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Sample records for pore complex localization

  1. Tpr is localized within the nuclear basket of the pore complex and has a role in nuclear protein export.

    PubMed

    Frosst, Phyllis; Guan, Tinglu; Subauste, Cecilia; Hahn, Klaus; Gerace, Larry

    2002-02-18

    Tpr is a coiled-coil protein found near the nucleoplasmic side of the pore complex. Since neither the precise localization of Tpr nor its functions are well defined, we generated antibodies to three regions of Tpr to clarify these issues. Using light and EM immunolocalization, we determined that mammalian Tpr is concentrated within the nuclear basket of the pore complex in a distribution similar to Nup153 and Nup98. Antibody localization together with imaging of GFP-Tpr in living cells revealed that Tpr is in discrete foci inside the nucleus similar to several other nucleoporins but is not present in intranuclear filamentous networks (Zimowska et al., 1997) or in long filaments extending from the pore complex (Cordes et al., 1997) as proposed. Injection of anti-Tpr antibodies into mitotic cells resulted in depletion of Tpr from the nuclear envelope without loss of other pore complex basket proteins. Whereas nuclear import mediated by a basic amino acid signal was unaffected, nuclear export mediated by a leucine-rich signal was retarded significantly. Nuclear injection of anti-Tpr antibodies in interphase cells similarly yielded inhibition of protein export but not import. These results indicate that Tpr is a nucleoporin of the nuclear basket with a role in nuclear protein export.

  2. SU-E-J-61: Electrodynamics and Nano-Scale Fluid Dynamics in Protein Localization of Nuclear Pore Complexes

    SciTech Connect

    Cunningham, J; Gatenby, R

    2014-06-01

    Purpose: To develop a simulation to catalyze a reevaluation of common assumptions about 3 dimensional diffusive processes and help cell biologists gain a more nuanced, intuitive understanding of the true physical hurdles of protein signaling cascades. Furthermore, to discuss the possibility of intracellular electrodynamics as a critical, unrecognized component of cellular biology and protein dynamics that is necessary for optimal information flow from the cell membrane to the nucleus. Methods: The Unity 3D gaming physics engine was used to build an accurate virtual scale model of the cytoplasm within a few hundred nanometers of the nuclear membrane. A cloud of simulated pERK proteins is controlled by the physics simulation, where diffusion is based on experimentally measured values and the electrodynamics are based on theoretical nano-fluid dynamics. The trajectories of pERK within the cytoplasm and through the 1250 nuclear pores on the nuclear surface is recorded and analyzed. Results: The simulation quickly demonstrates that pERKs moving solely by diffusion will rarely locate and come within capture distance of a nuclear pore. The addition of intracellular electrodynamics between charges on the nuclear pore complexes and on pERKs increases the number of successful translocations by allowing the electro-physical attractive effects to draw in pERKs from the cytoplasm. The effects of changes in intracellular shielding ion concentrations allowed for estimation of the “capture radius” under varying conditions. Conclusion: The simulation allows a shift in perspective that is paramount in attempting to communicate the scale and dynamics of intracellular protein cascade mechanics. This work has allowed researchers to more fully understand the parameters involved in intracellular electrodynamics, such as shielding anion concentration and protein charge. As these effects are still far below the spatial resolution of currently available measurement technology this

  3. Uncovering Nuclear Pore Complexity with Innovation

    PubMed Central

    Adams, Rebecca L.; Wente, Susan R.

    2013-01-01

    Advances in imaging and reductionist approaches provide a high-resolution understanding of nuclear pore complex structure and transport, revealing unexpected mechanistic complexities based on nucleoporin functions and specialized import and export pathways. PMID:23498931

  4. Localization of nucleoporin Tpr to the nuclear pore complex is essential for Tpr mediated regulation of the export of unspliced RNA.

    PubMed

    Rajanala, Kalpana; Nandicoori, Vinay Kumar

    2012-01-01

    Nucleoporin Tpr is a component of the nuclear pore complex (NPC) that localizes exclusively to intranuclear filaments. Tpr functions as a scaffolding element in the nuclear phase of the NPC and plays a role in mitotic spindle checkpoint signalling. Export of intron-containing mRNA in Mason Pfizer Monkey Virus is regulated by direct interaction of cellular proteins with the cis-acting Constitutive Transport Element (CTE). In mammalian cells, the transport of Gag/Pol-CTE reporter construct is not very efficient, suggesting a regulatory mechanism to retain this unspliced RNA. Here we report that the knockdown of Tpr in mammalian cells leads to a drastic enhancement in the levels of Gag proteins (p24) in the cytoplasm, which is rescued by siRNA resistant Tpr. Tpr's role in the retention of unspliced RNA is independent of the functions of Sam68 and Tap/Nxf1 proteins, which are reported to promote CTE dependent export. Further, we investigated the possible role for nucleoporins that are known to function in nucleocytoplasmic transport in modulating unspliced RNA export. Results show that depletion of Nup153, a nucleoporin required for NPC anchoring of Tpr, plays a role in regulating the export, while depletion of other FG repeat-containing nucleoporins did not alter the unspliced RNA export. Results suggest that Tpr and Nup153 both regulate the export of unspliced RNA and they are most likely functioning through the same pathway. Importantly, we find that localization of Tpr to the NPC is necessary for Tpr mediated regulation of unspliced RNA export. Collectively, the data indicates that perinuclear localization of Tpr at the nucleopore complex is crucial for regulating intron containing mRNA export by directly or indirectly participating in the processing and degradation of aberrant mRNA transcripts.

  5. The nuclear pore complex and nuclear transport.

    PubMed

    Wente, Susan R; Rout, Michael P

    2010-10-01

    Internal membrane bound structures sequester all genetic material in eukaryotic cells. The most prominent of these structures is the nucleus, which is bounded by a double membrane termed the nuclear envelope (NE). Though this NE separates the nucleoplasm and genetic material within the nucleus from the surrounding cytoplasm, it is studded throughout with portals called nuclear pore complexes (NPCs). The NPC is a highly selective, bidirectional transporter for a tremendous range of protein and ribonucleoprotein cargoes. All the while the NPC must prevent the passage of nonspecific macromolecules, yet allow the free diffusion of water, sugars, and ions. These many types of nuclear transport are regulated at multiple stages, and the NPC carries binding sites for many of the proteins that modulate and modify the cargoes as they pass across the NE. Assembly, maintenance, and repair of the NPC must somehow occur while maintaining the integrity of the NE. Finally, the NPC appears to be an anchor for localization of many nuclear processes, including gene activation and cell cycle regulation. All these requirements demonstrate the complex design of the NPC and the integral role it plays in key cellular processes. PMID:20630994

  6. Active genes at the nuclear pore complex.

    PubMed

    Taddei, Angela

    2007-06-01

    The nucleus is spatially and functionally organized and its architecture is now seen as a key contributor to genome functions. A central component of this architecture is the nuclear envelope, which is studded with nuclear pore complexes that serve as gateways for communication between the nucleoplasm and cytoplasm. Although the nuclear periphery has traditionally been described as a repressive compartment and repository for gene-poor chromosome regions, several recent studies in yeast have demonstrated that repressive and activating domains can both be positioned at the periphery of the nucleus. Moreover, association with the nuclear envelope favors the expression of particular genes, demonstrating that nuclear organization can play an active role in gene regulation. PMID:17467257

  7. In situ structural analysis of the human nuclear pore complex.

    PubMed

    von Appen, Alexander; Kosinski, Jan; Sparks, Lenore; Ori, Alessandro; DiGuilio, Amanda L; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S; Bui, Khanh Huy; Beck, Martin

    2015-10-01

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations.

  8. Correlative super-resolution fluorescence and electron microscopy of the nuclear pore complex with molecular resolution.

    PubMed

    Löschberger, Anna; Franke, Christian; Krohne, Georg; van de Linde, Sebastian; Sauer, Markus

    2014-10-15

    Here, we combine super-resolution fluorescence localization microscopy with scanning electron microscopy to map the position of proteins of nuclear pore complexes in isolated Xenopus laevis oocyte nuclear envelopes with molecular resolution in both imaging modes. We use the periodic molecular structure of the nuclear pore complex to superimpose direct stochastic optical reconstruction microscopy images with a precision of <20 nm on electron micrographs. The correlative images demonstrate quantitative molecular labeling and localization of nuclear pore complex proteins by standard immunocytochemistry with primary and secondary antibodies and reveal that the nuclear pore complex is composed of eight gp210 (also known as NUP210) protein homodimers. In addition, we find subpopulations of nuclear pore complexes with ninefold symmetry, which are found occasionally among the more typical eightfold symmetrical structures.

  9. Physical modelling of the nuclear pore complex

    PubMed Central

    Fassati, Ariberto; Ford, Ian J.; Hoogenboom, Bart W.

    2013-01-01

    Physically interesting behaviour can arise when soft matter is confined to nanoscale dimensions. A highly relevant biological example of such a phenomenon is the Nuclear Pore Complex (NPC) found perforating the nuclear envelope of eukaryotic cells. In the central conduit of the NPC, of ∼30–60 nm diameter, a disordered network of proteins regulates all macromolecular transport between the nucleus and the cytoplasm. In spite of a wealth of experimental data, the selectivity barrier of the NPC has yet to be explained fully. Experimental and theoretical approaches are complicated by the disordered and heterogeneous nature of the NPC conduit. Modelling approaches have focused on the behaviour of the partially unfolded protein domains in the confined geometry of the NPC conduit, and have demonstrated that within the range of parameters thought relevant for the NPC, widely varying behaviour can be observed. In this review, we summarise recent efforts to physically model the NPC barrier and function. We illustrate how attempts to understand NPC barrier function have employed many different modelling techniques, each of which have contributed to our understanding of the NPC.

  10. PoreFlow: A complex pore-network model for simulation of reactive transport in variably saturated porous media

    NASA Astrophysics Data System (ADS)

    Raoof, A.; Nick, H. M.; Hassanizadeh, S. M.; Spiers, C. J.

    2013-12-01

    This study introduces PoreFlow, a pore-network modeling tool capable of simulating fluid flow and multi-component reactive and adsorptive transport under saturated and variably saturated conditions. PoreFlow includes a variety of modules, such as: pore network generator, drainage simulator, calculation of pressure and velocity distributions, and modeling of reactive solute transport accounting for advection and diffusion. The pore space is represented using a multi-directional pore-network capable of capturing the random structure of a given porous media with user-defined directional connectivities for anisotropic pore structures. The chemical reactions can occur within the liquid phase, as well as between the liquid and solid phases which may result in an evolution of porosity and permeability. Under variably saturated conditions the area of interfaces changes with degree of the fluid saturation. PoreFlow uses complex formulations for more accurate modeling of transport problems in presence of the nonwetting phase. This is done by refining the discretization within drained pores. An implicit numerical scheme is used to solve the governing equations, and an efficient substitution method is applied to considerably minimize computational times. Several examples are provided, under saturated and variably saturated conditions, to demonstrate the model applicability in hydrogeology problems and petroleum fields. We show that PoreFlow is a powerful tool for upscaling of flow and transport in porous media, utilizing different pore scale information such as various interfaces, phase distributions and local fluxes and concentrations to determine macro scale properties such as average saturation, relative permeability, solute dispersivity, adsorption coefficients, effective diffusion and tortuosity. Such information can be used as constitutive relations within continuum scale governing equations to model physical and chemical processes more accurately at the larger scales.

  11. In situ structural analysis of the human nuclear pore complex

    PubMed Central

    Ori, Alessandro; DiGuilio, Amanda L.; Vollmer, Benjamin; Mackmull, Marie-Therese; Banterle, Niccolo; Parca, Luca; Kastritis, Panagiotis; Buczak, Katarzyna; Mosalaganti, Shyamal; Hagen, Wim; Andres-Pons, Amparo; Lemke, Edward A.; Bork, Peer; Antonin, Wolfram; Glavy, Joseph S.; Bui, Khanh Huy; Beck, Martin

    2016-01-01

    Summary Nuclear pore complexes (NPCs) are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Elucidating their 110 MDa structure imposes a formidable challenge and requires in situ structural biology approaches. Fifteen out of about thirty nucleoporins (Nups) are structured and form the Y- and inner ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ∼60 nm in diameter 1. The scaffold is decorated with transport channel Nups that often contain phenylalanine (FG)-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y-complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here, we combined cryo electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modeling to generate the most comprehensive architectural model of the NPC to date. Our data suggest previously unknown protein interfaces across Y-complexes and to inner ring complex members. We demonstrate that the higher eukaryotic transport channel Nup358 (RanBP2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport channel Nups. We conclude that, similarly to coated vesicles, multiple copies of the same structural building block - although compositionally identical - engage in different local sets of interactions and conformations. PMID:26416747

  12. Gating Immunity and Death at the Nuclear Pore Complex.

    PubMed

    Dasso, Mary; Fontoura, Beatriz M A

    2016-09-01

    The nuclear pore complex is the primary conduit for nuclear import and export of molecules. In this issue, Gu et al. uncover a novel mechanism in which immune signaling and programmed cell death require nuclear pore rearrangement and release of sequestered cyclin-dependent kinase inhibitors to elicit immunity and death. PMID:27610561

  13. An abiotic analogue of the nuclear pore complex hydrogel.

    PubMed

    Bird, Sean P; Baker, Lane A

    2011-09-12

    We describe an abiotic hydrogel that mimics selectivity of the nuclear pore complex. Copolymerization of peptide tetramers (phenylalanine-serine-phenylalanine-glycine, FSFG) with acrylamide results in hydrophobic interactions significant enough to allow the formation of freestanding hydrogel structures. Incorporation of FSFG motifs also renders the hydrogels selective. Selective binding of importins and nuclear transport receptor-cargo complexes is qualitatively demonstrated and compared with polyacrylamide, hydrogels prepared from a control peptide, and hydrogels prepared from the nuclear pore complex protein Nsp1. These abiotic hydrogels will enable further studies of the unique transport mechanisms of the nuclear pore complex and provide an interesting paradigm for the future development of synthetic platforms for separations and selective interfaces.

  14. Proteins Connecting the Nuclear Pore Complex with the Nuclear Interior

    PubMed Central

    Strambio-de-Castillia, Caterina; Blobel, Günter; Rout, Michael P.

    1999-01-01

    While much has been learned in recent years about the movement of soluble transport factors across the nuclear pore complex (NPC), comparatively little is known about intranuclear trafficking. We isolated the previously identified Saccharomyces protein Mlp1p (myosin-like protein) by an assay designed to find nuclear envelope (NE) associated proteins that are not nucleoporins. We localized both Mlp1p and a closely related protein that we termed Mlp2p to filamentous structures stretching from the nucleoplasmic face of the NE into the nucleoplasm, similar to the homologous vertebrate and Drosophila Tpr proteins. Mlp1p can be imported into the nucleus by virtue of a nuclear localization sequence (NLS) within its COOH-terminal domain. Overexpression experiments indicate that Mlp1p can form large structures within the nucleus which exclude chromatin but appear highly permeable to proteins. Remarkably, cells harboring a double deletion of MLP1 and MLP2 were viable, although they showed a slower net rate of active nuclear import and faster passive efflux of a reporter protein. Our data indicate that the Tpr homologues are not merely NPC-associated proteins but that they can be part of NPC-independent, peripheral intranuclear structures. In addition, we suggest that the Tpr filaments could provide chromatin-free conduits or tracks to guide the efficient translocation of macromolecules between the nucleoplasm and the NPC. PMID:10085285

  15. Lumenal interactions in nuclear pore complex assembly and stability

    PubMed Central

    Yewdell, William T.; Colombi, Paolo; Makhnevych, Taras; Lusk, C. Patrick

    2011-01-01

    Nuclear pore complexes (NPCs) provide a gateway for the selective transport of macromolecules across the nuclear envelope (NE). Although we have a solid understanding of NPC composition and structure, we do not have a clear grasp of the mechanism of NPC assembly. Here, we demonstrate specific defects in nucleoporin distribution in strains lacking Heh1p and Heh2p—two conserved members of the LEM (Lap2, emerin, MAN1) family of integral inner nuclear membrane proteins. These effects on nucleoporin localization are likely of functional importance as we have defined specific genetic interaction networks between HEH1 and HEH2, and genes encoding nucleoporins in the membrane, inner, and outer ring complexes of the NPC. Interestingly, expression of a domain of Heh1p that resides in the NE lumen is sufficient to suppress both the nucleoporin mislocalization and growth defects in heh1Δpom34Δ strains. We further demonstrate a specific physical interaction between the Heh1p lumenal domain and the massive cadherin-like lumenal domain of the membrane nucleoporin Pom152p. These findings support a role for Heh1p in the assembly or stability of the NPC, potentially through the formation of a lumenal bridge with Pom152p. PMID:21346187

  16. Molecular and functional characterization of the p62 complex, an assembly of nuclear pore complex glycoproteins

    PubMed Central

    1996-01-01

    Macromolecular trafficking across the nuclear envelope involves interactions between cytosolic transport factors and nuclear pore complex proteins. The p62 complex, an assembly of 62, 58, 54, and 45-kD O-linked glycoproteins-localized near the central gated channel of the nuclear pore complex, has been directly implicated in nuclear protein import. The cDNA cloning of rat p62 was reported previously. We have now carried out cDNA cloning of rat p58, p54, and p45. We found that p58 contains regions with FG (Phe, Gly) and PA (Pro, Ala) repeats at both its NH2 and COOH termini separated by a predicted alpha-helical coiled-coil region, while p54 has an NH2-terminal FG and PA repeat region and a COOH-terminal predicted coiled-coil region. p45 and p58 appear to be generated by alternative splicing, with p45 containing the NH2-terminal FG repeat region and the coiled-coil region of p58. Using immunogold electron microscopy, we found that p58/p45 and p54 are localized on both sides of the nuclear pore complex, like p62. Previous studies have shown that immobilized recombinant p62 can bind the cytosolic nuclear import factor NTF2 and thereby deplete transport activity from cytosol. We have now found that immobilized recombinant p58 and p54 also can deplete nuclear transport activity from cytosol, and that p62, p58, and p54 bind directly to the cytosolic nuclear import factors p97 and NTF2. At least in the case of p58, this involves FG repeat regions. Moreover, p58 can bind to a complex containing transport ligand, the nuclear localization sequence receptor (Srp1 alpha) and p97. These data support a model in which the p62 complex binds to a multicomponent particle consisting of transport ligand and cytosolic factors to achieve accumulation of ligand near the central gated channel of the nuclear pore complex. PMID:8707840

  17. Enriching the pore: Splendid complexity from humble origins

    PubMed Central

    Field, Mark C.; Koreny, Ludek; Rout, Michael P.

    2014-01-01

    The nucleus is the defining intracellular organelle of eukaryotic cells and represents a major structural innovation that differentiates the eukaryotic and prokaryotic cellular form. The presence of a nuclear envelope (NE) encapsulating the nucleus necessitates a mechanism for interchange between the contents of the nuclear interior and the cytoplasm, which is mediated via the nuclear pore complex (NPC), a large protein assembly residing in nuclear pores in the NE. Recent advances have begun to map the structure and functions of the NPC in multiple organisms, and to allow reconstruction of some of the evolutionary events that underpin the modern NPC form, highlighting common and differential NPC features across the eukaryotes. Here we discuss some of these advances and the questions being pursued, consider how the evolution of the NPC has been constrained, and finally propose a model for how the nuclear pore complex evolved. PMID:24279500

  18. Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells

    PubMed Central

    Raghunayakula, Sarita; Subramonian, Divya; Dasso, Mary; Kumar, Rita; Zhang, Xiang-Dong

    2015-01-01

    Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/β and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/β-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological significance of the

  19. Molecular Characterization and Functional Analysis of Annulate Lamellae Pore Complexes in Nuclear Transport in Mammalian Cells.

    PubMed

    Raghunayakula, Sarita; Subramonian, Divya; Dasso, Mary; Kumar, Rita; Zhang, Xiang-Dong

    2015-01-01

    Annulate lamellae are cytoplasmic organelles containing stacked sheets of membranes embedded with pore complexes. These cytoplasmic pore complexes at annulate lamellae are morphologically similar to nuclear pore complexes at the nuclear envelope. Although annulate lamellae has been observed in nearly all types of cells, their biological functions are still largely unknown. Here we show that SUMO1-modification of the Ran GTPase-activating protein RanGAP1 not only target RanGAP1 to its known sites at nuclear pore complexes but also to annulate lamellae pore complexes through interactions with the Ran-binding protein RanBP2 and the SUMO-conjugating enzyme Ubc9 in mammalian cells. Furthermore, upregulation of annulate lamellae, which decreases the number of nuclear pore complexes and concurrently increases that of annulate lamellae pore complexes, causes a redistribution of nuclear transport receptors including importin α/β and the exportin CRM1 from nuclear pore complexes to annulate lamellae pore complexes and also reduces the rates of nuclear import and export. Moreover, our results reveal that importin α/β-mediated import complexes initially accumulate at annulate lamellae pore complexes upon the activation of nuclear import and subsequently disassociate for nuclear import through nuclear pore complexes in cells with upregulation of annulate lamellae. Lastly, CRM1-mediated export complexes are concentrated at both nuclear pore complexes and annulate lamellae pore complexes when the disassembly of these export complexes is inhibited by transient expression of a Ran GTPase mutant arrested in its GTP-bound form, suggesting that RanGAP1/RanBP2-activated RanGTP hydrolysis at these pore complexes is required for the dissociation of the export complexes. Hence, our findings provide a foundation for further investigation of how upregulation of annulate lamellae decreases the rates of nuclear transport and also for elucidation of the biological significance of the

  20. Architecture of the fungal nuclear pore inner ring complex.

    PubMed

    Stuwe, Tobias; Bley, Christopher J; Thierbach, Karsten; Petrovic, Stefan; Schilbach, Sandra; Mayo, Daniel J; Perriches, Thibaud; Rundlet, Emily J; Jeon, Young E; Collins, Leslie N; Huber, Ferdinand M; Lin, Daniel H; Paduch, Marcin; Koide, Akiko; Lu, Vincent; Fischer, Jessica; Hurt, Ed; Koide, Shohei; Kossiakoff, Anthony A; Hoelz, André

    2015-10-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation.

  1. Energetics of Transport through the Nuclear Pore Complex

    PubMed Central

    Ghavami, Ali; van der Giessen, Erik; Onck, Patrick R.

    2016-01-01

    Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles. PMID:26894898

  2. Energetics of Transport through the Nuclear Pore Complex.

    PubMed

    Ghavami, Ali; van der Giessen, Erik; Onck, Patrick R

    2016-01-01

    Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown that the interaction between intrinsically disordered proteins that line the central channel of the NPC and the transporting cargoes is the determining factor, but the exact mechanism of transport is yet unknown. Here, we use coarse-grained molecular dynamics simulations to quantify the energy barrier that has to be overcome for molecules to pass through the NPC. We focus on two aspects of transport. First, the passive transport of model cargo molecules with different sizes is studied and the size selectivity feature of the NPC is investigated. Our results show that the transport probability of cargoes is significantly reduced when they are larger than ∼5 nm in diameter. Secondly, we show that incorporating hydrophobic binding spots on the surface of the cargo effectively decreases the energy barrier of the pore. Finally, a simple transport model is proposed which characterizes the energy barrier of the NPC as a function of diameter and hydrophobicity of the transporting particles.

  3. Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components

    PubMed Central

    1990-01-01

    Nuclear pore complexes (NPCs) prepared from Xenopus laevis oocyte nuclear envelopes were studied in "intact" form (i.e., unexposed to detergent) and after detergent treatment by a combination of conventional transmission electron microscopy (CTEM) and quantitative scanning transmission electron microscopy (STEM). In correlation- averaged CTEM pictures of negatively stained intact NPCs and of distinct NPC components (i.e., "rings," "spoke" complexes, and "plug- spoke" complexes), several fine structural features arranged with octagonal symmetry about a central axis could reproducibly be identified. STEM micrographs of unstained/freeze-dried intact NPCs as well as of their components yielded comparable but less distinct features. Mass determination by STEM revealed the following molecular masses: intact NPC with plug, 124 +/- 11 MD; intact NPC without plug, 112 +/- 11 MD; heavy ring, 32 +/- 5 MD; light ring, 21 +/- 4 MD; plug- spoke complex, 66 +/- 8 MD; and spoke complex, 52 +/- 3 MD. Based on these combined CTEM and STEM data, a three-dimensional model of the NPC exhibiting eightfold centrosymmetry about an axis perpendicular to the plane of the nuclear envelope but asymmetric along this axis is proposed. This structural polarity of the NPC across the nuclear envelope is in accord with its well-documented functional polarity facilitating mediated nucleocytoplasmic exchange of molecules and particles. PMID:2324201

  4. Probing nuclear pore complex architecture with proximity-dependent biotinylation.

    PubMed

    Kim, Dae In; Birendra, K C; Zhu, Wenhong; Motamedchaboki, Khatereh; Doye, Valérie; Roux, Kyle J

    2014-06-17

    Proximity-dependent biotin identification (BioID) is a method for identifying protein associations that occur in vivo. By fusing a promiscuous biotin ligase to a protein of interest expressed in living cells, BioID permits the labeling of proximate proteins during a defined labeling period. In this study we used BioID to study the human nuclear pore complex (NPC), one of the largest macromolecular assemblies in eukaryotes. Anchored within the nuclear envelope, NPCs mediate the nucleocytoplasmic trafficking of numerous cellular components. We applied BioID to constituents of the Nup107-160 complex and the Nup93 complex, two conserved NPC subcomplexes. A strikingly different set of NPC constituents was detected depending on the position of these BioID-fusion proteins within the NPC. By applying BioID to several constituents located throughout the extremely stable Nup107-160 subcomplex, we refined our understanding of this highly conserved subcomplex, in part by demonstrating a direct interaction of Nup43 with Nup85. Furthermore, by using the extremely stable Nup107-160 structure as a molecular ruler, we defined the practical labeling radius of BioID. These studies further our understanding of human NPC organization and demonstrate that BioID is a valuable tool for exploring the constituency and organization of large protein assemblies in living cells.

  5. Quantifying nucleoporin stoichiometry inside single nuclear pore complexes in vivo.

    PubMed

    Mi, Lan; Goryaynov, Alexander; Lindquist, Andre; Rexach, Michael; Yang, Weidong

    2015-03-23

    The nuclear pore complex (NPC) is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring-scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. NPCs are composed of ~30 different nucleoporins (Nups), averaged at 8, 16 or 32 copies per NPC. This estimate has not been confirmed for individual NPCs in living cells due to the inherent difficulty of counting proteins inside single supramolecular complexes. Here we used single-molecule SPEED microscopy to directly count the copy-number of twenty-four different Nups within individual NPCs of live yeast, and found agreement as well as significant deviation from previous estimates. As expected, we counted 8 copies of four peripheral Nups and 16 copies of fourteen scaffold Nups. Unexpectedly, we counted a maximum of 16 copies of Nsp1 and Nic96, rather than 32 as previously estimated; and found only 10-15 copies of six other Nups, rather than 8 or 16 copies as expected. This in situ molecular-counting technology can test structure-function models of NPCs and other supramolecular structures in cells.

  6. Characterisation of the passive permeability barrier of nuclear pore complexes

    PubMed Central

    Mohr, Dagmar; Frey, Steffen; Fischer, Torsten; Güttler, Thomas; Görlich, Dirk

    2009-01-01

    Nuclear pore complexes (NPCs) restrict uncontrolled nucleocytoplasmic fluxes of inert macromolecules but permit facilitated translocation of nuclear transport receptors and their cargo complexes. We probed the passive barrier of NPCs and observed sieve-like properties with a dominating mesh or channel radius of 2.6 nm, which is narrower than proposed earlier. A small fraction of diffusion channels has a wider opening, explaining the very slow passage of larger molecules. The observed dominant passive diameter approximates the distance of adjacent hydrophobic clusters of FG repeats, supporting the model that the barrier is made of FG repeat domains cross-linked with a spacing of an FG repeat unit length. Wheat germ agglutinin and the dominant-negative importin β45-462 fragment were previously regarded as selective inhibitors of facilitated NPC passage. We now observed that they do not distinguish between the passive and the facilitated mode. Instead, their inhibitory effect correlates with the size of the NPC-passing molecule. They have little effect on small species, inhibit the passage of green fluorescent protein-sized objects >10-fold and virtually block the translocation of larger ones. This suggests that passive and facilitated NPC passage proceed through one and the same permeability barrier. PMID:19680228

  7. Nuclear pore complexes: guardians of the nuclear genome.

    PubMed

    Capelson, M; Doucet, C; Hetzer, M W

    2010-01-01

    Eukaryotic cell function depends on the physical separation of nucleoplasmic and cytoplasmic components by the nuclear envelope (NE). Molecular communication between the two compartments involves active, signal-mediated trafficking, a function that is exclusively performed by nuclear pore complexes (NPCs). The individual NPC components and the mechanisms that are involved in nuclear trafficking are well documented and have become textbook knowledge. However, in addition to their roles as nuclear gatekeepers, NPC components-nucleoporins-have been shown to have critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multiprotein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our present view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition, we summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes. PMID:21502404

  8. Conserved Spatial Organization of FG Domains in the Nuclear Pore Complex

    PubMed Central

    Atkinson, Claire E.; Mattheyses, Alexa L.; Kampmann, Martin; Simon, Sanford M.

    2013-01-01

    Selective transport through the nuclear pore complex (NPC) requires nucleoporins containing natively unfolded phenylalanine-glycine (FG) domains. Several differing models for their dynamics within the pore have been proposed. We characterize the behavior of the FG nucleoporins in vivo using polarized fluorescence microscopy. Using nucleoporins tagged with green fluorescent protein along their FG domains, we show that some of these proteins are ordered, indicating an overall orientational organization within the NPC. This orientational ordering of the FG domains depends on their specific context within the NPC, but is independent of active transport and cargo load. For most nups, behavior does not depend on the FG motifs. These data support a model whereby local geometry constrains the orientational organization of the FG nups. Intriguingly, homologous yeast and mammalian proteins show conserved behavior, suggesting functional relevance. Our findings have implications for mechanistic models of NPC transport. PMID:23332057

  9. Primary Biliary Cirrhosis and the Nuclear Pore Complex

    PubMed Central

    Duarte-Rey, Carolina; Bogdanos, Dimitrios; Yang, Chen-Yen; Roberts, Krista; Leung, Patrick S.C.; Anaya, Juan-Manuel; Worman, Howard J.; Gershwin, M. Eric

    2012-01-01

    Experimental models of autoimmune diseases have led to the conclusion that an immune response to nuclear antigens is a sentinel marker for loss of tolerance and potential tissue damage. Various proteins are targets of antinuclear antibodies in a variety of autoimmune diseases, ranging from systemic rheumatologic disorders to diseases affecting specific organs such as the liver. Autoantibodies against specific nuclear constituents have also been used as probes to understand the structure and the function of the targeted components and their relevance to disease pathogenesis. Approximately a quarter of patients with primary biliary cirrhosis (PBC) have antibodies targeting proteins of the nuclear pore complex (NPC), a multi-protein structure that mediates molecular transport across the nuclear envelope. Autoantibodies against the integral membrane glycoprotein gp210 and nucleoporin p62 appear to be highly specific for PBC, an autoimmune disease characterized by progressive destruction of intrahepatic biliary epithelial cells. This review discusses the diagnostic and clinical relevance of anti-NPC antibodies in PBC and the possibility that this autoimmune response may arise as a result of molecular mimicry. PMID:22487189

  10. The Yeast Nuclear Pore Complex and Transport Through It

    PubMed Central

    Aitchison, John D.; Rout, Michael P.

    2012-01-01

    Exchange of macromolecules between the nucleus and cytoplasm is a key regulatory event in the expression of a cell’s genome. This exchange requires a dedicated transport system: (1) nuclear pore complexes (NPCs), embedded in the nuclear envelope and composed of proteins termed nucleoporins (or “Nups”), and (2) nuclear transport factors that recognize the cargoes to be transported and ferry them across the NPCs. This transport is regulated at multiple levels, and the NPC itself also plays a key regulatory role in gene expression by influencing nuclear architecture and acting as a point of control for various nuclear processes. Here we summarize how the yeast Saccharomyces has been used extensively as a model system to understand the fundamental and highly conserved features of this transport system, revealing the structure and function of the NPC; the NPC’s role in the regulation of gene expression; and the interactions of transport factors with their cargoes, regulatory factors, and specific nucleoporins. PMID:22419078

  11. Regulation of mRNA trafficking by nuclear pore complexes.

    PubMed

    Bonnet, Amandine; Palancade, Benoit

    2014-09-02

    Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed.

  12. Regulation of mRNA Trafficking by Nuclear Pore Complexes

    PubMed Central

    Bonnet, Amandine; Palancade, Benoit

    2014-01-01

    Over the last two decades, multiple studies have explored the mechanisms governing mRNA export out of the nucleus, a crucial step in eukaryotic gene expression. During transcription and processing, mRNAs are assembled into messenger ribonucleoparticles (mRNPs). mRNPs are then exported through nuclear pore complexes (NPCs), which are large multiprotein assemblies made of several copies of a limited number of nucleoporins. A considerable effort has been put into the dissection of mRNA export through NPCs at both cellular and molecular levels, revealing the conserved contributions of a subset of nucleoporins in this process, from yeast to vertebrates. Several reports have also demonstrated the ability of NPCs to sort out properly-processed mRNPs for entry into the nuclear export pathway. Importantly, changes in mRNA export have been associated with post-translational modifications of nucleoporins or changes in NPC composition, depending on cell cycle progression, development or exposure to stress. How NPC modifications also impact on cellular mRNA export in disease situations, notably upon viral infection, is discussed. PMID:25184662

  13. Multi-scale characterization of pore evolution in a combustion metamorphic complex, Hatrurim basin, Israel: Combining (ultra) small-angle neutron scattering and image analysis

    SciTech Connect

    Wang, Hsiu-Wen; Anovitz, Lawrence {Larry} M; Burg, Avihu; Cole, David; Allard Jr, Lawrence Frederick; Jackson, Andrew J; Stack, Andrew G; Rother, Gernot; Ciarlette, Diane D

    2013-01-01

    Backscattered scanning electron micrograph and ultra small- and small-angle neutron scattering data have been combined to provide statistically meaningful data on the pore/grain structure and pore evolution of combustion metamorphic complexes from the Hatrurim basin, Israel. Three processes, anti-sintering roughening, alteration of protolith (dehydration, decarbonation, and oxidation) and crystallization of high-temperature minerals, occurred simultaneously, leading to significant changes in observed pore/grain structures. Pore structures in the protoliths, and in lowand high-grade metamorphic rocks show surface (Ds) and mass (Dm) pore fractal geometries with gradual increases in both Ds and Dm values as a function of metamorphic grade. This suggests that increases in pore volume and formation of less branching pore networks are accompanied by a roughening of pore/grain interfaces. Additionally, pore evolution during combustion metamorphism is also characterized by reduced contributions from small-scale pores to the cumulative porosity in the high-grade rocks. At high temperatures, small-scale pores may be preferentially closed by the formation of high-temperature minerals, producing a rougher morphology with increasing temperature. Alternatively, large-scale pores may develop at the expense of small-scale pores. These observations (pore fractal geometry and cumulative porosity) indicate that the evolution of pore/grain structures is correlated with the growth of high-temperature phases and is a consequence of the energy balance between pore/grain surface energy and energy arising from heterogeneous phase contacts. The apparent pore volume density further suggests that the localized time/temperature development of the high-grade Hatrurim rocks is not simply an extension of that of the low-grade rocks. The former likely represents the "hot spots (burning foci)" in the overall metamorphic terrain while the latter may represent contact aureoles.

  14. More Than a Pore: Ion Channel Signaling Complexes

    PubMed Central

    Fakler, Bernd; Kaczmarek, Leonard K.; Isom, Lori L.

    2014-01-01

    Voltage- and ligand-gated ion channels form the molecular basis of cellular excitability. With >400 members and accounting for ∼1.5% of the human genome, ion channels are some of the most well studied of all proteins in heterologous expression systems. Yet, ion channels often exhibit unexpected properties in vivo because of their interaction with a variety of signaling/scaffolding proteins. Such interactions can influence the function and localization of ion channels, as well as their coupling to intracellular second messengers and pathways, thus increasing the signaling potential of these ion channels in neurons. Moreover, functions have been ascribed to ion channels that are largely independent of their ion-conducting roles. Molecular and functional dissection of the ion channel proteome/interactome has yielded new insights into the composition of ion channel complexes and how their dysregulation leads to human disease. PMID:25392484

  15. A characterization of the coupled evolution of grain fabric and pore space using complex networks: Pore connectivity and optimized flows in the presence of shear bands

    NASA Astrophysics Data System (ADS)

    Russell, Scott; Walker, David M.; Tordesillas, Antoinette

    2016-03-01

    A framework for the multiscale characterization of the coupled evolution of the solid grain fabric and its associated pore space in dense granular media is developed. In this framework, a pseudo-dual graph transformation of the grain contact network produces a graph of pores which can be readily interpreted as a pore space network. Survivability, a new metric succinctly summarizing the connectivity of the solid grain and pore space networks, measures material robustness. The size distribution and the connectivity of pores can be characterized quantitatively through various network properties. Assortativity characterizes the pore space with respect to the parity of the number of particles enclosing the pore. Multiscale clusters of odd parity versus even parity contact cycles alternate spatially along the shear band: these represent, respectively, local jamming and unjamming regions that continually switch positions in time throughout the failure regime. Optimal paths, established using network shortest paths in favor of large pores, provide clues on preferential paths for interstitial matter transport. In systems with higher rolling resistance at contacts, less tortuous shortest paths thread through larger pores in shear bands. Notably the structural patterns uncovered in the pore space suggest that more robust models of interstitial pore flow through deforming granular systems require a proper consideration of the evolution of in situ shear band and fracture patterns - not just globally, but also inside these localized failure zones.

  16. Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Rajarshi; Debnath, Ananya; Sebastian, K. L.

    2014-06-01

    Nuclear pore complexes (NPCs) are very selective filters that sit on the membrane of the nucleus and monitor the transport between the cytoplasm and the nucleoplasm. For the central plug of NPC two models have been suggested in the literature. The first suggests that the plug is a reversible hydrogel while the other suggests that it is a polymer brush. Here we propose a model for the transport of a protein through the plug, which is general enough to cover both the models. The protein stretches the plug and creates a local deformation, which together with the protein, we refer to as the bubble. We start with the free energy for creation of the bubble and consider its motion within the plug. The relevant coordinate is the center of the bubble which executes random walk. We find that for faster relaxation of the gel, the diffusion of the bubble is greater.

  17. Single-Molecule Imaging to Characterize the Transport Mechanism of the Nuclear Pore Complex.

    PubMed

    Jeremy, Grace; Stevens, James; Lowe, Alan R

    2016-01-01

    In the eukaryotic cell, a large macromolecular channel, known as the Nuclear Pore Complex (NPC), mediates all molecular transport between the nucleus and cytoplasm. In recent years, single-molecule fluorescence (SMF) imaging has emerged as a powerful tool to study the molecular mechanism of transport through the NPC. More recently, techniques such as single-molecule localization microscopy (SMLM) have enabled the spatial and temporal distribution of cargos, transport receptors and even structural components of the NPC to be determined with nanometre accuracy. In this protocol, we describe a method to study the position and/or motion of individual molecules transiting through the NPC with high spatial and temporal precision. PMID:27283299

  18. Direct numerical simulation of supercritical gas flow in complex nanoporous media: Elucidating the relationship between permeability and pore space geometry

    NASA Astrophysics Data System (ADS)

    Landry, C. J.; Prodanovic, M.; Eichhubl, P.

    2015-12-01

    Mudrocks and shales are currently a significant source of natural gas and understanding the basic transport properties of these formations is critical to predicting long-term production, however, the nanoporous nature of mudrocks presents a unique challenge. Mudrock pores are predominantly in the range of 1-100 nm, and within this size range the flow of gas at reservoir conditions will fall within the slip-flow and early transition-flow regime (0.001 < Kn < 1.0). Therefore, flow-rates will significantly deviate from Navier-Stokes predictions. Currently, the study of slip-flows is mostly limited to simple tube and channel geometries, but the geometry of mudrock pores is often sponge-like (organic matter) and/or platy (clays). Here we present a local effective viscosity lattice Boltzmann model (LEV-LBM) constructed for flow simulation in the slip- and early-transition flow regimes, adapted here for complex geometries. At the macroscopic scale the LEV-LBM is parameterized with local effective viscosities at each node to capture the variance of the mean free path of gas molecules in a bounded system. The LEV-LBM is first validated in simple tube geometries, where excellent agreement with linearized Boltzmann solutions is found for Knudsen numbers up to 1.0. The LEV-LBM is then employed to quantify the length effect on the apparent permeability of tubes, which suggests pore network modeling of flow in the slip and early-transition regime will result in overestimation unless the length effect is considered. Furthermore, the LEV-LBM is used to evaluate the predictive value of commonly measured pore geometry characteristics such as porosity, pore size distribution, and specific solid surface area for the calculation of permeability. We show that bundle of tubes models grossly overestimate apparent permeability, as well as underestimate the increase in apparent permeability with decreasing pressure as a result of excluding topology and pore shape from calculations.

  19. Assembly of anthrax toxin pore: Lethal-factor complexes into lipid nanodiscs

    PubMed Central

    Akkaladevi, N; Hinton-Chollet, L; Katayama, H; Mitchell, J; Szerszen, L; Mukherjee, S; Gogol, E P; Pentelute, B L; Collier, R J; Fisher, M T

    2013-01-01

    We have devised a procedure to incorporate the anthrax protective antigen (PA) pore complexed with the N-terminal domain of anthrax lethal factor (LFN) into lipid nanodiscs and analyzed the resulting complexes by negative-stain electron microscopy. Insertion into nanodiscs was performed without relying on primary and secondary detergent screens. The preparations were relatively pure, and the percentage of PA pore inserted into nanodiscs on EM grids was high (∼43%). Three-dimensional analysis of negatively stained single particles revealed the LFN-PA nanodisc complex mirroring the previous unliganded PA pore nanodisc structure, but with additional protein density consistent with multiple bound LFN molecules on the PA cap region. The assembly procedure will facilitate collection of higher resolution cryo-EM LFN-PA nanodisc structures and use of advanced automated particle selection methods. PMID:23389868

  20. The membrane attack complex, perforin and cholesterol-dependent cytolysin superfamily of pore-forming proteins.

    PubMed

    Lukoyanova, Natalya; Hoogenboom, Bart W; Saibil, Helen R

    2016-06-01

    The membrane attack complex and perforin proteins (MACPFs) and bacterial cholesterol-dependent cytolysins (CDCs) are two branches of a large and diverse superfamily of pore-forming proteins that function in immunity and pathogenesis. During pore formation, soluble monomers assemble into large transmembrane pores through conformational transitions that involve extrusion and refolding of two α-helical regions into transmembrane β-hairpins. These transitions entail a dramatic refolding of the protein structure, and the resulting assemblies create large holes in cellular membranes, but they do not use any external source of energy. Structures of the membrane-bound assemblies are required to mechanistically understand and modulate these processes. In this Commentary, we discuss recent advances in the understanding of assembly mechanisms and molecular details of the conformational changes that occur during MACPF and CDC pore formation. PMID:27179071

  1. Study of the protein complex, pore diameter, and pore-forming activity of the Borrelia burgdorferi P13 porin.

    PubMed

    Bárcena-Uribarri, Iván; Thein, Marcus; Barbot, Mariam; Sans-Serramitjana, Eulalia; Bonde, Mari; Mentele, Reinhard; Lottspeich, Friedrich; Bergström, Sven; Benz, Roland

    2014-07-01

    P13 is one of the major outer membrane proteins of Borrelia burgdorferi. Previous studies described P13 as a porin. In the present study some structure and function aspects of P13 were studied. P13 showed according to lipid bilayer studies a channel-forming activity of 0.6 nanosiemens in 1 m KCl. Single channel and selectivity measurements demonstrated that P13 had no preference for either cations or anions and showed no voltage-gating up to ±100 mV. Blue native polyacrylamide gel electrophoresis was used to isolate and characterize the P13 protein complex in its native state. The complex had a high molecular mass of about 300 kDa and was only composed of P13 monomers. The channel size was investigated using non-electrolytes revealing an apparent diameter of about 1.4 nm with a 400-Da molecular mass cut-off. Multichannel titrations with different substrates reinforced the idea that P13 forms a general diffusion channel. The identity of P13 within the complex was confirmed by second dimension SDS-PAGE, Western blotting, mass spectrometry, and the use of a p13 deletion mutant strain. The results suggested that P13 is the protein responsible for the 0.6-nanosiemens pore-forming activity in the outer membrane of B. burgdorferi.

  2. Micromechanics of Shear Localization under Elevated Temperature and Pore Pressure in Experimentally Deformed Quartz Sandstone

    NASA Astrophysics Data System (ADS)

    Kanaya, T.; Hirth, G.

    2014-12-01

    Triaxial compression experiments were conducted on a permeable quartz sandstone under argon pore fluid and vented conditions at temperatures to 900°C and effective pressures to 175 MPa. Vented tests exhibit a transition from brittle faulting towards thermally-activated cataclastic flow. Microfracture density and acoustic emissions indicate that the transition corresponds to a change in mechanism from rate-insensitive fracture to subcritical cracking. We conclude that the transition occurs when shear microfracture propagation and macroscopic shear localization are suppressed under increased grain-scale fracture energy and reduced dilatancy. A comparison of the two tests shows that pore fluid has little influence on the failure behavior at low temperatures. Conversely, pore fluid tests exhibit substantially smaller strengths and enhanced ductility than those of vented tests at high temperatures and pressures, similar to weakening induced by decreasing strain rate in the water-saturated sandstone at room temperature. We infer that the observed weakening results from an enhancement in intergranular frictional slip involving subcritical cracking where retained intracrystalline water reduced fracture energy. We are characterizing detailed microstructures and finite strain fields in samples deformed at varied strains, as well as evolution in volume strain and other inelastic properties, to further constrain the pore fluid effects on shear localization processes.

  3. An Autoimmune Myositis-Overlap Syndrome Associated With Autoantibodies to Nuclear Pore Complexes

    PubMed Central

    Senécal, Jean-Luc; Isabelle, Catherine; Fritzler, Marvin J.; Targoff, Ira N.; Goldstein, Rose; Gagné, Michel; Raynauld, Jean-Pierre; Joyal, France; Troyanov, Yves; Dabauvalle, Marie-Christine

    2014-01-01

    Abstract Autoimmune myositis encompasses various myositis-overlap syndromes, each being identified by the presence of serum marker autoantibodies. We describe a novel myositis-overlap syndrome in 4 patients characterized by the presence of a unique immunologic marker, autoantibodies to nuclear pore complexes. The clinical phenotype was characterized by prominent myositis in association with erosive, anti-CCP, and rheumatoid factor-positive arthritis, trigeminal neuralgia, mild interstitial lung disease, Raynaud phenomenon, and weight loss. The myositis was typically chronic, relapsing, and refractory to corticosteroids alone, but remitted with the addition of a second immunomodulating drug. There was no clinical or laboratory evidence for liver disease. The prognosis was good with 100% long-term survival (mean follow-up 19.5 yr). By indirect immunofluorescence on HEp-2 cells, sera from all 4 patients displayed a high titer of antinuclear autoantibodies (ANA) with a distinct punctate peripheral (rim) fluorescent pattern of the nuclear envelope characteristic of nuclear pore complexes. Reactivity with nuclear pore complexes was confirmed by immunoelectron microscopy. In a cohort of 100 French Canadian patients with autoimmune myositis, the nuclear pore complex fluorescent ANA pattern was restricted to these 4 patients (4%). It was not observed in sera from 393 adult patients with systemic sclerosis (n = 112), mixed connective tissue disease (n = 35), systemic lupus (n = 94), rheumatoid arthritis (n = 45), or other rheumatic diseases (n = 107), nor was it observed in 62 normal adults. Autoantibodies to nuclear pore complexes were predominantly of IgG isotype. No other IgG autoantibody markers for defined connective tissue diseases or overlap syndromes were present, indicating a selective and highly focused immune response. In 3 patients, anti-nuclear pore complex autoantibody titers varied in parallel with myositis activity, suggesting a pathogenic

  4. Structural basis for assembly and function of the Nup82 complex in the nuclear pore scaffold

    PubMed Central

    Gaik, Monika; Flemming, Dirk; von Appen, Alexander; Kastritis, Panagiotis; Mücke, Norbert; Fischer, Jessica; Stelter, Philipp; Ori, Alessandro; Bui, Khanh Huy; Baßler, Jochen; Barbar, Elisar

    2015-01-01

    Nuclear pore complexes (NPCs) are huge assemblies formed from ∼30 different nucleoporins, typically organized in subcomplexes. One module, the conserved Nup82 complex at the cytoplasmic face of NPCs, is crucial to terminate mRNA export. To gain insight into the structure, assembly, and function of the cytoplasmic pore filaments, we reconstituted in yeast the Nup82–Nup159–Nsp1–Dyn2 complex, which was suitable for biochemical, biophysical, and electron microscopy analyses. Our integrative approach revealed that the yeast Nup82 complex forms an unusual asymmetric structure with a dimeric array of subunits. Based on all these data, we developed a three-dimensional structural model of the Nup82 complex that depicts how this module might be anchored to the NPC scaffold and concomitantly can interact with the soluble nucleocytoplasmic transport machinery. PMID:25646085

  5. Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe.

    PubMed

    Asakawa, Haruhiko; Yang, Hui-Ju; Yamamoto, Takaharu G; Ohtsuki, Chizuru; Chikashige, Yuji; Sakata-Sogawa, Kumiko; Tokunaga, Makio; Iwamoto, Masaaki; Hiraoka, Yasushi; Haraguchi, Tokuko

    2014-01-01

    The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8-47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC.

  6. Characterization of nuclear pore complex components in fission yeast Schizosaccharomyces pombe

    PubMed Central

    Asakawa, Haruhiko; Yang, Hui-Ju; Yamamoto, Takaharu G; Ohtsuki, Chizuru; Chikashige, Yuji; Sakata-Sogawa, Kumiko; Tokunaga, Makio; Iwamoto, Masaaki; Hiraoka, Yasushi; Haraguchi, Tokuko

    2014-01-01

    The nuclear pore complex (NPC) is an enormous proteinaceous complex composed of multiple copies of about 30 different proteins called nucleoporins. In this study, we analyzed the composition of the NPC in the model organism Schizosaccharomyces pombe using strains in which individual nucleoporins were tagged with GFP. We identified 31 proteins as nucleoporins by their localization to the nuclear periphery. Gene disruption analysis in previous studies coupled with gene disruption analysis in the present study indicates that 15 of these nucleoporins are essential for vegetative cell growth and the other 16 nucleoporins are non-essential. Among the 16 non-essential nucleoporins, 11 are required for normal progression through meiosis and their disruption caused abnormal spore formation or poor spore viability. Based on fluorescence measurements of GFP-fused nucleoporins, we estimated the composition of the NPC in S. pombe and found that the organization of the S. pombe NPC is largely similar to that of other organisms; a single NPC was estimated as being 45.8–47.8 MDa in size. We also used fluorescence measurements of single NPCs and quantitative western blotting to analyze the composition of the Nup107-Nup160 subcomplex, which plays an indispensable role in NPC organization and function. Our analysis revealed low amounts of Nup107 and Nup131 and high amounts of Nup132 in the Nup107-Nup160 subcomplex, suggesting that the composition of this complex in S. pombe may differ from that in S. cerevisiae and humans. Comparative analysis of NPCs in various organisms will lead to a comprehensive understanding of the functional architecture of the NPC. PMID:24637836

  7. Optical recording of signal-mediated protein transport through single nuclear pore complexes.

    PubMed

    Keminer, O; Siebrasse, J P; Zerf, K; Peters, R

    1999-10-12

    Optical single-transporter recording, a recently established fluorescence microscopic method, was used to study the selective transport of proteins through single nuclear pore complexes (NPCs) of Xenopus oocytes. Recombinant proteins containing either a nuclear localization signal (import protein) or a nuclear export signal (export protein) were generated as transport substrates. To approximate in vivo conditions as closely as possible, a Xenopus egg extract was applied to the cytosolic side and a Xenopus oocyte nuclear extract to the nuclear side of the NPCs. It was found that protein transport through functionally isolated, "patched" NPCs depended on signal sequences, extracts, and metabolic energy, as in vivo. All NPCs were competent for both import and export. The transport direction was strictly determined by the transport signal, and at none of the conditions explored was the import protein exported or the export protein imported, even when the application sides of the extracts were reversed. The mean transport rates of the single NPC were approximately 2 dimers/s for the import protein and approximately 4 dimers/s for the export protein ( approximately 15 microM substrate concentration, 22-24 degrees C), in good agreement with in vivo rates estimated for mammalian cells by microinjection experiments. The study shows that optical single-transporter recording permits the analysis of membrane transport processes not previously accessible to single-transporter recording and thus provides additional possibilities for the elucidation of nucleocytoplasmic transport mechanisms. PMID:10518538

  8. Optical recording of signal-mediated protein transport through single nuclear pore complexes

    PubMed Central

    Keminer, Oliver; Siebrasse, Jan-Peter; Zerf, Katja; Peters, Reiner

    1999-01-01

    Optical single-transporter recording, a recently established fluorescence microscopic method, was used to study the selective transport of proteins through single nuclear pore complexes (NPCs) of Xenopus oocytes. Recombinant proteins containing either a nuclear localization signal (import protein) or a nuclear export signal (export protein) were generated as transport substrates. To approximate in vivo conditions as closely as possible, a Xenopus egg extract was applied to the cytosolic side and a Xenopus oocyte nuclear extract to the nuclear side of the NPCs. It was found that protein transport through functionally isolated, “patched” NPCs depended on signal sequences, extracts, and metabolic energy, as in vivo. All NPCs were competent for both import and export. The transport direction was strictly determined by the transport signal, and at none of the conditions explored was the import protein exported or the export protein imported, even when the application sides of the extracts were reversed. The mean transport rates of the single NPC were ≈2 dimers/s for the import protein and ≈4 dimers/s for the export protein (≈15 μM substrate concentration, 22–24°C), in good agreement with in vivo rates estimated for mammalian cells by microinjection experiments. The study shows that optical single-transporter recording permits the analysis of membrane transport processes not previously accessible to single-transporter recording and thus provides additional possibilities for the elucidation of nucleocytoplasmic transport mechanisms. PMID:10518538

  9. Pom121 links two essential subcomplexes of the nuclear pore complex core to the membrane

    PubMed Central

    Mitchell, Jana M.; Mansfeld, Jörg; Capitanio, Juliana; Kutay, Ulrike

    2010-01-01

    Nuclear pore complexes (NPCs) control the movement of molecules across the nuclear envelope (NE). We investigated the molecular interactions that exist at the interface between the NPC scaffold and the pore membrane. We show that key players mediating these interactions in mammalian cells are the nucleoporins Nup155 and Nup160. Nup155 depletion massively alters NE structure, causing a dramatic decrease in NPC numbers and the improper targeting of membrane proteins to the inner nuclear membrane. The role of Nup155 in assembly is likely closely linked to events at the membrane as we show that Nup155 interacts with pore membrane proteins Pom121 and NDC1. Furthermore, we demonstrate that the N terminus of Pom121 directly binds the β-propeller regions of Nup155 and Nup160. We propose a model in which the interactions of Pom121 with Nup155 and Nup160 are predicted to assist in the formation of the nuclear pore and the anchoring of the NPC to the pore membrane. PMID:20974814

  10. Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex

    PubMed Central

    Kampmann, Martin; Blobel, Günter

    2009-01-01

    Summary The Nuclear Pore Complex (NPC) mediates nucleocytoplasmic transport in all eukaryotes and is among the largest cellular assemblies of proteins, collectively referred to as nucleoporins (nups). Nups are organized into distinct subcomplexes. We optimized the isolation of a putative membrane-coating subcomplex of the NPC, the heptameric Nup84 complex, and analyzed its structure by electron microscopy (EM). Our data confirm the previously reported Y-shape. We discerned additional structural details, including specific hinge regions at which the particle shows great flexibility. We determined the three-dimensional structures of two conformers, mapped the localization of two nups within the subcomplex and docked known crystal structures into the EM maps. The free ends of the Y-shaped particle are formed by beta-propellers; the connecting segments consist of alpha-solenoids. Strikingly, the same organizational principle is found in the clathrin triskelion, which was proposed to share a common evolutionary origin with the heptameric complex. PMID:19503077

  11. The SUMO proteases SENP1 and SENP2 play a critical role in nucleoporin homeostasis and nuclear pore complex function.

    PubMed

    Chow, Kin-Hoe; Elgort, Suzanne; Dasso, Mary; Powers, Maureen A; Ullman, Katharine S

    2014-01-01

    Nuclear pore complexes are composed of ∼30 different proteins, each present at the pore in multiple copies. Together these proteins create specialized channels that convey cargo between the cytoplasm and the nuclear interior. With the building blocks of nuclear pores identified, one challenge is to decipher how these proteins are coordinately produced and assembled into macromolecular pore structures with each cell division. Specific individual pore proteins and protein cofactors have been probed for their role in the assembly process, as well as certain kinases that add a layer of regulation via the phosphorylation status of nucleoporins. Other posttranslational modifications are candidates for coordinating events of pore assembly as well. In this study of two pore-associated small ubiquitin-like modifier (SUMO) proteases, sentrin/SUMO-specific protease 1 (SENP1) and SENP2, we observe that many nucleoporins are mislocalized and, in some cases, reduced in level when SENP1 and SENP2 are codepleted. The pore complexes present under these conditions are still capable of transport, although the kinetics of specific cargo is altered. These results reveal a new role for the pore-associated SENPs in nucleoporin homeostasis and in achieving proper configuration of the nuclear pore complex. PMID:24196834

  12. Mislocalization of prelamin A Tyr646Phe mutant to the nuclear pore complex in human embryonic kidney 293 cells

    SciTech Connect

    Pan, Yong; Garg, Abhimanyu; Agarwal, Anil K. . E-mail: anil.agarwal@utsouthwestern.edu

    2007-03-30

    Mature lamin A is formed after post-translational processing of prelamin A, which includes prenylation and carboxymethylation of cysteine 661 in the CaaX motif, followed by two proteolytic cleavages by zinc metalloprotease (ZMPSTE24). We expressed several prelamin A mutants, C661S (defective in prenylation), Y646F (designed to undergo prenylation but not second proteolytic cleavage), double mutant, Y646F/C661S and Y646X (mature lamin A), and the wild-type construct in human embryonic kidney (HEK-293) cells. Only the Y646F mutant co-localized with nuclear pore complex proteins, including Nup53 and Nup98, whereas the other mutants localized to the nuclear envelope rim. The cells expressing Y646F mutant also revealed abnormal nuclear morphology which was partially rescued with the farnesyl transferase inhibitors. These data suggest that the unprenylated prelamin A is not toxic to the cells. The toxicity of prenylated prelamin A may be due to its association and/or accumulation at the nuclear pore complex which could be partially reversed by farnesyl transferase inhibitors.

  13. Targeting and function in mRNA export of nuclear pore complex protein Nup153

    PubMed Central

    1996-01-01

    Nup153 is a large (153 kD) O-linked glyco-protein which is a component of the basket structure located on the nucleoplasmic face of nuclear pore complexes. This protein exhibits a tripartite structure consisting of a zinc finger domain flanked by large (60-70 kD) NH2- and COOH- terminal domains. When full-length human Nup153 is expressed in BHK cells, it accumulates appropriately at the nucleoplasmic face of the nuclear envelope. Targeting information for Nup153 resides in the NH2- terminal domain since this region of the molecule can direct an ordinarily cytoplasmic protein, pyruvate kinase, to the nuclear face of the nuclear pore complex. Overexpression of Nup153 results in the dramatic accumulation of nuclear poly (A)+ RNA, suggesting an inhibition of RNA export from the nucleus. This is not due to a general decline in nucleocytoplasmic transport or to occlusion or loss of nuclear pore complexes since nuclear protein import is unaffected. While overexpression of certain Nup153 constructs was found to result in the formation of unusual intranuclear membrane arrays, this structural phenotype could not be correlated with the effects on poly (A)+ RNA distribution. The RNA trafficking defect was, however, dependent upon the Nup153 COOH-terminal domain which contains most of the XFXFG repeats. It is proposed that this region of Nup153, lying within the distal ring of the nuclear basket, represents a docking site for mRNA molecules exiting the nucleus. PMID:8794857

  14. The outer membrane usher forms a twin-pore secretion complex.

    PubMed

    Li, Huilin; Qian, Luping; Chen, Zhiqiang; Thibault, Danielle; Liu, Guang; Liu, Tianbo; Thanassi, David G

    2004-12-10

    The PapC usher is an outer membrane protein required for assembly and secretion of P pili in uropathogenic Escherichia coli. P pilus biogenesis occurs by the chaperone/usher pathway, a terminal branch of the general secretory pathway. Periplasmic chaperone-subunit complexes target to the PapC usher for fiber assembly and secretion through the usher to the cell surface. The molecular details of pilus biogenesis at the usher, and protein secretion across the outer membrane in general, are unclear. We studied the structure and oligomeric state of PapC by gel filtration, dynamic light scattering, and electron microscopy and image analysis. Two-dimensional crystals of wild-type PapC and a C-terminal deletion mutant of PapC were produced by reconstituting detergent purified usher into E.coli lipids. PapC formed a dimer both in detergent solution and in the phospholipid bilayer. Cryo-electron microscopy revealed that the usher forms a twin-pore complex. Removal of the C-terminal domain did not change the basic shape of the PapC molecule, but altered the dimeric association of the usher, suggesting that the C terminus forms part of the dimerization interface. The overall molecular size (11 nm), pore size (2 nm), and twin-pore configuration of PapC resemble that of the Tom40 complex, a mitochondrial outer membrane protein translocase.

  15. Pore-controlled formation of 0D metal complexes in anionic 3D metal-organic frameworks

    SciTech Connect

    Zhang, MW; Bosch, M; Zhou, HC

    2015-01-01

    The host-guest chemistry between a series of anionic MOFs and their trapped counterions was investigated by single crystal XRD. The PCN-514 series contains crystallographically identifiable metal complexes trapped in the pores, where their formation is controlled by the size and shape of the MOF pores. A change in the structure and pore size of PCN-518 indicates that the existence of guest molecules may reciprocally affect the formation of host MOFs.

  16. Local X-ray Computed Tomography Imaging for Mineralogical and Pore Characterization

    NASA Astrophysics Data System (ADS)

    Mills, G.; Willson, C. S.

    2015-12-01

    Sample size, material properties and image resolution are all tradeoffs that must be considered when imaging porous media samples with X-ray computed tomography. In many natural and engineered samples, pore and throat sizes span several orders of magnitude and are often correlated with the material composition. Local tomography is a nondestructive technique that images a subvolume, within a larger specimen, at high resolution and uses low-resolution tomography data from the larger specimen to reduce reconstruction error. The high-resolution, subvolume data can be used to extract important fine-scale properties but, due to the additional noise associated with the truncated dataset, it makes segmentation of different materials and mineral phases a challenge. The low-resolution data of a larger specimen is typically of much higher-quality making material characterization much easier. In addition, the imaging of a larger domain, allows for mm-scale bulk properties and heterogeneities to be determined. In this research, a 7 mm diameter and ~15 mm in length sandstone core was scanned twice. The first scan was performed to cover the entire diameter and length of the specimen at an image voxel resolution of 4.1 μm. The second scan was performed on a subvolume, ~1.3 mm in length and ~2.1 mm in diameter, at an image voxel resolution of 1.08 μm. After image processing and segmentation, the pore network structure and mineralogical features were extracted from the low-resolution dataset. Due to the noise in the truncated high-resolution dataset, several image processing approaches were applied prior to image segmentation and extraction of the pore network structure and mineralogy. Results from the different truncated tomography segmented data sets are compared to each other to evaluate the potential of each approach in identifying the different solid phases from the original 16 bit data set. The truncated tomography segmented data sets were also compared to the whole

  17. Ran-unassisted nuclear migration of a 97-kD component of nuclear pore-targeting complex.

    PubMed

    Kose, S; Imamoto, N; Tachibana, T; Shimamoto, T; Yoneda, Y

    1997-11-17

    A 97-kD component of nuclear pore-targeting complex (the beta-subunit of nuclear pore-targeting complex [PTAC]/importin/karyopherin) mediates the import of nuclear localization signal (NLS)-containing proteins by anchoring the NLS receptor protein (the alpha-subunit of PTAC/importin/karyopherin) to the nuclear pore complex (NPC). The import requires a small GTPase Ran, which interacts directly with the beta-subunit. The present study describes an examination of the behavior of the beta-subunit in living cells and in digitonin-permeabilized cells. In living cells, cytoplasmically injected beta-subunit rapidly migrates into the nucleus. The use of deletion mutants reveals that nuclear migration of the beta-subunit requires neither Ran- nor alpha-subunit-binding but only the NPC-binding domain of this molecule, which is also involved in NLS-mediated import. Furthermore, unlike NLS-mediated import, a dominant-negative Ran, defective in GTP-hydrolysis, did not inhibit nuclear migration of the beta-subunit. In the digitonin-permeabilized cell-free import assay, the beta-subunit transits rapidly through the NPC into the nucleus in a saturating manner in the absence of exogenous addition of soluble factors. These results show that the beta-subunit undergoes translocation at the NPC in a Ran-unassisted manner when it does not carry alpha-subunit/NLS substrate. Therefore, a requirement for Ran arises only when the beta-subunit undergoes a translocation reaction together with the alpha-subunit/NLS substrate. The results provide an insight to the yet unsolved question regarding the mechanism by which proteins are directionally transported through the NPC, and the role of Ran in this process.

  18. A Novel Saccharomyces cerevisiae FG Nucleoporin Mutant Collection for Use in Nuclear Pore Complex Functional Experiments.

    PubMed

    Adams, Rebecca L; Terry, Laura J; Wente, Susan R

    2015-11-03

    FG nucleoporins (Nups) are the class of proteins that both generate the permeability barrier and mediate selective transport through the nuclear pore complex (NPC). The FG Nup family has 11 members in Saccharomyces cerevisiae, and the study of mutants lacking different FG domains has been instrumental in testing transport models. To continue analyzing the distinct functional roles of FG Nups in vivo, additional robust genetic tools are required. Here, we describe a novel collection of S. cerevisiae mutant strains in which the FG domains of different groups of Nups are absent (Δ) in the greatest number documented to date. Using this plasmid-based ΔFG strategy, we find that a GLFG domain-only pore is sufficient for viability. The resulting extensive plasmid and strain resources are available to the scientific community for future in-depth in vivo studies of NPC transport.

  19. Structural Evidence for Common Ancestry of the Nuclear Pore Complex and Vesicle Coats

    SciTech Connect

    Brohawn, S.; Leksa, N; Spear, E; Rajashankar, K; Schwartz, T

    2008-01-01

    Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)bulletSeh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.

  20. Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex

    PubMed Central

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Upla, Paula; Rice, William J.; Phillips, Jeremy; Timney, Benjamin L.; Pieper, Ursula; Bonanno, Jeffrey B.; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Ketaren, Natalia E.; Matsui, Tsutomu; Weiss, Thomas M.; Stokes, David L.; Sauder, J. Michael; Burley, Stephen K.; Sali, Andrej; Rout, Michael P.; Almo, Steven C.

    2013-01-01

    Summary The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC’s inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2–960 [ScNup192(2–960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2–960) could undergo long-range transition between “open” and “closed” conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2–960), and homology modeling. Evolutionary analyses using the ScNup192(2–960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel. PMID:23499021

  1. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex.

    PubMed

    Sampathkumar, Parthasarathy; Kim, Seung Joong; Upla, Paula; Rice, William J; Phillips, Jeremy; Timney, Benjamin L; Pieper, Ursula; Bonanno, Jeffrey B; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Ketaren, Natalia E; Matsui, Tsutomu; Weiss, Thomas M; Stokes, David L; Sauder, J Michael; Burley, Stephen K; Sali, Andrej; Rout, Michael P; Almo, Steven C

    2013-04-01

    The nuclear pore complex, composed of proteins termed nucleoporins (Nups), is responsible for nucleocytoplasmic transport in eukaryotes. Nuclear pore complexes (NPCs) form an annular structure composed of the nuclear ring, cytoplasmic ring, a membrane ring, and two inner rings. Nup192 is a major component of the NPC's inner ring. We report the crystal structure of Saccharomyces cerevisiae Nup192 residues 2-960 [ScNup192(2-960)], which adopts an α-helical fold with three domains (i.e., D1, D2, and D3). Small angle X-ray scattering and electron microscopy (EM) studies reveal that ScNup192(2-960) could undergo long-range transition between "open" and "closed" conformations. We obtained a structural model of full-length ScNup192 based on EM, the structure of ScNup192(2-960), and homology modeling. Evolutionary analyses using the ScNup192(2-960) structure suggest that NPCs and vesicle-coating complexes are descended from a common membrane-coating ancestral complex. We show that suppression of Nup192 expression leads to compromised nuclear transport and hypothesize a role for Nup192 in modulating the permeability of the NPC central channel. PMID:23499021

  2. Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function

    PubMed Central

    Ando, David; Zandi, Roya; Kim, Yong Woon; Colvin, Michael; Rexach, Michael; Gopinathan, Ajay

    2014-01-01

    The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature. We perform coarse-grained simulations of both individual nucleoporins and grafted rings of nups mimicking the in vivo geometry of the NPC and supplement this with polymer brush modeling. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability. PMID:24806932

  3. Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

    PubMed Central

    Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

    2014-01-01

    The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ~5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC1. Whilst the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized2-5, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins5,6, and is therefore not well understood. Here, we show that stiffness topography7 with sharp atomic force microscopy tips can generate nanoscale cross sections of the NPC. The cross sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy2-5. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport, and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel. PMID:25420031

  4. Structural evolution of the membrane-coating module of the nuclear pore complex

    PubMed Central

    Liu, Xiaoping; Mitchell, Jana M.; Wozniak, Richard W.; Blobel, Günter; Fan, Jie

    2012-01-01

    The coatomer module of the nuclear pore complex borders the cylinder-like nuclear pore-membrane domain of the nuclear envelope. In evolution, a single coatomer module increases in size from hetero-heptamer (Saccharomyces cerevisiae) to hetero-octamer (Schizosaccharomyces pombe) to hetero-nonamer (Metazoa). Notably, the heptamer–octamer transition proceeds through the acquisition of the nucleoporin Nup37. How Nup37 contacts the heptamer remained unknown. Using recombinant nucleoporins, we show that Sp-Nup37 specifically binds the Sp-Nup120 member of the hetero-heptamer but does not bind an Sc-Nup120 homolog. To elucidate the Nup37–Nup120 interaction at the atomic level, we carried out crystallographic analyses of Sp-Nup37 alone and in a complex with an N-terminal, ∼110-kDa fragment of Sp-Nup120 comprising residues 1–950. Corroborating structural predictions, we determined that Nup37 folds into a seven-bladed β-propeller. Several disordered surface regions of the Nup37 β-propeller assume structure when bound to Sp-Nup120. The N-terminal domain of Sp-Nup1201–950 also folds into a seven-bladed propeller with a markedly protruding 6D–7A insert and is followed by a contorted helical domain. Conspicuously, this 6D–7A insert contains an extension of 50 residues which also is highly conserved in Metazoa but is absent in Sc-Nup120. Strikingly, numerous contacts with the Nup37 β-propeller are located on this extension of the 6D–7A insert. Another contact region is situated toward the end of the helical region of Sp-Nup1201–950. Our findings provide information about the evolution and the assembly of the coatomer module of the nuclear pore complex. PMID:23019579

  5. Fluorescence Anisotropy Reveals Order and Disorder of Protein Domains in the Nuclear Pore Complex

    PubMed Central

    Mattheyses, Alexa L.; Kampmann, Martin; Atkinson, Claire E.; Simon, Sanford M.

    2010-01-01

    We present a new approach for studying individual protein domains within the nuclear pore complex (NPC) using fluorescence polarization microscopy. The NPC is a large macromolecular complex, the size and complexity of which presents experimental challenges. Using fluorescence anisotropy and exploiting the symmetry of the NPC and its organization in the nuclear envelope, we have resolved order and disorder of individual protein domains. Fluorescently tagging specific domains of individual nucleoporins revealed both rigid and flexible domains: the tips of the FG domains are disordered, whereas the NPC-anchored domains are ordered. Our technique allows the collection of structural information in vivo, providing the ability to probe the organization of protein domains within the NPC. This has particular relevance for the FG domain nucleoporins, which are crucial for nucleocytoplasmic transport. PMID:20858414

  6. Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance

    PubMed Central

    Onischenko, Evgeny; Stanton, Leslie H.; Madrid, Alexis S.; Kieselbach, Thomas

    2009-01-01

    The nuclear pore complex (NPC) mediates all nucleocytoplasmic transport, yet its structure and biogenesis remain poorly understood. In this study, we have functionally characterized interaction partners of the yeast transmembrane nucleoporin Ndc1. Ndc1 forms a distinct complex with the transmembrane proteins Pom152 and Pom34 and two alternative complexes with the soluble nucleoporins Nup53 and Nup59, which in turn bind to Nup170 and Nup157. The transmembrane and soluble Ndc1-binding partners have redundant functions at the NPC, and disruption of both groups of interactions causes defects in Ndc1 targeting and in NPC structure accompanied by significant pore dilation. Using photoconvertible fluorescent protein fusions, we further show that the depletion of Pom34 in cells that lack NUP53 and NUP59 blocks new NPC assembly and leads to the reversible accumulation of newly made nucleoporins in cytoplasmic foci. Therefore, Ndc1 together with its interaction partners are collectively essential for the biosynthesis and structural integrity of yeast NPCs. PMID:19414609

  7. A negative loop within the nuclear pore complex controls global chromatin organization

    PubMed Central

    Breuer, Manuel; Ohkura, Hiroyuki

    2015-01-01

    The nuclear pore complex (NPC) tethers chromatin to create an environment for gene regulation, but little is known about how this activity is regulated to avoid excessive tethering of the genome. Here we propose a negative regulatory loop within the NPC controlling the chromatin attachment state, in which Nup155 and Nup93 recruit Nup62 to suppress chromatin tethering by Nup155. Depletion of Nup62 severely disrupts chromatin distribution in the nuclei of female germlines and somatic cells, which can be reversed by codepleting Nup155. Thus, this universal regulatory system within the NPC is crucial to control large-scale chromatin organization in the nucleus. PMID:26341556

  8. The nuclear pore complex mystery and anomalous diffusion in reversible gels.

    PubMed Central

    Bickel, Thomas; Bruinsma, Robijn

    2002-01-01

    The exchange of macromolecules between the cytoplasm and the nucleus of eukaryotic cells takes place through the nuclear pore complex (NPC), which contains a selective permeability barrier. Experiments on the physical properties of this barrier appear to be in conflict with current physical understanding of the rheology of reversible gels. This paper proposes that the NPC gel is anomalous and characterized by connectivity fluctuations. It develops a simplified model to demonstrate the possibility of enhanced diffusion constants of macromolecules trapped in such a gel. PMID:12496079

  9. Toward the atomic structure of the nuclear pore complex: when top down meets bottom up.

    PubMed

    Hoelz, André; Glavy, Joseph S; Beck, Martin

    2016-07-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, owing to its sheer size and flexibility, the NPC is unapproachable by classical structure determination techniques and requires a joint effort of complementary methods. Whereas bottom-up approaches rely on biochemical interaction studies and crystal-structure determination of NPC components, top-down approaches attempt to determine the structure of the intact NPC in situ. Recently, both approaches have converged, thereby bridging the resolution gap from the higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function.

  10. Complex resistivity spectra in relation to multiscale pore geometry in carbonates and mixed-siliciclastic rocks

    NASA Astrophysics Data System (ADS)

    Norbisrath, Jan Henrik

    Carbonate rocks are known to have complex and heterogeneous pore structures, which result from their biogenic origin and strong affinity for diagenetic processes that change their pore structure after burial. The combination of sheer endless variations of precursor biogenic material, depositional environments, and diagenetic effects results in rocks that are interesting to study but intricate to understand. Many schemes to categorize the diversity of carbonate rocks are in use today; most are based on the macropore structure and qualitative thin-section analysis. Many studies, however, acknowledge that micropores have a significant influence on the macroscopic petrophysical rock properties, which are essential to determine reservoir quality. Micropores are, by definition, smaller than the thickness of a thin-section (< 30 microm) and hence cannot be quantified with conventional methods. For their analysis, scanning electron microscopy (SEM) is the logical next step. The challenge is that mechanical polishing methods produce excessive surface roughness at micron scale; the resulting surfaces are not suited for quantification of micropores. Advances in broad-ion-beam (BIB) milling enable preparation of nanometer-precision 2D sections that are suited for quantitative analysis with the SEM. To accomplish the objective of accurate quantification of carbonate micropores, part one of this dissertation employs the BIB-SEM technique on a variety of carbonate rock samples and finds four major carbonate microporosity types: (1) small intercrystalline, (2) large inter-crystalline, (3) intercement, and (4) micromoldic. Each microporosity type shows a distinct capacity to conduct electrical charge, which largely controls the magnitude and range of cementation factors (m) in rocks with such microporosity type. The BIB-SEM method is also used on a dataset of mixed carbonate-siliciclastic (mudrock) samples with high kerogen and pyrite content. Results show that the nanopore

  11. GLE2, a Saccharomyces cerevisiae homologue of the Schizosaccharomyces pombe export factor RAE1, is required for nuclear pore complex structure and function.

    PubMed Central

    Murphy, R; Watkins, J L; Wente, S R

    1996-01-01

    To identify and characterize novel factors required for nuclear transport, a genetic screen was conducted in the yeast Saccharomyces cerevisiae. Mutations that were lethal in combination with a null allele of the gene encoding the nucleoporin Nup100p were isolated using a colony-sectoring assay. Three complementation groups of gle (for GLFG lethal) mutants were identified. In this report, the characterization of GLE2 is detailed. GLE2 encodes a 40.5-kDa polypeptide with striking similarity to that of Schizosaccharomyces pombe RAE1. In indirect immunofluorescence and nuclear pore complex fractionation experiments, Gle2p was associated with nuclear pore complexes. Mutated alleles of GLE2 displayed blockage of polyadenylated RNA export; however, nuclear protein import was not apparently diminished. Immunofluorescence and thin-section electron microscopic analysis revealed that the nuclear pore complex and nuclear envelope structure was grossly perturbed in gle2 mutants. Because the clusters of herniated pore complexes appeared subsequent to the export block, the structural perturbations were likely indirect consequences of the export phenotype. Interestingly, a two-hybrid interaction was detected between Gle2p and Srp1p, the nuclear localization signal receptor, as well as Rip1p, a nuclear export signal-interacting protein. We propose that Gle2p has a novel role in mediating nuclear transport. Images PMID:8970155

  12. Model Inspired by Nuclear Pore Complex Suggests Possible Roles for Nuclear Transport Receptors in Determining Its Structure

    PubMed Central

    Osmanović, Dino; Ford, Ian J.; Hoogenboom, Bart W.

    2013-01-01

    Nuclear transport receptors (NTRs) mediate nucleocytoplasmic transport via their affinity for unstructured proteins (polymers) in the nuclear pore complex (NPC). Here, we have modeled the effect of NTRs on polymeric structure in the nanopore confinement of the NPC central conduit. The model explicitly takes into account inter- and intramolecular interactions, as well as the finite size of the NTRs (∼20% of the NPC channel diameter). It reproduces various proposed scenarios for the channel structure, ranging from a central polymer condensate (selective phase) to brushlike polymer arrangements localized at the channel wall (virtual gate, reduction of dimensionality), with the transport receptors lining the polymer surface. In addition, it predicts a new structure in which NTRs become an integral part of the transport barrier by forming a cross-linked network with the unstructured proteins stretching across the pore. The model provides specific and distinctive predictions for the equilibrium spatial distributions of NTRs for these different scenarios that can be experimentally verified by, e.g., superresolution fluorescence microscopy. Moreover, it suggests mechanisms by which globular macromolecules (colloidal particles) can cause polymer-coated nanopores to switch between open and closed configurations, a possible explanation of the biological function of the NPC, and suggests potential technological applications for filtration and single-molecule sensing. PMID:24359750

  13. Saccharomyces cerevisiae Ndc1p Is a Shared Component of Nuclear Pore Complexes and Spindle Pole Bodies

    PubMed Central

    Chial, Heidi J.; Rout, Michael P.; Giddings, Thomas H.; Winey, Mark

    1998-01-01

    We report a novel connection between nuclear pore complexes (NPCs) and spindle pole bodies (SPBs) revealed by our studies of the Saccharomyces cerevisiae NDC1 gene. Although both NPCs and SPBs are embedded in the nuclear envelope (NE) in yeast, their known functions are quite distinct. Previous work demonstrated that NDC1 function is required for proper SPB duplication (Winey, M., M.A. Hoyt, C. Chan, L. Goetsch, D. Botstein, and B. Byers. 1993. J. Cell Biol. 122:743–751). Here, we show that Ndc1p is a membrane protein of the NE that localizes to both NPCs and SPBs. Indirect immunofluorescence microscopy shows that Ndc1p displays punctate, nuclear peripheral localization that colocalizes with a known NPC component, Nup49p. Additionally, distinct spots of Ndc1p localization colocalize with a known SPB component, Spc42p. Immunoelectron microscopy shows that Ndc1p localizes to the regions of NPCs and SPBs that interact with the NE. The NPCs in ndc1-1 mutant cells appear to function normally at the nonpermissive temperature. Finally, we have found that a deletion of POM152, which encodes an abundant but nonessential nucleoporin, suppresses the SPB duplication defect associated with a mutation in the NDC1 gene. We show that Ndc1p is a shared component of NPCs and SPBs and propose a shared function in the assembly of these organelles into the NE. PMID:9864355

  14. Selectivity Mechanism of the Nuclear Pore Complex Characterized by Single Cargo Tracking

    PubMed Central

    Lowe, Alan R.; Siegel, Jake J.; Kalab, Petr; Siu, Merek; Weis, Karsten; Liphardt, Jan T.

    2010-01-01

    The Nuclear Pore Complex (NPC) mediates all exchange between the cytoplasm and the nucleus. Small molecules can passively diffuse through the NPC, while larger cargos require transport receptors to translocate1. How the NPC facilitates the translocation of transport receptor/cargo complexes remains unclear. Here, we track single protein-functionalized Quantum Dot (QD) cargos as they translocate the NPC. Import proceeds by successive sub-steps comprising cargo capture, filtering and translocation, and release into the nucleus. The majority of QDs are rejected at one of these steps and return to the cytoplasm including very large cargos that abort at a size-selective barrier. Cargo movement in the central channel is subdiffusive and cargos that can bind more transport receptors diffuse more freely. Without Ran, cargos still explore the entire NPC, but have a markedly reduced probability of exit into the nucleus, suggesting that NPC entry and exit steps are not equivalent and that the pore is functionally asymmetric to importing cargos. The overall selectivity of the NPC appears to arise from the cumulative action of multiple reversible sub-steps and a final irreversible exit step. PMID:20811366

  15. Polymer brushes infiltrated by nanoparticles and applications to the nuclear pore complex

    NASA Astrophysics Data System (ADS)

    Opferman, Michael G.

    Systems of grafted polymers in the presence of additives are useful in a variety of contexts including industrial applications, solar cells, organic electronics, drug delivery, and nucleocytoplasmic transport. In this thesis, we will consider the morphologies that polymer brushes attain when exposed to a solution of additives (which we generically term "nanoparticles"), particularly when those nanparticles interact attractively with the polymers. We find that nanoparticles of this type can have a dramatic effect on the height of the polymer chains above the grafting surface, and they can induce highly non-uniform morphologies, including ones in which a dense layer of nanoparticles and monomers forms near the grafting surface. We consider especially the relevance of the system to several experiments performed on biopolymers in the nuclear pore complex when they interact attractively with transport factors that regulate nucleocytoplasmic transport. We find that, although these experiments appear to give inconsistent results, the inconsistencies can be reconciled through two simple models: the Alexander-de Gennes polymer brush, and the Milner-Witten-Cates polymer brush. Our findings should contribute to the understanding of the nuclear pore complex in that experiments can be better understood in the context of their relevant control parameters.

  16. Posttranslational marks control architectural and functional plasticity of the nuclear pore complex basket

    PubMed Central

    Niño, Carlos A.; Guet, David; Gay, Alexandre; Brutus, Sergine; Jourquin, Frédéric; Mendiratta, Shweta; Salamero, Jean; Géli, Vincent

    2016-01-01

    The nuclear pore complex (NPC) serves as both the unique gate between the nucleus and the cytoplasm and a major platform that coordinates nucleocytoplasmic exchanges, gene expression, and genome integrity. To understand how the NPC integrates these functional constraints, we dissected here the posttranslational modifications of the nuclear basket protein Nup60 and analyzed how they intervene to control the plasticity of the NPC. Combined approaches highlight the role of monoubiquitylation in regulating the association dynamics of Nup60 and its partner, Nup2, with the NPC through an interaction with Nup84, a component of the Y complex. Although major nuclear transport routes are not regulated by Nup60 modifications, monoubiquitylation of Nup60 is stimulated upon genotoxic stress and regulates the DNA-damage response and telomere repair. Together, these data reveal an original mechanism contributing to the plasticity of the NPC at a molecular-organization and functional level. PMID:26783300

  17. Influence of pore fluid chemistry on the complex conductivity and induced polarization responses of Berea sandstone

    NASA Astrophysics Data System (ADS)

    Lesmes, David P.; Frye, Kevin M.

    2001-01-01

    The spectral induced-polarization (IP) response of rocks and soils is a complex function of pore solution chemistry, sample microgeometry, and surface chemical properties. We measure the complex conductivity and the time domain IP responses of Berea sandstone as a function of pore fluid ionic strength and pH. Complex conductivity is measured over the frequency range 10-3 to 106 Hz, and chargeability is computed using a time window of 0.16 to 1.74 s. The field IP parameters: phase, percent frequency effect, and chargeability are functions of both the surface and bulk electrical properties of the sample and are observed to decrease with increasing solution conductivity. Dividing these parameters by the sample resistivity yields normalized IP parameters (quadrature conductivity, metal factor, normalized chargeability) that are proportional to the imaginary component of the complex surface conductivity. Normalized IP parameters increase with ionic strength up to concentrations of 10-1 M NaCl and show a reduced response at pH 3, the point of zero charge for quartz-dominated systems. For concentrations >10-1 M NaCl, the normalized parameters decrease with increasing concentration. This decrease in surface polarization may indicate a decrease in the effective mobility of polarizing charges at high solution concentration. Our data indicate that normalized IP parameters are directly related to the physiochemical parameters that control the surface conductivity responses of rocks and soils. Normalization of IP measurements in environmental investigations should increase the effectiveness of IP surveys, especially in high-conductivity environments.

  18. Local Geometrical Machinery for Complexity and Control

    NASA Astrophysics Data System (ADS)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    In this Chapter, we present local geometrical machinery for studying complexity and control, consisting of dynamics on Kähler manifolds, which combine three geometrical structures-Riemannian, symplectic and complex (Hermitian)-in a mutually compatible way. In other words, every Kähler manifold is simultaneously Riemannian, symplectic and complex (Hermitian). It is well known that Riemannian manifolds represent the stage on which Lagrangian dynamics is set, symplectic manifolds represent the stage for Hamiltonian dynamics, and complex (Hermitian) varieties comprise the stage for quantum dynamics. Therefore, Kähler manifolds represent the richest dynamical stage available where Lagrangian, Hamiltonian, and quantum dynamics all dance together.

  19. Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic framework.

    PubMed

    Alzahrani, Khalid A H; Deeth, Robert J

    2016-04-01

    A new all-atom first-principles force field (FF) is constructed for the bimetallic, four-bladed zinc paddlewheel (ZPW) motif. Zinc-ligand interactions are described via Morse functions and the angular geometry at the metal centers is modeled with a pure ligand-ligand repulsion term. The ZPW-FF is principally based on 15 DFT-optimized model systems of general formula ZnPR.nL, where ZnP is the base Zn2(O2CR)4 unit, R = H, CH3 or CF3, L = NH3 or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn2(O2CR)4] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D4h transition state conformations. The zinc-ligand Morse function reference distance, r 0 , is further refined against 30 complexes located in the Cambridge Structural Database and this FF is applied to pore models of the flexible metal-organic framework (MOF) [Zn(bdc)2(dabco)]n (bdc = 1,4-benzendicarboxylate; dabco = 1,4-diazabicyclo(2.2.2)octane). A single pore model reproduces the unit cell of the evacuated MOF system while a 3×3 grid model is necessary to provide good agreement with the observed pronounced structural changes upon adsorption of either dimethylformamide or benzene. PMID:26979608

  20. The human TREX-2 complex is stably associated with the nuclear pore basket.

    PubMed

    Umlauf, David; Bonnet, Jacques; Waharte, François; Fournier, Marjorie; Stierle, Matthieu; Fischer, Benoit; Brino, Laurent; Devys, Didier; Tora, László

    2013-06-15

    In eukaryotes, mRNA export involves many evolutionarily conserved factors that carry the nascent transcript to the nuclear pore complex (NPC). The THO/TREX complex couples transcription to mRNA export and recruits the mRNA export receptor NXF1 for the transport of messenger ribonucleoprotein particles (mRNP) to the NPC. The transcription and export complex 2 (TREX-2) was suggested to interact with NXF1 and to shuttle between transcription sites and the NPC. Here, we characterize the dynamics of human TREX-2 and show that it stably associates with the NPC basket. Moreover, the association of TREX-2 with the NPC requires the basket nucleoporins NUP153 and TPR, but is independent of transcription. Differential profiles of mRNA nuclear accumulation reveal that TREX-2 functions similarly to basket nucleoporins, but differently from NXF1. Thus, our results show that TREX-2 is an NPC-associated complex in mammalian cells and suggest that it is involved in putative NPC basket-related functions.

  1. The transmission of nuclear pore complexes to daughter cells requires a cytoplasmic pool of Nsp1.

    PubMed

    Colombi, Paolo; Webster, Brant M; Fröhlich, Florian; Lusk, C Patrick

    2013-10-28

    Nuclear pore complexes (NPCs) are essential protein assemblies that span the nuclear envelope and establish nuclear-cytoplasmic compartmentalization. We have investigated mechanisms that control NPC number in mother and daughter cells during the asymmetric division of budding yeast. By simultaneously tracking existing NPCs and newly synthesized NPC protomers (nups) through anaphase, we uncovered a pool of the central channel nup Nsp1 that is actively targeted to the bud in association with endoplasmic reticulum. Bud targeting required an intact actin cytoskeleton and the class V myosin, Myo2. Selective inhibition of cytoplasmic Nsp1 or inactivation of Myo2 reduced the inheritance of NPCs in daughter cells, leading to a daughter-specific loss of viability. Our data are consistent with a model in which Nsp1 releases a barrier that otherwise prevents NPC passage through the bud neck. It further supports the finding that NPC inheritance, not de novo NPC assembly, is primarily responsible for controlling NPC number in daughter cells.

  2. Clathrin inhibitor Pitstop-2 disrupts the nuclear pore complex permeability barrier

    PubMed Central

    Liashkovich, Ivan; Pasrednik, Dzmitry; Prystopiuk, Valeria; Rosso, Gonzalo; Oberleithner, Hans; Shahin, Victor

    2015-01-01

    Existence of a selective nucleocytoplasmic permeability barrier is attributed to Phenylalanine-Glycine rich proteins (FG-nups) within the central channel of the nuclear pore complex (NPC). Limited understanding of the FG-nup structural arrangement hinders development of strategies directed at disrupting the NPC permeability barrier. In this report we explore an alternative approach to enhancing the NPC permeability for exogenous macromolecules. We demonstrate that the recently discovered inhibitor of clathrin coat assembly Pitstop-2 compromises the NPC permeability barrier in a rapid and effective manner. Treatment with Pitstop-2 causes a collapse of the NPC permeability barrier and a reduction of Importin β binding accompanied by alteration of the NPC ultrastructure. Interestingly, the effects are induced by the same chemical agent that is capable of inhibiting clathrin-mediated endocytosis. To our knowledge, this is the first functional indication of the previously postulated evolutionary relation between clathrin and NPC scaffold proteins. PMID:25944393

  3. Molecular Architecture of the Transport Channel of the Nuclear Pore Complex

    SciTech Connect

    Solmaz, Sozanne R.; Chauhan, Radha; Blobel, Günter; Mel; #269; ák, Ivo

    2012-05-22

    The nuclear pore complex encloses a central channel for nucleocytoplasmic transport, which is thought to consist of three nucleoporins, Nup54, Nup58, and Nup62. However, the structure and composition of the channel are elusive. We determined the crystal structures of the interacting domains between these nucleoporins and pieced together the molecular architecture of the mammalian transport channel. Located in the channel midplane is a flexible Nup54Nup58 ring that can undergo large rearrangements yielding diameter changes from {approx}20 to {approx}40 nm. Nup62Nup54 triple helices project alternately up and down from either side of the midplane ring and form nucleoplasmic and cytoplasmic entries. The channel consists of as many as 224 copies of the three nucleoporins, amounting to a molar mass of 12.3 MDa and contributing 256 phenylalanine-glycine repeat regions. We propose that the occupancy of these repeat regions with transport receptors modulates ring diameter and transport activity.

  4. Cargo surface hydrophobicity is sufficient to overcome the nuclear pore complex selectivity barrier.

    PubMed

    Naim, Bracha; Zbaida, David; Dagan, Shlomi; Kapon, Ruti; Reich, Ziv

    2009-09-16

    To fulfil their function, nuclear pore complexes (NPCs) must discriminate between inert proteins and nuclear transport receptors (NTRs), admitting only the latter. This specific permeation is thought to depend on interactions between hydrophobic patches on NTRs and phenylalanine-glycine (FG) or related repeats that line the NPC. Here, we tested this premise directly by conjugating different hydrophobic amino-acid analogues to the surface of an inert protein and examining its ability to cross NPCs unassisted by NTRs. Conjugation of as few as four hydrophobic moieties was sufficient to enable passage of the protein through NPCs. Transport of the modified protein proceeded with rates comparable to those measured for the innate protein when bound to an NTR and was relatively insensitive both to the nature and density of the amino acids used to confer hydrophobicity. The latter observation suggests a non-specific, small, and plant interaction network between cargo and FG repeats.

  5. Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes.

    PubMed

    Labokha, Aksana A; Gradmann, Sabine; Frey, Steffen; Hülsmann, Bastian B; Urlaub, Henning; Baldus, Marc; Görlich, Dirk

    2013-01-23

    Nuclear pore complexes (NPCs) control the traffic between cell nucleus and cytoplasm. While facilitating translocation of nuclear transport receptors (NTRs) and NTR·cargo complexes, they suppress passive passage of macromolecules 30 kDa. Previously, we reconstituted the NPC barrier as hydrogels comprising S. cerevisiae FG domains. We now studied FG domains from 10 Xenopus nucleoporins and found that all of them form hydrogels. Related domains with low FG motif density also substantially contribute to the NPC's hydrogel mass. We characterized all these hydrogels and observed the strictest sieving effect for the Nup98-derived hydrogel. It fully blocks entry of GFP-sized inert objects, permits facilitated entry of the small NTR NTF2, but arrests importin β-type NTRs at its surface. O-GlcNAc modification of the Nup98 FG domain prevented this arrest and allowed also large NTR·cargo complexes to enter. Solid-state NMR spectroscopy revealed that the O-GlcNAc-modified Nup98 gel lacks amyloid-like β-structures that dominate the rigid regions in the S. cerevisiae Nsp1 FG hydrogel. This suggests that FG hydrogels can assemble through different structural principles and yet acquire the same NPC-like permeability.

  6. Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

    PubMed Central

    Obado, Samson O.; Brillantes, Marc; Uryu, Kunihiro; Zhang, Wenzhu; Ketaren, Natalia E.; Chait, Brian T.; Field, Mark C.; Rout, Michael P.

    2016-01-01

    The nuclear pore complex (NPC) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression. The components of NPCs from several eukaryotic lineages have been determined, but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level. Significantly, recent evidence indicates that compositional similarity does not necessarily correspond to homologous architecture between NPCs from different taxa. To address this, we describe the interactome of the trypanosome NPC, a representative, highly divergent eukaryote. We identify numerous new NPC components and report an exhaustive interactome, allowing assignment of trypanosome nucleoporins to discrete NPC substructures. Remarkably, despite retaining similar protein composition, there are exceptional architectural dissimilarities between opisthokont (yeast and vertebrates) and excavate (trypanosomes) NPCs. Whilst elements of the inner core are conserved, numerous peripheral structures are highly divergent, perhaps reflecting requirements to interface with divergent nuclear and cytoplasmic functions. Moreover, the trypanosome NPC has almost complete nucleocytoplasmic symmetry, in contrast to the opisthokont NPC; this may reflect divergence in RNA export processes at the NPC cytoplasmic face, as we find evidence supporting Ran-dependent mRNA export in trypanosomes, similar to protein transport. We propose a model of stepwise acquisition of nucleocytoplasmic mechanistic complexity and demonstrate that detailed dissection of macromolecular complexes provides fuller understanding of evolutionary processes. PMID:26891179

  7. Complex Patterns of Local Adaptation in Teosinte

    PubMed Central

    Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

    2013-01-01

    Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

  8. An evaluation of factors influencing pore pressure in accretionary complexes: Implications for taper angle and wedge mechanics

    USGS Publications Warehouse

    Saffer, D.M.; Bekins, B.A.

    2006-01-01

    At many subduction zones, accretionary complexes form as sediment is off-scraped from the subducting plate. Mechanical models that treat accretionary complexes as critically tapered wedges of sediment demonstrate that pore pressure controls their taper angle by modifying basal and internal shear strength. Here, we combine a numerical model of groundwater flow with critical taper theory to quantify the effects of sediment and de??collement permeability, sediment thickness, sediment partitioning between accretion and underthrusting, and plate convergence rate on steady state pore pressure. Our results show that pore pressure in accretionary wedges can be viewed as a dynamically maintained response to factors which drive pore pressure (source terms) and those that limit flow (permeability and drainage path length). We find that sediment permeability and incoming sediment thickness are the most important factors, whereas fault permeability and the partitioning of sediment have a small effect. For our base case model scenario, as sediment permeability is increased, pore pressure decreases from near-lithostatic to hydrostatic values and allows stable taper angles to increase from ??? 2.5?? to 8??-12.5??. With increased sediment thickness in our models (from 100 to 8000 m), increased pore pressure drives a decrease in stable taper angle from 8.4??-12.5?? to 15?? to <4??) with increased sediment thickness (from <1 to 7 km). One key implication is that hydrologic properties may strongly influence the strength of the crust in a wide range of geologic settings. Copyright 2006 by the American Geophysical Union.

  9. An alternative explanation for evidence that xenon depletion, pore formation, and grain subdivision begin at different local burnups

    NASA Astrophysics Data System (ADS)

    Rest, J.; Hofman, G. L.

    2000-01-01

    In order to interpret the recent observation that xenon depletion, pore formation, and grain subdivision occur successively at increasing local burnups, a rate-theory-based model is used to investigate the nucleation and growth of cavities during low-temperature irradiation of UO 2 in the presence of irradiation-induced interstitial-loop formation and growth. Consolidation of the dislocation structure takes into account the generation of forest dislocations and capture of interstitial dislocation loops. The loops accumulate and ultimately evolve into a low-energy cellular dislocation structure. The cell walls have been previously identified as recrystallization nuclei. The calculations indicate that nanometer-size bubbles are associated with this cellular dislocation structure while the observed micron-size bubbles are presumed to be either preexisting pores deformed by adjacent grains and/or new pores formed in the new recrystallized grain-boundary junctions. Subsequent to recrystallization, gas released from the recrystallized grains feeds the preexisting pores and the recrystallized grains may appear to form a preferential concentration of subdivided grains around the growing pores. This picture is illustrated in a sequence of photomicrographs of irradiated U 3O 8.

  10. Porosity-Tortuosity Relations in Complex Porous Media Using Pore-Scale Numerical Simulation

    NASA Astrophysics Data System (ADS)

    Xiao, F.; Yin, X.

    2015-12-01

    Diffusive transport is an important mechanism of mass transfer in gas or liquid phases in porous media. The continuous presence of solids in porous media causes the diffusion paths to deviate from straight lines, and this behavior is descried as the tortuosity of porous media. In this contribution, the porosity-tortuosity relations were studied using a random walk particle tracking (RWPT) code for three-dimensional complex porous medium geometries. The RWPT code was massively parallelized and has been tested on Titan (Cray XK7) at the Oak Ridge National Laboratory and on Mira (IBM Blue Gene/Q) at the Argonne National Laboratory with up to 16,384 cores. The porous medium geometries were synthetically created based on Voronoi tessellations, and include homogeneous fibrous/tubular/granular geometries as well as heterogeneous (vuggy) tubular/granular geometries. Simulation results show that the homogenous granular geometry is the least tortuous, the homogeneous tubular geometry is intermediately tortuous, and the homogeneous fibrous geometry is the most tortuous. For homogeneous granular and tubular geometries, as porosity increases, the difference between the tortuosity of tubular geometry and that of granular geometry decreases. The vuggy porosity increases the tortuosity, due to the fact that mass "particles" trapped in a vug cannot exit the vug except along specific directions where the vug has narrow openings. The size of vugs relative to the size of inter-vug pores also affects tortuosity: the larger the vug size relative to the inter-vug pores, the higher the tortuosity, because in smaller vugs (with the same vuggy porosity and total porosity) the chance is higher for mass "particles" to diffuse into the exiting cylindrical pores. To test the effect of vuggy porosity and tortuosity on permeability, three vuggy geometries were set up with the same vuggy porosity, but different vug sizes. It is found, interestingly, that they have the same dimensionless

  11. F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling.

    PubMed

    Heemskerk, Niels; Schimmel, Lilian; Oort, Chantal; van Rijssel, Jos; Yin, Taofei; Ma, Bin; van Unen, Jakobus; Pitter, Bettina; Huveneers, Stephan; Goedhart, Joachim; Wu, Yi; Montanez, Eloi; Woodfin, Abigail; van Buul, Jaap D

    2016-01-27

    During immune surveillance and inflammation, leukocytes exit the vasculature through transient openings in the endothelium without causing plasma leakage. However, the exact mechanisms behind this intriguing phenomenon are still unknown. Here we report that maintenance of endothelial barrier integrity during leukocyte diapedesis requires local endothelial RhoA cycling. Endothelial RhoA depletion in vitro or Rho inhibition in vivo provokes neutrophil-induced vascular leakage that manifests during the physical movement of neutrophils through the endothelial layer. Local RhoA activation initiates the formation of contractile F-actin structures that surround emigrating neutrophils. These structures that surround neutrophil-induced endothelial pores prevent plasma leakage through actomyosin-based pore confinement. Mechanistically, we found that the initiation of RhoA activity involves ICAM-1 and the Rho GEFs Ect2 and LARG. In addition, regulation of actomyosin-based endothelial pore confinement involves ROCK2b, but not ROCK1. Thus, endothelial cells assemble RhoA-controlled contractile F-actin structures around endothelial pores that prevent vascular leakage during leukocyte extravasation.

  12. F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling

    PubMed Central

    Heemskerk, Niels; Schimmel, Lilian; Oort, Chantal; van Rijssel, Jos; Yin, Taofei; Ma, Bin; van Unen, Jakobus; Pitter, Bettina; Huveneers, Stephan; Goedhart, Joachim; Wu, Yi; Montanez, Eloi; Woodfin, Abigail; van Buul, Jaap D.

    2016-01-01

    During immune surveillance and inflammation, leukocytes exit the vasculature through transient openings in the endothelium without causing plasma leakage. However, the exact mechanisms behind this intriguing phenomenon are still unknown. Here we report that maintenance of endothelial barrier integrity during leukocyte diapedesis requires local endothelial RhoA cycling. Endothelial RhoA depletion in vitro or Rho inhibition in vivo provokes neutrophil-induced vascular leakage that manifests during the physical movement of neutrophils through the endothelial layer. Local RhoA activation initiates the formation of contractile F-actin structures that surround emigrating neutrophils. These structures that surround neutrophil-induced endothelial pores prevent plasma leakage through actomyosin-based pore confinement. Mechanistically, we found that the initiation of RhoA activity involves ICAM-1 and the Rho GEFs Ect2 and LARG. In addition, regulation of actomyosin-based endothelial pore confinement involves ROCK2b, but not ROCK1. Thus, endothelial cells assemble RhoA-controlled contractile F-actin structures around endothelial pores that prevent vascular leakage during leukocyte extravasation. PMID:26814335

  13. Nuclear pore protein NUP88 activates anaphase-promoting complex to promote aneuploidy.

    PubMed

    Naylor, Ryan M; Jeganathan, Karthik B; Cao, Xiuqi; van Deursen, Jan M

    2016-02-01

    The nuclear pore complex protein NUP88 is frequently elevated in aggressive human cancers and correlates with reduced patient survival; however, it is unclear whether and how NUP88 overexpression drives tumorigenesis. Here, we show that mice overexpressing NUP88 are cancer prone and form intestinal tumors. To determine whether overexpression of NUP88 drives tumorigenesis, we engineered transgenic mice with doxycycline-inducible expression of Nup88. Surprisingly, NUP88 overexpression did not alter global nuclear transport, but was a potent inducer of aneuploidy and chromosomal instability. We determined that NUP88 and the nuclear transport factors NUP98 and RAE1 comprise a regulatory network that inhibits premitotic activity of the anaphase-promoting complex/cyclosome (APC/C). When overexpressed, NUP88 sequesters NUP98-RAE1 away from APC/CCDH1, triggering proteolysis of polo-like kinase 1 (PLK1), a tumor suppressor and multitasking mitotic kinase. Premitotic destruction of PLK1 disrupts centrosome separation, causing mitotic spindle asymmetry, merotelic microtubule-kinetochore attachments, lagging chromosomes, and aneuploidy. These effects were replicated by PLK1 insufficiency, indicating that PLK1 is responsible for the mitotic defects associated with NUP88 overexpression. These findings demonstrate that the NUP88-NUP98-RAE1-APC/CCDH1 axis contributes to aneuploidy and suggest that it may be deregulated in the initiating stages of a broad spectrum of human cancers. PMID:26731471

  14. Influenza virus targets the mRNA export machinery and the nuclear pore complex.

    PubMed

    Satterly, Neal; Tsai, Pei-Ling; van Deursen, Jan; Nussenzveig, Daniel R; Wang, Yaming; Faria, Paula A; Levay, Agata; Levy, David E; Fontoura, Beatriz M A

    2007-02-01

    The NS1 protein of influenza A virus is a major virulence factor that is essential for pathogenesis. NS1 functions to impair innate and adaptive immunity by inhibiting host signal transduction and gene expression, but its mechanisms of action remain to be fully elucidated. We show here that NS1 forms an inhibitory complex with NXF1/TAP, p15/NXT, Rae1/mrnp41, and E1B-AP5, which are key constituents of the mRNA export machinery that interact with both mRNAs and nucleoporins to direct mRNAs through the nuclear pore complex. Increased levels of NXF1, p15, or Rae1 revert the mRNA export blockage induced by NS1. Furthermore, influenza virus down-regulates Nup98, a nucleoporin that is a docking site for mRNA export factors. Reduced expression of these mRNA export factors renders cells highly permissive to influenza virus replication, demonstrating that proper levels of key constituents of the mRNA export machinery protect against influenza virus replication. Because Nup98 and Rae1 are induced by interferons, down-regulation of this pathway is likely a viral strategy to promote viral replication. These findings demonstrate previously undescribed influenza-mediated viral-host interactions and provide insights into potential molecular therapies that may interfere with influenza infection.

  15. Nuclear pore protein NUP88 activates anaphase-promoting complex to promote aneuploidy

    PubMed Central

    Naylor, Ryan M.; Jeganathan, Karthik B.; Cao, Xiuqi; van Deursen, Jan M.

    2016-01-01

    The nuclear pore complex protein NUP88 is frequently elevated in aggressive human cancers and correlates with reduced patient survival; however, it is unclear whether and how NUP88 overexpression drives tumorigenesis. Here, we show that mice overexpressing NUP88 are cancer prone and form intestinal tumors. To determine whether overexpression of NUP88 drives tumorigenesis, we engineered transgenic mice with doxycycline-inducible expression of Nup88. Surprisingly, NUP88 overexpression did not alter global nuclear transport, but was a potent inducer of aneuploidy and chromosomal instability. We determined that NUP88 and the nuclear transport factors NUP98 and RAE1 comprise a regulatory network that inhibits premitotic activity of the anaphase-promoting complex/cyclosome (APC/C). When overexpressed, NUP88 sequesters NUP98-RAE1 away from APC/CCDH1, triggering proteolysis of polo-like kinase 1 (PLK1), a tumor suppressor and multitasking mitotic kinase. Premitotic destruction of PLK1 disrupts centrosome separation, causing mitotic spindle asymmetry, merotelic microtubule-kinetochore attachments, lagging chromosomes, and aneuploidy. These effects were replicated by PLK1 insufficiency, indicating that PLK1 is responsible for the mitotic defects associated with NUP88 overexpression. These findings demonstrate that the NUP88-NUP98-RAE1-APC/CCDH1 axis contributes to aneuploidy and suggest that it may be deregulated in the initiating stages of a broad spectrum of human cancers. PMID:26731471

  16. Percolation of localized attack on complex networks

    NASA Astrophysics Data System (ADS)

    Shao, Shuai; Huang, Xuqing; Stanley, H. Eugene; Havlin, Shlomo

    2015-02-01

    The robustness of complex networks against node failure and malicious attack has been of interest for decades, while most of the research has focused on random attack or hub-targeted attack. In many real-world scenarios, however, attacks are neither random nor hub-targeted, but localized, where a group of neighboring nodes in a network are attacked and fail. In this paper we develop a percolation framework to analytically and numerically study the robustness of complex networks against such localized attack. In particular, we investigate this robustness in Erdős-Rényi networks, random-regular networks, and scale-free networks. Our results provide insight into how to better protect networks, enhance cybersecurity, and facilitate the design of more robust infrastructures.

  17. Pore water distributions of dissolved copper and copper-complexing ligands in estuarine and coastal marine sediments

    SciTech Connect

    Skrabal, S.A.; Donat, J.R.; Burdige, D.J.

    2000-06-01

    The distributions and seasonal variability of total dissolved Cu (TDCu) and Cu-complexing ligands in sediment pore waters have been investigated at two contrasting sites in the Chesapeake Bay. Two ligand classes, which differ on the basis of the conditional stability constants (K{prime}{sub cond}) of their Cu complexes, were detected at all depths at both sites. For comparison, one pore water profile from a slope station off of the Chesapeake Bay also showed the presence of two ligand classes. Virtually all TDCu fluxing from these sediments is complexed during sediment-water exchange. A relatively small fraction of the TDCu is exchanged as inorganic species, which are widely regarded as the most bioavailable form of Cu. Total ligand concentrations are 15 to >100 times higher in the upper intervals of the pore waters relative to ligand concentrations in the bottom waters of the Chesapeake Bay (30--60 nM), consistent with previous observations of fluxes of these ligands from the sediments to overlying waters. These results suggest that sediments are potentially significant sources of Cu-complexing ligands to the overlying waters of the Chesapeake Bay, and perhaps, other shallow water estuarine and coastal environments. Copper-complexing ligands released from sediment pore waters may play an important role in influencing Cu speciation in overlying waters.

  18. How local factors affect the exponents of forced polymer translocation through a nano-pore

    NASA Astrophysics Data System (ADS)

    Bhattacharyaa, Aniket

    2010-02-01

    We study polymer translocation through a narrow pore driven by a bias present inside the pore with an aim to compare predictions of the existing theoretical results with those that we obtain using Langevin dynamics simulation in three dimensions(3D). We find that the translocation exponent α(< τ > ˜Nα) decreases from 1.35 to 1.2 as the width of the pore is decreased from 1.5 σ to 1.1 σ. The exponent ℵ = 1.2 (extracted from chain lengths up to N = 256) not only violates the lower limit 1 + ν proposed by Kantor and Kardar (Y. Kantor and M. Kardar, Phys. Rev. E, 69, 021806 (2004)) earlier but also lower than the more recently proposed lower limit (1 + 2 ν) /(1 + ν) by Vocks et al. (H. Vocks, D. Panja, G. T. Barkema, and R. C. Ball, J. Phys.: Condens. Matter 20, 095224 (2008)). We find that the average calculated during the entire translocation process is dominated by the equilibrium configurations at the cis side and therefore, relatively insensitive to the pore width and approximately described by the equilibrium Flory exponent ν. The velocity of the center of mass of the translocating chain on the contrary exhibits a systematic variation. Therefore, if we assume (< τ > ˜ / ) , the dependence of on the pore width appears to be the primary factor that affects the translocation exponent.

  19. Artificial nanopores that mimic the transport selectivity of the nuclear pore complex

    PubMed Central

    Jovanovic-Talisman, Tijana; Tetenbaum-Novatt, Jaclyn; McKenney, Anna Sophia; Zilman, Anton; Peters, Reiner; Rout, Michael P.; Chait, Brian T.

    2009-01-01

    Nuclear pore complexes (NPCs) act as effective and robust gateways between the nucleus and the cytoplasm, selecting for the passage of particular macromolecules across the nuclear envelope. NPCs are comprised of an elaborate scaffold that defines a ∼30nm diameter passageway connecting the nucleus and the cytoplasm. This scaffold anchors proteins termed ‘phenylalanine-glycine’ (FG)-nucleoporins, the natively disordered domains of which line the passageway and extend into its lumen1. Passive diffusion through this lined passageway is hindered in a size-dependent manner. However, transport factors and their cargo-bound complexes overcome this restriction by transient binding to the FG-nucleoporins2–10. To test whether a simple passageway and a lining of transport-factor-binding FG-nucleoporins are sufficient for selective transport, we designed a functionalized membrane that incorporates just these two elements. Here we demonstrate that this membrane functions as a nanoselective filter, efficiently passing transport factors and transport-factor–cargo complexes that specifically bind FG-nucleoporins, while significantly inhibiting the passage of proteins that do not. This inhibition is greatly enhanced when transport factor is present. Determinants of selectivity include the passageway diameter, the length of the nanopore region coated with FG-nucleoporins, the binding strength to FG-nucleoporins, and the antagonistic effect of transport factors on the passage of proteins that do not specifically bind FG-nucleoporins. We show that this artificial system faithfully reproduces key features of trafficking through the NPC, including transport-factor-mediated cargo import. PMID:19098896

  20. Complex earthquake rupture and local tsunamis

    USGS Publications Warehouse

    Geist, E.L.

    2002-01-01

    In contrast to far-field tsunami amplitudes that are fairly well predicted by the seismic moment of subduction zone earthquakes, there exists significant variation in the scaling of local tsunami amplitude with respect to seismic moment. From a global catalog of tsunami runup observations this variability is greatest for the most frequently occuring tsunamigenic subduction zone earthquakes in the magnitude range of 7 < Mw < 8.5. Variability in local tsunami runup scaling can be ascribed to tsunami source parameters that are independent of seismic moment: variations in the water depth in the source region, the combination of higher slip and lower shear modulus at shallow depth, and rupture complexity in the form of heterogeneous slip distribution patterns. The focus of this study is on the effect that rupture complexity has on the local tsunami wave field. A wide range of slip distribution patterns are generated using a stochastic, self-affine source model that is consistent with the falloff of far-field seismic displacement spectra at high frequencies. The synthetic slip distributions generated by the stochastic source model are discretized and the vertical displacement fields from point source elastic dislocation expressions are superimposed to compute the coseismic vertical displacement field. For shallow subduction zone earthquakes it is demonstrated that self-affine irregularities of the slip distribution result in significant variations in local tsunami amplitude. The effects of rupture complexity are less pronounced for earthquakes at greater depth or along faults with steep dip angles. For a test region along the Pacific coast of central Mexico, peak nearshore tsunami amplitude is calculated for a large number (N = 100) of synthetic slip distribution patterns, all with identical seismic moment (Mw = 8.1). Analysis of the results indicates that for earthquakes of a fixed location, geometry, and seismic moment, peak nearshore tsunami amplitude can vary by a

  1. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

    PubMed Central

    Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; Rout, Michael P.; Sali, Andrej; Cowburn, David

    2016-01-01

    Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport. PMID:27091992

  2. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

    PubMed Central

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick YH; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. DOI: http://dx.doi.org/10.7554/eLife.10785.001 PMID:27198189

  3. Nuclear pore complex integrity requires Lnp1, a regulator of cortical endoplasmic reticulum

    PubMed Central

    Casey, Amanda K.; Chen, Shuliang; Novick, Peter; Ferro-Novick, Susan; Wente, Susan R.

    2015-01-01

    The nuclear envelope (NE) and endoplasmic reticulum (ER) are components of the same contiguous membrane system and yet have distinct cellular functions. Mounting evidence suggests roles for some ER proteins in the NE for proper nuclear pore complex (NPC) structure and function. In this study, we identify a NE role in Saccharomyces cerevisiae for Lnp1 and Sey1, proteins required for proper cortical ER formation. Both lnp1Δ and sey1Δ mutants exhibit synthetic genetic interactions with mutants in genes encoding key NPC structural components. Both Lnp1 and Sey1 physically associate with other ER components that have established NPC roles, including Rtn1, Yop1, Pom33, and Per33. Of interest, lnp1Δ rtn1Δ mutants but not rtn1Δ sey1Δ mutants exhibit defects in NPC distribution. Furthermore, the essential NPC assembly factor Ndc1 has altered interactions in the absence of Sey1. Lnp1 dimerizes in vitro via its C-terminal zinc finger motif, a property that is required for proper ER structure but not NPC integrity. These findings suggest that Lnp1's role in NPC integrity is separable from functions in the ER and is linked to Ndc1 and Rtn1 interactions. PMID:26041935

  4. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex.

    PubMed

    Raveh, Barak; Karp, Jerome M; Sparks, Samuel; Dutta, Kaushik; Rout, Michael P; Sali, Andrej; Cowburn, David

    2016-05-01

    Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport. PMID:27091992

  5. Molecular Architecture of the Transport Channel of the Nuclear Pore Complex

    PubMed Central

    Solmaz, Sozanne R.; Chauhan, Radha; Blobel, Günter; Melčák, Ivo

    2012-01-01

    SUMMARY The nuclear pore complex encloses a central channel for nucleocytoplasmic transport, which is thought to consist of three nucleoporins, Nup54, Nup58, and Nup62. However, the structure and composition of the channel are elusive. We determined the crystal structures of the interacting domains between these nucleoporins and pieced together the molecular architecture of the mammalian transport channel. Located in the channel midplane is a flexible Nup54·Nup58 ring that can undergo large rearrangements yielding diameter changes from ~20 to ~40 nm. Nup62·Nup54 triple helices project alternately up and down from either side of the midplane ring and form nucleoplasmic and cytoplasmic entries. The channel consists of as many as 224 copies of the three nucleoporins, amounting to a molar mass of 12.3 MDa and contributing 256 phenylalanine-glycine repeat regions. We propose that the occupancy of these repeat regions with transport receptors modulates ring diameter and transport activity. PMID:22036567

  6. Changes of the local pore space structure quantified in heterogeneous porous media by 1H magnetic resonance relaxation tomography

    NASA Astrophysics Data System (ADS)

    Borgia, G. C.; Bortolotti, V.; Fantazzini, P.

    2001-08-01

    Magnetic resonance imaging and relaxation analysis are combined in a spatially resolved technique (relaxation tomography), which is able to quantify the parameters connected to the local structure in the internal regions of a porous material saturated by water, giving information on the pore space structure beyond the nominal instrumental resolution. Voxel-by-voxel longitudinal (T1) and transverse (T2) relaxation curves are acquired in order to obtain T1, T2 and S(0) maps, where S(0) is the extrapolation to zero time of the total equilibrium magnetization corrected for T2 decay. The proposed method permits evaluation of the porosity (ratio of pore space to total volume), at different length scales, from the sample to the voxel, not all achievable by traditional methods. More striking is its ability to describe how porosity is shared among different classes of surface-to-volume ratios of diffusion cells (the regions that the individual water molecules, starting at their particular positions, can experience by diffusion before relaxing). This is a consequence of the fact that relaxation times of water confined in a porous material can, under favorable circumstances, distinguish regions with the same local porosity but with different pore sizes and connections. So, parameters can be introduced, such as the microporosity fraction, defined as the fraction of the "micropore" volume with respect to the total pore volume, and several voxel average porosities, defined as the average porosities of the voxels characterized by particular classes of diffusion cells. Moreover, the imaging methods enable us to get all this information in a user-defined region of interest. The method has been applied to quantify changes in the structure of carbonate cores with wide distributions of pore sizes induced by repeated cycles of freezing and heating of the sample. With freezing, the microporosity fraction decreases significantly; the voxel average porosity of voxels with T1 shorter than

  7. Localized recovery of complex networks against failure

    PubMed Central

    Shang, Yilun

    2016-01-01

    Resilience of complex networks to failure has been an important issue in network research for decades, and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood, and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks, and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the “complement network” of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems. PMID:27456202

  8. Localized recovery of complex networks against failure

    NASA Astrophysics Data System (ADS)

    Shang, Yilun

    2016-07-01

    Resilience of complex networks to failure has been an important issue in network research for decades, and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood, and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks, and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the “complement network” of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems.

  9. Localized recovery of complex networks against failure.

    PubMed

    Shang, Yilun

    2016-01-01

    Resilience of complex networks to failure has been an important issue in network research for decades, and recent studies have begun to focus on the inverse recovery of network functionality through strategically healing missing nodes or edges. However, the effect of network recovery is far from fully understood, and a general theory is still missing. Here we propose and study a general model of localized recovery, where a group of neighboring nodes are restored in an invasive way from a seed node. We develop a theoretical framework to compare the effect of random recovery (RR) and localized recovery (LR) in complex networks including Erdős-Rényi networks, random regular networks, and scale-free networks. We find detailed phase diagrams for the subnetwork of occupied nodes and the "complement network" of failed nodes under RR and LR. By identifying the two competitive forces behind LR, we present an analytical and numerical approach to guide us in choosing the appropriate recovery strategy and provide estimation on its effect by using the degree distribution of the original network as the only input. Our work therefore provides insight for quantitatively understanding recovery process and its implications in infrastructure protection in various complex systems. PMID:27456202

  10. Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex.

    PubMed

    Tagliazucchi, Mario; Peleg, Orit; Kröger, Martin; Rabin, Yitzhak; Szleifer, Igal

    2013-02-26

    The molecular structure of the yeast nuclear pore complex (NPC) and the translocation of model particles have been studied with a molecular theory that accounts for the geometry of the pore and the sequence and anchoring position of the unfolded domains of the nucleoporin proteins (the FG-Nups), which control selective transport through the pore. The theory explicitly models the electrostatic, hydrophobic, steric, conformational, and acid-base properties of the FG-Nups. The electrostatic potential within the pore, which arises from the specific charge distribution of the FG-Nups, is predicted to be negative close to pore walls and positive along the pore axis. The positive electrostatic potential facilitates the translocation of negatively charged particles, and the free energy barrier for translocation decreases for increasing particle hydrophobicity. These results agree with the experimental observation that transport receptors that form complexes with hydrophilic/neutral or positively charged proteins to transport them through the NPC are both hydrophobic and strongly negatively charged. The molecular theory shows that the effects of electrostatic and hydrophobic interactions on the translocating potential are cooperative and nonequivalent due to the interaction-dependent reorganization of the FG-Nups in the presence of the translocating particle. The combination of electrostatic and hydrophobic interactions can give rise to complex translocation potentials displaying a combination of wells and barriers, in contrast to the simple barrier potential observed for a hydrophilic/neutral translocating particle. This work demonstrates the importance of explicitly considering the amino acid sequence and hydrophobic, electrostatic, and steric interactions in understanding the translocation through the NPC.

  11. Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex.

    PubMed

    Tagliazucchi, Mario; Peleg, Orit; Kröger, Martin; Rabin, Yitzhak; Szleifer, Igal

    2013-02-26

    The molecular structure of the yeast nuclear pore complex (NPC) and the translocation of model particles have been studied with a molecular theory that accounts for the geometry of the pore and the sequence and anchoring position of the unfolded domains of the nucleoporin proteins (the FG-Nups), which control selective transport through the pore. The theory explicitly models the electrostatic, hydrophobic, steric, conformational, and acid-base properties of the FG-Nups. The electrostatic potential within the pore, which arises from the specific charge distribution of the FG-Nups, is predicted to be negative close to pore walls and positive along the pore axis. The positive electrostatic potential facilitates the translocation of negatively charged particles, and the free energy barrier for translocation decreases for increasing particle hydrophobicity. These results agree with the experimental observation that transport receptors that form complexes with hydrophilic/neutral or positively charged proteins to transport them through the NPC are both hydrophobic and strongly negatively charged. The molecular theory shows that the effects of electrostatic and hydrophobic interactions on the translocating potential are cooperative and nonequivalent due to the interaction-dependent reorganization of the FG-Nups in the presence of the translocating particle. The combination of electrostatic and hydrophobic interactions can give rise to complex translocation potentials displaying a combination of wells and barriers, in contrast to the simple barrier potential observed for a hydrophilic/neutral translocating particle. This work demonstrates the importance of explicitly considering the amino acid sequence and hydrophobic, electrostatic, and steric interactions in understanding the translocation through the NPC. PMID:23404701

  12. Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex

    PubMed Central

    Tagliazucchi, Mario; Peleg, Orit; Kröger, Martin; Rabin, Yitzhak; Szleifer, Igal

    2013-01-01

    The molecular structure of the yeast nuclear pore complex (NPC) and the translocation of model particles have been studied with a molecular theory that accounts for the geometry of the pore and the sequence and anchoring position of the unfolded domains of the nucleoporin proteins (the FG-Nups), which control selective transport through the pore. The theory explicitly models the electrostatic, hydrophobic, steric, conformational, and acid-base properties of the FG-Nups. The electrostatic potential within the pore, which arises from the specific charge distribution of the FG-Nups, is predicted to be negative close to pore walls and positive along the pore axis. The positive electrostatic potential facilitates the translocation of negatively charged particles, and the free energy barrier for translocation decreases for increasing particle hydrophobicity. These results agree with the experimental observation that transport receptors that form complexes with hydrophilic/neutral or positively charged proteins to transport them through the NPC are both hydrophobic and strongly negatively charged. The molecular theory shows that the effects of electrostatic and hydrophobic interactions on the translocating potential are cooperative and nonequivalent due to the interaction-dependent reorganization of the FG-Nups in the presence of the translocating particle. The combination of electrostatic and hydrophobic interactions can give rise to complex translocation potentials displaying a combination of wells and barriers, in contrast to the simple barrier potential observed for a hydrophilic/neutral translocating particle. This work demonstrates the importance of explicitly considering the amino acid sequence and hydrophobic, electrostatic, and steric interactions in understanding the translocation through the NPC. PMID:23404701

  13. Distinct, but not completely separate spatial transport routes in the nuclear pore complex

    PubMed Central

    2013-01-01

    The nuclear pore complex (NPC), which provides the permeable and selective transport path between the nucleus and cytoplasm of eukaryotic cells, allows both the passive diffusion of small molecules in a signal-independent manner and the transport receptor-facilitated translocation of cargo molecules in a signal-dependent manner. However, the spatial and functional relationships between these two transport pathways, which represent critical information for unraveling the fundamental nucleocytoplasmic transport mechanism, remain in dispute. The direct experimental examination of passive and facilitated transport with a high spatiotemporal resolution under real-time trafficking conditions in native NPCs is still difficult. To address this issue and further define these transport mechanisms, we recently developed single-point edge-excitation sub-diffraction (SPEED) microscopy and a deconvolution algorithm to directly map both passive and facilitated transport routes in three dimensions (3D) in native NPCs. Our findings revealed that passive and facilitated transport occur through spatially distinct transport routes. Signal-independent small molecules exhibit a high probability of passively diffusing through an axial central viscous channel, while transport receptors and their cargo complexes preferentially travel through the periphery, around this central channel, after interacting with phenylalanine-glycine (FG) filaments. Strikingly, these two distinct transport zones are not completely separate either spatially or functionally. Instead, their conformations are closely correlated and simultaneously regulated. In this review, we will specifically highlight a detailed procedure for 3D mapping of passive and facilitated transport routes, demonstrate the correlation between these two distinct pathways, and finally, speculate regarding the regulation of the transport pathways driven by the conformational changes of FG filaments in NPCs. PMID:23669120

  14. Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating

    PubMed Central

    Gamini, Ramya; Han, Wei; Stone, John E.; Schulten, Klaus

    2014-01-01

    Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups are arranged in the interior of the NPC may explain how NPC functions as a selectivity filter for transport of large molecules and a sieve-like filter for diffusion of small molecules (< or ). We employed molecular dynamics to model the structures formed by various assemblies of one kind of nup, namely the 609-aa-long FG domain of Nsp1 (Nsp1-FG). The simulations started from different initial conformations and geometrical arrangements of Nsp1-FGs. In all cases Nsp1-FGs collectively formed brush-like structures with bristles made of bundles of 2–27 nups, however, the bundles being cross-linked through single nups leaving one bundle and joining a nearby one. The degree of cross-linking varies with different initial nup conformations and arrangements. Structural analysis reveals that FG-repeats of the nups not only involve formation of bundle structures, but are abundantly present in cross-linking regions where the epitopes of FG-repeats are highly accessible. Large molecules that are assisted by transport factors (TFs) are selectively transported through NPC apparently by binding to FG-nups through populated FG-binding pockets on the TF surface. Therefore, our finding suggests that TFs bind concertedly to multiple FGs in cross-linking regions and break-up the bundles to create wide pores for themselves and their cargoes to pass. In addition, the cross-linking between Nsp1-FG bundles, arising from simulations, is found to set a molecular size limit of < for passive diffusion of molecules. Our simulations suggest that the NPC central channel, near the periphery where tethering of nups is dominant, features brush-like moderately cross-linked bundles, but in the central region, where tethering loses its effect, features a

  15. Importin beta negatively regulates nuclear membrane fusion and nuclear pore complex assembly.

    PubMed

    Harel, Amnon; Chan, Rene C; Lachish-Zalait, Aurelie; Zimmerman, Ella; Elbaum, Michael; Forbes, Douglass J

    2003-11-01

    Assembly of a eukaryotic nucleus involves three distinct events: membrane recruitment, fusion to form a double nuclear membrane, and nuclear pore complex (NPC) assembly. We report that importin beta negatively regulates two of these events, membrane fusion and NPC assembly. When excess importin beta is added to a full Xenopus nuclear reconstitution reaction, vesicles are recruited to chromatin but their fusion is blocked. The importin beta down-regulation of membrane fusion is Ran-GTP reversible. Indeed, excess RanGTP (RanQ69L) alone stimulates excessive membrane fusion, leading to intranuclear membrane tubules and cytoplasmic annulate lamellae-like structures. We propose that a precise balance of importin beta to Ran is required to create a correct double nuclear membrane and simultaneously to repress undesirable fusion events. Interestingly, truncated importin beta 45-462 allows membrane fusion but produces nuclei lacking any NPCs. This reveals distinct importin beta-regulation of NPC assembly. Excess full-length importin beta and beta 45-462 act similarly when added to prefused nuclear intermediates, i.e., both block NPC assembly. The importin beta NPC block, which maps downstream of GTPgammaS and BAPTA-sensitive steps in NPC assembly, is reversible by cytosol. Remarkably, it is not reversible by 25 microM RanGTP, a concentration that easily reverses fusion inhibition. This report, using a full reconstitution system and natural chromatin substrates, significantly expands the repertoire of importin beta. Its roles now encompass negative regulation of two of the major events of nuclear assembly: membrane fusion and NPC assembly.

  16. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145

    SciTech Connect

    Sampathkumar, Parthasarathy; Ozyurt, Sinem A.; Do, Johnny; Bain, Kevin T.; Dickey, Mark; Rodgers, Logan A.; Gheyi, Tarun; Sali, Andrej; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Martel, Anne; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sauder, J. Michael; Burley, Stephen K.

    2012-04-30

    Nuclear pore complexes (NPCs) are large, octagonally symmetric dynamic macromolecular assemblies responsible for exchange of proteins and RNAs between the nucleus and cytoplasm. NPCs are made up of at least 456 polypeptides from {approx}30 distinct nucleoporins. Several of these components, sharing similar structural motifs, form stable subcomplexes that form a coaxial structure containing two outer rings (the nuclear and cytoplasmic rings), two inner rings, and a membrane ring. The yeast (Saccharomyces cerevisiae) Nup145 and its human counterpart are unique among the nucleoporins, in that they undergo autoproteolysis to generate functionally distinct proteins. The human counterpart of Nup145 is expressed as two alternatively spliced mRNA transcripts. The larger 190 kDa precursor undergoes post-translational autoproteolysis at the Phe863-Ser864 peptide bond yielding the 92 kDa Nup98 and the 96 kDa Nup96. The smaller 98 kDa precursor is also autoproteolysed at an analogous site giving 92 kDa Nup98-N and a 6 kDa C-terminal fragment, which may form a noncovalent complex. The yeast Nup145 precursor [Fig. 1(A)] contains twelve repeats of a 'GLFG' peptide motif (FG repeats) at its N-terminus, an internal autoproteolytic domain (a region of high conservation with the homologous yeast nucleoporins Nup110 and Nup116, neither of which undergo autoproteolysis), followed by the C-terminal domain. Various forms of the FG repeats are present in nearly half of all nucleoporins; they form intrinsically disordered regions implicated in gating mechanisms that control passage of macromolecules through NPCs. Nup145 undergoes autoproteolysis at the Phe605-Ser606 peptide bond to generate two functionally distinct proteins, Nup145N and Nup145C. Subsequently, Nup145C associates with six other proteins to form the heptameric Y-complex, a component of the outer rings of the NPC. Nup145N, on the other hand, can shuttle between the NPC and the nuclear interior. It has been suggested that Nup

  17. Self-assembly of hybrid dendrons with complex primary structure into functional helical pores.

    PubMed

    Percec, Virgil; Smidrkal, Jan; Peterca, Mihai; Mitchell, Catherine M; Nummelin, Sami; Dulcey, Andrés E; Sienkowska, Monika J; Heiney, Paul A

    2007-01-01

    The synthesis of three libraries of self-assembling hybrid dendrons containing a primary structure based on the sequence (4-3,4-3,5)12G2-CO(2)CH(3) generated from benzyl ether, biphenyl-4-methyl ether, and AB(2) repeat units constructed from (AB)(y)--AB(2) combinations of benzyl ethers, is reported. The structural and retrostructural analysis of their supramolecular dendrimers facilitated the discovery of new architectural principles that lead to the assembly of functional helical pores. The self-assembly of an example of hybrid dendron containing -H, -CO(2)CH(3), -CH(2)OH, -COOH, -COOK, -CONH(2), -CONHCH(3), -CO(2)(CH(2))(2)OCH(3), -(R) and -(S)-CONHCH(CH(3))C(2)H(5) as X-groups at the apex demonstrated that these self-assembling dendrons provide the simplest strategy for the design and synthesis of porous columns containing a diversity of hydrophilic and hydrophobic functional groups in the inner part of the pore. The results reported here expand the scope and limitations of dendrons available for the self-assembly of functional pores that previously were generated mostly from dendritic dipeptides, to simpler architectures based on hybrid dendrons. PMID:17304597

  18. Pustular psoriasis elicited by streptococcal antigen and localized to the sweat pore.

    PubMed

    Shelley, W B; Wood, M G; Beerman, H

    1975-11-01

    A woman, aged 39 years, presented with a localized, painful, pustular eruption of the neck, scalp, and finger of five years' duration. A diagnosis of pustular psoriasis was made clinically and histologically. It was possible to reproduce the disease by the intradermal injection of killed Group A streptococcal organisms. The induced pustules, as well as those appearing clinically, were intraepidermal and indistinguishable from the Kogoj spongiform abscess, and on serial sectioning showed a distinctive localization to the acryosyringium. Immunosuppressant as well as antistreptococcal therapy in the form of cyclophosphamide and clindamycin was of help. The process is classified as a nonvasculitic pustular bacterid, and as a prototype for antigen localization of lesions to the occluded epidermal sweat duct unit.

  19. The development of a single molecule fluorescence standard and its application in estimating the stoichiometry of the nuclear pore complex.

    PubMed

    Tie, Hieng Chiong; Madugula, Viswanadh; Lu, Lei

    2016-09-30

    We report here an image-based method to quantify the stoichiometry of diffraction-limited sub-cellular protein complexes in vivo under spinning disk confocal microscopy. A GFP single molecule fluorescence standard was first established by immobilizing His-tagged GFP molecules onto the glass surface via nickel nitrilotriacetic acid functionalized polyethylene glycol. When endogenous nucleoporins were knocked down and replaced by the exogenously expressed and knockdown-resistant GFP-nucleoporins, the stoichiometry of the nucleoporin was estimated by the ratio of its fluorescence intensity to that of the GFP single molecules. Our measured stoichiometry of Nup35, Nup93, Nup133 and Nup88 is 23, 18, 14 and 9 and there are possibly16 copies of Nup107-160 complex per nuclear pore complex.

  20. The development of a single molecule fluorescence standard and its application in estimating the stoichiometry of the nuclear pore complex.

    PubMed

    Tie, Hieng Chiong; Madugula, Viswanadh; Lu, Lei

    2016-09-30

    We report here an image-based method to quantify the stoichiometry of diffraction-limited sub-cellular protein complexes in vivo under spinning disk confocal microscopy. A GFP single molecule fluorescence standard was first established by immobilizing His-tagged GFP molecules onto the glass surface via nickel nitrilotriacetic acid functionalized polyethylene glycol. When endogenous nucleoporins were knocked down and replaced by the exogenously expressed and knockdown-resistant GFP-nucleoporins, the stoichiometry of the nucleoporin was estimated by the ratio of its fluorescence intensity to that of the GFP single molecules. Our measured stoichiometry of Nup35, Nup93, Nup133 and Nup88 is 23, 18, 14 and 9 and there are possibly16 copies of Nup107-160 complex per nuclear pore complex. PMID:27613095

  1. Importin-β modulates the permeability of the nuclear pore complex in a Ran-dependent manner

    PubMed Central

    Lowe, Alan R; Tang, Jeffrey H; Yassif, Jaime; Graf, Michael; Huang, William YC; Groves, Jay T; Weis, Karsten; Liphardt, Jan T

    2015-01-01

    Soluble karyopherins of the importin-β (impβ) family use RanGTP to transport cargos directionally through the nuclear pore complex (NPC). Whether impβ or RanGTP regulate the permeability of the NPC itself has been unknown. In this study, we identify a stable pool of impβ at the NPC. A subpopulation of this pool is rapidly turned-over by RanGTP, likely at Nup153. Impβ, but not transportin-1 (TRN1), alters the pore's permeability in a Ran-dependent manner, suggesting that impβ is a functional component of the NPC. Upon reduction of Nup153 levels, inert cargos more readily equilibrate across the NPC yet active transport is impaired. When purified impβ or TRN1 are mixed with Nup153 in vitro, higher-order, multivalent complexes form. RanGTP dissolves the impβ•Nup153 complexes but not those of TRN1•Nup153. We propose that impβ and Nup153 interact at the NPC's nuclear face to form a Ran-regulated mesh that modulates NPC permeability. DOI: http://dx.doi.org/10.7554/eLife.04052.001 PMID:25748139

  2. Nuclear pore complex remodeling by p75NTR cleavage controls TGF-β signaling and astrocyte functions

    PubMed Central

    Schachtrup, Christian; Ryu, Jae Kyu; Mammadzada, Könül; Khan, Abdullah S.; Carlton, Peter M.; Perez, Alex; Christian, Frank; Le Moan, Natacha; Vagena, Eirini; Baeza-Raja, Bernat; Rafalski, Victoria; Chan, Justin P.; Nitschke, Roland; Houslay, Miles D.; Ellisman, Mark H.; Wyss-Coray, Tony; Palop, Jorge J.; Akassoglou, Katerina

    2016-01-01

    Astrocytes play critical roles in neuronal activity and inhibition of regeneration. Here we show that the cleaved p75 neurotrophin receptor (p75NTR) is a component of the nuclear pore complex (NPC) required for glial scar formation and reduced gamma oscillations in mice via regulation of TGF-β signaling. The cleaved p75NTR interacts with nucleoporins to promote Smad2 nucleocytoplasmic shuttling. Thus, NPC remodeling by regulated intramembrane cleavage of p75NTR controls astrocyte-neuronal communication in response to profibrotic factors. PMID:26120963

  3. Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

    SciTech Connect

    Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.; Blobel, Günter; Hoelz, André

    2012-07-25

    So far, only a few of the interactions between the {approx}30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 {angstrom} resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed {beta}-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 {beta}-propeller and the other one from the {beta}-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic {alpha}-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 {beta}-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 {beta}-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 {beta}-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82 {center_dot} Nup159 {center_dot} Nup116 complex.

  4. Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

    PubMed Central

    Yoshida, Kimihisa; Seo, Hyuk-Soo; Debler, Erik W.; Blobel, Günter; Hoelz, André

    2011-01-01

    So far, only a few of the interactions between the ≈30 nucleoporins comprising the modular structure of the nuclear pore complex have been defined at atomic resolution. Here we report the crystal structure, at 2.6 Å resolution, of a heterotrimeric complex, composed of fragments of three cytoplasmically oriented nucleoporins of yeast: Nup82, Nup116, and Nup159. Our data show that the Nup82 fragment, representing more than the N-terminal half of the molecule, folds into an extensively decorated, seven-bladed β-propeller that forms the centerpiece of this heterotrimeric complex and anchors both a C-terminal fragment of Nup116 and the C-terminal tail of Nup159. Binding between Nup116 and Nup82 is mutually reinforced via two loops, one emanating from the Nup82 β-propeller and the other one from the β-sandwich fold of Nup116, each contacting binding pockets in their counterparts. The Nup82-Nup159 interaction occurs through an amphipathic α-helix of Nup159, which is cradled in a large hydrophobic groove that is generated from several large surface decorations of the Nup82 β-propeller. Although Nup159 and Nup116 fragments bind to the Nup82 β-propeller in close vicinity, there are no direct contacts between them, consistent with the noncooperative binding that was detected biochemically. Extensive mutagenesis delineated hot-spot residues for these interactions. We also showed that the Nup82 β-propeller binds to other yeast Nup116 family members, Nup145N, Nup100 and to the mammalian homolog, Nup98. Notably, each of the three nucleoporins contains additional nuclear pore complex binding sites, distinct from those that were defined here in the heterotrimeric Nup82•Nup159•Nup116 complex. PMID:21930948

  5. High-Resolution Scanning Electron Microscopy and Immuno-Gold Labeling of the Nuclear Lamina and Nuclear Pore Complex.

    PubMed

    Goldberg, Martin W

    2016-01-01

    Scanning electron microscopy (SEM) is a technique used to image surfaces. Field emission SEMs (feSEMs) can resolve structures that are ~0.5-1.5 nm apart. FeSEM, therefore is a useful technique for imaging molecular structures that exist at surfaces such as membranes. The nuclear envelope consists of four membrane surfaces, all of which may be accessible for imaging. Imaging of the cytoplasmic face of the outer membrane gives information about ribosomes and cytoskeletal attachments, as well as details of the cytoplasmic peripheral components of the nuclear pore complex, and is the most easily accessed surface. The nucleoplasmic face of the inner membrane is easily accessible in some cells, such as amphibian oocytes, giving valuable details about the organization of the nuclear lamina and how it interacts with the nuclear pore complexes. The luminal faces of both membranes are difficult to access, but may be exposed by various fracturing techniques. Protocols are presented here for the preparation, labeling, and feSEM imaging of Xenopus laevis oocyte nuclear envelopes.

  6. Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice

    SciTech Connect

    Brohawn, Stephen G; Schwartz, Thomas U; MIT,

    2010-02-02

    Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y complex and the heteromeric Nic96 complex. We previously showed that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat, and we proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134-kDa complex of Nup84-Nup145C-Sec13 of the Y complex. The heterotypic ACE1 interaction of Nup84 and Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative 'fence-like' NPC model. We construct a molecular model of the Y complex and compare the architectural principles of COPII and NPC lattices.

  7. Nup93, a Vertebrate Homologue of Yeast Nic96p, Forms a Complex with a Novel 205-kDa Protein and Is Required for Correct Nuclear Pore Assembly

    PubMed Central

    Grandi, Paola; Dang, Tam; Pané, Nelly; Shevchenko, Andrej; Mann, Matthias; Forbes, Douglass; Hurt, Ed

    1997-01-01

    Yeast and vertebrate nuclear pores display significant morphological similarity by electron microscopy, but sequence similarity between the respective proteins has been more difficult to observe. Herein we have identified a vertebrate nucleoporin, Nup93, in both human and Xenopus that has proved to be an evolutionarily related homologue of the yeast nucleoporin Nic96p. Polyclonal antiserum to human Nup93 detects corresponding proteins in human, rat, and Xenopus cells. Immunofluorescence and immunoelectron microscopy localize vertebrate Nup93 at the nuclear basket and at or near the nuclear entry to the gated channel of the pore. Immunoprecipitation from both mammalian and Xenopus cell extracts indicates that a small fraction of Nup93 physically interacts with the nucleoporin p62, just as yeast Nic96p interacts with the yeast p62 homologue. However, a large fraction of vertebrate Nup93 is extracted from pores and is also present in Xenopus egg extracts in complex with a newly discovered 205-kDa protein. Mass spectrometric sequencing of the human 205-kDa protein reveals that this protein is encoded by an open reading frame, KIAAO225, present in the human database. The putative human nucleoporin of 205 kDa has related sequence homologues in Caenorhabditis elegans and Saccharomyces cerevisiae. To analyze the role of the Nup93 complex in the pore, nuclei were assembled that lack the Nup93 complex after immunodepletion of a Xenopus nuclear reconstitution extract. The Nup93-complex–depleted nuclei are clearly defective for correct nuclear pore assembly. From these experiments, we conclude that the vertebrate and yeast pore have significant homology in their functionally important cores and that, with the identification of Nup93 and the 205-kDa protein, we have extended the knowledge of the nearest-neighbor interactions of this core in both yeast and vertebrates. PMID:9348540

  8. Putative members of the Arabidopsis Nup107-160 nuclear pore sub-complex contribute to pathogen defense.

    PubMed

    Wiermer, Marcel; Cheng, Yu Ti; Imkampe, Julia; Li, Meilan; Wang, Dongmei; Lipka, Volker; Li, Xin

    2012-06-01

    In eukaryotic cells, transduction of external stimuli into the nucleus to induce transcription and export of mRNAs for translation in the cytoplasm is mediated by nuclear pore complexes (NPCs) composed of nucleoporin proteins (Nups). We previously reported that Arabidopsis MOS3, encoding the homolog of vertebrate Nup96, is required for plant immunity and constitutive resistance mediated by the de-regulated Toll interleukin 1 receptor/nucleotide-binding/leucine-rich repeat (TNL)-type R gene snc1. In vertebrates, Nup96 is a component of the conserved Nup107-160 nuclear pore sub-complex, and implicated in immunity-related mRNA export. Here, we used a reverse genetics approach to examine the requirement for additional subunits of the predicted Arabidopsis Nup107-160 complex in plant immunity. We show that, among eight putative complex members, beside MOS3, only plants with defects in Nup160 or Seh1 are impaired in basal resistance. Constitutive resistance in the snc1 mutant and immunity mediated by TNL-type R genes also depend on functional Nup160 and have a partial requirement for Seh1. Conversely, resistance conferred by coiled coil-type immune receptors operates largely independently of both genes, demonstrating specific contributions to plant defense signaling. Our functional analysis further revealed that defects in nup160 and seh1 result in nuclear accumulation of poly(A) mRNA, and, in the case of nup160, considerable depletion of EDS1, a key positive regulator of basal and TNL-triggered resistance. These findings suggest that Nup160 is required for nuclear mRNA export and full expression of EDS1-conditioned resistance pathways in Arabidopsis.

  9. Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex.

    PubMed

    Peyro, Mohaddeseh; Soheilypour, Mohammad; Ghavami, Ali; Mofrad, Mohammad R K

    2015-01-01

    Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has shifted from studies of the overall function of the nuclear pore complex (NPC) to the examination of the role of different domains of phenylalanine-glycine nucleoporin (FG Nup) sequences on the NPC function. In our recent bioinformatics study, we showed that FG Nups have some evolutionarily conserved sequence-based features that might govern their physical behavior inside the NPC. We proposed the 'like charge regions' (LCRs), sequences of charged residues with only one type of charge, as one of the features that play a significant role in the formation of FG network inside the central channel. In this study, we further explore the role of LCRs in the distribution of FG Nups, using a recently developed coarse-grained molecular dynamics model. Our results demonstrate how LCRs affect the formation of two transport pathways. While some FG Nups locate their FG network at the center of the NPC forming a homogeneous meshwork of FG repeats, other FG Nups cover the space adjacent to the NPC wall. LCRs in the former group, i.e. FG Nups that form an FG domain at the center, tend to regulate the size of the highly dense, doughnut-shaped FG meshwork and leave a small low FG density area at the center of the pore for passive diffusion. On the other hand, LCRs in the latter group of FG Nups enable them to maximize their interactions and cover a larger space inside the NPC to increase its capability to transport numerous cargos at the same time. Finally, a new viewpoint is proposed that reconciles different models for the nuclear pore selective barrier function.

  10. Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex.

    PubMed

    Peyro, Mohaddeseh; Soheilypour, Mohammad; Ghavami, Ali; Mofrad, Mohammad R K

    2015-01-01

    Nucleocytoplasmic transport has been the subject of a large body of research in the past few decades. Recently, the focus of investigations in this field has shifted from studies of the overall function of the nuclear pore complex (NPC) to the examination of the role of different domains of phenylalanine-glycine nucleoporin (FG Nup) sequences on the NPC function. In our recent bioinformatics study, we showed that FG Nups have some evolutionarily conserved sequence-based features that might govern their physical behavior inside the NPC. We proposed the 'like charge regions' (LCRs), sequences of charged residues with only one type of charge, as one of the features that play a significant role in the formation of FG network inside the central channel. In this study, we further explore the role of LCRs in the distribution of FG Nups, using a recently developed coarse-grained molecular dynamics model. Our results demonstrate how LCRs affect the formation of two transport pathways. While some FG Nups locate their FG network at the center of the NPC forming a homogeneous meshwork of FG repeats, other FG Nups cover the space adjacent to the NPC wall. LCRs in the former group, i.e. FG Nups that form an FG domain at the center, tend to regulate the size of the highly dense, doughnut-shaped FG meshwork and leave a small low FG density area at the center of the pore for passive diffusion. On the other hand, LCRs in the latter group of FG Nups enable them to maximize their interactions and cover a larger space inside the NPC to increase its capability to transport numerous cargos at the same time. Finally, a new viewpoint is proposed that reconciles different models for the nuclear pore selective barrier function. PMID:26658558

  11. Local rewiring rules for evolving complex networks

    NASA Astrophysics Data System (ADS)

    Colman, E. R.; Rodgers, G. J.

    2014-12-01

    The effects of link rewiring are considered for the class of directed networks where each node has the same fixed out-degree. We model a network generated by three mechanisms that are present in various networked systems; growth, global rewiring and local rewiring. During a rewiring phase a node is randomly selected, one of its out-going edges is detached from its destination then re-attached to the network in one of two possible ways; either globally to a randomly selected node, or locally to a descendant of a descendant of the originally selected node. Although the probability of attachment to a node increases with its connectivity, the probability of detachment also increases, the result is an exponential degree distribution with a small number of outlying nodes that have extremely large degree. We explain these outliers by identifying the circumstances for which a set of nodes can grow to very high degree.

  12. The nuclear pore complex protein Tpr is a common autoantigen in sera that demonstrate nuclear envelope staining by indirect immunofluorescence.

    PubMed

    Ou, Y; Enarson, P; Rattner, J B; Barr, S G; Fritzler, M J

    2004-05-01

    We studied the autoantigen targets of 75 human sera that had antibodies to the nuclear envelope (NE) as identified by indirect immunofluorescence (IIF) on HEp-2 cells. Several different IIF staining patterns could be identified when antibodies to different components of the nuclear membrane (NM) and nuclear pore complexes (NuPC) were identified: a smooth membrane pattern characteristic of antibodies to nuclear lamins, a punctate pattern typical of antibodies to the nuclear pore complex and more complex patterns that included antibodies to nuclear and cytoplasmic organelles. Western immunoblotting of isolated nuclear and NE proteins and immunoprecipitation of radiolabelled recombinant proteins prepared by using the full-length cDNAs of the Translocated promoter region (Tpr), gp210 and p62 were used to identify specific autoantibody targets. Fifty-two of the 75 (70%) sera bound to Tpr, 25 (33%) bound to lamins A, B or C, 15 (20%) reacted with gp210 and none reacted with p62. Sixteen (21%) did not react with any of the NE components tested in our assays. The clinical features of 37 patients with anti-NE showed that there were 34 females and three males with an age range of 16-88 years (mean 59 years). The most frequent clinical diagnosis (9/37 = 24%) was autoimmune liver disease (ALD; two with primary biliary cirrhosis), followed by seven (19%) with systemic lupus erythematosus (SLE), four (11%) with a motor and/or sensory neuropathy, three (8%) with anti-phospholipid syndrome (APS), two with systemic sclerosis (SSc), two with Sjögren's syndrome (SjS), and others with a variety of diagnoses. This report indicates that Tpr, a component of the NuPC, is a common target of human autoantibodies that react with the NE.

  13. Spatiotemporal dynamics of the nuclear pore complex transport barrier resolved by high-speed atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Sakiyama, Yusuke; Mazur, Adam; Kapinos, Larisa E.; Lim, Roderick Y. H.

    2016-08-01

    Nuclear pore complexes (NPCs) are biological nanomachines that mediate the bidirectional traffic of macromolecules between the cytoplasm and nucleus in eukaryotic cells. This process involves numerous intrinsically disordered, barrier-forming proteins known as phenylalanine-glycine nucleoporins (FG Nups) that are tethered inside each pore. The selective barrier mechanism has so far remained unresolved because the FG Nups have eluded direct structural analysis within NPCs. Here, high-speed atomic force microscopy is used to visualize the nanoscopic spatiotemporal dynamics of FG Nups inside Xenopus laevis oocyte NPCs at timescales of ∼100 ms. Our results show that the cytoplasmic orifice is circumscribed by highly flexible, dynamically fluctuating FG Nups that rapidly elongate and retract, consistent with the diffusive motion of tethered polypeptide chains. On this basis, intermingling FG Nups exhibit transient entanglements in the central channel, but do not cohere into a tightly crosslinked meshwork. Therefore, the basic functional form of the NPC barrier is comprised of highly dynamic FG Nups that manifest as a central plug or transporter when averaged in space and time.

  14. A monoclonal antibody against the nuclear pore complex inhibits nucleocytoplasmic transport of protein and RNA in vivo

    PubMed Central

    1988-01-01

    A monoclonal antibody that reacts with proteins in the nuclear pore complex of rat liver (Snow, C. M., A. Senior, and L. Gerace. 1987. J. Cell Biol. 104:1143-1156) has been shown to cross react with similar components in Xenopus oocytes, as determined by immunofluorescence microscopy and immunoblotting. We have microinjected the antibody into oocytes to study the possible role of these polypeptides in nucleocytoplasmic transport. The antibody inhibits import of a large nuclear protein, nucleoplasmin, in a time- and concentration-dependent manner. It also inhibits export of 5S ribosomal RNA and mature tRNA, but has no effect on transcription or intranuclear tRNA processing. The antibody does not affect the rate of diffusion into the nucleus of two small proteins, myoglobin and ovalbumin, indicating that antibody binding does not result in occlusion of the channel for diffusion. This suggests that inhibition of protein and RNA transport occurs by binding of the antibody at or near components of the pore that participate in mediated transport. PMID:2459127

  15. B-type nuclear lamin and the nuclear pore complex Nup107-160 influences maintenance of the spindle envelope required for cytokinesis in Drosophila male meiosis

    PubMed Central

    Hayashi, Daisuke; Tanabe, Karin; Katsube, Hiroka

    2016-01-01

    ABSTRACT In higher eukaryotes, nuclear envelope (NE) disassembly allows chromatin to condense and spindle microtubules to access kinetochores. The nuclear lamina, which strengthens the NE, is composed of a polymer meshwork made of A- and B-type lamins. We found that the B-type lamin (Lam) is not fully disassembled and continues to localize along the spindle envelope structure during Drosophila male meiosis I, while the A-type lamin (LamC) is completely dispersed throughout the cytoplasm. Among the nuclear pore complex proteins, Nup107 co-localized with Lam during this meiotic division. Surprisingly, Lam depletion resulted in a higher frequency of cytokinesis failure in male meiosis. We also observed the similar meiotic phenotype in Nup107-depleted cells. Abnormal localization of Lam was found in the Nup-depleted cells at premeiotic and meiotic stages. The central spindle microtubules became abnormal and recruitment of a contractile ring component to the cleavage sites was disrupted in Lam-depleted cells and Nup107-depleted cells. Therefore, we speculate that both proteins are required for a reinforcement of the spindle envelope, which supports the formation of central spindle microtubules essential for cytokinesis in Drosophila male meiosis. PMID:27402967

  16. B-type nuclear lamin and the nuclear pore complex Nup107-160 influences maintenance of the spindle envelope required for cytokinesis in Drosophila male meiosis.

    PubMed

    Hayashi, Daisuke; Tanabe, Karin; Katsube, Hiroka; Inoue, Yoshihiro H

    2016-08-15

    In higher eukaryotes, nuclear envelope (NE) disassembly allows chromatin to condense and spindle microtubules to access kinetochores. The nuclear lamina, which strengthens the NE, is composed of a polymer meshwork made of A- and B-type lamins. We found that the B-type lamin (Lam) is not fully disassembled and continues to localize along the spindle envelope structure during Drosophila male meiosis I, while the A-type lamin (LamC) is completely dispersed throughout the cytoplasm. Among the nuclear pore complex proteins, Nup107 co-localized with Lam during this meiotic division. Surprisingly, Lam depletion resulted in a higher frequency of cytokinesis failure in male meiosis. We also observed the similar meiotic phenotype in Nup107-depleted cells. Abnormal localization of Lam was found in the Nup-depleted cells at premeiotic and meiotic stages. The central spindle microtubules became abnormal and recruitment of a contractile ring component to the cleavage sites was disrupted in Lam-depleted cells and Nup107-depleted cells. Therefore, we speculate that both proteins are required for a reinforcement of the spindle envelope, which supports the formation of central spindle microtubules essential for cytokinesis in Drosophila male meiosis.

  17. Linking local riverbed flow patterns and pore-water chemistry to hydrogeologic and geomorphic features across scales

    NASA Astrophysics Data System (ADS)

    Ibrahim, T. G.; Thornton, S.; Surridge, B.; Wainwright, J.

    2009-12-01

    The groundwater-surface water interface (GSI) is a critical environmental hotspot, a key area influencing the fate of carbon, nutrients and contaminants of surface and subsurface origin, and a zone of ecological importance. Policy seeking to mitigate issues relating to dissolved contaminants and to improve stream health, increasingly recognizes its significance, particularly in the context of integrated management of streams and aquifers. Techniques assessing riverbed flow and solute patterns are often limited to the local scale. When related to the multi-scale pattern of hydrogeologic and geomorphic features controlling stream, hyporheic and groundwater fluxes, they can improve larger scale predictions of flow and solute behaviour at the GSI. This study develops a conceptual model of riverbed flow and solute patterns, and tests it in a 4th order stream in the UK. It assesses the interaction between large scale subsurface flowpaths, driven by the distribution of bedrock outcrops, and the expansion and closure of alluvial deposits, and small-scale hyporheic flowpaths, driven by riffle-pool sequences. It uses two networks of riverbed mini-piezometers and multi-level samplers: network 1, across fifteen sites in a 7.2 km length of river in unconstrained (open alluvial valley), asymmetric (bedrock outcropping on one bank) and constrained (bedrock on both banks) contexts; and network 2, across six riffle-pool sequences in a 350-m reach, at the transition between asymmetric/unconstrained and constrained contexts. Subsurface flowpaths and stream-water infiltration were deduced by relating vertical exchange fluxes to stream and pore-water patterns of conservative natural tracers. Biogeochemical processes were highlighted using reactive natural tracers. At network 2, measurements of surface water profiles and riverbed coring were also undertaken, and dissolved metal concentrations in the first 15 cm of sediments assessed using gel probes. Network 1 was sampled twice. Monthly

  18. Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export.

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

    The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1Δ strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1.

  19. Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export.

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

    The conserved Sac3:Thp1:Sem1:Sus1:Cdc31 (TREX2) complex binds to nuclear pore complexes (NPCs) and, in addition to integrating mRNA nuclear export with preceding steps in the gene expression pathway, facilitates re-positioning of highly regulated actively transcribing genes (such as GAL1) to NPCs. Although TREX2 is thought to bind NPC protein Nup1, defining the precise role of this interaction has been frustrated by the complex pleiotropic phenotype exhibited by nup1Δ strains. To provide a structural framework for understanding the binding of TREX2 to NPCs and its function in the gene expression pathway, we have determined the structure of the Nup1:TREX2 interaction interface and used this information to engineer a Sac3 variant that impairs NPC binding while not compromising TREX2 assembly. This variant inhibited the NPC association of both de-repressed and activated GAL1 and also produced mRNA export and growth defects. These results indicate that the TREX2:Nup1 interaction facilitates the efficient nuclear export of bulk mRNA together with the re-positioning of GAL1 to NPCs that is required for transcriptional control that is mediated by removal of SUMO from repressors by NPC-bound Ulp1. PMID:24705649

  20. Positively charged amino acids at the SNAP-25 C terminus determine fusion rates, fusion pore properties, and energetics of tight SNARE complex zippering.

    PubMed

    Fang, Qinghua; Zhao, Ying; Herbst, Adam Drew; Kim, Brian N; Lindau, Manfred

    2015-02-18

    SNAP-25 is a Q-SNARE protein mediating exocytosis of neurosecretory vesicles including chromaffin granules. Previous results with a SNAP-25 construct lacking the nine C terminal residues (SNAP-25Δ9) showed changed fusion pore properties (Fang et al., 2008), suggesting a model for fusion pore mechanics that couple C terminal zipping of the SNARE complex to the opening of the fusion pore. The deleted fragment contains the positively charged residues R198 and K201, adjacent to layers 7 and 8 of the SNARE complex. To determine how fusion pore conductance and dynamics depend on these residues, single exocytotic events in bovine chromaffin cells expressing R198Q, R198E, K201Q, or K201E mutants were investigated by carbon fiber amperometry and cell-attached patch capacitance measurements. Coarse grain molecular dynamics simulations revealed spontaneous transitions between a loose and tightly zippered state at the SNARE complex C terminus. The SNAP-25 K201Q mutant showed no changes compared with SNAP-25 wild-type. However, K201E, R198Q, and R198E displayed reduced release frequencies, slower release kinetics, and prolonged fusion pore duration that were correlated with reduced probability to engage in the tightly zippered state. The results show that the positively charged amino acids at the SNAP-25 C terminus promote tight SNARE complex zippering and are required for high release frequency and rapid release in individual fusion events.

  1. Nup84, A Novel Nucleoporin That Is Associated With CAN/Nup214 on the Cytoplasmic Face of the Nuclear Pore Complex

    PubMed Central

    Bastos, Ricardo; Pouplana, Lluis Ribas de; Enarson, Mark; Bodoor, Khaldon; Burke, Brian

    1997-01-01

    The short filaments extending from the cytoplasmic face of nuclear pore complexes are thought to contain docking sites for nuclear import substrates. One component of these filaments is the large O-linked glycoprotein CAN/Nup214. Immunoprecipitation studies carried out under nondenaturing conditions, and using a variety of antibodies, reveal a novel nonglycosylated nucleoporin, Nup84, that is tightly associated with CAN/Nup214. Consistent with such an association, Nup84 is found to be exposed on the cytoplasmic face of the nuclear pore complex. cDNA sequence analyses indicate that Nup84 contains neither the GLFG nor the XFXFG repeats that are a characteristic of a number of other nuclear pore complex proteins. Secondary structure predictions, however, suggest that Nup84 contains a coiled–coil COOH-terminal domain, a conclusion supported by the observation of significant sequence similarity between this region of the molecule and various members of the tropomyosin family. Mutagenesis and expression studies indicate that the putative coiled–coil domain is required for association with the cytoplasmic face of the nuclear pore complex, whereas it is the NH2-terminal region of Nup84 that contains the site of interaction with CAN/Nup214. These findings suggest a model in which Nup84 may function in the attachment of CAN/Nup214 to the central framework of the nuclear pore complex. In this way, Nup84 could play a central role in the organization of the interface between the pore complex and the cytoplasm. PMID:9166401

  2. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

    The hydroxide anion OH−(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH−(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH−(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions. PMID:27550616

  3. On the complex structural diffusion of proton holes in nanoconfined alkaline solutions within slit pores

    NASA Astrophysics Data System (ADS)

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-08-01

    The hydroxide anion OH-(aq) in homogeneous bulk water, that is, the solvated proton hole, is known to feature peculiar properties compared with excess protons solvated therein. In this work, it is disclosed that nanoconfinement of such alkaline aqueous solutions strongly affects the key structural and dynamical properties of OH-(aq) compared with the bulk limit. The combined effect of the preferred hypercoordinated solvation pattern of OH-(aq), its preferred perpendicular orientation relative to the confining surfaces, the pronounced layering of nanoconfined water and the topology of the hydrogen bond network required for proton hole transfer lead to major changes of the charge transport mechanism, in such a way that the proton hole migration mechanism depends exquisitely on the width of the confined space that hosts the water film. Moreover, the anionic Zundel complex, which is of transient nature in homogeneous bulk solutions, can be dynamically trapped as a shallow intermediate species by suitable nanoconfinement conditions.

  4. Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity

    PubMed Central

    Holden, Jennifer M.; Koreny, Ludek; Obado, Samson; Ratushny, Alexander V.; Chen, Wei-Ming; Chiang, Jung-Hsien; Kelly, Steven; Chait, Brian T.; Aitchison, John D.; Rout, Michael P.; Field, Mark C.

    2014-01-01

    The nuclear pore complex (NPC) has dual roles in nucleocytoplasmic transport and chromatin organization. In many eukaryotes the coiled-coil Mlp/Tpr proteins of the NPC nuclear basket have specific functions in interactions with chromatin and defining specialized regions of active transcription, whereas Mlp2 associates with the mitotic spindle/NPC in a cell cycle–dependent manner. We previously identified two putative Mlp-related proteins in African trypanosomes, TbNup110 and TbNup92, the latter of which associates with the spindle. We now provide evidence for independent ancestry for TbNup92/TbNup110 and Mlp/Tpr proteins. However, TbNup92 is required for correct chromosome segregation, with knockout cells exhibiting microaneuploidy and lowered fidelity of telomere segregation. Further, TbNup92 is intimately associated with the mitotic spindle and spindle anchor site but apparently has minimal roles in control of gene transcription, indicating that TbNup92 lacks major barrier activity. TbNup92 therefore acts as a functional analogue of Mlp/Tpr proteins, and, together with the lamina analogue NUP-1, represents a cohort of novel proteins operating at the nuclear periphery of trypanosomes, uncovering complex evolutionary trajectories for the NPC and nuclear lamina. PMID:24600046

  5. Patch clamp and atomic force microscopy demonstrate TATA-binding protein (TBP) interactions with the nuclear pore complex.

    PubMed

    Bustamante, J O; Liepins, A; Prendergast, R A; Hanover, J A; Oberleithner, H

    1995-08-01

    The universal TATA-binding protein, TBP, is an essential component of the multiprotein complex known as transcription factor IID (TFIID). This complex, which consists of TBP and TBP-associated factors (TAFs), is essential for RNA polymerase II-mediated transcription. The molecular size of human TBP (37.7 kD) is close to the passive diffusion limit along the transport channel of the nuclear pore complex (NPC). Therefore, the possibility exists that NPCs restrict TBP translocation to the nuclear interior. Here we show for the first time, with patch-clamp and atomic force microscopy (AFM), that NPCs regulate TBP movement into the nucleus and that TBP (10(-15)-10(-10)M) is capable of modifying NPC structure and function. The translocation of TBP was ATP-dependent and could be detected as a transient plugging of the NPC channels, with a concomitant transient reduction in single NPC channel conductance, gamma, to a negligible value. NPC unplugging was accompanied by permanent channel opening at concentrations greater than 250 pM. AFM images demonstrated that the TBP molecules attached to and accumulated on the NPC cytosolic side. NPC channel activity could be recorded for more than 48 hr. These observations suggest that three novel functions of TBP are: to stabilize NPC, to force the NPC channels into an open state, and to increase the number of functional channels. Since TBP is a major component of transcription, our observations are relevant to the understanding of the gene expression mechanisms underlying normal and pathological cell structure and function. PMID:8568841

  6. One Single Static Measurement Predicts Wave Localization in Complex Structures

    NASA Astrophysics Data System (ADS)

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-01

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.

  7. One Single Static Measurement Predicts Wave Localization in Complex Structures.

    PubMed

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-12

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible. PMID:27563967

  8. High-resolution imaging reveals new features of nuclear export of mRNA through the nuclear pore complexes.

    PubMed

    Kelich, Joseph M; Yang, Weidong

    2014-01-01

    The nuclear envelope (NE) of eukaryotic cells provides a physical barrier for messenger RNA (mRNA) and the associated proteins (mRNPs) traveling from sites of transcription in the nucleus to locations of translation processing in the cytoplasm. Nuclear pore complexes (NPCs) embedded in the NE serve as a dominant gateway for nuclear export of mRNA. However, the fundamental characterization of export dynamics of mRNPs through the NPC has been hindered by several technical limits. First, the size of NPC that is barely below the diffraction limit of conventional light microscopy requires a super-resolution microscopy imaging approach. Next, the fast transit of mRNPs through the NPC further demands a high temporal resolution by the imaging approach. Finally, the inherent three-dimensional (3D) movements of mRNPs through the NPC demand the method to provide a 3D mapping of both transport kinetics and transport pathways of mRNPs. This review will highlight the recently developed super-resolution imaging techniques advanced from 1D to 3D for nuclear export of mRNPs and summarize the new features in the dynamic nuclear export process of mRNPs revealed from these technical advances. PMID:25141104

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

    SciTech Connect

    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.

    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.

  10. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena.

    PubMed

    Iwamoto, Masaaki; Koujin, Takako; Osakada, Hiroko; Mori, Chie; Kojidani, Tomoko; Matsuda, Atsushi; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2015-05-01

    Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates.

  11. Atomic Structure of the Nuclear Pore Complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata

    PubMed Central

    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.

    2012-01-01

    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 cytoplasm. The yeast NPC is an eight-fold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins (Nups). 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 (GLEBS 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 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by Small Angle X-ray Scattering (SAXS). Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiaeNup145N, and human Nup98 are discussed. PMID:22544723

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

    PubMed

    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

    2012-08-01

    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 ~456 polypeptide chains contributed by ~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 Å 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. PMID:22544723

  13. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex

    SciTech Connect

    Sampathkumar, Parthasarathy; Gheyi, Tarun; Miller, Stacy A.; Bain, Kevin T.; Dickey, Mark; Bonanno, Jeffrey B.; Kim, Seung Joong; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Martel, Anne; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sali, Andrej; Sauder, J. Michael; Burley, Stephen K.

    2012-10-23

    Nuclear pore complexes (NPCs), responsible for the nucleo-cytoplasmic exchange of proteins and nucleic acids, are dynamic macromolecular assemblies forming an eight-fold symmetric co-axial ring structure. Yeast (Saccharomyces cerevisiae) NPCs are made up of at least 456 polypeptide chains of {approx}30 distinct sequences. Many of these components (nucleoporins, Nups) share similar structural motifs and form stable subcomplexes. We have determined a high-resolution crystal structure of the C-terminal domain of yeast Nup133 (ScNup133), a component of the heptameric Nup84 subcomplex. Expression tests yielded ScNup133(944-1157) that produced crystals diffracting to 1.9{angstrom} resolution. ScNup133(944-1157) adopts essentially an all {alpha}-helical fold, with a short two stranded {beta}-sheet at the C-terminus. The 11 {alpha}-helices of ScNup133(944-1157) form a compact fold. In contrast, the previously determined structure of human Nup133(934-1156) bound to a fragment of human Nup107 has its constituent {alpha}-helices are arranged in two globular blocks. These differences may reflect structural divergence among homologous nucleoporins.

  14. Biased assembly of the nuclear pore complex is required for somatic and germline nuclear differentiation in Tetrahymena

    PubMed Central

    Iwamoto, Masaaki; Koujin, Takako; Osakada, Hiroko; Mori, Chie; Kojidani, Tomoko; Matsuda, Atsushi; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2015-01-01

    Ciliates have two functionally distinct nuclei, a somatic macronucleus (MAC) and a germline micronucleus (MIC) that develop from daughter nuclei of the last postzygotic division (PZD) during the sexual process of conjugation. Understanding this nuclear dimorphism is a central issue in ciliate biology. We show, by live-cell imaging of Tetrahymena, that biased assembly of the nuclear pore complex (NPC) occurs immediately after the last PZD, which generates anterior-posterior polarized nuclei: MAC-specific NPCs assemble in anterior presumptive MACs but not in posterior presumptive MICs. MAC-specific NPC assembly in the anterior nuclei occurs much earlier than transport of Twi1p, which is required for MAC genome rearrangement. Correlative light-electron microscopy shows that addition of new nuclear envelope (NE) precursors occurs through the formation of domains of redundant NE, where the outer double membrane contains the newly assembled NPCs. Nocodazole inhibition of the second PZD results in assembly of MAC-specific NPCs in the division-failed zygotic nuclei, leading to failure of MIC differentiation. Our findings demonstrate that NPC type switching has a crucial role in the establishment of nuclear differentiation in ciliates. PMID:25788697

  15. The influence of bedding and pore space-anisotropy on strain localization, mechanical anisotropy and transport properties in porous sandstone

    NASA Astrophysics Data System (ADS)

    Baud, P.; Louis, L.; Meredith, P. G..; Townend, E.; Wong, T.-F.

    2009-04-01

    Significant anisotropy in mechanical behaviour and failure strength may arise from planar rock fabrics such as bedding or preferred alignment of inequant voids in sedimentary rocks, cleavage in slates, and preferred orientation and/or arrangement of minerals and cracks in crystalline igneous and metamorphic rocks. Elastic anisotropy of a rock can be related to its fabric, a seismic manifestation of which is shear-wave splitting. Textural anisotropy can also result in pronounced anisotropy of tensile and compressive strength, which may be associated with different failure modes and deformation mechanisms, depending on how stress is applied relative to the anisotropy planes. On the borehole scale mechanical anisotropy and anisotropic rock strength can significantly influence the morphology and interpretation of wellbore breakout as well as the inference of in situ stress. In this study, we focussed on sedimentary rocks and studied the microstructural attributes that govern anisotropic failure in Rothbach and Diemelstadt sandstones of nominal porosities 20 and 24%, respectively. Rothbach sandstone has a relatively heterogeneous structure with granulometric layering that alternates between zones with significant contrasts in porosity and grain size. Diemelstadt sandstone presents a relatively more homogeneous structure, significant P-Wave anisotropy and a mean pore space geometry inferred by magnetic susceptibility (AMS) approximating to an oblate spheroid. Conventional triaxial experiments were performed at constant strain rate and room temperature on saturated samples of both rocks cored at various orientations with respect to the sedimentary bedding. For Diemelstadt sandstone, the samples cored parallel to bedding were stronger than those cored perpendicular to bedding. The mechanical anisotropy was more pronounced and significantly different in Rothbach sandstone. The sample cored perpendicular to bedding were stronger than those cored parallel to bedding, while

  16. Nup2 requires a highly divergent partner, NupA, to fulfill functions at nuclear pore complexes and the mitotic chromatin region

    PubMed Central

    Markossian, Sarine; Suresh, Subbulakshmi; Osmani, Aysha H.; Osmani, Stephen A.

    2015-01-01

    Chromatin and nuclear pore complexes (NPCs) undergo dramatic changes during mitosis, which in vertebrates and Aspergillus nidulans involves movement of Nup2 from NPCs to the chromatin region to fulfill unknown functions. This transition is shown to require the Cdk1 mitotic kinase and be promoted prematurely by ectopic expression of the NIMA kinase. Nup2 localizes with a copurifying partner termed NupA, a highly divergent yet essential NPC protein. NupA and Nup2 locate throughout the chromatin region during prophase but during anaphase move to surround segregating DNA. NupA function is shown to involve targeting Nup2 to its interphase and mitotic locations. Deletion of either Nup2 or NupA causes identical mitotic defects that initiate a spindle assembly checkpoint (SAC)–dependent mitotic delay and also cause defects in karyokinesis. These mitotic problems are not caused by overall defects in mitotic NPC disassembly–reassembly or general nuclear import. However, without Nup2 or NupA, although the SAC protein Mad1 locates to its mitotic locations, it fails to locate to NPCs normally in G1 after mitosis. Collectively the study provides new insight into the roles of Nup2 and NupA during mitosis and in a surveillance mechanism that regulates nucleokinesis when mitotic defects occur after SAC fulfillment. PMID:25540430

  17. Nup2 requires a highly divergent partner, NupA, to fulfill functions at nuclear pore complexes and the mitotic chromatin region.

    PubMed

    Markossian, Sarine; Suresh, Subbulakshmi; Osmani, Aysha H; Osmani, Stephen A

    2015-02-15

    Chromatin and nuclear pore complexes (NPCs) undergo dramatic changes during mitosis, which in vertebrates and Aspergillus nidulans involves movement of Nup2 from NPCs to the chromatin region to fulfill unknown functions. This transition is shown to require the Cdk1 mitotic kinase and be promoted prematurely by ectopic expression of the NIMA kinase. Nup2 localizes with a copurifying partner termed NupA, a highly divergent yet essential NPC protein. NupA and Nup2 locate throughout the chromatin region during prophase but during anaphase move to surround segregating DNA. NupA function is shown to involve targeting Nup2 to its interphase and mitotic locations. Deletion of either Nup2 or NupA causes identical mitotic defects that initiate a spindle assembly checkpoint (SAC)-dependent mitotic delay and also cause defects in karyokinesis. These mitotic problems are not caused by overall defects in mitotic NPC disassembly-reassembly or general nuclear import. However, without Nup2 or NupA, although the SAC protein Mad1 locates to its mitotic locations, it fails to locate to NPCs normally in G1 after mitosis. Collectively the study provides new insight into the roles of Nup2 and NupA during mitosis and in a surveillance mechanism that regulates nucleokinesis when mitotic defects occur after SAC fulfillment.

  18. Integral membrane proteins Brr6 and Apq12 link assembly of the nuclear pore complex to lipid homeostasis in the endoplasmic reticulum

    PubMed Central

    Hodg, Christine A.; Choudhary, Vineet; Wolyniak, Michael J.; Scarcelli, John J.; Schneiter, Roger; Col, Charles N.

    2010-01-01

    Summary Cells of Saccharomyces cerevisiae lacking Apq12, a nuclear envelope (NE)-endoplasmic reticulum (ER) integral membrane protein, are defective in assembly of nuclear pore complexes (NPCs), possibly because of defects in regulating membrane fluidity. We identified BRR6, which encodes an essential integral membrane protein of the NE-ER, as a dosage suppressor of apq12 Δ. Cells carrying the temperature-sensitive brr6-1 allele have been shown to have defects in nucleoporin localization, mRNA metabolism and nuclear transport. Electron microscopy revealed that brr6-1 cells have gross NE abnormalities and proliferation of the ER. brr6-1 cells were hypersensitive to compounds that affect membrane biophysical properties and to inhibitors of lipid biosynthetic pathways, and displayed strong genetic interactions with genes encoding non-essential lipid biosynthetic enzymes. Strikingly, brr6-1 cells accumulated, in or near the NE, elevated levels of the two classes of neutral lipids, steryl esters and triacylglycerols, and over-accumulated sterols when they were provided exogenously. Although neutral lipid synthesis is dispensable in wild-type cells, viability of brr6-1 cells was fully dependent on neutral lipid production. These data indicate that Brr6 has an essential function in regulating lipid homeostasis in the NE-ER, thereby impacting NPC formation and nucleocytoplasmic transport. PMID:20016074

  19. Local modularity for community detection in complex networks

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Tao; Zhang, Yan; Hu, Ke; Li, Jian-Ming; Xu, Xiao-Ke; Liu, Cui-Cui; Chen, Shi

    2016-02-01

    Community detection is a topic of interest in the study of complex networks such as the protein-protein interaction networks and metabolic networks. In recent years, various methods were proposed to detect community structures of the networks. Here, a kind of local modularity with tunable parameter is derived from the Newman-Girvan modularity by a special self-loop strategy that depends on the community division of the networks. By the self-loop strategy, one can easily control the definition of modularity, and the resulting modularity can be optimized by using the existing modularity optimization algorithms. The local modularity is used as the target function for community detection, and a self-consistent method is proposed for the optimization of the local modularity. We analyze the behaviors of the local modularity and show the validity of the local modularity in detecting community structures on various networks.

  20. Dependence on injection temperature and on aquifer's petrophysical properties of the local stress applying on the pore wall of a crystallized pore in the context of CO2 storage in deep saline aquifers

    NASA Astrophysics Data System (ADS)

    Osselin, Florian; Fen-Chong, Teddy; Fabbri, Antonin; Lassin, Arnault; Pereira, Jean-Michel; Dangla, Patrick

    2013-11-01

    The development of CCS (carbon capture and storage) currently faces numerous problems and particularly the precipitation of salts induced by the drying of the porous medium during injection of carbon dioxide in deep saline aquifers. This precipitation has several consequences, and particularly the creation of a crystallization pressure which can have an important mechanical impact on the host rock. Literature on crystallization pressure is one century rich of experimental and theoretical works. However, applications have been performed in the field of civil engineering and building science only, and, despite they are of paramount importance in the context of CCS, studies about this phenomenon in deep reservoir conditions are currently lacking. In this paper, we retrieve the classic crystallization pressure equation within the framework of geochemistry and present its explicit form of dependence with temperature, pressure, and composition. Evaluation of the crystallization pressure has then been proceeded considering the injection conditions and a sketch of in-pore crystallization process. The evolution of the local stress transmitted to a crystallized pore wall is found to be strongly related to the petrophysical properties of the medium and to the injection temperature of the carbon dioxide under the assumption of constant salt concentration during the precipitation process. Values differ strongly with the considered mineral, depending particularly on the solubility, and can reach in some conditions 165 MPa, making crystallization pressure a major factor in the mechanical behavior of the aquifer.

  1. Dynamic subcellular localization of a respiratory complex controls bacterial respiration.

    PubMed

    Alberge, François; Espinosa, Leon; Seduk, Farida; Sylvi, Léa; Toci, René; Walburger, Anne; Magalon, Axel

    2015-01-01

    Respiration, an essential process for most organisms, has to optimally respond to changes in the metabolic demand or the environmental conditions. The branched character of their respiratory chains allows bacteria to do so by providing a great metabolic and regulatory flexibility. Here, we show that the native localization of the nitrate reductase, a major respiratory complex under anaerobiosis in Escherichia coli, is submitted to tight spatiotemporal regulation in response to metabolic conditions via a mechanism using the transmembrane proton gradient as a cue for polar localization. These dynamics are critical for controlling the activity of nitrate reductase, as the formation of polar assemblies potentiates the electron flux through the complex. Thus, dynamic subcellular localization emerges as a critical factor in the control of respiration in bacteria.

  2. Dynamic subcellular localization of a respiratory complex controls bacterial respiration

    PubMed Central

    Alberge, François; Espinosa, Leon; Seduk, Farida; Sylvi, Léa; Toci, René; Walburger, Anne; Magalon, Axel

    2015-01-01

    Respiration, an essential process for most organisms, has to optimally respond to changes in the metabolic demand or the environmental conditions. The branched character of their respiratory chains allows bacteria to do so by providing a great metabolic and regulatory flexibility. Here, we show that the native localization of the nitrate reductase, a major respiratory complex under anaerobiosis in Escherichia coli, is submitted to tight spatiotemporal regulation in response to metabolic conditions via a mechanism using the transmembrane proton gradient as a cue for polar localization. These dynamics are critical for controlling the activity of nitrate reductase, as the formation of polar assemblies potentiates the electron flux through the complex. Thus, dynamic subcellular localization emerges as a critical factor in the control of respiration in bacteria. DOI: http://dx.doi.org/10.7554/eLife.05357.001 PMID:26077726

  3. Isolation and characterization of a proteinaceous subnuclear fraction composed of nuclear matrix, peripheral lamina, and nuclear pore complexes from embryos of Drosophila melanogaster.

    PubMed

    Fisher, P A; Berrios, M; Blobel, G

    1982-03-01

    Morphologically intact nuclei have been prepared from embryos of Drosophila melanogaster by a simple and rapid procedure. These nuclei have been further treated with high concentrations of DNase I and RNase A followed by sequential extraction with 2% Triton X-100 and 1 M NaCl to produce a structurally and biochemically distinct preparation designated Drosophila subnuclear fraction I (DSNF-I). As seen by phase-contrast microscopy, DSNF-I is composed of material which closely resembles unfractionated nuclei; residual internal nuclear structures including nucleolar remnants are clearly visible. By transmission electron microscopy, nuclear lamina, pore complexes, and a nuclear matrix are similarly identified. Biochemically, DSNF-I is composed almost entirely of protein (greater than 93%). SDS PAGE analysis reveals several major polypeptides; species at 174,000, 74,000, and 42,000 predominate. A polypeptide coincident with the Coomassie Blue-stainable 174-kdalton band has been shown by a novel technique of lectin affinity labeling to be a glycoprotein; a glycoprotein of similar or identical molecular weight has been found to be a component of nuclear envelope fractions isolated from the livers of rats, guinea pigs, opossums, and chickens. Antisera against several of the polypeptides in DSNF-I have been obtained from rabbits, and all of them show only little or no cross-reactivity with Drosophila cytoplasmic fractions. Initial results of immunocytochemical studies, while failing to positively localize either the 174- or 16-kdalton polypeptides, demonstrate a nuclear localization of the 74-kdalton antigen in all of several interphase cell types obtained from both Drosophila embryos and third-instar larvae. PMID:6177701

  4. The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope

    SciTech Connect

    Kind, Barbara; Koehler, Katrin; Lorenz, Mike; Huebner, Angela

    2009-12-11

    The nuclear pore complex (NPC) consists of {approx}30 different proteins and provides the only sites for macromolecular transport between cytoplasm and nucleus. ALADIN was discovered as a new member of the NPC. Mutations in ALADIN are known to cause triple A syndrome, a rare autosomal recessive disorder characterized by adrenal insufficiency, alacrima, and achalasia. The function and exact location of the nucleoporin ALADIN within the NPC multiprotein complex is still unclear. Using a siRNA-based approach we downregulated the three known membrane integrated nucleoporins NDC1, GP210, and POM121 in stably expressing GFP-ALADIN HeLa cells. We identified NDC1 but not GP210 and POM121 as the main anchor of ALADIN within the NPC. Solely the depletion of NDC1 caused mislocalization of ALADIN. Vice versa, the depletion of ALADIN led also to disappearance of NDC1 at the NPC. However, the downregulation of two further membrane-integral nucleoporins GP210 and POM121 had no effect on ALADIN localization. Furthermore, we could show a direct association of NDC1 and ALADIN in NPCs by fluorescence resonance energy transfer (FRET) measurements. Based on our findings we conclude that ALADIN is anchored in the nuclear envelope via NDC1 and that this interaction gets lost, if ALADIN is mutated. The loss of integration of ALADIN in the NPC is a main pathogenetic aspect for the development of the triple A syndrome and suggests that the interaction between ALADIN and NDC1 may be involved in the pathogenesis of the disease.

  5. A laboratory study to estimate pore geometric parameters of sandstones using complex conductivity and nuclear magnetic resonance for permeability prediction

    NASA Astrophysics Data System (ADS)

    Osterman, Gordon; Keating, Kristina; Binley, Andrew; Slater, Lee

    2016-06-01

    We estimate parameters from the Katz and Thompson permeability model using laboratory complex electrical conductivity (CC) and nuclear magnetic resonance (NMR) data to build permeability models parameterized with geophysical measurements. We use the Katz and Thompson model based on the characteristic hydraulic length scale, determined from mercury injection capillary pressure estimates of pore throat size, and the intrinsic formation factor, determined from multisalinity conductivity measurements, for this purpose. Two new permeability models are tested, one based on CC data and another that incorporates CC and NMR data. From measurements made on forty-five sandstone cores collected from fifteen different formations, we evaluate how well the CC relaxation time and the NMR transverse relaxation times compare to the characteristic hydraulic length scale and how well the formation factor estimated from CC parameters compares to the intrinsic formation factor. We find: (1) the NMR transverse relaxation time models the characteristic hydraulic length scale more accurately than the CC relaxation time (R2 of 0.69 and 0.33 and normalized root mean square errors (NRMSE) of 0.16 and 0.21, respectively); (2) the CC estimated formation factor is well correlated with the intrinsic formation factor (NRMSE=0.23). We demonstrate that that permeability estimates from the joint-NMR-CC model (NRMSE=0.13) compare favorably to estimates from the Katz and Thompson model (NRMSE=0.074). This model advances the capability of the Katz and Thompson model by employing parameters measureable in the field giving it the potential to more accurately estimate permeability using geophysical measurements than are currently possible.

  6. Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket.

    PubMed

    Krull, Sandra; Thyberg, Johan; Björkroth, Birgitta; Rackwitz, Hans-Richard; Cordes, Volker C

    2004-09-01

    The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.

  7. Numerical and Experimental Pore-scale Analyses of Inert and Reactive Multiple Colloidal Particles in Complex Flow Domains

    NASA Astrophysics Data System (ADS)

    Basagaoglu, H.; Succi, S.; Melchionna, S.; Allwein, S.; Dixon, H.

    2008-12-01

    A fluctuating lattice-Boltzmann model was developed to simulate pore-scale flow and transport of multiple particles in geometrically complex porous and fractured domains. The model is based on the original work of Ladd [J. Fluid Mech., 271, 285, 1994] and the modeling approach based on the virtual intraparticle fluid nodes as proposed by Ding and Aidun [J. Stat. Phys., 112, 685, 2003]. The model has been improved by introducing two-body electrostatic and van der Waals potentials. Moreover, the commonly used bounce-back algorithm to simulate no-slip conditions has been replaced by an immersed boundary condition to simulate softer particle-wall interactions. The simulation results captured the wall and inertial effects on trajectories of a single particle in different Reynolds number flows in smooth-walled channels, consistent with earlier numerical simulation results. Multiple-particle simulations in porous and fractured domains captured trains of particles crossing multiple streamlines in fast-flow paths and lagged particles in slow-flow paths as has been observed in our experiments and reported in the literature. Experimental studies are focused on two-dimensional flow for three microflow cell geometries and use monodispersed particles in dense and dilute concentrations. The average particle sizes are 2, 10 and 30 microns, and the interaction between particle surfaces is controlled by the use of surfactants. Three two- dimensional flow cells with a 50 to 500 micron width have been manufactured to evaluate scale effects. Preliminary results are available for the flow of 2 micron poly(lactic-co-glycolic acid) [PLGA] microspheres dispersed in polyvinyl alcohol solution (PVA) in a 500-micron tube with inline flow obstruction with dilute and concentrated solutions. These results demonstrate particle streamlines and show particle-particle and particle-wall interactions. The experimental findings are compared with simulation results.

  8. Two conformational states of the membrane-associated Bacillus thuringiensis Cry4Ba {delta}-endotoxin complex revealed by electron crystallography: Implications for toxin-pore formation

    SciTech Connect

    Ounjai, Puey; Unger, Vinzenz M.; Sigworth, Fred J.; Angsuthanasombat, Chanan

    2007-10-05

    The insecticidal nature of Cry {delta}-endotoxins produced by Bacillus thuringiensis is generally believed to be caused by their ability to form lytic pores in the midgut cell membrane of susceptible insect larvae. Here we have analyzed membrane-associated structures of the 65-kDa dipteran-active Cry4Ba toxin by electron crystallography. The membrane-associated toxin complex was crystallized in the presence of DMPC via detergent dialysis. Depending upon the charge of the adsorbed surface, 2D crystals of the oligomeric toxin complex have been captured in two distinct conformations. The projection maps of those crystals have been generated at 17 A resolution. Both complexes appeared to be trimeric; as in one crystal form, its projection structure revealed a symmetrical pinwheel-like shape with virtually no depression in the middle of the complex. The other form revealed a propeller-like conformation displaying an obvious hole in the center region, presumably representing the toxin-induced pore. These crystallographic data thus demonstrate for the first time that the 65-kDa activated Cry4Ba toxin in association with lipid membranes could exist in at least two different trimeric conformations, conceivably implying the closed and open states of the pore.

  9. Disulfide bridge formation between SecY and a translocating polypeptide localizes the translocation pore to the center of SecY.

    PubMed

    Cannon, Kurt S; Or, Eran; Clemons, William M; Shibata, Yoko; Rapoport, Tom A

    2005-04-25

    During their biosynthesis, many proteins pass through the membrane via a hydrophilic channel formed by the heterotrimeric Sec61/SecY complex. Whether this channel forms at the interface of multiple copies of Sec61/SecY or is intrinsic to a monomeric complex, as suggested by the recently solved X-ray structure of the Methanococcus jannaschii SecY complex, is a matter of contention. By introducing a single cysteine at various positions in Escherichia coli SecY and testing its ability to form a disulfide bond with a single cysteine in a translocating chain, we provide evidence that translocating polypeptides pass through the center of the SecY complex. The strongest cross-links were observed with residues that would form a constriction in an hourglass-shaped pore. This suggests that the channel makes only limited contact with a translocating polypeptide, thus minimizing the energy required for translocation. PMID:15851514

  10. Advanced Algorithms for Local Routing Strategy on Complex Networks

    PubMed Central

    Lin, Benchuan; Chen, Bokui; Gao, Yachun; Tse, Chi K.; Dong, Chuanfei; Miao, Lixin; Wang, Binghong

    2016-01-01

    Despite the significant improvement on network performance provided by global routing strategies, their applications are still limited to small-scale networks, due to the need for acquiring global information of the network which grows and changes rapidly with time. Local routing strategies, however, need much less local information, though their transmission efficiency and network capacity are much lower than that of global routing strategies. In view of this, three algorithms are proposed and a thorough investigation is conducted in this paper. These algorithms include a node duplication avoidance algorithm, a next-nearest-neighbor algorithm and a restrictive queue length algorithm. After applying them to typical local routing strategies, the critical generation rate of information packets Rc increases by over ten-fold and the average transmission time 〈T〉 decreases by 70–90 percent, both of which are key physical quantities to assess the efficiency of routing strategies on complex networks. More importantly, in comparison with global routing strategies, the improved local routing strategies can yield better network performance under certain circumstances. This is a revolutionary leap for communication networks, because local routing strategy enjoys great superiority over global routing strategy not only in terms of the reduction of computational expense, but also in terms of the flexibility of implementation, especially for large-scale networks. PMID:27434502

  11. Advanced Algorithms for Local Routing Strategy on Complex Networks.

    PubMed

    Lin, Benchuan; Chen, Bokui; Gao, Yachun; Tse, Chi K; Dong, Chuanfei; Miao, Lixin; Wang, Binghong

    2016-01-01

    Despite the significant improvement on network performance provided by global routing strategies, their applications are still limited to small-scale networks, due to the need for acquiring global information of the network which grows and changes rapidly with time. Local routing strategies, however, need much less local information, though their transmission efficiency and network capacity are much lower than that of global routing strategies. In view of this, three algorithms are proposed and a thorough investigation is conducted in this paper. These algorithms include a node duplication avoidance algorithm, a next-nearest-neighbor algorithm and a restrictive queue length algorithm. After applying them to typical local routing strategies, the critical generation rate of information packets Rc increases by over ten-fold and the average transmission time 〈T〉 decreases by 70-90 percent, both of which are key physical quantities to assess the efficiency of routing strategies on complex networks. More importantly, in comparison with global routing strategies, the improved local routing strategies can yield better network performance under certain circumstances. This is a revolutionary leap for communication networks, because local routing strategy enjoys great superiority over global routing strategy not only in terms of the reduction of computational expense, but also in terms of the flexibility of implementation, especially for large-scale networks. PMID:27434502

  12. Extracellular signal-regulated kinase 2 (ERK2) phosphorylation sites and docking domain on the nuclear pore complex protein Tpr cooperatively regulate ERK2-Tpr interaction.

    PubMed

    Vomastek, Tomás; Iwanicki, Marcin P; Burack, W Richard; Tiwari, Divya; Kumar, Devanand; Parsons, J Thomas; Weber, Michael J; Nandicoori, Vinay Kumar

    2008-11-01

    Identifying direct substrates of mitogen-activated protein kinases (MAPKs) and understanding how those substrates are selected is central to understanding how these ubiquitously activated enzymes generate diverse biological responses. In previous work, we identified several new candidate substrates for the MAPK ERK2 (extracellular signal-regulated kinase 2), including the nuclear pore complex protein Tpr (translocated promoter region). In this report, we identify sites on Tpr for ERK2 phosphorylation and binding and demonstrate their functional interaction. ERK2 phosphorylation and dimerization are necessary for ERK2-Tpr binding, and this occurs through a DEF (docking site for ERK2, FXF) domain on Tpr. Surprisingly, the DEF domain and the phosphorylation sites displayed positive cooperativity to promote ERK2 binding to Tpr, in contrast to substrates where phosphorylation reduces binding. Ectopic expression or depletion of Tpr resulted in decreased movement of activated ERK2 from the cytoplasm to the nucleus, implying a role for Tpr in ERK2 translocation. Collectively, the data provide direct evidence that a component of the nuclear pore complex is a bona fide substrate of ERK2 in vivo and that activated ERK2 stably associates with this substrate after phosphorylation, where it could play a continuing role in nuclear pore function. We propose that Tpr is both a substrate and a scaffold for activated ERKs.

  13. Diaphanous regulates SCAR complex localization during Drosophila myoblast fusion.

    PubMed

    Deng, Su; Bothe, Ingo; Baylies, Mary

    2016-10-01

    From Drosophila to man, multinucleated muscle cells form through cell-cell fusion. Using Drosophila as a model system, researchers first identified, and then demonstrated, the importance of actin cytoskeletal rearrangements at the site of fusion. These actin rearrangements at the fusion site are regulated by SCAR and WASp mediated Arp2/3 activation, which nucleates branched actin networks. Loss of SCAR, WASp or both leads to defects in myoblast fusion. Recently, we have found that the actin regulator Diaphanous (Dia) also plays a role both in organizing actin and in regulating Arp2/3 activity at the fusion site. In this Extra View article, we provide additional data showing that the Abi-SCAR complex accumulates at the fusion site and that excessive SCAR activity impairs myoblast fusion. Using constitutively active Dia constructs, we provide additional evidence that Dia functions upstream of SCAR activity to regulate actin dynamics at the fusion site and to localize the Abi-SCAR complex.

  14. Soil pore structure and substrate C mineralization

    NASA Astrophysics Data System (ADS)

    Sleutel, Steven; Maenhout, Peter; Vanhoorebeke, Luc; Cnudde, Veerle; De Neve, Stefaan

    2014-05-01

    Our aim was to investigate the complex interactions between soil pore structure, soil biota and decomposition of added OM substrates. We report on a lab incubation experiment in which CO2 respiration from soil cores was monitored (headspace GC analysis) and an X-ray CT approach yielded soil pore size distributions. Such combined use of X-ray CT with soil incubation studies was obstructed, until now, by many practical constraints such as CT-volume quality, limited resolution, scanning time and complex soil pore network quantification, which have largely been overcome in this study. We incubated a sandy loam soil (with application of ground grass or sawdust) in 18 small aluminium rings (Ø 1 cm, h 1 cm). Bulk density was adjusted to 1.1 or 1.3 Mg m-3 (compaction) and 6 rings were filled at a coarser Coarse Sand:Fine Sand:Silt+Clay ratio. While compaction induced a strong reduction in the cumulative C mineralization for both grass and sawdust substrates, artificial change to a coarser soil texture only reduced net C mineralization from the added sawdust. There thus appears to be a strong interaction effect between soil pore structure and substrate type on substrate decomposition. Correlation coefficients between the C mineralization rates and volumes of 7 pore size classes (from the X-ray CT data) also showed an increasing positive correlation with increasing pore size. Since any particulate organic matter initially present in the soil was removed prior to the experiment (sieving, ashing the >53µm fraction and recombining with the <53µm fraction), the added OM can be localized by means of X-ray CT. Through on-going image analysis the surrounding porosity of the added grass or sawdust particles is being quantified to further study the interaction between the soil pore structure and substrate decomposition.

  15. Cilia and Nuclear Pore Proteins: Pore No More?

    PubMed

    Obado, Samson O; Rout, Michael P

    2016-09-12

    Nuclear pore proteins at the base of cilia were thought to regulate transport into cilia. In this issue of Developmental Cell, Del Viso et al. (2016) challenge this view, showing instead that pore proteins localize to ciliary basal bodies and that their perturbation leads to congenital heart disease. PMID:27623377

  16. Velocity Profiles in Pores with Undulating Opening Diameter and Their Importance for Resistive-Pulse Experiments

    PubMed Central

    2015-01-01

    Pores with undulating opening diameters have emerged as an analytical tool enhancing the speed of resistive-pulse experiments, with a potential to simultaneously characterize size and mechanical properties of translocating objects. In this work, we present a detailed study of the characteristics of resistive-pulses of charged and uncharged polymer particles in pores with different aspect ratios and pore topography. Although no external pressure difference was applied, our experiments and modeling indicated the existence of local pressure drops, which modified axial and radial velocities of the solution. As a consequence of the complex velocity profiles, pores with undulating pore diameter and low-aspect ratio exhibited large dispersion of the translocation times. Distribution of the pulse amplitude, which is a measure of the object size, was not significantly affected by the pore topography. The importance of tuning pore geometry for the application in resistive-sensing and multipronged characterization of physical properties of translocating objects is discussed. PMID:25245282

  17. FgKin1 kinase localizes to the septal pore and plays a role in hyphal growth, ascospore germination, pathogenesis, and localization of Tub1 beta-tubulins in Fusarium graminearum.

    PubMed

    Luo, Yongping; Zhang, Hongchang; Qi, Linlu; Zhang, Shijie; Zhou, Xiaoying; Zhang, Yimei; Xu, Jin-Rong

    2014-12-01

    The Kin1/Par-1/MARK kinases regulate various cellular processes in eukaryotic organisms. Kin1 orthologs are well conserved in fungal pathogens but none of them have been functionally characterized. Here, we show that KIN1 is important for pathogenesis and growth in two phytopathogenic fungi and that FgKin1 regulates ascospore germination and the localization of Tub1 β-tubulins in Fusarium graminearum. The Fgkin1 mutant and putative FgKIN1(S172A) kinase dead (nonactivatable) transformants were characterized for defects in plant infection, sexual and asexual reproduction, and stress responses. The localization of FgKin1 and two β-tubulins were examined in the wild-type and mutant backgrounds. Deletion of FgKIN1 resulted in reduced virulence and defects in ascospore germination and release. FgKin1 localized to the center of septal pores. FgKIN1 deletion had no effect on Tub2 microtubules but disrupted Tub1 localization. In the mutant, Tub1 appeared to be enriched in the nucleolus. In Magnaporthe oryzae, MoKin1 has similar functions in growth and infection and it also localizes to septal pores. The S172A mutation had no effect on the localization and function of FgKIN1 during sexual reproduction. These results indicate that FgKIN1 has kinase-dependent and independent functions and it specifically regulates Tub1 β-tubulins. FgKin1 plays a critical role in ascospore discharge, germination, and plant infection. PMID:25078365

  18. Neural correlates of sound localization in complex acoustic environments.

    PubMed

    Zündorf, Ida C; Lewald, Jörg; Karnath, Hans-Otto

    2013-01-01

    Listening to and understanding people in a "cocktail-party situation" is a remarkable feature of the human auditory system. Here we investigated the neural correlates of the ability to localize a particular sound among others in an acoustically cluttered environment with healthy subjects. In a sound localization task, five different natural sounds were presented from five virtual spatial locations during functional magnetic resonance imaging (fMRI). Activity related to auditory stream segregation was revealed in posterior superior temporal gyrus bilaterally, anterior insula, supplementary motor area, and frontoparietal network. Moreover, the results indicated critical roles of left planum temporale in extracting the sound of interest among acoustical distracters and the precuneus in orienting spatial attention to the target sound. We hypothesized that the left-sided lateralization of the planum temporale activation is related to the higher specialization of the left hemisphere for analysis of spectrotemporal sound features. Furthermore, the precuneus - a brain area known to be involved in the computation of spatial coordinates across diverse frames of reference for reaching to objects - seems to be also a crucial area for accurately determining locations of auditory targets in an acoustically complex scene of multiple sound sources. The precuneus thus may not only be involved in visuo-motor processes, but may also subserve related functions in the auditory modality.

  19. Classifying Urban Land Covers Using Local Indices of Spatial Complexity

    NASA Technical Reports Server (NTRS)

    Arumugam, Mahesh; Emerson, Charles W.; Lam, Nina Siu-Ngan; Quattrochi, Dale A.

    2003-01-01

    The skewed statistical distributions of land cover types in complex, heterogeneous urban areas limits the effectiveness of traditional spectrally based maximum-likelihood classifiers. This work examines the utility of fractal dimension and Moran's I index of spatial autocorrelation in segmenting high-resolution panchromatic and lower-resolution multispectral imagery. Tools available in the Image Characterization and Modeling System (ICAMS) were used to analyze multi-temporal and multi-platform imagery of Atlanta, Georgia. In this example, land cover change trajectories from forest or grassland to built up land covers lead to decreased spatial autocorrelation. In lower resolution imagery such as Landsat MSS, the complex details of forested land covers and urbanized areas are smoothed, and texture-based change detection is less effective. Although segmentation of panchromatic images is possible using fractal dimension or Moran's I, widely differing land covers often yield similar values of these indices. Better results are obtained when a surface of local fractal dimension or spatial autocorrelation is combined as an additional layer in a supervised maximum-likelihood multispectral classification.

  20. Local structure analysis of some Cu(II) theophylline complexes

    NASA Astrophysics Data System (ADS)

    David, L.; Cozar, O.; Forizs, E.; Cr ăciun, C.; Ristoiu, D.; B ălan, C.

    1999-10-01

    The CuT 2L 2·2H 2O complexes [T=Theophylline (1,3-dimethylxanthine); L=NH 3, n-propylamine (npa), 2-aminoethanol (ae)] were prepared and investigated by ESR spectroscopy. Powder ESR spectrum of CuT 2(NH 3) 2·2H 2O is axial ( g||=2.255, g⊥=2.059). ESR spectrum of CuT 2(npa) 2·2H 2O with ( g||=2.299, g⊥=2.081) is a superposition of one axial ( g||=2.299, g⊥=2.073) and one isotropic component ( g0≈2.089), in the same amount. The axial spectra of the former complexes are due to a static Jahn-Teller effect ( EJT≈2880 cm -1). ESR spectrum of CuT 2(ae) 2·2H 2O is orthorhombic ( g1c=2.199, g2c=2.095, g3c=2.037). The local symmetries around the Cu(II) ions remain unchanged by DMF solvating, by adsorbing these solutions on NaY zeolite or by lowering the temperature.

  1. Structural and functional studies of Nup107/Nup133 interaction and its implications for the architecture of the nuclear pore complex

    SciTech Connect

    Boehmer, T.; Jeudy, S.; Berke, I.C.; Schwartz, T.U.

    2008-07-03

    Nuclear pore complexes (NPCs) are 4060 MDa protein assemblies embedded in the nuclear envelope of eukaryotic cells. NPCs exclusively mediate all transport between cytoplasm and nucleus. The nucleoporins that build the NPC are arranged in a stable core of module-like subcomplexes with eight-fold rotational symmetry. To gain insight into the intricate assembly of the NPC, we have solved the crystal structure of a protein complex between two nucleoporins, human Nup107 and Nup133. Both proteins form elongated structures that interact tightly via a compact interface in tail-to-tail fashion. Additional experiments using structure-guided mutants show that Nup107 is the critical anchor for Nup133 to the NPC, positioning Nup133 at the periphery of the NPC. The significant topological differences between Nup107 and Nup133 suggest that {alpha}-helical nucleoporin domains of the NPC scaffold fall in different classes and fulfill largely nonredundant functions.

  2. Local algorithm for computing complex travel time based on the complex eikonal equation

    NASA Astrophysics Data System (ADS)

    Huang, Xingguo; Sun, Jianguo; Sun, Zhangqing

    2016-04-01

    The traditional algorithm for computing the complex travel time, e.g., dynamic ray tracing method, is based on the paraxial ray approximation, which exploits the second-order Taylor expansion. Consequently, the computed results are strongly dependent on the width of the ray tube and, in regions with dramatic velocity variations, it is difficult for the method to account for the velocity variations. When solving the complex eikonal equation, the paraxial ray approximation can be avoided and no second-order Taylor expansion is required. However, this process is time consuming. In this case, we may replace the global computation of the whole model with local computation by taking both sides of the ray as curved boundaries of the evanescent wave. For a given ray, the imaginary part of the complex travel time should be zero on the central ray. To satisfy this condition, the central ray should be taken as a curved boundary. We propose a nonuniform grid-based finite difference scheme to solve the curved boundary problem. In addition, we apply the limited-memory Broyden-Fletcher-Goldfarb-Shanno technology for obtaining the imaginary slowness used to compute the complex travel time. The numerical experiments show that the proposed method is accurate. We examine the effectiveness of the algorithm for the complex travel time by comparing the results with those from the dynamic ray tracing method and the Gauss-Newton Conjugate Gradient fast marching method.

  3. Local algorithm for computing complex travel time based on the complex eikonal equation.

    PubMed

    Huang, Xingguo; Sun, Jianguo; Sun, Zhangqing

    2016-04-01

    The traditional algorithm for computing the complex travel time, e.g., dynamic ray tracing method, is based on the paraxial ray approximation, which exploits the second-order Taylor expansion. Consequently, the computed results are strongly dependent on the width of the ray tube and, in regions with dramatic velocity variations, it is difficult for the method to account for the velocity variations. When solving the complex eikonal equation, the paraxial ray approximation can be avoided and no second-order Taylor expansion is required. However, this process is time consuming. In this case, we may replace the global computation of the whole model with local computation by taking both sides of the ray as curved boundaries of the evanescent wave. For a given ray, the imaginary part of the complex travel time should be zero on the central ray. To satisfy this condition, the central ray should be taken as a curved boundary. We propose a nonuniform grid-based finite difference scheme to solve the curved boundary problem. In addition, we apply the limited-memory Broyden-Fletcher-Goldfarb-Shanno technology for obtaining the imaginary slowness used to compute the complex travel time. The numerical experiments show that the proposed method is accurate. We examine the effectiveness of the algorithm for the complex travel time by comparing the results with those from the dynamic ray tracing method and the Gauss-Newton Conjugate Gradient fast marching method. PMID:27176428

  4. Local algorithm for computing complex travel time based on the complex eikonal equation.

    PubMed

    Huang, Xingguo; Sun, Jianguo; Sun, Zhangqing

    2016-04-01

    The traditional algorithm for computing the complex travel time, e.g., dynamic ray tracing method, is based on the paraxial ray approximation, which exploits the second-order Taylor expansion. Consequently, the computed results are strongly dependent on the width of the ray tube and, in regions with dramatic velocity variations, it is difficult for the method to account for the velocity variations. When solving the complex eikonal equation, the paraxial ray approximation can be avoided and no second-order Taylor expansion is required. However, this process is time consuming. In this case, we may replace the global computation of the whole model with local computation by taking both sides of the ray as curved boundaries of the evanescent wave. For a given ray, the imaginary part of the complex travel time should be zero on the central ray. To satisfy this condition, the central ray should be taken as a curved boundary. We propose a nonuniform grid-based finite difference scheme to solve the curved boundary problem. In addition, we apply the limited-memory Broyden-Fletcher-Goldfarb-Shanno technology for obtaining the imaginary slowness used to compute the complex travel time. The numerical experiments show that the proposed method is accurate. We examine the effectiveness of the algorithm for the complex travel time by comparing the results with those from the dynamic ray tracing method and the Gauss-Newton Conjugate Gradient fast marching method.

  5. Solvation-driven charge transfer and localization in metal complexes.

    PubMed

    Rondi, Ariana; Rodriguez, Yuseff; Feurer, Thomas; Cannizzo, Andrea

    2015-05-19

    In any physicochemical process in liquids, the dynamical response of the solvent to the solutes out of equilibrium plays a crucial role in the rates and products: the solvent molecules react to the changes in volume and electron density of the solutes to minimize the free energy of the solution, thus modulating the activation barriers and stabilizing (or destabilizing) intermediate states. In charge transfer (CT) processes in polar solvents, the response of the solvent always assists the formation of charge separation states by stabilizing the energy of the localized charges. A deep understanding of the solvation mechanisms and time scales is therefore essential for a correct description of any photochemical process in dense phase and for designing molecular devices based on photosensitizers with CT excited states. In the last two decades, with the advent of ultrafast time-resolved spectroscopies, microscopic models describing the relevant case of polar solvation (where both the solvent and the solute molecules have a permanent electric dipole and the mutual interaction is mainly dipole-dipole) have dramatically progressed. Regardless of the details of each model, they all assume that the effect of the electrostatic fields of the solvent molecules on the internal electronic dynamics of the solute are perturbative and that the solvent-solute coupling is mainly an electrostatic interaction between the constant permanent dipoles of the solute and the solvent molecules. This well-established picture has proven to quantitatively rationalize spectroscopic effects of environmental and electric dynamics (time-resolved Stokes shifts, inhomogeneous broadening, etc.). However, recent computational and experimental studies, including ours, have shown that further improvement is required. Indeed, in the last years we investigated several molecular complexes exhibiting photoexcited CT states, and we found that the current description of the formation and stabilization of CT

  6. Landsliding as the progressive growth of a slipping region: Initiating dynamic rupture propagation by local pore-pressure increase and its potential for arrest

    NASA Astrophysics Data System (ADS)

    Viesca-Falguières, R. C.; Rice, J. R.

    2010-12-01

    Given the low angles of continental slopes, sedimentation alone may not be sufficient to initiate failure, in which case a source of locally elevated pore pressure p is a likely candidate. Heterogeneities in p may arise from spatially variable sources of gas (e.g., Fleischer et al., Geo-Mar. Lett. 2001), variations in permeability, and channelized seepage, and are expected in regions affected by methane hydrates and their dissociation (e.g., Xu & Germanovich, JGR 2006). Additionally, while marine sediments are ideally considered as normally consolidated sediments (for which shear strength is expected to increase with deformation), given typical sedimentation rates on these slopes (~mm/yr or less) strength may develop due to the long lifetime of interparticle contacts. Such behavior is indicated by increased sample stiffness following long periods of fixed loads in consolidation tests (e.g., Karig & Ask, JGR 2003); as well as by the development of increasingly peaked stress-strain profiles under triaxial loading conditions for normally consolidated samples previously held under loads for increasingly long times (e.g., Bjerrum & Lo, Geotechniqué 1963). Such strength would be lost upon sufficient disruption of contacts (i.e., the sediments are considered sensitive), and if weakening is sufficiently strong, localized deformation may be expected as traditionally is for overconsolidated sediments. Consequently, we apply a fracture-mechanics model of the quasistatic growth of a thin zone of localized shear (represented as a slipping crack surface) due to a locally peaked and increasing p profile of a generic nature. Strength on the slip surface weakens with slip and we find that the ruptured region may reach a limit at which the quasistatically calculated crack growth rates become unbounded, corresponding to initiation of dynamic rupture and landsliding. In some cases rupture propagation may not be indefinite, because another equilibrium crack length and slip

  7. Respiratory complex I dysfunction due to mitochondrial DNA mutations shifts the voltage threshold for opening of the permeability transition pore toward resting levels.

    PubMed

    Porcelli, Anna Maria; Angelin, Alessia; Ghelli, Anna; Mariani, Elisa; Martinuzzi, Andrea; Carelli, Valerio; Petronilli, Valeria; Bernardi, Paolo; Rugolo, Michela

    2009-01-23

    We have studied mitochondrial bioenergetics in HL180 cells (a cybrid line harboring the T14484C/ND6 and G14279A/ND6 mtDNA mutations of Leber hereditary optic neuropathy, leading to an approximately 50% decrease of ATP synthesis) and XTC.UC1 cells (derived from a thyroid oncocytoma bearing a disruptive frameshift mutation in MT-ND1, which impairs complex I assembly). The addition of rotenone to HL180 cells and of antimycin A to XTC.UC1 cells caused fast mitochondrial membrane depolarization that was prevented by treatment with cyclosporin A, intracellular Ca2+ chelators, and antioxidant. Both cell lines also displayed an anomalous response to oligomycin, with rapid onset of depolarization that was prevented by cyclosporin A and by overexpression of Bcl-2. These findings indicate that depolarization by respiratory chain inhibitors and oligomycin was due to opening of the mitochondrial permeability transition pore (PTP). A shift of the threshold voltage for PTP opening close to the resting potential may therefore be the underlying cause facilitating cell death in diseases affecting complex I activity. This study provides a unifying reading frame for previous observations on mitochondrial dysfunction, bioenergetic defects, and Ca2+ deregulation in mitochondrial diseases. Therapeutic strategies aimed at normalizing the PTP voltage threshold may be instrumental in ameliorating the course of complex I-dependent mitochondrial diseases.

  8. The Nectin-4/Afadin Protein Complex and Intercellular Membrane Pores Contribute to Rapid Spread of Measles Virus in Primary Human Airway Epithelia

    PubMed Central

    Singh, Brajesh K.; Hornick, Andrew L.; Krishnamurthy, Sateesh; Locke, Anna C.; Mendoza, Crystal A.; Mateo, Mathieu; Miller-Hunt, Catherine L.; Cattaneo, Roberto

    2015-01-01

    ABSTRACT The discovery that measles virus (MV) uses the adherens junction protein nectin-4 as its epithelial receptor provides a new vantage point from which to characterize its rapid spread in the airway epithelium. We show here that in well-differentiated primary cultures of airway epithelial cells from human donors (HAE), MV infectious centers form rapidly and become larger than those of other respiratory pathogens: human respiratory syncytial virus, parainfluenza virus 5, and Sendai virus. While visible syncytia do not form after MV infection of HAE, the cytoplasm of an infected cell suddenly flows into an adjacent cell, as visualized through wild-type MV-expressed cytoplasmic green fluorescent protein (GFP). High-resolution video microscopy documents that GFP flows through openings that form on the lateral surfaces between columnar epithelial cells. To assess the relevance of the protein afadin, which connects nectin-4 to the actin cytoskeleton, we knocked down its mRNA. This resulted in more-limited infectious-center formation. We also generated a nectin-4 mutant without the afadin-binding site in its cytoplasmic tail. This mutant was less effective than wild-type human nectin-4 at promoting MV infection in primary cultures of porcine airway epithelia. Thus, in airway epithelial cells, MV spread requires the nectin-4/afadin complex and is based on cytoplasm transfer between columnar cells. Since the viral membrane fusion apparatus may open the passages that allow cytoplasm transfer, we refer to them as intercellular membrane pores. Virus-induced intercellular pores may contribute to extremely efficient measles contagion by promoting the rapid spread of the virus through the upper respiratory epithelium. IMPORTANCE Measles virus (MV), while targeted for eradication, still causes about 120,000 deaths per year worldwide. The recent reemergence of measles in insufficiently vaccinated populations in Europe and North America reminds us that measles is extremely

  9. Shape index distribution based local surface complexity applied to the human cortex

    PubMed Central

    Kim, Sun Hyung; Fonov, Vladimir; Collins, D. Louis; Gerig, Guido; Styner, Martin A.

    2015-01-01

    The quantification of local surface complexity in the human cortex has shown to be of interest in investigating population differences as well as developmental changes in neurodegenerative or neurodevelopment diseases. We propose a novel assessment method that represents local complexity as the difference between the observed distributions of local surface topology to its best-fit basic topology model within a given local neighborhood. This distribution difference is estimated via Earth Move Distance (EMD) over the histogram within the local neighborhood of the surface topology quantified via the Shape Index (SI) measure. The EMD scores have a range from simple complexity (0.0), which indicates a consistent local surface topology, up to high complexity (1.0), which indicates a highly variable local surface topology. The basic topology models are categorized as 9 geometric situation modeling situations such as crowns, ridges and fundi of cortical gyro and sulci. We apply a geodesic kernel to calculate the local SI histrogram distribution within a given region. In our experiments, we obtained the results of local complexity that shows generally higher complexity in the gyral/sulcal wall regions and lower complexity in some gyral ridges and lowest complexity in sulcal fundus areas. In addition, we show expected, preliminary results of increased surface complexity across most of the cortical surface within the first years of postnatal life, hypothesized to be due to the changes such as development of sulcal pits. PMID:26028803

  10. Shape index distribution based local surface complexity applied to the human cortex

    NASA Astrophysics Data System (ADS)

    Kim, Sun Hyung; Fonov, Vladimir; Collins, D. Louis; Gerig, Guido; Styner, Martin A.

    2015-03-01

    The quantification of local surface complexity in the human cortex has shown to be of interest in investigating population differences as well as developmental changes in neurodegenerative or neurodevelopment diseases. We propose a novel assessment method that represents local complexity as the difference between the observed distributions of local surface topology to its best-fit basic topology model within a given local neighborhood. This distribution difference is estimated via Earth Move Distance (EMD) over the histogram within the local neighborhood of the surface topology quantified via the Shape Index (SI) measure. The EMD scores have a range from simple complexity (0.0), which indicates a consistent local surface topology, up to high complexity (1.0), which indicates a highly variable local surface topology. The basic topology models are categorized as 9 geometric situation modeling situations such as crowns, ridges and fundi of cortical gyro and sulci. We apply a geodesic kernel to calculate the local SI histogram distribution within a given region. In our experiments, we obtained the results of local complexity that shows generally higher complexity in the gyral/sulcal wall regions and lower complexity in some gyral ridges and lowest complexity in sulcal fundus areas. In addition, we show expected, preliminary results of increased surface complexity across most of the cortical surface within the first years of postnatal life, hypothesized to be due to the changes such as development of sulcal pits.

  11. Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex.

    PubMed

    Moussavi-Baygi, R; Mofrad, M R K

    2016-01-01

    Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores. PMID:27470900

  12. Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex

    PubMed Central

    Moussavi-Baygi, R.; Mofrad, M. R. K.

    2016-01-01

    Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores. PMID:27470900

  13. Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex*

    PubMed Central

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M.; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B.; Sauder, J. Michael; Burley, Stephen K.; Chait, Brian T.; Almo, Steven C.; Rout, Michael P.; Sali, Andrej

    2014-01-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup13355–502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes. PMID:25139911

  14. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

    PubMed

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Chait, Brian T; Almo, Steven C; Rout, Michael P; Sali, Andrej

    2014-11-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133(55-502)) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup133(2-1157). Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes. PMID:25139911

  15. Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.

    PubMed

    Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B; Sauder, J Michael; Burley, Stephen K; Chait, Brian T; Almo, Steven C; Rout, Michael P; Sali, Andrej

    2014-11-01

    The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133(55-502)) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup133(2-1157). Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.

  16. Novel in situ multiharmonic EQCM-D approach to characterize complex carbon pore architectures for capacitive deionization of brackish water.

    PubMed

    Shpigel, Netanel; Levi, Mikhael D; Sigalov, Sergey; Aurbach, Doron; Daikhin, Leonid; Presser, Volker

    2016-03-23

    Multiharmonic analysis by electrochemical quartz-crystal microbalance with dissipation monitoring (EQCM-D) is introduced as an excellent tool for quantitative studying electrosorption of ions from aqueous solution in mesoporous (BP-880) or mixed micro-mesoporous (BP-2000) carbon electrodes. Finding the optimal conditions for gravimetric analysis of the ionic content in the charged carbon electrodes, we propose a novel approach to modeling the charge-dependent gravimetric characteristics by incorporation of Gouy-Chapman-Stern electric double layer model for ions electrosorption into meso- and micro-mesoporous carbon electrodes. All three parameters of the gravimetric equation evaluated by fitting it to the experimental mass changes curves were validated using supplementary nitrogen gas sorption analysis and complementing atomic force microscopy. Important overlap between gravimetric EQCM-D analysis of the ionic content of porous carbon electrodes and the classical capacitive deionization models has been established. The necessity and usefulness of non-gravimetric EQCM-D characterizations of complex carbon architectures, providing insight into their unique viscoelastic behavior and porous structure changes, have been discussed in detail.

  17. SUMO modification through rapamycin-mediated heterodimerization reveals a dual role for Ubc9 in targeting RanGAP1 to nuclear pore complexes

    SciTech Connect

    Zhu Shanshan; Zhang Hong; Matunis, Michael J. . E-mail: mmatunis@jhsph.edu

    2006-04-15

    SUMOs (small ubiquitin-related modifiers) are eukaryotic proteins that are covalently conjugated to other proteins and thereby regulate a wide range of important cellular processes. The molecular mechanisms by which SUMO modification influences the functions of most target proteins and cellular processes, however, remain poorly defined. A major obstacle to investigating the effects of SUMO modification is the availability of a system for selectively inducing the modification or demodification of an individual protein. To address this problem, we have developed a procedure using the rapamycin heterodimerizer system. This procedure involves co-expression of rapamycin-binding domain fusion proteins of SUMO and candidate SUMO substrates in living cells. Treating cells with rapamycin induces a tight association between SUMO and a single SUMO substrate, thereby allowing specific downstream effects to be analyzed. Using RanGAP1 as a model SUMO substrate, the heterodimerizer system was used to investigate the molecular mechanism by which SUMO modification targets RanGAP1 from the cytoplasm to nuclear pore complexes (NPCs). Our results revealed a dual role for Ubc9 in targeting RanGAP1 to NPCs: In addition to conjugating SUMO-1 to RanGAP1, Ubc9 is also required to form a stable ternary complex with SUMO-1 modified RanGAP1 and Nup358. As illustrated by our studies, the rapamycin heterodimerizer system represents a novel tool for studying the molecular effects of SUMO modification.

  18. Structural and Functional Studies of Nup107/Nup133 Interaction and Its Implications for the Architecture of the Nuclear Pore Complex

    PubMed Central

    Boehmer, Thomas; Jeudy, Sandra; Berke, Ian C.; Schwartz, Thomas U.

    2008-01-01

    SUMMARY Nuclear pore complexes (NPCs) are 40–60 MDa protein assemblies embedded in the nuclear envelope of eukaryotic cells. NPCs exclusively mediate all transport between cytoplasm and nucleus. The nucleoporins that build the NPC are arranged in a stable core of module-like subcomplexes with 8-fold rotational symmetry. To gain insight into the intricate assembly of the NPC, we have solved the crystal structure of a protein complex between two nucleoporins, human Nup107 and Nup133. Both proteins form elongated structures that interact tightly via a compact interface in tail-to-tail fashion. Additional experiments using structure-guided mutants show that Nup107 is the critical anchor for Nup133 to the NPC, positioning Nup133 at the periphery of the NPC. Structure predictions suggest these domains to be composed of simple α-helical repeats, yet we find that they are highly individualized and non-repeating. This favors an NPC model assembled from non-redundant architectural nucleoporins. PMID:18570875

  19. Local cortical surface complexity maps from spherical harmonic reconstructions.

    PubMed

    Yotter, Rachel A; Nenadic, Igor; Ziegler, Gabriel; Thompson, Paul M; Gaser, Christian

    2011-06-01

    Altered cortical surface complexity and gyrification differences may be a potentially sensitive marker for several neurodevelopmental disorders. We propose to use spherical harmonic (SPH) constructions to measure cortical surface folding complexity. First, we demonstrate that the complexity measure is accurate, by applying our SPH approach and the more traditional box-counting method to von Koch fractal surfaces with known fractal dimension (FD) values. The SPH approach is then applied to study complexity differences between 87 patients with DSM-IV schizophrenia (with stable psychopathology and treated with antipsychotic medication; 48 male/39 female; mean age=35.5 years, SD=11.0) and 108 matched healthy controls (68 male/40 female; mean age=32.1 years, SD=10.0). The global FD for the right hemisphere in the schizophrenia group was significantly reduced. Regionally, reduced complexity was also found in temporal, frontal, and cingulate regions in the right hemisphere, and temporal and prefrontal regions in the left hemisphere. These results are discussed in terms of previously published findings. Finally, the anatomical implications of a reduced FD are highlighted through comparison of two subjects with vastly different complexity maps.

  20. Photonic hybrid crystals constructed from in situ host-guest nanoconfinement of a light-emitting complex in metal-organic framework pores

    NASA Astrophysics Data System (ADS)

    Chaudhari, Abhijeet K.; Ryder, Matthew R.; Tan, Jin-Chong

    2016-03-01

    We report the concept underpinning the facile nanoconfinement of a bulky luminous guest molecule in the pores of a metal-organic framework (MOF) host, which yields a hybrid host ⊃ guest nanomaterial with tunable opto-electronic characteristics and enhanced photostability. Utilizing an in situ host-guest confinement strategy enabled by molecular self-assembly, we show that the highly emitting ZnQ [Zn-(bis-8-hydroxyquinoline)] guest complexes could be rapidly encapsulated within the sodalite nanocages of zeolitic imidazolate framework (ZIF-8) host crystals. The nature of optical and electronic transitions phenomena of the guest-encapsulated ZIF-8 ⊃ ZnQ has been elucidated by means of fluorescence and absorption spectroscopy measurements, and substantiated further via theoretical molecular orbital calculations revealing the plausible host-guest charge transfer mechanism involved. Evidence suggests that its photophysical properties are not only strongly determined by the host-guest co-operative bonding interactions within the environment of the confined MOF nanocage, but also can be engineered to manipulate its emission color chromaticity or to shield light-sensitive emitting guests against rapid photochemical degradation.We report the concept underpinning the facile nanoconfinement of a bulky luminous guest molecule in the pores of a metal-organic framework (MOF) host, which yields a hybrid host ⊃ guest nanomaterial with tunable opto-electronic characteristics and enhanced photostability. Utilizing an in situ host-guest confinement strategy enabled by molecular self-assembly, we show that the highly emitting ZnQ [Zn-(bis-8-hydroxyquinoline)] guest complexes could be rapidly encapsulated within the sodalite nanocages of zeolitic imidazolate framework (ZIF-8) host crystals. The nature of optical and electronic transitions phenomena of the guest-encapsulated ZIF-8 ⊃ ZnQ has been elucidated by means of fluorescence and absorption spectroscopy measurements, and

  1. Structure of local interactions in complex financial dynamics

    PubMed Central

    Jiang, X. F.; Chen, T. T.; Zheng, B.

    2014-01-01

    With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906

  2. Towards quantifying cochlear implant localization performance in complex acoustic environments.

    PubMed

    Kerber, S; Seeber, B U

    2011-08-01

    Cochlear implant (CI) users frequently report listening difficulties in reverberant and noisy spaces. While it is common to assess speech understanding with implants in background noise, binaural hearing performance has rarely been quantified in the presence of other sources, although the binaural system is a major contributor to the robustness of speech understanding in noisy situations with normal hearing. Here, a pointing task was used to measure horizontal localization ability of a bilateral CI user in quiet and in a continuous diffuse noise interferer at a signal-to-noise ratio of 0 dB. Results were compared to localization performance of six normal hearing listeners. The average localization error of the normal hearing listeners was within normal ranges reported previously and only increased by 1.8° when the interfering noise was introduced. In contrast, the bilateral CI user showed a localization error of 22° in quiet which rose to 31° in noise. This increase was partly due to target sounds being inaudible when presented from frontal locations between -20° and +20°. With the noise present, the implant user was only able to reliably hear target sounds presented from locations well off the median plane. The results give support to the informal complaints raised by CI users and can help to define targets for the design of, e.g., noise reduction algorithms for implant processors.

  3. Electron localization in a mixed-valence diniobium benzene complex

    DOE PAGES

    Gianetti, Thomas L.; Nocton, Grégory; Minasian, Stefan G.; Kaltsoyannis, Nikolas; Kilcoyne, A. L. David; Kozimor, Stosh A.; Shuh, David K.; Tyliszczak, Tolek; Bergman, Robert G.; Arnold, John

    2014-11-11

    Reaction of the neutral diniobium benzene complex {[Nb(BDI)NtBu]2(μ-C6H6)} (BDI = N,N'-diisopropylbenzene-β-diketiminate) with Ag[B(C6F5)4] results in a single electron oxidation to produce a cationic diniobium arene complex, {[Nb(BDI)NtBu]2(μ-C6H6)}{B(C6F5)4}. Investigation of the solid state and solution phase structure using single-crystal X-ray diffraction, cyclic voltammetry, magnetic susceptibility, and multinuclear NMR spectroscopy indicates that the oxidation results in an asymmetric molecule with two chemically inequivalent Nb atoms. Further characterization using density functional theory (DFT) calculations, UV-visible, Nb L3,2-edge X-ray absorption near-edge structure (XANES), and EPR spectroscopies supports assignment of a diniobium complex, in which one Nb atom carries a single unpaired electron that ismore » not largely delocalized on the second Nb atom. During the oxidative transformation, one electron is removed from the δ-bonding HOMO, which causes a destabilization of the molecule and formation of an asymmetric product. Subsequent reactivity studies indicate that the oxidized product allows access to metal-based chemistry with substrates that did not exhibit reactivity with the starting neutral complex.« less

  4. Electron localization in a mixed-valence diniobium benzene complex

    SciTech Connect

    Gianetti, Thomas L.; Nocton, Grégory; Minasian, Stefan G.; Kaltsoyannis, Nikolas; Kilcoyne, A. L. David; Kozimor, Stosh A.; Shuh, David K.; Tyliszczak, Tolek; Bergman, Robert G.; Arnold, John

    2014-11-11

    Reaction of the neutral diniobium benzene complex {[Nb(BDI)NtBu]2(μ-C6H6)} (BDI = N,N'-diisopropylbenzene-β-diketiminate) with Ag[B(C6F5)4] results in a single electron oxidation to produce a cationic diniobium arene complex, {[Nb(BDI)NtBu]2(μ-C6H6)}{B(C6F5)4}. Investigation of the solid state and solution phase structure using single-crystal X-ray diffraction, cyclic voltammetry, magnetic susceptibility, and multinuclear NMR spectroscopy indicates that the oxidation results in an asymmetric molecule with two chemically inequivalent Nb atoms. Further characterization using density functional theory (DFT) calculations, UV-visible, Nb L3,2-edge X-ray absorption near-edge structure (XANES), and EPR spectroscopies supports assignment of a diniobium complex, in which one Nb atom carries a single unpaired electron that is not largely delocalized on the second Nb atom. During the oxidative transformation, one electron is removed from the δ-bonding HOMO, which causes a destabilization of the molecule and formation of an asymmetric product. Subsequent reactivity studies indicate that the oxidized product allows access to metal-based chemistry with substrates that did not exhibit reactivity with the starting neutral complex.

  5. NSF- and SNARE-mediated membrane fusion is required for nuclear envelope formation and completion of nuclear pore complex assembly in Xenopus laevis egg extracts.

    PubMed

    Baur, Tina; Ramadan, Kristijan; Schlundt, Andreas; Kartenbeck, Jürgen; Meyer, Hemmo H

    2007-08-15

    Despite the progress in understanding nuclear envelope (NE) reformation after mitosis, it has remained unclear what drives the required membrane fusion and how exactly this is coordinated with nuclear pore complex (NPC) assembly. Here, we show that, like other intracellular fusion reactions, NE fusion in Xenopus laevis egg extracts is mediated by SNARE proteins that require activation by NSF. Antibodies against Xenopus NSF, depletion of NSF or the dominant-negative NSF(E329Q) variant specifically inhibited NE formation. Staging experiments further revealed that NSF was required until sealing of the envelope was completed. Moreover, excess exogenous alpha-SNAP that blocks SNARE function prevented membrane fusion and caused accumulation of non-flattened vesicles on the chromatin surface. Under these conditions, the nucleoporins Nup107 and gp210 were fully recruited, whereas assembly of FxFG-repeat-containing nucleoporins was blocked. Together, we define NSF- and SNARE-mediated membrane fusion events as essential steps during NE formation downstream of Nup107 recruitment, and upstream of membrane flattening and completion of NPC assembly.

  6. Phosphomimetic mutation of the mitotically phosphorylated serine 1880 compromises the interaction of the transmembrane nucleoporin gp210 with the nuclear pore complex

    SciTech Connect

    Onischenko, Evgeny A.; Crafoord, Ellinor; Hallberg, Einar . E-mail: einar.hallberg@sh.se

    2007-07-15

    The nuclear pore complexes (NPCs) reversibly disassemble and reassemble during mitosis. Disassembly of the NPC is accompanied by phosphorylation of many nucleoporins although the function of this is not clear. It was previously shown that in the transmembrane nucleoporin gp210 a single serine residue at position 1880 is specifically phosphorylated during mitosis. Using amino acid substitution combined with live cell imaging, time-lapse microscopy and FRAP, we investigated the role of serine 1880 in binding of gp210 to the NPC in vivo. An alanine substitution mutant (S1880A) was significantly more dynamic at the NPC compared to the wild-type protein, suggesting that serine 1880 is important for binding of gp210 to the NPC. Moreover a glutamate substitution (S1880E) closely mimicking phosphorylated serine specifically interfered with incorporation of gp210 into the NPC and compromised its post-mitotic recruitment to the nuclear envelope of daughter nuclei. Our findings are consistent with the idea that mitotic phosphorylation acts to dissociate gp210 from the structural elements of the NPC.

  7. Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus.

    PubMed

    Paul, Biplab; Montpetit, Ben

    2016-09-01

    Many protein factors are required for mRNA biogenesis and nuclear export, which are central to the eukaryotic gene expression program. It is unclear, however, whether all factors have been identified. Here we report on a screen of >1000 essential gene mutants in Saccharomyces cerevisiae for defects in mRNA processing and export, identifying 26 mutants with defects in this process. Single-molecule FISH data showed that the majority of these mutants accumulated mRNA within specific regions of the nucleus, which included 1) mRNAs within the nucleolus when nucleocytoplasmic transport, rRNA biogenesis, or RNA processing and surveillance was disrupted, 2) the buildup of mRNAs near transcription sites in 3'-end processing and chromosome segregation mutants, and 3) transcripts being enriched near nuclear pore complexes when components of the mRNA export machinery were mutated. These data show that alterations to various nuclear processes lead to the retention of mRNAs at discrete locations within the nucleus.

  8. Global efficiency of local immunization on complex networks

    NASA Astrophysics Data System (ADS)

    Hébert-Dufresne, Laurent; Allard, Antoine; Young, Jean-Gabriel; Dubé, Louis J.

    2013-07-01

    Epidemics occur in all shapes and forms: infections propagating in our sparse sexual networks, rumours and diseases spreading through our much denser social interactions, or viruses circulating on the Internet. With the advent of large databases and efficient analysis algorithms, these processes can be better predicted and controlled. In this study, we use different characteristics of network organization to identify the influential spreaders in 17 empirical networks of diverse nature using 2 epidemic models. We find that a judicious choice of local measures, based either on the network's connectivity at a microscopic scale or on its community structure at a mesoscopic scale, compares favorably to global measures, such as betweenness centrality, in terms of efficiency, practicality and robustness. We also develop an analytical framework that highlights a transition in the characteristic scale of different epidemic regimes. This allows to decide which local measure should govern immunization in a given scenario.

  9. Global efficiency of local immunization on complex networks

    PubMed Central

    Hébert-Dufresne, Laurent; Allard, Antoine; Young, Jean-Gabriel; Dubé, Louis J.

    2013-01-01

    Epidemics occur in all shapes and forms: infections propagating in our sparse sexual networks, rumours and diseases spreading through our much denser social interactions, or viruses circulating on the Internet. With the advent of large databases and efficient analysis algorithms, these processes can be better predicted and controlled. In this study, we use different characteristics of network organization to identify the influential spreaders in 17 empirical networks of diverse nature using 2 epidemic models. We find that a judicious choice of local measures, based either on the network's connectivity at a microscopic scale or on its community structure at a mesoscopic scale, compares favorably to global measures, such as betweenness centrality, in terms of efficiency, practicality and robustness. We also develop an analytical framework that highlights a transition in the characteristic scale of different epidemic regimes. This allows to decide which local measure should govern immunization in a given scenario. PMID:23842121

  10. Poring over two-pore channel pore mutants

    PubMed Central

    Penny, Christopher J.; Patel, Sandip

    2016-01-01

    Two-pore channels are members of the voltage-gated ion channel superfamily. They localise to the endolysosomal system and are likely targets for the Ca2+ mobilising messenger NAADP. In this brief review, we relate mutagenesis of the TPC pore to a recently published homology model and discuss how pore mutants are informing us of TPC function. Molecular physiology of these ubiquitous proteins is thus emerging. PMID:27226934

  11. Multimodal cues improve prey localization under complex environmental conditions

    PubMed Central

    Rhebergen, F.; Taylor, R. C.; Ryan, M. J.; Page, R. A.; Halfwerk, W.

    2015-01-01

    Predators often eavesdrop on sexual displays of their prey. These displays can provide multimodal cues that aid predators, but the benefits in attending to them should depend on the environmental sensory conditions under which they forage. We assessed whether bats hunting for frogs use multimodal cues to locate their prey and whether their use varies with ambient conditions. We used a robotic set-up mimicking the sexual display of a male túngara frog (Physalaemus pustulosus) to test prey assessment by fringe-lipped bats (Trachops cirrhosus). These predatory bats primarily use sound of the frog's call to find their prey, but the bats also use echolocation cues returning from the frog's dynamically moving vocal sac. In the first experiment, we show that multimodal cues affect attack behaviour: bats made narrower flank attack angles on multimodal trials compared with unimodal trials during which they could only rely on the sound of the frog. In the second experiment, we explored the bat's use of prey cues in an acoustically more complex environment. Túngara frogs often form mixed-species choruses with other frogs, including the hourglass frog (Dendropsophus ebraccatus). Using a multi-speaker set-up, we tested bat approaches and attacks on the robofrog under three different levels of acoustic complexity: no calling D. ebraccatus males, two calling D. ebraccatus males and five D. ebraccatus males. We found that bats are more directional in their approach to the robofrog when more D. ebraccatus males were calling. Thus, bats seemed to benefit more from multimodal cues when confronted with increased levels of acoustic complexity in their foraging environments. Our data have important consequences for our understanding of the evolution of multimodal sexual displays as they reveal how environmental conditions can alter the natural selection pressures acting on them. PMID:26336176

  12. Multimodal cues improve prey localization under complex environmental conditions.

    PubMed

    Rhebergen, F; Taylor, R C; Ryan, M J; Page, R A; Halfwerk, W

    2015-09-01

    Predators often eavesdrop on sexual displays of their prey. These displays can provide multimodal cues that aid predators, but the benefits in attending to them should depend on the environmental sensory conditions under which they forage. We assessed whether bats hunting for frogs use multimodal cues to locate their prey and whether their use varies with ambient conditions. We used a robotic set-up mimicking the sexual display of a male túngara frog (Physalaemus pustulosus) to test prey assessment by fringe-lipped bats (Trachops cirrhosus). These predatory bats primarily use sound of the frog's call to find their prey, but the bats also use echolocation cues returning from the frog's dynamically moving vocal sac. In the first experiment, we show that multimodal cues affect attack behaviour: bats made narrower flank attack angles on multimodal trials compared with unimodal trials during which they could only rely on the sound of the frog. In the second experiment, we explored the bat's use of prey cues in an acoustically more complex environment. Túngara frogs often form mixed-species choruses with other frogs, including the hourglass frog (Dendropsophus ebraccatus). Using a multi-speaker set-up, we tested bat approaches and attacks on the robofrog under three different levels of acoustic complexity: no calling D. ebraccatus males, two calling D. ebraccatus males and five D. ebraccatus males. We found that bats are more directional in their approach to the robofrog when more D. ebraccatus males were calling. Thus, bats seemed to benefit more from multimodal cues when confronted with increased levels of acoustic complexity in their foraging environments. Our data have important consequences for our understanding of the evolution of multimodal sexual displays as they reveal how environmental conditions can alter the natural selection pressures acting on them. PMID:26336176

  13. Mesangial Localization of Immune Complexes in Experimental Canine Adenovirus Glomerulonephritis

    PubMed Central

    Wright, N. G.; Morrison, W. I.; Thompson, H.; Cornwell, H. J. C.

    1974-01-01

    Each of a group of 14 dogs was infected experimentally by an intravenous dose of canine adenovirus calculated to allow survival until the initial stages of antibody production; the kidneys of infected dogs were examined during the period of 4-14 days after administration of virus. Proliferative glomerulonephritis with localization of IgG, C3 and viral antigen in mesangial regions was demonstrated. With the electron microscope, electron dense deposits were found scattered throughout the mesangium. There was proliferation of mesangial cells, infiltration into the glomerular tuft of polymorphonuclear leucocytes and, in some cases, focal glomerular necrosis with intracapsular and tubular haemorrhage. By means of an indirect immunofluorescence test, anti-viral antibody was detected in kidney eluates; anti-kidney antibody was not present. ImagesFigs. 5-8Figs. 9-10Figs. 1-4 PMID:4375485

  14. Effect of the ostreolysin A/pleurotolysin B pore-forming complex on neuroblastoma cell morphology and intracellular Ca²⁺ activity.

    PubMed

    Vrecl, Milka; Babnik, Monika; Diacci, Uroš; Benoit, Evelyne; Frangež, Robert

    2015-04-01

    Ostreolysin A (OlyA) and pleurotolysin B (PlyB), isolated from edible oyster mushrooms, form a cytolytic complex (OlyA/PlyB) in membrane cells that causes respiratory arrest. This study evaluated the mechanisms underlying cytotoxic OlyA/PlyB activity in neuroblastoma NG108-15 cells. Confocal microscopy with morphometric analysis revealed that OlyA/PlyB increased the 3-dimensional projected area of differentiated cells. Iso-osmotic replacement of NaCl by sucrose or Na-isethionate prevented the cellular swelling. This suggests that formation of cellular edema requires the presence of Na(+) and/or Cl(-) in the extracellular space and may be related to an influx of Na(+) and/or a shift in Cl(-), which induce a marked influx of water that is ultimately responsible for cellular swelling. In addition, extracellular Ca(2+) moderately contributed to the swelling because benzamil (10 µM), a 3Na(+)/Ca(2+) exchange (NCX) inhibitor, and Ca(2+)-free medium partially prevented this response. Fluorometric measurements revealed that OlyA/PlyB, at approximately 15-fold higher concentrations, increased the intracellular Ca(2+) activity [Ca(2+)]i. This increase was dependent on the presence of Na(+) and Ca(2+) in the external medium and was sensitive to benzamil. It is thus likely that a switch in the NCX mode, associated with the de novo formation of non-selective ion pores by OlyA/PlyB in cellular plasma membranes, plays an important role in this effect. Overall, OlyA/PlyB affects neuroblastoma cell morphology and Ca(2+) homeostasis to influence the toxin-induced respiratory arrest. PMID:25556216

  15. The Nup155-mediated organisation of inner nuclear membrane proteins is independent of Nup155 anchoring to the metazoan nuclear pore complex.

    PubMed

    Busayavalasa, Kiran; Chen, Xin; Farrants, Ann-Kristin Östlund; Wagner, Nicole; Sabri, Nafiseh

    2012-09-15

    The nuclear envelope (NE), an important barrier between the nucleus and the cytoplasm, is composed of three structures: the outer nuclear membrane, which is continuous with the ER, the inner nuclear membrane (INM), which interfaces with chromatin, and nuclear pore complexes (NPCs), which are essential for the exchange of macromolecules between the two compartments. The NPC protein Nup155 has an evolutionarily conserved role in the metazoan NE formation; but the in vivo analysis of Nup155 has been severely hampered by the essential function of this protein in cell viability. Here, we take advantage of the hypomorphicity of RNAi systems and use a combination of protein binding and rescue assays to map the interaction sites of two neighbouring NPC proteins Nup93 and Nup53 on Nup155, and to define the requirements of these interactions in INM protein organization. We show that different parts of Drosophila Nup155 have distinct functions: the Nup155 β-propeller anchors the protein to the NPC, whereas the α-solenoid part of Nup155 is essential for the correct localisation of INM proteins lamin-B receptor (LBR) and otefin. Using chromatin extracts from semi-synchronized cells, we also provide evidence that the Nup155 α-solenoid has a chromatin-binding activity that is stronger at the end of mitosis. Our results argue that the role of Nup155 in INM protein localisation is not mediated through the NPC anchoring activity of the protein and suggest that regions other than Nup155 β-propeller are necessary for the targeting of proteins to the INM. PMID:22718353

  16. A recurrent KCNQ2 pore mutation causing early onset epileptic encephalopathy has a moderate effect on M current but alters subcellular localization of Kv7 channels.

    PubMed

    Abidi, Affef; Devaux, Jérôme J; Molinari, Florence; Alcaraz, Gisèle; Michon, François-Xavier; Sutera-Sardo, Julie; Becq, Hélène; Lacoste, Caroline; Altuzarra, Cécilia; Afenjar, Alexandra; Mignot, Cyril; Doummar, Diane; Isidor, Bertrand; Guyen, Sylvie N; Colin, Estelle; De La Vaissière, Sabine; Haye, Damien; Trauffler, Adeline; Badens, Catherine; Prieur, Fabienne; Lesca, Gaetan; Villard, Laurent; Milh, Mathieu; Aniksztejn, Laurent

    2015-08-01

    Mutations in the KCNQ2 gene encoding the voltage-dependent potassium M channel Kv7.2 subunit cause either benign epilepsy or early onset epileptic encephalopathy (EOEE). It has been proposed that the disease severity rests on the inhibitory impact of mutations on M current density. Here, we have analyzed the phenotype of 7 patients carrying the p.A294V mutation located on the S6 segment of the Kv7.2 pore domain (Kv7.2(A294V)). We investigated the functional and subcellular consequences of this mutation and compared it to another mutation (Kv7.2(A294G)) associated with a benign epilepsy and affecting the same residue. We report that all the patients carrying the p.A294V mutation presented the clinical and EEG characteristics of EOEE. In CHO cells, the total expression of Kv7.2(A294V) alone, assessed by western blotting, was only 20% compared to wild-type. No measurable current was recorded in CHO cells expressing Kv7.2(A294V) channel alone. Although the total Kv7.2(A294V) expression was rescued to wild-type levels in cells co-expressing the Kv7.3 subunit, the global current density was still reduced by 83% compared to wild-type heteromeric channel. In a configuration mimicking the patients' heterozygous genotype i.e., Kv7.2(A294V)/Kv7.2/Kv7.3, the global current density was reduced by 30%. In contrast to Kv7.2(A294V), the current density of homomeric Kv7.2(A294G) was not significantly changed compared to wild-type Kv7.2. However, the current density of Kv7.2(A294G)/Kv7.2/Kv7.3 and Kv7.2(A294G)/Kv7.3 channels were reduced by 30% and 50% respectively, compared to wild-type Kv7.2/Kv7.3. In neurons, the p.A294V mutation induced a mislocalization of heteromeric mutant channels to the somato-dendritic compartment, while the p.A294G mutation did not affect the localization of the heteromeric channels to the axon initial segment. We conclude that this position is a hotspot of mutation that can give rise to a severe or a benign epilepsy. The p.A294V mutation does not exert a

  17. Intergovernmental complexity in nuclear waste disposal policy: The indeterminate role of local government

    SciTech Connect

    Herzik, E.B.; Mushkatel, A.H.

    1991-12-31

    Local governments play a critical, albeit often overlooked, role in nuclear waste disposal policymaking. The centrality of local governments in the policymaking process rests on the simple fact that impacts would be borne disproportionately by local jurisdictions hosting and immediately adjacent to waste disposal sites. This article focuses on the capacity of local jurisdictions in Southern and rural Nevada to absorb and support an undertaking as large and technically complex as the proposed high-level nuclear waste repository. The article also examines the perceptions of local government officials concerning a number of management and policy issues related to the construction and operation of the proposed waste repository.

  18. Common and distinctive localization patterns of Crumbs polarity complex proteins in the mammalian eye

    PubMed Central

    Kim, Jin Young; Song, Ji Yun; Karnam, Santi; Park, Jun Young; Lee, Jamie JH; Kim, Seonhee; Cho, Seo-Hee

    2016-01-01

    Crumbs polarity complex proteins are essential for cellular and tissue polarity, and for adhesion of epithelial cells. In epithelial tissues deletion of any of three core proteins disrupts localization of the other proteins, indicating structural and functional interdependence among core components. Despite previous studies of function and co-localization that illustrated the properties that these proteins share, it is not known whether an individual component of the complex plays a distinct role in a unique cellular and developmental context. In order to investigate this question, we primarily used confocal imaging to determine the expression and subcellular localization of the core Crumbs polarity complex proteins during ocular development. Here we show that in developing ocular tissues core Crumbs polarity complex proteins, Crb, Pals1 and Patj, generally appear in an overlapping pattern with some exceptions. All three core complex proteins localize to the apical junction of the retinal and lens epithelia. Pals1 is also localized in the Golgi of the retinal cells and Patj localizes to the nuclei of the apically located subset of progenitor cells. These findings suggest that core Crumbs polarity complex proteins exert common and independent functions depending on cellular context. PMID:25636444

  19. Characterization of Fus3 localization: active Fus3 localizes in complexes of varying size and specific activity.

    PubMed

    Choi, K Y; Kranz, J E; Mahanty, S K; Park, K S; Elion, E A

    1999-05-01

    The MAP kinase Fus3 regulates many different signal transduction outputs that govern the ability of Saccharomyces cerevisiae haploid cells to mate. Here we characterize Fus3 localization and association with other proteins. By indirect immunofluorescence, Fus3 localizes in punctate spots throughout the cytoplasm and nucleus, with slightly enhanced nuclear localization after pheromone stimulation. This broad distribution is consistent with the critical role Fus3 plays in mating and contrasts that of Kss1, which concentrates in the nucleus and is not required for mating. The majority of Fus3 is soluble and not bound to any one protein; however, a fraction is stably bound to two proteins of approximately 60 and approximately 70 kDa. Based on fractionation and gradient density centrifugation properties, Fus3 exists in a number of complexes, with its activity critically dependent upon association with other proteins. In the presence of alpha factor, nearly all of the active Fus3 localizes in complexes of varying size and specific activity, whereas monomeric Fus3 has little activity. Fus3 has highest specific activity within a 350- to 500-kDa complex previously shown to contain Ste5, Ste11, and Ste7. Ste5 is required for Fus3 to exist in this complex. Upon alpha factor withdrawal, a pool of Fus3 retains activity for more than one cell cycle. Collectively, these results support Ste5's role as a tether and suggest that association of Fus3 in complexes in the presence of pheromone may prevent inactivation in addition to enhancing activation. PMID:10233162

  20. Circulating and localized immune complexes in experimental mycoplasma-induced arthritis-associated ocular inflammation.

    PubMed Central

    Thirkill, C E; Tyler, N K; Roth, A M

    1992-01-01

    Ocular deposits of immune complexes are believed to contribute to the anterior segment inflammations observed in association with the human arthritides. Arthritis-related ocular inflammations may be reproduced in animals by infection with certain species of mycoplasma. To evaluate the role of immune complexes in the production of ocular lesions, we studied their involvement in the rodent model of experimental arthritis-associated ocular inflammation induced by Mycoplasma arthritidis. Sprague-Dawley rats were infected with viable concentrates of M. arthritidis and monitored for the production of related circulating and intraocular immune complexes. Circulating immune complexes were monitored by antigen capture systems, and localized intraocular complexes were identified by indirect immunohistochemistry. Polyacrylamide gel immunoblot analysis of captured complexes confirmed the antigen(s) involved as proteins derived from M. arthritidis. Indirect immunofluorescence revealed localized complexes containing mycoplasma antigens within the ciliary-iris vasculature. Concentrations of the generated complexes diminished rapidly over a 30-day period. While complex deposits within ocular tissues could represent a contributing cause to the localized anterior segment inflammation reported in this rodent model, secondary challenge with viable M. arthritidis, which reproduced high concentrations of intraocular and circulating immune complexes, failed to elicit any ocular response. Images PMID:1730469

  1. Measuring kinetic drivers of pneumolysin pore structure.

    PubMed

    Gilbert, Robert J C; Sonnen, Andreas F-P

    2016-05-01

    Most membrane attack complex-perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins are thought to form pores in target membranes by assembling into pre-pore oligomers before undergoing a pre-pore to pore transition. Assembly during pore formation is into both full rings of subunits and incomplete rings (arcs). The balance between arcs and full rings is determined by a mechanism dependent on protein concentration in which arc pores arise due to kinetic trapping of the pre-pore forms by the depletion of free protein subunits during oligomerization. Here we describe the use of a kinetic assay to study pore formation in red blood cells by the MACPF/CDC pneumolysin from Streptococcus pneumoniae. We show that cell lysis displays two kinds of dependence on protein concentration. At lower concentrations, it is dependent on the pre-pore to pore transition of arc oligomers, which we show to be a cooperative process. At higher concentrations, it is dependent on the amount of pneumolysin bound to the membrane and reflects the affinity of the protein for its receptor, cholesterol. A lag occurs before cell lysis begins; this is dependent on oligomerization of pneumolysin. Kinetic dissection of cell lysis by pneumolysin demonstrates the capacity of MACPF/CDCs to generate pore-forming oligomeric structures of variable size with, most likely, different functional roles in biology. PMID:26906727

  2. Aubergine is a component of a nanos mRNA localization complex

    PubMed Central

    Becalska, Agata N.; Kim, YoungJung R.; Belletier, Nicolette G.; Lerit, Dorothy A.; Sinsimer, Kristina S.; Gavis, Elizabeth R.

    2010-01-01

    Localization of nanos (nos) mRNA to the posterior pole of the Drosophila oocyte is essential for abdominal segmentation and germline development during embryogenesis. Posterior localization is mediated by a complex cis-acting localization signal in the nos 3′ untranslated region that comprises multiple partially redundant elements. Genetic analysis suggests that this signal is recognized by RNA-binding proteins and associated factors that package nos mRNA into a localization competent ribonucleoprotein complex. However, functional redundancy among localization elements has made the identification of individual localization factors difficult. Indeed, only a single direct-acting nos localization factor, Rumpelstiltskin (Rump), has been identified thus far. Through a sensitized genetic screen, we have now identified the Argonaute family member Aubergine (Aub) as a nos localization factor. Aub interacts with nos mRNA in vivo and co-purifies with Rump in an RNA-dependent manner. Our results support a role for Aub, independent of its function in RNA silencing, as a component of a nos mRNA localization complex. PMID:20937269

  3. Dissecting the Sequential Assembly and Localization of Intraflagellar Transport Particle Complex B in Chlamydomonas

    PubMed Central

    Richey, Elizabeth A.; Qin, Hongmin

    2012-01-01

    Intraflagellar transport (IFT), the key mechanism for ciliogenesis, involves large protein particles moving bi-directionally along the entire ciliary length. IFT particles contain two large protein complexes, A and B, which are constructed with proteins in a core and several peripheral proteins. Prior studies have shown that in Chlamydomonas reinhardtii, IFT46, IFT52, and IFT88 directly interact with each other and are in a subcomplex of the IFT B core. However, ift46, bld1, and ift88 mutants differ in phenotype as ift46 mutants are able to form short flagella, while the other two lack flagella completely. In this study, we investigated the functional differences of these individual IFT proteins contributing to complex B assembly, stability, and basal body localization. We found that complex B is completely disrupted in bld1 mutant, indicating an essential role of IFT52 for complex B core assembly. Ift46 mutant cells are capable of assembling a relatively intact complex B, but such complex is highly unstable and prone to degradation. In contrast, in ift88 mutant cells the complex B core still assembles and remains stable, but the peripheral proteins no longer attach to the B core. Moreover, in ift88 mutant cells, while complex A and the anterograde IFT motor FLA10 are localized normally to the transition fibers, complex B proteins instead are accumulated at the proximal ends of the basal bodies. In addition, in bld2 mutant, the IFT complex B proteins still localize to the proximal ends of defective centrioles which completely lack transition fibers. Taken together, these results revealed a step-wise assembly process for complex B, and showed that the complex first localizes to the proximal end of the centrioles and then translocates onto the transition fibers via an IFT88-dependent mechanism. PMID:22900094

  4. Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field

    PubMed Central

    Eizaguirre, Christophe; Lenz, Tobias L; Kalbe, Martin; Milinski, Manfred

    2012-01-01

    Although crucial for the understanding of adaptive evolution, genetically resolved examples of local adaptation are rare. To maximize survival and reproduction in their local environment, hosts should resist their local parasites and pathogens. The major histocompatibility complex (MHC) with its key function in parasite resistance represents an ideal candidate to investigate parasite-mediated local adaptation. Using replicated field mesocosms, stocked with second-generation lab-bred three-spined stickleback hybrids of a lake and a river population, we show local adaptation of MHC genotypes to population-specific parasites, independently of the genetic background. Increased allele divergence of lake MHC genotypes allows lake fish to fight the broad range of lake parasites, whereas more specific river genotypes confer selective advantages against the less diverse river parasites. Hybrids with local MHC genotype gained more body weight and thus higher fitness than those with foreign MHC in either habitat, suggesting the evolutionary significance of locally adapted MHC genotypes. PMID:22583762

  5. Laser powder-bed fusion additive manufacturing: Physics of complex melt flow and formation mechanisms of pores, spatter, and denudation zones

    DOE PAGES

    Khairallah, Saad A.; Anderson, Andrew T.; Rubenchik, Alexander; King, Wayne E.

    2016-02-23

    Our study demonstrates the significant effect of the recoil pressure and Marangoni convection in laser powder bed fusion (L-PBF) of 316L stainless steel. A three-dimensional high fidelity powder-scale model reveals how the strong dynamical melt flow generates pore defects, material spattering (sparking), and denudation zones. The melt track is divided into three sections: a topological depression, a transition and a tail region, each being the location of specific physical effects. The inclusion of laser ray-tracing energy deposition in the powder-scale model improves over traditional volumetric energy deposition. It enables partial particle melting, which impacts pore defects in the denudation zone.more » Different pore formation mechanisms are observed at the edge of a scan track, at the melt pool bottom (during collapse of the pool depression), and at the end of the melt track (during laser power ramp down). Finally, we discuss remedies to these undesirable pores are discussed. The results are validated against the experiments and the sensitivity to laser absorptivity.« less

  6. Polar localization of Escherichia coli chemoreceptors requires an intact Tol–Pal complex

    PubMed Central

    Santos, Thiago M. A.; Lin, Ti-Yu; Rajendran, Madhusudan; Anderson, Samantha M.; Weibel, Douglas B.

    2014-01-01

    Summary Subcellular biomolecular localization is critical for the metabolic and structural properties of the cell. The functional implications of the spatiotemporal distribution of protein complexes during the bacterial cell cycle have long been acknowledged; however, the molecular mechanisms for generating and maintaining their dynamic localization in bacteria are not completely understood. Here we demonstrate that the trans-envelope Tol–Pal complex, a widely conserved component of the cell envelope of Gram-negative bacteria, is required to maintain the polar positioning of chemoreceptor clusters in Escherichia coli. Localization of the chemoreceptors was independent of phospholipid composition of the membrane and the curvature of the cell wall. Instead, our data indicate that chemoreceptors interact with components of the Tol–Pal complex and that this interaction is required to polarly localize chemoreceptor clusters. We found that disruption of the Tol–Pal complex perturbs the polar localization of chemoreceptors, alters cell motility, and affects chemotaxis. We propose that the E. coli Tol–Pal complex restricts mobility of the chemoreceptor clusters at the cell poles and may be involved in regulatory mechanisms that co-ordinate cell division and segregation of the chemosensory machinery. PMID:24720726

  7. Distinct localization of the complement C5b-9 complex on Gram-positive bacteria.

    PubMed

    Berends, Evelien T M; Dekkers, Johanna F; Nijland, Reindert; Kuipers, Annemarie; Soppe, Jasper A; van Strijp, Jos A G; Rooijakkers, Suzan H M

    2013-12-01

    The plasma proteins of the complement system fulfil important immune defence functions, including opsonization of bacteria for phagocytosis, generation of chemo-attractants and direct bacterial killing via the Membrane Attack Complex (MAC or C5b-9). The MAC is comprised of C5b, C6, C7, C8, and multiple copies of C9 that generate lytic pores in cellular membranes. Gram-positive bacteria are protected from MAC-dependent lysis by their thick peptidoglycan layer. Paradoxically, several Gram-positive pathogens secrete small proteins that inhibit C5b-9 formation. In this study, we found that complement activation on Gram-positive bacteria in serum results in specific surface deposition of C5b-9 complexes. Immunoblotting revealed that C9 occurs in both monomeric and polymeric (SDS-stable) forms, indicating the presence of ring-structured C5b-9. Surprisingly, confocal microscopy demonstrated that C5b-9 deposition occurs at specialized regions on the bacterial cell. On Streptococcus pyogenes, C5b-9 deposits near the division septum whereas on Bacillus subtilis the complex is located at the poles. This is in contrast to C3b deposition, which occurs randomly on the bacterial surface. Altogether, these results show a previously unrecognized interaction between the C5b-9 complex and Gram-positive bacteria, which might ultimately lead to a new model of MAC assembly and functioning.

  8. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    SciTech Connect

    Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; Perkins, William A.; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; Krafczyk, Manfred; Luo, Li -Shi; Tartakovsky, Alexandre M.; Yang, Xiaofan; Scheibe, Timothy D.; Trask, Nathaniel

    2015-09-28

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for confidence

  9. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    DOE PAGES

    Mehmani, Yashar; Schoenherr, Martin; Pasquali, Andrea; Perkins, William A.; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; et al

    2015-09-28

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based onmore » the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This paper provides support for

  10. Benchmark Study of 3D Pore-scale Flow and Solute Transport Simulation Methods

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Yang, X.; Mehmani, Y.; Perkins, W. A.; Pasquali, A.; Schoenherr, M.; Kim, K.; Perego, M.; Parks, M. L.; Trask, N.; Balhoff, M.; Richmond, M. C.; Geier, M.; Krafczyk, M.; Luo, L. S.; Tartakovsky, A. M.

    2015-12-01

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that benchmark study to include additional models of the first type based on the immersed-boundary method (IMB), lattice Boltzmann method (LBM), and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries in the manner of PNMs has not been fully determined. We apply all five approaches (FVM-based CFD, IMB, LBM, SPH and PNM) to simulate pore-scale velocity distributions and nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The benchmark study was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence in a variety of pore-scale modeling methods, and motivates further development and application of pore-scale simulation methods.

  11. Intercomparison of 3D pore-scale flow and solute transport simulation methods

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.; Pasquali, Andrea; Schönherr, Martin; Kim, Kyungjoo; Perego, Mauro; Parks, Michael L.; Trask, Nathaniel; Balhoff, Matthew T.; Richmond, Marshall C.; Geier, Martin; Krafczyk, Manfred; Luo, Li-Shi; Tartakovsky, Alexandre M.; Scheibe, Timothy D.

    2016-09-01

    Multiple numerical approaches have been developed to simulate porous media fluid flow and solute transport at the pore scale. These include 1) methods that explicitly model the three-dimensional geometry of pore spaces and 2) methods that conceptualize the pore space as a topologically consistent set of stylized pore bodies and pore throats. In previous work we validated a model of the first type, using computational fluid dynamics (CFD) codes employing a standard finite volume method (FVM), against magnetic resonance velocimetry (MRV) measurements of pore-scale velocities. Here we expand that validation to include additional models of the first type based on the lattice Boltzmann method (LBM) and smoothed particle hydrodynamics (SPH), as well as a model of the second type, a pore-network model (PNM). The PNM approach used in the current study was recently improved and demonstrated to accurately simulate solute transport in a two-dimensional experiment. While the PNM approach is computationally much less demanding than direct numerical simulation methods, the effect of conceptualizing complex three-dimensional pore geometries on solute transport in the manner of PNMs has not been fully determined. We apply all four approaches (FVM-based CFD, LBM, SPH and PNM) to simulate pore-scale velocity distributions and (for capable codes) nonreactive solute transport, and intercompare the model results. Comparisons are drawn both in terms of macroscopic variables (e.g., permeability, solute breakthrough curves) and microscopic variables (e.g., local velocities and concentrations). Generally good agreement was achieved among the various approaches, but some differences were observed depending on the model context. The intercomparison work was challenging because of variable capabilities of the codes, and inspired some code enhancements to allow consistent comparison of flow and transport simulations across the full suite of methods. This study provides support for confidence

  12. A novel low-complexity post-processing algorithm for precise QRS localization.

    PubMed

    Fonseca, Pedro; Aarts, Ronald M; Foussier, Jérôme; Long, Xi

    2014-01-01

    Precise localization of QRS complexes is an essential step in the analysis of small transient changes in instant heart rate and before signal averaging in QRS morphological analysis. Most localization algorithms reported in literature are either not robust to artifacts, depend on the sampling rate of the ECG recordings or are too computationally expensive for real-time applications, especially in low-power embedded devices. This paper proposes a localization algorithm based on the intersection of tangents fitted to the slopes of R waves detected by any QRS detector. Despite having a lower complexity, this algorithm achieves comparable trigger jitter to more complex localization methods without requiring the data to first be upsampled. It also achieves high localization precision regardless of which QRS detector is used as input. It is robust to clipping artifacts and to noise, achieving an average localization error below 2 ms and a trigger jitter below 1 ms on recordings where no additional artifacts were added, and below 8 ms for recordings where the signal was severely degraded. Finally, it increases the accuracy of template-based false positive rejection, allowing nearly all mock false positives added to a set of QRS detections to be removed at the cost of a very small decrease in sensitivity. The localization algorithm proposed is particularly well-suited for implementation in embedded, low-power devices for real-time applications. PMID:26034664

  13. A novel low-complexity post-processing algorithm for precise QRS localization.

    PubMed

    Fonseca, Pedro; Aarts, Ronald M; Foussier, Jérôme; Long, Xi

    2014-01-01

    Precise localization of QRS complexes is an essential step in the analysis of small transient changes in instant heart rate and before signal averaging in QRS morphological analysis. Most localization algorithms reported in literature are either not robust to artifacts, depend on the sampling rate of the ECG recordings or are too computationally expensive for real-time applications, especially in low-power embedded devices. This paper proposes a localization algorithm based on the intersection of tangents fitted to the slopes of R waves detected by any QRS detector. Despite having a lower complexity, this algorithm achieves comparable trigger jitter to more complex localization methods without requiring the data to first be upsampled. It also achieves high localization precision regardless of which QRS detector is used as input. It is robust to clipping artifacts and to noise, achieving an average localization error below 2 ms and a trigger jitter below 1 ms on recordings where no additional artifacts were added, and below 8 ms for recordings where the signal was severely degraded. Finally, it increases the accuracy of template-based false positive rejection, allowing nearly all mock false positives added to a set of QRS detections to be removed at the cost of a very small decrease in sensitivity. The localization algorithm proposed is particularly well-suited for implementation in embedded, low-power devices for real-time applications.

  14. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

    PubMed Central

    Ilca, Serban L.; Kotecha, Abhay; Sun, Xiaoyu; Poranen, Minna M.; Stuart, David I.; Huiskonen, Juha T.

    2015-01-01

    Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems. PMID:26534841

  15. Localized vibrational modes of carbon-hydrogen complexes in GaN

    SciTech Connect

    Manasreh, M.O.; Baranowski, J.M.; Pakula, K.; Jiang, H.X.; Lin, J.

    1999-08-01

    Localized vibrational modes of carbon-hydrogen complexes in metalorganic chemical vapor deposition grown GaN on sapphire were studied using a Fourier-transform infrared spectroscopy technique. Three distinctive localized vibrational modes were observed around 2850, 2922, and 2959 cm{sup {minus}1} for undoped, Si-, and Mg-doped samples. These peaks are related to CH, CH{sub 2}, and CH{sub 3} defect complexes, respectively. However, the localized vibrational modes were not observed in some undoped samples, which is indicative of high quality grown epitaxial layers. It is also observed that the frequencies and intensities of the localized vibrational modes are sample dependent. {copyright} {ital 1999 American Institute of Physics.}

  16. Direct numerical simulation of pore-scale flow in a bead pack: Comparison with magnetic resonance imaging observations

    NASA Astrophysics Data System (ADS)

    Yang, Xiaofan; Scheibe, Timothy D.; Richmond, Marshall C.; Perkins, William A.; Vogt, Sarah J.; Codd, Sarah L.; Seymour, Joseph D.; McKinley, Matthew I.

    2013-04-01

    A significant body of current research is aimed at developing methods for numerical simulation of flow and transport in porous media that explicitly resolve complex pore and solid geometries, and at utilizing such models to study the relationships between fundamental pore-scale processes and macroscopic manifestations at larger (i.e., Darcy) scales. A number of different numerical methods for pore-scale simulation have been developed, and have been extensively tested and validated for simplified geometries. However, validation of pore-scale simulations of fluid velocity for complex, three-dimensional (3D) pore geometries that are representative of natural porous media is challenging due to our limited ability to measure pore-scale velocity in such systems. Recent advances in magnetic resonance imaging (MRI) offer the opportunity to measure not only the pore geometry, but also local fluid velocities under steady-state flow conditions in 3D and with high spatial resolution. In this paper, we present a 3D velocity field measured at sub-pore resolution (tens of micrometers) over a centimeter-scale 3D domain using MRI methods. We have utilized the measured pore geometry to perform 3D simulations of Navier-Stokes flow over the same domain using direct numerical simulation techniques. We present a comparison of the numerical simulation results with the measured velocity field. It is shown that the numerical results match the observed velocity patterns well overall except for a variance and small systematic scaling which can be attributed to the known experimental uncertainty in the MRI measurements. The comparisons presented here provide strong validation of the pore-scale simulation methods and new insights for interpretation of uncertainty in MRI measurements of pore-scale velocity. This study also provides a potential benchmark for future comparison of other pore-scale simulation methods. 2012 Elsevier Science.

  17. Inertial effects during irreversible meniscus reconfiguration in angular pores

    NASA Astrophysics Data System (ADS)

    Ferrari, Andrea; Lunati, Ivan

    2014-12-01

    In porous media, the dynamics of the invading front between two immiscible fluids is often characterized by abrupt reconfigurations caused by local instabilities of the interface. As a prototype of these phenomena we consider the dynamics of a meniscus in a corner as it can be encountered in angular pores. We investigate this process in detail by means of direct numerical simulations that solve the Navier-Stokes equations in the pore space and employ the Volume of Fluid method (VOF) to track the evolution of the interface. We show that for a quasi-static displacement, the numerically calculated surface energy agrees well with the analytical solutions that we have derived for pores with circular and square cross sections. However, the spontaneous reconfigurations are irreversible and cannot be controlled by the injection rate: they are characterized by the amount of surface energy that is spontaneously released and transformed into kinetic energy. The resulting local velocities can be orders of magnitude larger than the injection velocity and they induce damped oscillations of the interface that possess their own time scales and depend only on fluid properties and pore geometry. In complex media (we consider a network of cubic pores) reconfigurations are so frequent and oscillations last long enough that increasing inertial effects leads to a different fluid distribution by influencing the selection of the next pore to be invaded. This calls into question simple pore-filling rules based only on capillary forces. Also, we demonstrate that inertial effects during irreversible reconfigurations can influence the work done by the external forces that is related to the pressure drop in Darcy's law. This suggests that these phenomena have to be considered when upscaling multiphase flow because local oscillations of the menisci affect macroscopic quantities and modify the constitutive relationships to be used in macro-scale models. These results can be extrapolated to other

  18. Gas Hydrate and Pore Pressure

    NASA Astrophysics Data System (ADS)

    Tinivella, Umberta; Giustiniani, Michela

    2014-05-01

    Many efforts have been devoted to quantify excess pore pressures related to gas hydrate dissociation in marine sediments below the BSR using several approaches. Dissociation of gas hydrates in proximity of the BSR, in response to a change in the physical environment (i.e., temperature and/or pressure regime), can liberate excess gas incrising the local pore fluid pressure in the sediment, so decreasing the effective normal stress. So, gas hydrate dissociation may lead to excess pore pressure resulting in sediment deformation or failure, such as submarine landslides, sediment slumping, pockmarks and mud volcanoes, soft-sediment deformation and giant hummocks. Moreover, excess pore pressure may be the result of gas hydrate dissociation due to continuous sedimentation, tectonic uplift, sea level fall, heating or inhibitor injection. In order to detect the presence of the overpressure below the BSR, we propose two approachs. The fist approach models the BSR depth versus pore pressure; in fact, if the free gas below the BSR is in overpressure condition, the base of the gas hydrate stability is deeper with respect to the hydrostatic case. This effect causes a discrepancy between seismic and theoretical BSR depths. The second approach models the velocities versus gas hydrate and free gas concentrations and pore pressure, considering the approximation of the Biot theory in case of low frequency, i.e. seismic frequency. Knowing the P and S seismic velocity from seismic data analysis, it is possibile to jointly estimate the gas hydrate and free gas concentrations and the pore pressure regime. Alternatively, if the S-wave velocity is not availbale (due to lack of OBS/OBC data), an AVO analysis can be performed in order to extract information about Poisson ratio. Our modeling suggests that the areas characterized by shallow waters (i.e., areas in which human infrastructures, such as pipelines, are present) are significantly affected by the presence of overpressure condition

  19. Pore-Scale Modeling of Pore Structure Effects on P-Wave Scattering Attenuation in Dry Rocks

    PubMed Central

    Li, Tianyang; Qiu, Hao; Wang, Feifei

    2015-01-01

    Underground rocks usually have complex pore system with a variety of pore types and a wide range of pore size. The effects of pore structure on elastic wave attenuation cannot be neglected. We investigated the pore structure effects on P-wave scattering attenuation in dry rocks by pore-scale modeling based on the wave theory and the similarity principle. Our modeling results indicate that pore size, pore shape (such as aspect ratio), and pore density are important factors influencing P-wave scattering attenuation in porous rocks, and can explain the variation of scattering attenuation at the same porosity. From the perspective of scattering attenuation, porous rocks can safely suit to the long wavelength assumption when the ratio of wavelength to pore size is larger than 15. Under the long wavelength condition, the scattering attenuation coefficient increases as a power function as the pore density increases, and it increases exponentially with the increase in aspect ratio. For a certain porosity, rocks with smaller aspect ratio and/or larger pore size have stronger scattering attenuation. When the pore aspect ratio is larger than 0.5, the variation of scattering attenuation at the same porosity is dominantly caused by pore size and almost independent of the pore aspect ratio. These results lay a foundation for pore structure inversion from elastic wave responses in porous rocks. PMID:25961729

  20. Pore-scale modeling of pore structure effects on P-wave scattering attenuation in dry rocks.

    PubMed

    Wang, Zizhen; Wang, Ruihe; Li, Tianyang; Qiu, Hao; Wang, Feifei

    2015-01-01

    Underground rocks usually have complex pore system with a variety of pore types and a wide range of pore size. The effects of pore structure on elastic wave attenuation cannot be neglected. We investigated the pore structure effects on P-wave scattering attenuation in dry rocks by pore-scale modeling based on the wave theory and the similarity principle. Our modeling results indicate that pore size, pore shape (such as aspect ratio), and pore density are important factors influencing P-wave scattering attenuation in porous rocks, and can explain the variation of scattering attenuation at the same porosity. From the perspective of scattering attenuation, porous rocks can safely suit to the long wavelength assumption when the ratio of wavelength to pore size is larger than 15. Under the long wavelength condition, the scattering attenuation coefficient increases as a power function as the pore density increases, and it increases exponentially with the increase in aspect ratio. For a certain porosity, rocks with smaller aspect ratio and/or larger pore size have stronger scattering attenuation. When the pore aspect ratio is larger than 0.5, the variation of scattering attenuation at the same porosity is dominantly caused by pore size and almost independent of the pore aspect ratio. These results lay a foundation for pore structure inversion from elastic wave responses in porous rocks.

  1. Evaluation of a Florida coastal golf complex as a local and watershed source of bioavailable contaminants

    EPA Science Inventory

    Lewis, Michael A., Robert L. Quarles, Darrin D. Dantin and James C. Moore. 2004. Evaluation of a Coastal Golf Complex as a Local and Watershed Source of Bioavailable Contaminants. Mar. Pollut. Bull. 48(3-4):254-262. (ERL,GB 1183).

    Contaminant fate in coastal areas impacte...

  2. Peripheral Stimulus Localization by Infants of Moving Stimuli on Complex Backgrounds

    ERIC Educational Resources Information Center

    Mallin, Brittany M.; Richards, John E.

    2012-01-01

    This study examined the effect of attention in young infants on the saccadic localization of dynamic peripheral stimuli presented on complex and interesting backgrounds. Infants at 14, 20, and 26 weeks of age were presented with scenes from a Sesame Street movie until fixation on a moving character occurred and then presented with a second segment…

  3. A Local Discontinuous Galerkin Method for the Complex Modified KdV Equation

    SciTech Connect

    Li Wenting; Jiang Kun

    2010-09-30

    In this paper, we develop a local discontinuous Galerkin(LDG) method for solving complex modified KdV(CMKdV) equation. The LDG method has the flexibility for arbitrary h and p adaptivity. We prove the L{sup 2} stability for general solutions.

  4. Local pressure components and interfacial tensions of a liquid film in the vicinity of a solid surface with a nanometer-scale slit pore obtained by the perturbative method

    SciTech Connect

    Fujiwara, K.; Shibahara, M.

    2015-03-07

    A classical molecular dynamics simulation was conducted for a liquid-solid interfacial system with a nanometer-scale slit pore in order to reveal local thermodynamic states: local pressure components and interfacial tensions of a liquid film in the vicinity of the slit. The simulation also examined the transition mechanism between the two states of the liquid film: (a) liquid film on the slit and (b) liquid film in the slit, based on the local thermodynamic quantities from a molecular point of view. An instantaneous expression of the local pressure components and interfacial tensions, which is based on a volume perturbation, was presented to investigate time-dependent phenomena in molecular dynamics simulations. The interactions between the particles were described by the 12-6 Lennard-Jones potential, and effects of the fluid-solid interaction intensity on the local pressure components and interfacial tensions of the fluid in the vicinity of the slit were examined in detail by the presented perturbative method. The results revealed that the local pressure components tangential to the solid surface in the vicinity of the 1st fluid layer from the solid surface are different in a two dimensional plane, and the difference became pronounced in the vicinity of the corner of the slit, for cases where the fluid-solid interaction intensities are relatively strong. The results for the local interfacial tensions of the fluid inside the slit suggested that the local interfacial tensions in the vicinity of the 2nd and 3rd layers of the solid atoms from the entrance of the slit act as a trigger for the transition between the two states under the influence of a varying fluid-solid interaction.

  5. Mono- and Dinuclear Phosphorescent Rhenium(I) Complexes: Impact of Subcellular Localization on Anticancer Mechanisms.

    PubMed

    Ye, Rui-Rong; Tan, Cai-Ping; Chen, Mu-He; Hao, Liang; Ji, Liang-Nian; Mao, Zong-Wan

    2016-06-01

    Elucidation of relationship among chemical structure, cellular uptake, localization, and biological activity of anticancer metal complexes is important for the understanding of their mechanisms of action. Organometallic rhenium(I) tricarbonyl compounds have emerged as potential multifunctional anticancer drug candidates that can integrate therapeutic and imaging capabilities in a single molecule. Herein, two mononuclear phosphorescent rhenium(I) complexes (Re1 and Re2), along with their corresponding dinuclear complexes (Re3 and Re4), were designed and synthesized as potent anticancer agents. The subcellular accumulation of Re1-Re4 was conveniently analyzed by confocal microscopy in situ in live cells by utilizing their intrinsic phosphorescence. We found that increased lipophilicity of the bidentate ligands could enhance their cellular uptake, leading to improved anticancer efficacy. The dinuclear complexes were more potent than the mononuclear counterparts. The molecular anticancer mechanisms of action evoked by Re3 and Re4 were explored in detail. Re3 with a lower lipophilicity localizes to lysosomes and induces caspase-independent apoptosis, whereas Re4 with higher lipophilicity specially accumulates in mitochondria and induces caspase-independent paraptosis in cancer cells. Our study demonstrates that subcellular localization is crucial for the anticancer mechanisms of these phosphorescent rhenium(I) complexes. PMID:27106876

  6. Mono- and Dinuclear Phosphorescent Rhenium(I) Complexes: Impact of Subcellular Localization on Anticancer Mechanisms.

    PubMed

    Ye, Rui-Rong; Tan, Cai-Ping; Chen, Mu-He; Hao, Liang; Ji, Liang-Nian; Mao, Zong-Wan

    2016-06-01

    Elucidation of relationship among chemical structure, cellular uptake, localization, and biological activity of anticancer metal complexes is important for the understanding of their mechanisms of action. Organometallic rhenium(I) tricarbonyl compounds have emerged as potential multifunctional anticancer drug candidates that can integrate therapeutic and imaging capabilities in a single molecule. Herein, two mononuclear phosphorescent rhenium(I) complexes (Re1 and Re2), along with their corresponding dinuclear complexes (Re3 and Re4), were designed and synthesized as potent anticancer agents. The subcellular accumulation of Re1-Re4 was conveniently analyzed by confocal microscopy in situ in live cells by utilizing their intrinsic phosphorescence. We found that increased lipophilicity of the bidentate ligands could enhance their cellular uptake, leading to improved anticancer efficacy. The dinuclear complexes were more potent than the mononuclear counterparts. The molecular anticancer mechanisms of action evoked by Re3 and Re4 were explored in detail. Re3 with a lower lipophilicity localizes to lysosomes and induces caspase-independent apoptosis, whereas Re4 with higher lipophilicity specially accumulates in mitochondria and induces caspase-independent paraptosis in cancer cells. Our study demonstrates that subcellular localization is crucial for the anticancer mechanisms of these phosphorescent rhenium(I) complexes.

  7. Calculating interaction energies in transition metal complexes with local electron correlation methods

    NASA Astrophysics Data System (ADS)

    Hill, J. Grant; Platts, James A.

    2008-10-01

    The results of density fitting and local approximations applied to the calculation of transition metal-ligand binding energies using second order Møller-Plesset perturbation theory are reported. This procedure accurately reproduces counterpoise corrected binding energies from the canonical method for a range of test complexes. While counterpoise corrections for basis set superposition error are generally small, this procedure can be time consuming, and in some cases gives rise to unphysical dissociation of complexes. In circumventing this correction, a local treatment of electron correlation offers major efficiency savings with little loss of accuracy. The use of density fitting for the underlying Hartree-Fock calculations is also tested for sample Ru complexes, leading to further efficiency gains but essentially no loss in accuracy.

  8. Grainsize and pore size changes due to the flow of granular materials

    NASA Astrophysics Data System (ADS)

    Marks, Benjy; Einav, Itai

    2014-05-01

    Granular materials exhibit behaviour which can cause spatial or local changes in their grainsize distribution, such as crushing, mixing and segregation. These mechanisms are modelled simultaneously using a cellular automaton, and the complex phenomena that emerge as they interact are explored. We find that either power law or log-normal grainsize distributions can develop. Finally, detailed information about the evolution of the local grainsize distribution is used to describe the evolution of the pore size distribution.

  9. Local and landscape associations between wintering dabbling ducks and wetland complexes in Mississippi

    USGS Publications Warehouse

    Pearse, Aaron T.; Kaminski, Richard M.; Reinecke, Kenneth J.; Dinsmore, Stephen J.

    2012-01-01

    Landscape features influence distribution of waterbirds throughout their annual cycle. A conceptual model, the wetland habitat complex, may be useful in conservation of wetland habitats for dabbling ducks (Anatini). The foundation of this conceptual model is that ducks seek complexes of wetlands containing diverse resources to meet dynamic physiological needs. We included flooded croplands, wetlands and ponds, public-land waterfowl sanctuary, and diversity of habitats as key components of wetland habitat complexes and compared their relative influence at two spatial scales (i.e., local, 0.25-km radius; landscape, 4-km) on dabbling ducks wintering in western Mississippi, USA during winters 2002–2004. Distribution of mallard (Anas platyrhynchos) groups was positively associated with flooded cropland at local and landscape scales. Models representing flooded croplands at the landscape scale best explained occurrence of other dabbling ducks. Habitat complexity measured at both scales best explained group size of other dabbling ducks. Flooded croplands likely provided food that had decreased in availability due to conversion of wetlands to agriculture. Wetland complexes at landscape scales were more attractive to wintering ducks than single or structurally simple wetlands. Conservation of wetland complexes at large spatial scales (≥5,000 ha) on public and private lands will require coordination among multiple stakeholders.

  10. Measuring streetscape complexity based on the statistics of local contrast and spatial frequency.

    PubMed

    Cavalcante, André; Mansouri, Ahmed; Kacha, Lemya; Barros, Allan Kardec; Takeuchi, Yoshinori; Matsumoto, Naoji; Ohnishi, Noboru

    2014-01-01

    Streetscapes are basic urban elements which play a major role in the livability of a city. The visual complexity of streetscapes is known to influence how people behave in such built spaces. However, how and which characteristics of a visual scene influence our perception of complexity have yet to be fully understood. This study proposes a method to evaluate the complexity perceived in streetscapes based on the statistics of local contrast and spatial frequency. Here, 74 streetscape images from four cities, including daytime and nighttime scenes, were ranked for complexity by 40 participants. Image processing was then used to locally segment contrast and spatial frequency in the streetscapes. The statistics of these characteristics were extracted and later combined to form a single objective measure. The direct use of statistics revealed structural or morphological patterns in streetscapes related to the perception of complexity. Furthermore, in comparison to conventional measures of visual complexity, the proposed objective measure exhibits a higher correlation with the opinion of the participants. Also, the performance of this method is more robust regarding different time scenarios. PMID:24498292

  11. Measuring Streetscape Complexity Based on the Statistics of Local Contrast and Spatial Frequency

    PubMed Central

    Cavalcante, André; Mansouri, Ahmed; Kacha, Lemya; Barros, Allan Kardec; Takeuchi, Yoshinori; Matsumoto, Naoji; Ohnishi, Noboru

    2014-01-01

    Streetscapes are basic urban elements which play a major role in the livability of a city. The visual complexity of streetscapes is known to influence how people behave in such built spaces. However, how and which characteristics of a visual scene influence our perception of complexity have yet to be fully understood. This study proposes a method to evaluate the complexity perceived in streetscapes based on the statistics of local contrast and spatial frequency. Here, 74 streetscape images from four cities, including daytime and nighttime scenes, were ranked for complexity by 40 participants. Image processing was then used to locally segment contrast and spatial frequency in the streetscapes. The statistics of these characteristics were extracted and later combined to form a single objective measure. The direct use of statistics revealed structural or morphological patterns in streetscapes related to the perception of complexity. Furthermore, in comparison to conventional measures of visual complexity, the proposed objective measure exhibits a higher correlation with the opinion of the participants. Also, the performance of this method is more robust regarding different time scenarios. PMID:24498292

  12. Latest Progress of Fault Detection and Localization in Complex Electrical Engineering

    NASA Astrophysics Data System (ADS)

    Zhao, Zheng; Wang, Can; Zhang, Yagang; Sun, Yi

    2014-01-01

    In the researches of complex electrical engineering, efficient fault detection and localization schemes are essential to quickly detect and locate faults so that appropriate and timely corrective mitigating and maintenance actions can be taken. In this paper, under the current measurement precision of PMU, we will put forward a new type of fault detection and localization technology based on fault factor feature extraction. Lots of simulating experiments indicate that, although there are disturbances of white Gaussian stochastic noise, based on fault factor feature extraction principal, the fault detection and localization results are still accurate and reliable, which also identifies that the fault detection and localization technology has strong anti-interference ability and great redundancy.

  13. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Cesnik, Carlos E. S.

    2016-09-01

    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin-Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  14. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Cesnik, Carlos E. S.

    2016-09-01

    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin–Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  15. Identification of Essential Proteins Based on a New Combination of Local Interaction Density and Protein Complexes

    PubMed Central

    Luo, Jiawei; Qi, Yi

    2015-01-01

    Background Computational approaches aided by computer science have been used to predict essential proteins and are faster than expensive, time-consuming, laborious experimental approaches. However, the performance of such approaches is still poor, making practical applications of computational approaches difficult in some fields. Hence, the development of more suitable and efficient computing methods is necessary for identification of essential proteins. Method In this paper, we propose a new method for predicting essential proteins in a protein interaction network, local interaction density combined with protein complexes (LIDC), based on statistical analyses of essential proteins and protein complexes. First, we introduce a new local topological centrality, local interaction density (LID), of the yeast PPI network; second, we discuss a new integration strategy for multiple bioinformatics. The LIDC method was then developed through a combination of LID and protein complex information based on our new integration strategy. The purpose of LIDC is discovery of important features of essential proteins with their neighbors in real protein complexes, thereby improving the efficiency of identification. Results Experimental results based on three different PPI(protein-protein interaction) networks of Saccharomyces cerevisiae and Escherichia coli showed that LIDC outperformed classical topological centrality measures and some recent combinational methods. Moreover, when predicting MIPS datasets, the better improvement of performance obtained by LIDC is over all nine reference methods (i.e., DC, BC, NC, LID, PeC, CoEWC, WDC, ION, and UC). Conclusions LIDC is more effective for the prediction of essential proteins than other recently developed methods. PMID:26125187

  16. Conserved motif of CDK5RAP2 mediates its localization to centrosomes and the Golgi complex.

    PubMed

    Wang, Zhe; Wu, Tao; Shi, Lin; Zhang, Lin; Zheng, Wei; Qu, Jianan Y; Niu, Ruifang; Qi, Robert Z

    2010-07-16

    As the primary microtubule-organizing centers, centrosomes require gamma-tubulin for microtubule nucleation and organization. Located in close vicinity to centrosomes, the Golgi complex is another microtubule-organizing organelle in interphase cells. CDK5RAP2 is a gamma-tubulin complex-binding protein and functions in gamma-tubulin attachment to centrosomes. In this study, we find that CDK5RAP2 localizes to the Golgi complex in an ATP- and centrosome-dependent manner and associates with Golgi membranes independently of microtubules. CDK5RAP2 contains a centrosome-targeting domain with its core region highly homologous to the Motif 2 (CM2) of centrosomin, a functionally related protein in Drosophila. This sequence, referred to as the CM2-like motif, is also conserved in related proteins in chicken and zebrafish. Therefore, CDK5RAP2 may undertake a conserved mechanism for centrosomal localization. Using a mutational approach, we demonstrate that the CM2-like motif plays a crucial role in the centrosomal and Golgi localization of CDK5RAP2. Furthermore, the CM2-like motif is essential for the association of the centrosome-targeting domain to pericentrin and AKAP450. The binding with pericentrin is required for the centrosomal and Golgi localization of CDK5RAP2, whereas the binding with AKAP450 is required for the Golgi localization. Although the CM2-like motif possesses the activity of Ca(2+)-independent calmodulin binding, binding of calmodulin to this sequence is dispensable for centrosomal and Golgi association. Altogether, CDK5RAP2 may represent a novel mechanism for centrosomal and Golgi localization. PMID:20466722

  17. Synergy and destructive interferences between local magnetic anisotropies in binuclear complexes

    NASA Astrophysics Data System (ADS)

    Guihéry, Nathalie; Ruamps, Renaud; Maurice, Rémi; de Graaf, Coen

    2015-12-01

    Magnetic anisotropy is responsible for the single molecule magnet behavior of transition metal complexes. This behavior is characterized by a slow relaxation of the magnetization for low enough temperatures, and thus for a possible blocking of the magnetization. This bistable behavior can lead to possible technological applications in the domain of data storage or quantum computing. Therefore, the understanding of the microscopic origin of magnetic anisotropy has received a considerable interest during the last two decades. The presentation focuses on the determination of the anisotropy parameters of both mono-nuclear and bi-nuclear types of complexes and on the control and optimization of the anisotropic properties. The validity of the model Hamiltonians commonly used to characterize such complexes has been questioned and it is shown that neither the standard multispin Hamiltonian nor the giant spin Hamiltonian are appropriate for weakly coupled ions. Alternative models have been proposed and used to properly extract the relevant parameters. Rationalizations of the magnitude and nature of both local anisotropies of single ions and the molecular anisotropy of polynuclear complexes are provided. The synergy and interference effects between local magnetic anisotropies are studied in a series of binuclear complexes.

  18. Synergy and destructive interferences between local magnetic anisotropies in binuclear complexes

    SciTech Connect

    Guihéry, Nathalie; Ruamps, Renaud; Maurice, Rémi

    2015-12-31

    Magnetic anisotropy is responsible for the single molecule magnet behavior of transition metal complexes. This behavior is characterized by a slow relaxation of the magnetization for low enough temperatures, and thus for a possible blocking of the magnetization. This bistable behavior can lead to possible technological applications in the domain of data storage or quantum computing. Therefore, the understanding of the microscopic origin of magnetic anisotropy has received a considerable interest during the last two decades. The presentation focuses on the determination of the anisotropy parameters of both mono-nuclear and bi-nuclear types of complexes and on the control and optimization of the anisotropic properties. The validity of the model Hamiltonians commonly used to characterize such complexes has been questioned and it is shown that neither the standard multispin Hamiltonian nor the giant spin Hamiltonian are appropriate for weakly coupled ions. Alternative models have been proposed and used to properly extract the relevant parameters. Rationalizations of the magnitude and nature of both local anisotropies of single ions and the molecular anisotropy of polynuclear complexes are provided. The synergy and interference effects between local magnetic anisotropies are studied in a series of binuclear complexes.

  19. Complex-time singularity and locality estimates for quantum lattice systems

    SciTech Connect

    Bouch, Gabriel

    2015-12-15

    We present and prove a well-known locality bound for the complex-time dynamics of a general class of one-dimensional quantum spin systems. Then we discuss how one might hope to extend this same procedure to higher dimensions using ideas related to the Eden growth process and lattice trees. Finally, we demonstrate with a specific family of lattice trees in the plane why this approach breaks down in dimensions greater than one and prove that there exist interactions for which the complex-time dynamics blows-up in finite imaginary time. .

  20. Complex-time singularity and locality estimates for quantum lattice systems

    NASA Astrophysics Data System (ADS)

    Bouch, Gabriel

    2015-12-01

    We present and prove a well-known locality bound for the complex-time dynamics of a general class of one-dimensional quantum spin systems. Then we discuss how one might hope to extend this same procedure to higher dimensions using ideas related to the Eden growth process and lattice trees. Finally, we demonstrate with a specific family of lattice trees in the plane why this approach breaks down in dimensions greater than one and prove that there exist interactions for which the complex-time dynamics blows-up in finite imaginary time.

  1. On the cavitation and pore blocking in slit-shaped ink-bottle pores.

    PubMed

    Fan, Chunyan; Do, D D; Nicholson, D

    2011-04-01

    We present GCMC simulations of argon adsorption in slit pores of different channel geometry. We show that the isotherm for an ink-bottle pore can be reconstructed as a linear combination of the local isotherms of appropriately chosen independent unit cells. Second, depending on the system parameters and operating conditions, the phenomena of cavitation and pore blocking can occur for a given configuration of the ink-bottle pore by varying the geometrical aspect ratio. Although it has been argued in the literature that the geometrical aspects of the system govern the evaporation mechanism (either cavitation or pore blocking), we here put forward an argument that the local compressibility in different parts of the ink-bottle pore is the deciding factor for evaporation. When the fluid in the small neck is strongly bound, cavitation is the governing process, and molecules in the cavity evaporate to the surrounding bulk gas via a mass transfer mechanism through the pore neck. When the pore neck is sufficiently large, the system of neck and cavity evaporates at the same pressure, which is a consequence of the comparable compressibility between the fluid in the neck and that in the cavity. This suggests that local compressibility is the measure of cohesiveness of the fluid prior to evaporation. One consequence that we derive from the analysis of isotherms of a number of connected pores is that by analyzing the adsorption branch or the desorption branch of an experimental isotherm may not lead to the correct pore sizes and the correct pore volume distribution. PMID:21370903

  2. Precipitation in pores: A geochemical frontier

    DOE PAGES

    Stack, Andrew G.

    2015-07-29

    This article's purpose is to review some of the recent research in which geochemists have examined precipitation of solid phases in porous media, particularly in pores a few nanometers in diameter (nanopores). While this is a “review,” it is actually more forward-looking in that the list of things about this phenomenon that we do not know or cannot control at this time is likely longer than what we do know and can control. For example, there are three directly contradictory theories on how to predict how precipitation proceeds in a medium of varying pore size, as will be discussed below.more » The confusion on this subject likely stems from the complexity of the phenomenon itself: One can easily clog a porous medium by inducing a rapid, homogeneous precipitation directly from solution, or have limited precipitation occur that does not affect permeability or even porosity substantially. It is more difficult to engineer mineral precipitation in order to obtain a specific outcome, such as filling all available pore space over a targeted area for the purposes of contaminant sequestration. However, breakthrough discoveries could occur in the next five to ten years that enhance our ability to predict robustly and finely control precipitation in porous media by understanding how porosity and permeability evolve in response to system perturbations. These discoveries will likely stem (at least in part) from advances in our ability to 1) perform and interpret X-ray/neutron scattering experiments that reveal the extent of precipitation and its locales within porous media (Anovitz and Cole 2015, this volume), and 2) utilize increasingly powerful simulations to test concepts and models about the evolution of porosity and permeability as precipitation occurs (Steefel et al. 2015, this volume). A further important technique to isolate specific phenomena and understand reactivity is also microfluidics cell experiments that allow specific control of flow paths and fluid

  3. Precipitation in pores: A geochemical frontier

    SciTech Connect

    Stack, Andrew G.

    2015-07-29

    This article's purpose is to review some of the recent research in which geochemists have examined precipitation of solid phases in porous media, particularly in pores a few nanometers in diameter (nanopores). While this is a “review,” it is actually more forward-looking in that the list of things about this phenomenon that we do not know or cannot control at this time is likely longer than what we do know and can control. For example, there are three directly contradictory theories on how to predict how precipitation proceeds in a medium of varying pore size, as will be discussed below. The confusion on this subject likely stems from the complexity of the phenomenon itself: One can easily clog a porous medium by inducing a rapid, homogeneous precipitation directly from solution, or have limited precipitation occur that does not affect permeability or even porosity substantially. It is more difficult to engineer mineral precipitation in order to obtain a specific outcome, such as filling all available pore space over a targeted area for the purposes of contaminant sequestration. However, breakthrough discoveries could occur in the next five to ten years that enhance our ability to predict robustly and finely control precipitation in porous media by understanding how porosity and permeability evolve in response to system perturbations. These discoveries will likely stem (at least in part) from advances in our ability to 1) perform and interpret X-ray/neutron scattering experiments that reveal the extent of precipitation and its locales within porous media (Anovitz and Cole 2015, this volume), and 2) utilize increasingly powerful simulations to test concepts and models about the evolution of porosity and permeability as precipitation occurs (Steefel et al. 2015, this volume). A further important technique to isolate specific phenomena and understand reactivity is also microfluidics cell experiments that allow specific control of flow paths and fluid velocities

  4. Structure, Function, and Localization of Gβ5–RGS Complexes

    PubMed Central

    Slepak, Vladlen Z.

    2012-01-01

    Members of the R7 subfamily of regulator of G protein signaling (RGS) proteins (RGS6, 7, 9, and 11) exist as heterodimers with the G protein beta subunit Gβ5. These protein complexes are only found in neurons and are defined by the presence of three domains: DEP/DHEX, Gβ5/GGL, and RGS. This article summarizes published work in the following areas: (1) the functional significance of structural organization of Gβ5–R7 complexes, (2) regional distribution of Gβ5–R7 in the nervous system and regulation of R7 family expression, (3) subcellular localization of Gβ5–R7 complexes, and (4) novel binding partners of Gβ5–R7 proteins. The review points out some contradictions between observations made by different research groups and highlights the importance of using alternative experimental approaches to obtain conclusive information about Gβ5–R7 function in vivo. PMID:20374716

  5. Adaptive Multi-Scale Pore Network Method for Two-Phase Flow in Porous Media

    NASA Astrophysics Data System (ADS)

    Meyer, D. W.; Khayrat, K.; Jenny, P.

    2015-12-01

    Dynamic pore network simulators are important tools in studying macroscopic quantities in two-phase flow through porous media. However, these simulators have a time complexity of order N2 for N pore bodies, which limits their usage to small domains. Quasi-static pore network simulators, which assume capillary dominated flow, are more efficient with a time complexity of order N log(N), but are unable to capture phenomena caused by viscous effects such as viscous fingering and stable displacement. It has been experimentally observed that, in several flow scenarios, capillary forces are dominant at the pore scale and viscous forces at larger scales. In order to take advantage of this behaviour and to reduce the time complexity of existing dynamic pore network simulators, we propose a multi-scale pore-network method for two phase flow. In our solution algorithm, the pore network is first divided into smaller subnetworks. The algorithm to advance the fluid interfaces within each subnetwork consists of three steps: 1) The saturation rate of each subnetwork is obtained by solving a two-phase meso-scale mass balance equation over the domain of subnetworks. Here, a multi-point flux scheme is used. 2) Depending on the local capillary number computed in the subnetwork, either an invasion percolation algorithm or a dynamic network algorithm is used to locally advance the fluid-fluid interfaces within each subnetwork until a new saturation value is matched. 3) The transmissibilities for the meso-scale equation are updated based on the updated fluid configurations in each subnetwork. For this purpose the methodoloy of the existing multi-scale finite volume (MSFV) method is employed. An important feature of the multi-scale pore-network method is that it maintains consistency of both fluid occupancy and fluxes at subnetwork interfaces. Viscous effects such as viscous fingering (see figure) can be captured at a decreased computational cost compared to dynamic pore network

  6. Non-iterative holographic axial localization using complex amplitude of diffraction-free vortices.

    PubMed

    Bouchal, Petr; Bouchal, Zdeněk

    2014-12-01

    We present a novel technique of digital holography using digitally implemented diffraction-free vortices for a precise three-dimensional (3D) localization of point-like objects. The localization is realized by the processing of the holographic image reconstructed at arbitrarily selected plane. Separating a single radial component of the spatial spectrum and modulating its phase by a virtual spiral mask, the holographic images of individual object points are transformed to the image structures analogous to the diffraction-free vortex beams. The real part of the complex amplitude of the digital vortices creates the shape-invariant patterns rotating due to a defocusing. Determining the angular rotation, the axial positions of the individual point objects are specified over a wide axial range. In the proposed method, a single in-line hologram is processed without phase shifting and multiplane reconstruction, so that a dynamic localization and tracking of particles becomes possible. The principle of the method is presented in a unified computational model valid for both coherent and incoherent techniques of digital holography. The functionality of the method has been verified in experiments of the Fresnel incoherent correlation holography (FINCH) and its flexibility presented by controlled variations of the localization sensitivity. The application potential has been demonstrated by the defocusing image rotation of fixed fluorescent microspheres and the 3D localization and tracking of moving polystyrene beads resulting in the trajectory reconstruction of a selected particle. PMID:25606951

  7. Norepinephrine Modulates Coding of Complex Vocalizations in the Songbird Auditory Cortex Independent of Local Neuroestrogen Synthesis

    PubMed Central

    Ikeda, Maaya Z.; Jeon, Sung David; Cowell, Rosemary A.

    2015-01-01

    The catecholamine norepinephrine plays a significant role in auditory processing. Most studies to date have examined the effects of norepinephrine on the neuronal response to relatively simple stimuli, such as tones and calls. It is less clear how norepinephrine shapes the detection of complex syntactical sounds, as well as the coding properties of sensory neurons. Songbirds provide an opportunity to understand how auditory neurons encode complex, learned vocalizations, and the potential role of norepinephrine in modulating the neuronal computations for acoustic communication. Here, we infused norepinephrine into the zebra finch auditory cortex and performed extracellular recordings to study the modulation of song representations in single neurons. Consistent with its proposed role in enhancing signal detection, norepinephrine decreased spontaneous activity and firing during stimuli, yet it significantly enhanced the auditory signal-to-noise ratio. These effects were all mimicked by clonidine, an α-2 receptor agonist. Moreover, a pattern classifier analysis indicated that norepinephrine enhanced the ability of single neurons to accurately encode complex auditory stimuli. Because neuroestrogens are also known to enhance auditory processing in the songbird brain, we tested the hypothesis that norepinephrine actions depend on local estrogen synthesis. Neither norepinephrine nor adrenergic receptor antagonist infusion into the auditory cortex had detectable effects on local estradiol levels. Moreover, pretreatment with fadrozole, a specific aromatase inhibitor, did not block norepinephrine's neuromodulatory effects. Together, these findings indicate that norepinephrine enhances signal detection and information encoding for complex auditory stimuli by suppressing spontaneous “noise” activity and that these actions are independent of local neuroestrogen synthesis. PMID:26109659

  8. Ligand-dependent localization and function of ORP-VAP complexes at membrane contact sites.

    PubMed

    Weber-Boyvat, Marion; Kentala, Henriikka; Peränen, Johan; Olkkonen, Vesa M

    2015-05-01

    Oxysterol-binding protein/OSBP-related proteins (ORPs) constitute a conserved family of sterol/phospholipid-binding proteins with lipid transporter or sensor functions. We investigated the spatial occurrence and regulation of the interactions of human OSBP/ORPs or the S. cerevisiae orthologs, the Osh (OSBP homolog) proteins, with their endoplasmic reticulum (ER) anchors, the VAMP-associated proteins (VAPs), by employing bimolecular fluorescence complementation and pull-down set-ups. The ORP-VAP interactions localize frequently at distinct subcellular sites, shown in several cases to represent membrane contact sites (MCSs). Using established ORP ligand-binding domain mutants and pull-down assays with recombinant proteins, we show that ORP liganding regulates the ORP-VAP association, alters the subcellular targeting of ORP-VAP complexes, or modifies organelle morphology. There is distinct protein specificity in the effects of the mutants on subcellular targeting of ORP-VAP complexes. We provide evidence that complexes of human ORP2 and VAPs at ER-lipid droplet interfaces regulate the hydrolysis of triglycerides and lipid droplet turnover. The data suggest evolutionarily conserved, complex ligand-dependent functions of ORP-VAP complexes at MCSs, with implications for cellular lipid homeostasis and signaling.

  9. Ligand-dependent localization and function of ORP-VAP complexes at membrane contact sites.

    PubMed

    Weber-Boyvat, Marion; Kentala, Henriikka; Peränen, Johan; Olkkonen, Vesa M

    2015-05-01

    Oxysterol-binding protein/OSBP-related proteins (ORPs) constitute a conserved family of sterol/phospholipid-binding proteins with lipid transporter or sensor functions. We investigated the spatial occurrence and regulation of the interactions of human OSBP/ORPs or the S. cerevisiae orthologs, the Osh (OSBP homolog) proteins, with their endoplasmic reticulum (ER) anchors, the VAMP-associated proteins (VAPs), by employing bimolecular fluorescence complementation and pull-down set-ups. The ORP-VAP interactions localize frequently at distinct subcellular sites, shown in several cases to represent membrane contact sites (MCSs). Using established ORP ligand-binding domain mutants and pull-down assays with recombinant proteins, we show that ORP liganding regulates the ORP-VAP association, alters the subcellular targeting of ORP-VAP complexes, or modifies organelle morphology. There is distinct protein specificity in the effects of the mutants on subcellular targeting of ORP-VAP complexes. We provide evidence that complexes of human ORP2 and VAPs at ER-lipid droplet interfaces regulate the hydrolysis of triglycerides and lipid droplet turnover. The data suggest evolutionarily conserved, complex ligand-dependent functions of ORP-VAP complexes at MCSs, with implications for cellular lipid homeostasis and signaling. PMID:25420878

  10. Velocities in Solar Pores

    NASA Astrophysics Data System (ADS)

    Balasubramaniam, K. S.; Keil, S. L.; Smaldone, L. A.

    1996-05-01

    We investigate the three dimensional structure of solar pores and their surroundings using high spatial and spectral resolution data. We present evidence that surface velocities decrease around pores with a corresponding increase in the line-of-sight (LOS) velocities. LOS velocities in pores increase with the strength of the magnetic field. Surface velocities show convergence toward a weak downflow which appear to trace boundaries resembling meso-granular and super granular flows. The observed magnetic fields in the pores appear near these boundaries. We analyze the vertical velocity structure in pores and show that they generally have downflows decreasing exponentially with height, with a scale height of about 90 km. Evidence is also presented for the expanding nature of flux tubes. Finally we describe a phenomenological model for pores. This work was supported by AFOSR Task 2311G3. LAS was partially supported by the Progetto Nazionale Astrofisica e Fisica Cosmica of MURST and Scambi Internazionali of the Universita degli Studi di Napoli Frederico II. National Solar Observatory, NOAO, is operated for the National Science Foundation by AURA, Inc.

  11. Local weather conditions have complex effects on the growth of blue tit nestlings.

    PubMed

    Mainwaring, Mark C; Hartley, Ian R

    2016-08-01

    Adverse weather conditions are expected to result in impaired nestling development in birds, but empirical studies have provided equivocal support for such a relationship. This may be because the negative effects of adverse weather conditions are masked by parental effects. Globally, ambient temperatures, rainfall levels and wind speeds are all expected to increase in a changing climate and so there is a need for a better understanding of the relationship between weather conditions and nestling growth. Here, we describe a correlative study that examined the relationships between local temperatures, rainfall levels and wind speeds and the growth of individual blue tit (Cyanistes caeruleus) nestlings in relation to their hatching order and sex. We found that changes in a range of morphological characters were negatively related to both temperature and wind speed, but positively related to rainfall. These patterns were further influenced by the hatching order of the nestlings but not by nestling sex. This suggests that the predicted changes in local weather conditions may have complex effects on nestling growth, but that parents may be able to mitigate the adverse effects via adaptive parental effects. We therefore conclude that local weather conditions have complex effects on avian growth and the implications for patterns of avian growth in a changing climate are discussed.

  12. Local weather conditions have complex effects on the growth of blue tit nestlings.

    PubMed

    Mainwaring, Mark C; Hartley, Ian R

    2016-08-01

    Adverse weather conditions are expected to result in impaired nestling development in birds, but empirical studies have provided equivocal support for such a relationship. This may be because the negative effects of adverse weather conditions are masked by parental effects. Globally, ambient temperatures, rainfall levels and wind speeds are all expected to increase in a changing climate and so there is a need for a better understanding of the relationship between weather conditions and nestling growth. Here, we describe a correlative study that examined the relationships between local temperatures, rainfall levels and wind speeds and the growth of individual blue tit (Cyanistes caeruleus) nestlings in relation to their hatching order and sex. We found that changes in a range of morphological characters were negatively related to both temperature and wind speed, but positively related to rainfall. These patterns were further influenced by the hatching order of the nestlings but not by nestling sex. This suggests that the predicted changes in local weather conditions may have complex effects on nestling growth, but that parents may be able to mitigate the adverse effects via adaptive parental effects. We therefore conclude that local weather conditions have complex effects on avian growth and the implications for patterns of avian growth in a changing climate are discussed. PMID:27503711

  13. Hydrogen Exchange Differences between Chemoreceptor Signaling Complexes Localize to Functionally Important Subdomains

    PubMed Central

    2015-01-01

    The goal of understanding mechanisms of transmembrane signaling, one of many key life processes mediated by membrane proteins, has motivated numerous studies of bacterial chemotaxis receptors. Ligand binding to the receptor causes a piston motion of an α helix in the periplasmic and transmembrane domains, but it is unclear how the signal is then propagated through the cytoplasmic domain to control the activity of the associated kinase CheA. Recent proposals suggest that signaling in the cytoplasmic domain involves opposing changes in dynamics in different subdomains. However, it has been difficult to measure dynamics within the functional system, consisting of extended arrays of receptor complexes with two other proteins, CheA and CheW. We have combined hydrogen exchange mass spectrometry with vesicle template assembly of functional complexes of the receptor cytoplasmic domain to reveal that there are significant signaling-associated changes in exchange, and these changes localize to key regions of the receptor involved in the excitation and adaptation responses. The methylation subdomain exhibits complex changes that include slower hydrogen exchange in complexes in a kinase-activating state, which may be partially consistent with proposals that this subdomain is stabilized in this state. The signaling subdomain exhibits significant protection from hydrogen exchange in complexes in a kinase-activating state, suggesting a tighter and/or larger interaction interface with CheA and CheW in this state. These first measurements of the stability of protein subdomains within functional signaling complexes demonstrate the promise of this approach for measuring functionally important protein dynamics within the various physiologically relevant states of multiprotein complexes. PMID:25420045

  14. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis

    NASA Astrophysics Data System (ADS)

    Ding, Hang

    2014-01-01

    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  15. Diego interacts with Prickle and Strabismus/Van Gogh to localize planar cell polarity complexes.

    PubMed

    Das, Gishnu; Jenny, Andreas; Klein, Thomas J; Eaton, Suzanne; Mlodzik, Marek

    2004-09-01

    Planar cell polarity (PCP) in the Drosophila eye is established by the distinct fate specifications of photoreceptors R3 and R4, and is regulated by the Frizzled (Fz)/PCP signaling pathway. Before the PCP proteins become asymmetrically localized to opposite poles of the cell in response to Fz/PCP signaling, they are uniformly apically colocalized. Little is known about how the apical localization is maintained. We provide evidence that the PCP protein Diego (Dgo) promotes the maintenance of apical localization of Flamingo (Fmi), an atypical Cadherin-family member, which itself is required for the apical localization of the other PCP factors. This function of Dgo is redundant with Prickle (Pk) and Strabismus (Stbm), and only appreciable in double mutant tissue. We show that the initial membrane association of Dgo depends on Fz, and that Dgo physically interacts with Stbm and Pk through its Ankyrin repeats, providing evidence for a PCP multiprotein complex. These interactions suggest a positive feedback loop initiated by Fz that results in the apical maintenance of other PCP factors through Fmi.

  16. Decomposing Complex, Macroscopic Phenomena Through A Set of Local Nonlinear Rules In A Cellular Automata Environment.

    NASA Astrophysics Data System (ADS)

    Avolio, M. V.; Crisci, G. M.; D'Ambrosio, D.; di Gregorio, S.; Iovine, G.; Rongo, R.; Spataro, W.

    Cellular Automata (CA) are able to capture the peculiar characteristics of systems, whose global evolution can be exclusively described on the basis of local interactions among their constituent parts ("a-centrism"). Such systems match the paradigm of parallelism with the a-centrism one. In modelling complex phenomena by means of classical CA, elementary automata characterised by few states and simple transition function have usually been involved. On the other hand, many complex macroscopic phenomena (even though characterised by properties of parallelism and a-centrism) can be very difficult to be modelled through classical CA, because of their hetero- geneous characteristics, which require a very large number of states. For such cases, which perfectly fit the general definition of CA, more complex transition rules (differ- ing from typical transition functions) would be, in fact, needed. Aiming at modelling these latter phenomena, an empirical method has been developed, based on the decom- position of the phenomenon into "elementary" components, whose behaviour can be described through local rules. Furthermore, criteria and conditions have been defined, in order to translate the local rules into a transition function, as needed for perform- ing cellular automata simulations. Applications of CA models to real cases of study have recently been attempted: landslides (earth flows, rock avalanches, debris flows), lava flows, soil erosion, soil contamination and bioremediation, forest fires have all been analysed through CA simulations, and encouraging results have been obtained. In the present paper, examples of application of the method for hazard evaluation are described, with particular reference to the Sarno 1998 debris flows and the Etna 2001 lava flows.

  17. Magnetic Exchange Couplings in Heterodinuclear Complexes Based on Differential Local Spin Rotations.

    PubMed

    Joshi, Rajendra P; Phillips, Jordan J; Peralta, Juan E

    2016-04-12

    We analyze the performance of a new method for the calculation of magnetic exchange coupling parameters for the particular case of heterodinuclear transition metals complexes of Cu, Ni, and V. This method is based on a generalized perturbative approach which uses differential local spin rotations via formal Lagrange multipiers (Phillips, J. J.; Peralta, J. E. J. Chem. Phys. 2013, 138, 174115). The reliability of the calculated couplings has been assessed by comparing with results from traditional energy differences with different density functional approximations and with experimental values. Our results show that this method to calculate magnetic exchange couplings can be reliably used for heteronuclear transition metal complexes, and at the same time, that it is independent from the different mapping schemes used in energy difference methods. PMID:26953521

  18. Thermal analysis of porous medium with ellipsoidal pores using a homogenization method

    NASA Astrophysics Data System (ADS)

    Asakuma, Yusuke; Yamamoto, Tsuyoshi

    2016-10-01

    Effective thermal conductivity including radiation is analyzed using a homogenization method. This method can precisely represent the microstructure of a porous medium with ellipsoidal pores. Here, the effects of parameters such as porosity, pore shape, pore distribution, and temperature of the porous medium on the conductivity are estimated to clarify the mechanisms in complex pore structures. For example, heat transfer by radiation does not dominate if the medium has pores of less than 1 mm in size. Moreover, the anisotropy of the effective thermal conductivity is found to depend on temperature, pore shape, pore size, and pore distribution.

  19. Complex mineral zoning patterns caused by ultra-local equilibrium at reaction interfaces

    NASA Astrophysics Data System (ADS)

    Pearce, Mark; Liu, Weihua; Borg, Stacey; Cleverley, James

    2014-05-01

    Chemical compositions of zoned minerals record a time-series of conditions experienced by the rock. They are a function of the prevailing pressure, temperature and effective bulk chemical composition as well as any post-growth modification processes e.g. volume diffusion and deformation. In fluid-buffered systems, zoned mineral compositions should be expected to reflect directly the evolution of fluid composition. Here we show that during rapid fluid-rock reactions, ultra-local equilibrium can form complex mineral zoning patterns, even when the overall system is highly fluid buffered. We reacted calcite single crystals with arsenate-phosphate solutions with molar ratios of As/(As+P) between 0.011 - 0.145 at 250°C and water-saturated pressure with fluid-rock mass ratios in excess of 2500%. Porous, fine-grained apatite polycrystals with varying arsenic contents replaced the calcite by an interface-coupled dissolution reprecipitation mechanism. During the first few hours of the reaction, complex zoning patterns of arsenic content within the apatite formed. The scale of the arsenic variations corresponds with the scale of corrugations of the reaction interface. The variations in arsenic content of the apatite result from spatially and temporally varying increases in the arsenic content of the reaction interface fluid. Since phosphate diffusion cannot keep pace with the reaction rate arsenic becomes enriched in the reaction interface fluid as phosphate is preferentially used in the reaction. The most arsenic rich parts of the apatite crystal show an 8-fold enrichment in arsenic with respect to the bulk fluid composition but only at an ultra-local scale. Once the calcite is completely consumed, the porous crystal equilibrates with the bulk fluid over a few days because the grain size is much finer and diffusion can keep pace with the equilibration reaction. This study highlights the complexity that can arise from ultra-local fluid composition variations due to rapid

  20. Implications of rupture complexity for hazard assessment and forecasting of local and regional tsunami

    NASA Astrophysics Data System (ADS)

    Müller, Christof; Power, William; Fraser, Stuart; Wang, Xiaoming; Ristau, John

    2014-05-01

    Traditionally hazard assessment for tsunami does not take rupture complexity, i.e. the heterogeneity of the slip distribution across the earthquake rupture interface, into account. The authors have demonstrated that the potential extent of inundation will be significantly underestimated if rupture complexity is ignored. For local tsunami it has also been shown that for a target site a strict proportionality between earthquake moment magnitude and inundation extent does not exist. The main difficulty in including the effects of rupture complexity in Probabilistic Tsunami Hazard Assessment (PTHA) for local and regional tsunami lies in the fact that calculations to full inundation need to solve non-linear wave equations. These calculations are so computationally expensive that simulating a statistically significant number of scenarios becomes impractical. The hazard assessment process thus requires a de-aggregation procedure that can rely on simulations based on the linear wave equations alone, to identify scenarios significant enough to be considered for full inundation modelling. We correlate properties of the offshore wave field derived from linear simulations with the extent of inundation derived from non-linear tsunami simulations, allowing us to reduce non-linear calculations in our hazard assessment to a practical number. The effect of rupture complexity on the tsunami wave field is routinely considered in tsunami forecasting for distant and regional sources. Source models are inverted from DART buoy readings as soon as this information becomes available. However, depending on the location of the earthquake causing the tsunami, DART buoy information will not be provided immediately after the event, which poses a challenge to tsunami forecasting for local and regional sources. We propose a concept of tsunami forecasting for regional tsunami, which also provides probabilistic hazard assessment for the event in question. This approach considers rupture complexity

  1. Pore Scale View of Fluid Displacement Fronts in Porous Media

    NASA Astrophysics Data System (ADS)

    Or, D.; Moebius, F.

    2014-12-01

    The macroscopically smooth and regular motion of fluid fronts in porous media is composed of abrupt pore-scale interfacial jumps involving intense interfacial energy release marked by pressure bursts and acoustic emissions. The characteristics of these pore scale events affect residual phase entrapment and the resulting unsaturated transport properties behind the front. Experimental studies using acoustic emissions technique (AE), rapid imaging, and pressure measurements help characterize pore scale processes during drainage and imbibition in model porous media. Imbibition and drainage produce different AE signatures (obeying a power law). For rapid drainage, AE signals persist long after cessation of front motion indicative of redistribution and interfacial relaxation. Rapid imaging revealed that interfacial jumps exceed mean front velocity and are highly inertial (Re>1000). Imaged pore invasion volumes and pore volumes deduced from waiting times between pressure fluctuations were in remarkable agreement with geometric pores. Differences between invaded volumes and geometrical pores increase with increasing capillary numbers due to shorter pore evacuation times and onset of simultaneous invasion events. A new mechanistic model for interfacial motions through a pore-throat network enabled systematic evaluation of inertia in interfacial dynamics. Results suggest that in contrast to great sensitivity of pore scale dynamics to variations in pore geometry and boundary conditions, inertia exerts only a minor effect on average phase entrapment. Pore scale invasion events paint a complex picture of rapid and inertial motions and provide new insights on mechanisms at displacement fronts essential for improving the macroscopic description of multiphase flow in porous media.

  2. Magnetic localization and orientation of the capsule endoscope based on a random complex algorithm

    PubMed Central

    He, Xiaoqi; Zheng, Zizhao; Hu, Chao

    2015-01-01

    The development of the capsule endoscope has made possible the examination of the whole gastrointestinal tract without much pain. However, there are still some important problems to be solved, among which, one important problem is the localization of the capsule. Currently, magnetic positioning technology is a suitable method for capsule localization, and this depends on a reliable system and algorithm. In this paper, based on the magnetic dipole model as well as magnetic sensor array, we propose nonlinear optimization algorithms using a random complex algorithm, applied to the optimization calculation for the nonlinear function of the dipole, to determine the three-dimensional position parameters and two-dimensional direction parameters. The stability and the antinoise ability of the algorithm is compared with the Levenberg–Marquart algorithm. The simulation and experiment results show that in terms of the error level of the initial guess of magnet location, the random complex algorithm is more accurate, more stable, and has a higher “denoise” capacity, with a larger range for initial guess values. PMID:25914561

  3. Complexity of Low-Frequency BOLD Fluctuations Covaries with Local Connectivity

    PubMed Central

    Anderson, Jeffrey S.; Zielinski, Brandon A.; Nielsen, Jared A.; Ferguson, Michael A.

    2014-01-01

    Very low frequency blood oxygen level dependent (BOLD) fluctuations have emerged as a valuable tool for describing brain anatomy, neuropathology, and development. Such fluctuations exhibit power law frequency dynamics, with largest amplitude at lowest frequencies. The biophysical mechanisms generating such fluctuations are poorly understood. Using publicly available data from 1019 subjects of age 7-30, we show that BOLD fluctuations exhibit temporal complexity that is linearly related to local connectivity (regional homogeneity), consistently and significantly covarying across subjects and across gray matter regions. This relationship persisted independently of covariance with gray matter density or standard deviation of BOLD signal. During late neurodevelopment, BOLD fluctuations were unchanged with age in association cortex while becoming more random throughout the rest of the brain. These data suggest that local interconnectivity may play a key role in establishing the complexity of low frequency BOLD fluctuations underlying functional MRI connectivity. Stable low frequency power dynamics may emerge through segmentation and integration of connectivity during development of distributed large-scale brain networks. PMID:23417795

  4. Learning and inference using complex generative models in a spatial localization task.

    PubMed

    Bejjanki, Vikranth R; Knill, David C; Aslin, Richard N

    2016-01-01

    A large body of research has established that, under relatively simple task conditions, human observers integrate uncertain sensory information with learned prior knowledge in an approximately Bayes-optimal manner. However, in many natural tasks, observers must perform this sensory-plus-prior integration when the underlying generative model of the environment consists of multiple causes. Here we ask if the Bayes-optimal integration seen with simple tasks also applies to such natural tasks when the generative model is more complex, or whether observers rely instead on a less efficient set of heuristics that approximate ideal performance. Participants localized a "hidden" target whose position on a touch screen was sampled from a location-contingent bimodal generative model with different variances around each mode. Over repeated exposure to this task, participants learned the a priori locations of the target (i.e., the bimodal generative model), and integrated this learned knowledge with uncertain sensory information on a trial-by-trial basis in a manner consistent with the predictions of Bayes-optimal behavior. In particular, participants rapidly learned the locations of the two modes of the generative model, but the relative variances of the modes were learned much more slowly. Taken together, our results suggest that human performance in a more complex localization task, which requires the integration of sensory information with learned knowledge of a bimodal generative model, is consistent with the predictions of Bayes-optimal behavior, but involves a much longer time-course than in simpler tasks.

  5. Learning and inference using complex generative models in a spatial localization task.

    PubMed

    Bejjanki, Vikranth R; Knill, David C; Aslin, Richard N

    2016-01-01

    A large body of research has established that, under relatively simple task conditions, human observers integrate uncertain sensory information with learned prior knowledge in an approximately Bayes-optimal manner. However, in many natural tasks, observers must perform this sensory-plus-prior integration when the underlying generative model of the environment consists of multiple causes. Here we ask if the Bayes-optimal integration seen with simple tasks also applies to such natural tasks when the generative model is more complex, or whether observers rely instead on a less efficient set of heuristics that approximate ideal performance. Participants localized a "hidden" target whose position on a touch screen was sampled from a location-contingent bimodal generative model with different variances around each mode. Over repeated exposure to this task, participants learned the a priori locations of the target (i.e., the bimodal generative model), and integrated this learned knowledge with uncertain sensory information on a trial-by-trial basis in a manner consistent with the predictions of Bayes-optimal behavior. In particular, participants rapidly learned the locations of the two modes of the generative model, but the relative variances of the modes were learned much more slowly. Taken together, our results suggest that human performance in a more complex localization task, which requires the integration of sensory information with learned knowledge of a bimodal generative model, is consistent with the predictions of Bayes-optimal behavior, but involves a much longer time-course than in simpler tasks. PMID:26967015

  6. Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon

    PubMed Central

    Kerber, Sarah; Minyem, Jacques C.; Um Boock, Alphonse; Vogel, Moritz; Bayi, Pierre Franklin; Junghanss, Thomas; Brites, Daniela; Harris, Simon R.; Parkhill, Julian; Pluschke, Gerd; Lamelas Cabello, Araceli

    2015-01-01

    Background Mycobacterium ulcerans is the causative agent of the necrotizing skin disease Buruli ulcer (BU), which has been reported from over 30 countries worldwide. The majority of notified patients come from West African countries, such as Côte d’Ivoire, Ghana, Benin and Cameroon. All clinical isolates of M. ulcerans from these countries are closely related and their genomes differ only in a limited number of single nucleotide polymorphisms (SNPs). Methodology/Principal Findings We performed a molecular epidemiological study with clinical isolates from patients from two distinct BU endemic regions of Cameroon, the Nyong and the Mapé river basins. Whole genome sequencing of the M. ulcerans strains from these two BU endemic areas revealed the presence of two phylogenetically distinct clonal complexes. The strains from the Nyong river basin were genetically more diverse and less closely related to the M. ulcerans strain circulating in Ghana and Benin than the strains causing BU in the Mapé river basin. Conclusions Our comparative genomic analysis revealed that M. ulcerans clones diversify locally by the accumulation of SNPs. Case isolates coming from more recently emerging BU endemic areas, such as the Mapé river basin, may be less diverse than populations from longer standing disease foci, such as the Nyong river basin. Exchange of strains between distinct endemic areas seems to be rare and local clonal complexes can be easily distinguished by whole genome sequencing. PMID:26046531

  7. X-ray microtomography application in pore space reservoir rock.

    PubMed

    Oliveira, M F S; Lima, I; Borghi, L; Lopes, R T

    2012-07-01

    Characterization of porosity in carbonate rocks is important in the oil and gas industry since a major hydrocarbons field is formed by this lithology and they have a complex media porous. In this context, this research presents a study of the pore space in limestones rocks by x-ray microtomography. Total porosity, type of porosity and pore size distribution were evaluated from 3D high resolution images. Results show that carbonate rocks has a complex pore space system with different pores types at the same facies.

  8. Hydrogeology and hydrodynamics of coral reef pore waters

    SciTech Connect

    Buddemeier, R.W.; Oberdorfer, J.A.

    1988-06-29

    A wide variety of forces can produce head gradients that drive the flow and advective mixing of internal coral reef pore waters. Oscillatory gradients that produce mixing result from wave and tide action. Sustained gradients result from wave and tide-induced setup and ponding, from currents impinging on the reef structure, from groundwater heads, and from density differenced (temperature or salinity gradients). These gradients and the permeabilities and porosities of reef sediments are such that most macropore environments are dominated by advection rather than diffusion. The various driving forces must be analyzed to determine the individual and combined magnitudes of their effects on a specific reef pore-water system. Pore-water movement controls sediment diagenesis, the exchange of nutrients between sediments and benthos, and coastal/island groundwater resources. Because of the complexity of forcing functions, their interactions with specific local reef environments, experimental studies require careful incorporation of these considerations into their design and interpretation. 8 refs., 3 figs., 1 tab.

  9. A new view of transcriptome complexity and regulation through the lens of local splicing variations

    PubMed Central

    Vaquero-Garcia, Jorge; Barrera, Alejandro; Gazzara, Matthew R; González-Vallinas, Juan; Lahens, Nicholas F; Hogenesch, John B; Lynch, Kristen W; Barash, Yoseph

    2016-01-01

    Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSVs). LSVs capture previously defined types of alternative splicing as well as more complex transcript variations. Building the first genome wide map of LSVs from twelve mouse tissues, we find complex LSVs constitute over 30% of tissue dependent transcript variations and affect specific protein families. We show the prevalence of complex LSVs is conserved in humans and identify hundreds of LSVs that are specific to brain subregions or altered in Alzheimer's patients. Amongst those are novel isoforms in the Camk2 family and a novel poison exon in Ptbp1, a key splice factor in neurogenesis. We anticipate the approach presented here will advance the ability to relate tissue-specific splice variation to genetic variation, phenotype, and disease. DOI: http://dx.doi.org/10.7554/eLife.11752.001 PMID:26829591

  10. Kinetochore-localized BUB-1/BUB-3 complex promotes anaphase onset in C. elegans

    PubMed Central

    Kim, Taekyung; Moyle, Mark W.; Lara-Gonzalez, Pablo; De Groot, Christian; Oegema, Karen

    2015-01-01

    The conserved Bub1/Bub3 complex is recruited to the kinetochore region of mitotic chromosomes, where it initiates spindle checkpoint signaling and promotes chromosome alignment. Here we show that, in contrast to the expectation for a checkpoint pathway component, the BUB-1/BUB-3 complex promotes timely anaphase onset in Caenorhabditis elegans embryos. This activity of BUB-1/BUB-3 was independent of spindle checkpoint signaling but required kinetochore localization. BUB-1/BUB-3 inhibition equivalently delayed separase activation and other events occurring during mitotic exit. The anaphase promotion function required BUB-1’s kinase domain, but not its kinase activity, and this function was independent of the role of BUB-1/BUB-3 in chromosome alignment. These results reveal an unexpected role for the BUB-1/BUB-3 complex in promoting anaphase onset that is distinct from its well-studied functions in checkpoint signaling and chromosome alignment, and suggest a new mechanism contributing to the coordination of the metaphase-to-anaphase transition. PMID:25987605

  11. Electromagnetic vacuum of complex media: Dipole emission versus light propagation, vacuum energy, and local field factors

    SciTech Connect

    Donaire, M.

    2011-02-15

    We offer a unified approach to several phenomena related to the electromagnetic vacuum of a complex medium made of point electric dipoles. To this aim, we apply the linear response theory to the computation of the polarization field propagator and study the spectrum of vacuum fluctuations. The physical distinction among the local density of states which enter the spectra of light propagation, total dipole emission, coherent emission, total vacuum energy, and Schwinger-bulk energy is made clear. Analytical expressions for the spectrum of dipole emission and for the vacuum energy are derived. Their respective relations with the spectrum of external light and with the Schwinger-bulk energy are found. The light spectrum and the Schwinger-bulk energy are determined by the Dyson propagator. The emission spectrum and the total vacuum energy are determined by the polarization propagator. An exact relationship of proportionality between both propagators is found in terms of local field factors. A study of the nature of stimulated emission from a single dipole is carried out. Regarding coherent emission, it contains two components. A direct one which is transferred radiatively and directly from the emitter into the medium and whose spectrum is that of external light. And an indirect one which is radiated by induced dipoles. The induction is mediated by one (and only one) local field factor. Regarding the vacuum energy, we find that in addition to the Schwinger-bulk energy the vacuum energy of an effective medium contains local field contributions proportional to the resonant frequency and to the spectral line width.

  12. Visualization of enzyme activities inside earthworm pores

    NASA Astrophysics Data System (ADS)

    Hoang, Duyen; Razavi, Bahar S.

    2015-04-01

    In extremely dynamic microhabitats as bio-pores made by earthworm, the in situ enzyme activities are assumed as a footprint of complex biotic interactions. Our study focused on the effect of earthworm on the enzyme activities inside bio-pores and visualizing the differences between bio-pores and earthworm-free soil by zymography technique (Spohn and Kuzyakov, 2013). For the first time, we aimed at quantitative imaging of enzyme activities in bio-pores. Lumbricus terrestris L. was placed into transparent box (15×20×15cm). After two weeks when bio-pore systems were formed by earthworms, we visualized in situ enzyme activities of five hydrolytic enzymes (β-glucosidase, cellobiohydrolase, chitinase, xylanase, leucine-aminopeptidase, and phosphatase. Zymography showed higher activity of β-glucosidase, chitinase, xylanase and phosphatase in biopores comparing to bulk soil. However, the differences in activity of cellobiohydrolase and leucine aminopeptidase between bio-pore and bulk soil were less pronounced. This demonstrated an applicability of zymography approach to monitor and to distinguish the in situ activity of hydrolytic enzymes in soil biopores.

  13. The Arabidopsis Nuclear Pore and Nuclear Envelope

    PubMed Central

    Meier, Iris; Brkljacic, Jelena

    2010-01-01

    The nuclear envelope is a double membrane structure that separates the eukaryotic cytoplasm from the nucleoplasm. The nuclear pores embedded in the nuclear envelope are the sole gateways for macromolecular trafficking in and out of the nucleus. The nuclear pore complexes assembled at the nuclear pores are large protein conglomerates composed of multiple units of about 30 different nucleoporins. Proteins and RNAs traffic through the nuclear pore complexes, enabled by the interacting activities of nuclear transport receptors, nucleoporins, and elements of the Ran GTPase cycle. In addition to directional and possibly selective protein and RNA nuclear import and export, the nuclear pore gains increasing prominence as a spatial organizer of cellular processes, such as sumoylation and desumoylation. Individual nucleoporins and whole nuclear pore subcomplexes traffic to specific mitotic locations and have mitotic functions, for example at the kinetochores, in spindle assembly, and in conjunction with the checkpoints. Mutants of nucleoporin genes and genes of nuclear transport components lead to a wide array of defects from human diseases to compromised plant defense responses. The nuclear envelope acts as a repository of calcium, and its inner membrane is populated by functionally unique proteins connected to both chromatin and—through the nuclear envelope lumen—the cytoplasmic cytoskeleton. Plant nuclear pore and nuclear envelope research—predominantly focusing on Arabidopsis as a model—is discovering both similarities and surprisingly unique aspects compared to the more mature model systems. This chapter gives an overview of our current knowledge in the field and of exciting areas awaiting further exploration. PMID:22303264

  14. Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis.

    PubMed

    Zhang, Yi; Nikolovski, Nino; Sorieul, Mathias; Vellosillo, Tamara; McFarlane, Heather E; Dupree, Ray; Kesten, Christopher; Schneider, René; Driemeier, Carlos; Lathe, Rahul; Lampugnani, Edwin; Yu, Xiaolan; Ivakov, Alexander; Doblin, Monika S; Mortimer, Jenny C; Brown, Steven P; Persson, Staffan; Dupree, Paul

    2016-01-01

    As the most abundant biopolymer on Earth, cellulose is a key structural component of the plant cell wall. Cellulose is produced at the plasma membrane by cellulose synthase (CesA) complexes (CSCs), which are assembled in the endomembrane system and trafficked to the plasma membrane. While several proteins that affect CesA activity have been identified, components that regulate CSC assembly and trafficking remain unknown. Here we show that STELLO1 and 2 are Golgi-localized proteins that can interact with CesAs and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. Hence, we have uncovered proteins that regulate CSC assembly in the plant Golgi apparatus. PMID:27277162

  15. S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization.

    PubMed

    Kumar, Manoj; Wightman, Raymond; Atanassov, Ivan; Gupta, Anjali; Hurst, Charlotte H; Hemsley, Piers A; Turner, Simon

    2016-07-01

    Plant cellulose microfibrils are synthesized by a process that propels the cellulose synthase complex (CSC) through the plane of the plasma membrane. How interactions between membranes and the CSC are regulated is currently unknown. Here, we demonstrate that all catalytic subunits of the CSC, known as cellulose synthase A (CESA) proteins, are S-acylated. Analysis of Arabidopsis CESA7 reveals four cysteines in variable region 2 (VR2) and two cysteines at the carboxy terminus (CT) as S-acylation sites. Mutating both the VR2 and CT cysteines permits CSC assembly and trafficking to the Golgi but prevents localization to the plasma membrane. Estimates suggest that a single CSC contains more than 100 S-acyl groups, which greatly increase the hydrophobic nature of the CSC and likely influence its immediate membrane environment. PMID:27387950

  16. Complex Plasmas in Narrow Channels: Impact of Confinement on the Local Order

    SciTech Connect

    Klumov, B. A.

    2008-10-15

    Two-dimensional (2D) and three-dimensional (3D) quasi-equilibrium configurations of a complex (dusty) plasma in narrow channels are investigated using the molecular dynamics simulations for various confining potentials (confinements). The dynamics of the microparticles is described within the framework of a Langevin thermostat with allowance for the pair interaction between charged particles, which is described by a screened Coulomb potential (Yukawa potential). Two types of confinement: the parabolic electrostatic potential and hard elastic wall are considered. It is shown that the confinement strongly affects the crystallization and the local order of the microparticles in the system under consideration; in particular, the appearance of a new quasicrystalline phase induced by the hard wall confinement is revealed in 3D case.

  17. Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis

    PubMed Central

    Zhang, Yi; Nikolovski, Nino; Sorieul, Mathias; Vellosillo, Tamara; McFarlane, Heather E.; Dupree, Ray; Kesten, Christopher; Schneider, René; Driemeier, Carlos; Lathe, Rahul; Lampugnani, Edwin; Yu, Xiaolan; Ivakov, Alexander; Doblin, Monika S.; Mortimer, Jenny C.; Brown, Steven P.; Persson, Staffan; Dupree, Paul

    2016-01-01

    As the most abundant biopolymer on Earth, cellulose is a key structural component of the plant cell wall. Cellulose is produced at the plasma membrane by cellulose synthase (CesA) complexes (CSCs), which are assembled in the endomembrane system and trafficked to the plasma membrane. While several proteins that affect CesA activity have been identified, components that regulate CSC assembly and trafficking remain unknown. Here we show that STELLO1 and 2 are Golgi-localized proteins that can interact with CesAs and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. Hence, we have uncovered proteins that regulate CSC assembly in the plant Golgi apparatus. PMID:27277162

  18. Unexpected Outcomes of Thai Cassava Trade: A Case of Global Complexity and Local Unsustainability

    PubMed Central

    CURRAN, SARA R.; COOKE, ABIGAIL M.

    2014-01-01

    Tracing the Thai cassava (Manihot esculenta) trade network, between 1960 and 2000, offers a compelling example of global complexity at work. The emergence of Thailand’s dominance of world export markets caught the world by surprise. The opening up of a European market for cassava was supposed to be met by Brazilian and Indonesian producers. Instead, Thailand took over the market by 1975. Several factors facilitated this emergence including: entrepreneurial diasporic networks of Thai-Chinese traders, local political economy conditions in both Europe and Thailand, and ecological conditions in Thailand. These same factors also shaped the subsequent timing of the closing of the European market, the emergence of a new industry association, the creation of new cassava products, and the expansion to other markets. Furthermore, the dynamic nature of cassava market yielded equivocal outcomes for both Europe and Thai farmers. PMID:25328444

  19. Learning and inference using complex generative models in a spatial localization task

    PubMed Central

    Bejjanki, Vikranth R.; Knill, David C.; Aslin, Richard N.

    2016-01-01

    A large body of research has established that, under relatively simple task conditions, human observers integrate uncertain sensory information with learned prior knowledge in an approximately Bayes-optimal manner. However, in many natural tasks, observers must perform this sensory-plus-prior integration when the underlying generative model of the environment consists of multiple causes. Here we ask if the Bayes-optimal integration seen with simple tasks also applies to such natural tasks when the generative model is more complex, or whether observers rely instead on a less efficient set of heuristics that approximate ideal performance. Participants localized a “hidden” target whose position on a touch screen was sampled from a location-contingent bimodal generative model with different variances around each mode. Over repeated exposure to this task, participants learned the a priori locations of the target (i.e., the bimodal generative model), and integrated this learned knowledge with uncertain sensory information on a trial-by-trial basis in a manner consistent with the predictions of Bayes-optimal behavior. In particular, participants rapidly learned the locations of the two modes of the generative model, but the relative variances of the modes were learned much more slowly. Taken together, our results suggest that human performance in a more complex localization task, which requires the integration of sensory information with learned knowledge of a bimodal generative model, is consistent with the predictions of Bayes-optimal behavior, but involves a much longer time-course than in simpler tasks. PMID:26967015

  20. The COPII complex and lysosomal VAMP7 determine intracellular Salmonella localization and growth.

    PubMed

    Santos, José Carlos; Duchateau, Magalie; Fredlund, Jennifer; Weiner, Allon; Mallet, Adeline; Schmitt, Christine; Matondo, Mariette; Hourdel, Véronique; Chamot-Rooke, Julia; Enninga, Jost

    2015-12-01

    Salmonella invades epithelial cells and survives within a membrane-bound compartment, the Salmonella-containing vacuole (SCV). We isolated and determined the host protein composition of the SCV at 30 min and 3 h of infection to identify and characterize novel regulators of intracellular bacterial localization and growth. Quantitation of the SCV protein content revealed 392 host proteins specifically enriched at SCVs, out of which 173 associated exclusively with early SCVs, 124 with maturing SCV and 95 proteins during both time-points. Vacuole interactions with endoplasmic reticulum-derived coat protein complex II vesicles modulate early steps of SCV maturation, promoting SCV rupture and bacterial hyper-replication within the host cytosol. On the other hand, SCV interactions with VAMP7-positive lysosome-like vesicles promote Salmonella-induced filament formation and bacterial growth within the late SCV. Our results reveal that the dynamic communication between the SCV and distinct host organelles affects both intracellular Salmonella localization and growth at successive steps of host cell invasion.

  1. Effects of rupture complexity on local tsunami inundation: Implications for probabilistic tsunami hazard assessment by example

    NASA Astrophysics Data System (ADS)

    Mueller, Christof; Power, William; Fraser, Stuart; Wang, Xiaoming

    2015-01-01

    We investigated the influence of earthquake source complexity on the extent of inundation caused by the resulting tsunami. We simulated 100 scenarios with collocated sources of variable slip on the Hikurangi subduction interface in the vicinity of Hawke's Bay and Poverty Bay in New Zealand and investigated the tsunami effects on the cities of Napier and Gisborne. Rupture complexity was found to have a first-order effect on flow depth and inundation extent for local tsunami sources. The position of individual asperities in the slip distribution on the rupture interface control to some extent how severe inundation will be. However, predicting inundation extent in detail from investigating the distribution of slip on the rupture interface proves difficult. Assuming uniform slip on the rupture interface in tsunami models can underestimate the potential impact and extent of inundation. For example, simulation of an Mw 8.7 to Mw 8.8 earthquake with uniform slip reproduced the area that could potentially be inundated by equivalent nonuniform slip events of Mw 8.4. Deaggregation, to establish the contribution of different sources with different slip distributions to the probabilistic hazard, cannot be performed based on magnitude considerations alone. We propose two predictors for inundation severity based on the offshore tsunami wavefield using the linear wave equations in an attempt to keep costly simulations of full inundation to a minimum.

  2. Generalized CNF satisfiability, local reductions and complexity of succinctly specified problems

    SciTech Connect

    Marathe, M.V.; Hunt, H.B. III; Stearns, R.E.; Radhakrishnan, V.

    1995-02-01

    We, study the complexity and efficient approximability of various decision, counting and optimization problems when instances are specified using (1) the 1-dimensional finite periodic narrow specifications of Wanke, (2) the 2-way infinite 1-dimensional narrow periodic (sometimes called dynamic) specifications of Karp and Orlin et al., and (3) the hierarchical specification language of Lengauer et al. We outline how generalized CNF satisfiability problems and local reductions can be used to obtain both hardness and easiness results for a number of decision, counting, optimization and approximate optimization problems when instances are specified as in (1), (2) or (3). As corollaries we obtain a number of new PSPACE-hardness and {number_sign}PSPACE-hardness,9 results and a number of new polynomial time approximation algorithms for natural PSPACE-hard optimization problems. In particular assuming P {ne} PSPACE, we characterize completely the complexities of the generalized CNF satisfiability problems SAT(S) of Schaefer [Sc78], when instances are specified as in (1), (2) or (3).

  3. CIN85 is localized at synapses and forms a complex with S-SCAM via dendrin.

    PubMed

    Kawata, Akira; Iida, Junko; Ikeda, Mitsunobu; Sato, Yuji; Mori, Hiroki; Kansaku, Ai; Sumita, Kazutaka; Fujiwara, Naoyuki; Rokukawa, Chiaki; Hamano, Mamiko; Hirabayashi, Susumu; Hata, Yutaka

    2006-05-01

    Membrane-associated guanylate kinase inverted (MAGI)-1 plays a role as a scaffold at cell junctions in non-neuronal cells, while S-SCAM, its neuronal isoform, is involved in the organization of synapses. A search for MAGI-1-interacting proteins by yeast two-hybrid screening of a kidney cDNA library yielded dendrin. As dendrin was originally reported as a brain-specific postsynaptic protein, we tested the interaction between dendrin and S-SCAM and revealed that dendrin binds to the WW domains of S-SCAM. Dendrin is known to be dendritically translated but its function is largely unknown. To gain insights into the physiological meaning of the interaction, we performed a second yeast two-hybrid screening using dendrin as a bait. We identified CIN85, an endocytic scaffold protein, as a putative dendrin-interactor. Immunocytochemistry and subcellular fractionation analysis supported the synaptic localization of CIN85. The first SH3 domain and the C-terminal region of CIN85 bind to the proline-rich region and the N-terminal region of dendrin, respectively. In vitro experiments suggest that dendrin forms a ternary complex with CIN85 and S-SCAM and that this complex formation facilitates the recruitment of dendrin and S-SCAM to vesicle-like structures where CIN85 is accumulated.

  4. Influence of pore pressure and production-induced changes in pore pressure on in situ stress

    SciTech Connect

    Teufel, L.W.

    1996-02-01

    Knowledge of in situ stress and how stress changes with reservoir depletion and pore pressure drawdown is important in a multi-disciplinary approach to reservoir characterization, reservoir management, and improved oil recovery projects. This report summarizes a compilation of in situ stress data from six fields showing the effects of pore pressure and production-induced changes in pore pressure on the minimum horizontal stress. The in situ stress data and corresponding pore pressure data were obtained from field records of the operating companies and published reports. Horizontal stress was determined from closure pressure data of hydraulic fractures and leak-off tests. The stress measurements clearly demonstrate that the total minimum-horizontal stress is dependent on pore pressure. A decrease in pore pressure either by geologic processes or production of a reservoir will result in a decrease in the total minimum-horizontal stress. The magnitude of changes in stress state with net changes in pore pressure is dependent on local field conditions and cannot be accurately predicted by the uniaxial strain model that is commonly used by the petroleum industry.

  5. Transient carbon isotope changes in complex systems: Finding the global signal, embracing the local signal

    NASA Astrophysics Data System (ADS)

    Bowen, G. J.; Schneider-Mor, A.; Filley, T. R.

    2008-12-01

    Global, transient carbon isotope excursions (CIEs) in the geological record are increasingly invoked as evidence of short-lived changes in carbon fluxes to/from the ocean-atmosphere-biosphere (exogenic) system. Reconstructing the dynamics of carbon cycle perturbation and response during such events requires that the global extent, magnitude, and temporal pattern of carbon isotope change are well understood. Unfortunately, no simple, globally integrated measure of exogenic δ13C change exists in the geological record: during major global perturbations even the best-case candidates such as deep-ocean carbonate δ13C values likely respond to a complex of factors including ocean carbonate chemistry and circulation. Here we consider the utility of organic carbon isotope records from two complex depositional systems common in the geological record, fossil soils and continental margin sediments, which are of interest in terms of their relationship to organic carbon cycling and records of past ecological change. Within both systems changes in ecology, climate, carbon source, residence time, and molecular composition have clear potential to modulate the preserved record of global exogenic δ13C change, compromising 1st-order interpretations of bulk or compound-specific isotopic records. Process-explicit eco- geochemical models, ideally combined with multi-substrate data, provide one approach to the isolation of global δ13C change and identification of local or regional processes reflected in such records. Examples from both systems drawn from ongoing work on the Paleocene-Eocene thermal maximum illustrate the potential pitfalls, as well as opportunities, afforded by coupled data/model assessment of transient δ13C changes in complex systems.

  6. Unstable Pore-Water Flow in Intertidal Wetlands

    NASA Astrophysics Data System (ADS)

    Barry, D. A.; Shen, C.; Li, L.

    2014-12-01

    Salt marshes are important intertidal wetlands strongly influenced by interactions between surface water and groundwater. Bordered by coastal water, the marsh system undergoes cycles of inundation and exposure driven by the tide. This leads to dynamic, complex pore-water flow and solute transport in the marsh soil. Pore-water circulations occur over vastly different spatial and temporal scales with strong link to the marsh topography. These circulations control solute transport between the marsh soil and the tidal creek, and ultimately affect the overall nutrient exchange between the marsh and coastal water. The pore-water flows also dictate the soil condition, particularly aeration, which influences the marsh plant growth. Numerous studies have been carried out to examine the pore-water flow process in the marsh soil driven by tides, focusing on stable flow with the assumption of homogeneity in soil and fluid properties. This assumption, however, is questionable given the actual inhomogeneous conditions in the field. For example, the salinity of surface water in the tidal creek varies temporally and spatially due to the influence of rainfall and evapotranspiration as well as the freshwater input from upland areas to the estuary, creating density gradients across the marsh surface and within the marsh soil. Many marshes possess soil stratigraphy with low-permeability mud typically overlying high-permeability sandy deposits. Macropores such as crab burrows are commonly distributed in salt marsh sediments. All these conditions are prone to the development of non-uniform, unstable preferential pore-water flow in the marsh soil, for example, funnelling and fingering. Here we present results from laboratory experiments and numerical simulations to explore such unstable flow. In particular, the analysis aims to address how the unstable flow modifies patterns of local pore-water movement and solute transport, as well as the overall exchange between the marsh soil and

  7. The pore space scramble

    NASA Astrophysics Data System (ADS)

    Gormally, Alexandra; Bentham, Michelle; Vermeylen, Saskia; Markusson, Nils

    2015-04-01

    Climate change and energy security continue to be the context of the transition to a secure, affordable and low carbon energy future, both in the UK and beyond. This is reflected in for example, binding climate policy targets at the EU level, the introduction of renewable energy targets, and has also led to an increasing interest in Carbon Capture and Storage (CCS) technology with its potential to help mitigate against the effects of CO2 emissions from fossil fuel burning. The UK has proposed a three phase strategy to integrate CCS into its energy system in the long term focussing on off-shore subsurface storage (DECC, 2014). The potential of CCS therefore, raises a number of challenging questions and issues surrounding the long-term storage of CO2 captured and injected into underground spaces and, alongside other novel uses of the subsurface, contributes to opening a new field for discussion on the governance of the subsurface. Such 'novel' uses of the subsurface have lead to it becoming an increasingly contested space in terms of its governance, with issues emerging around the role of ownership, liability and property rights of subsurface pore space. For instance, questions over the legal ownership of pore space have arisen with ambiguity over the legal standpoint of the surface owner and those wanting to utilise the pore space for gas storage, and suggestions of whether there are depths at which legal 'ownership' becomes obsolete (Barton, 2014). Here we propose to discuss this 'pore space scramble' and provide examples of the competing trajectories of different stakeholders, particularly in the off-shore context given its priority in the UK. We also propose to highlight the current ambiguity around property law of pore space in the UK with reference to approaches currently taken in different national contexts. Ultimately we delineate contrasting models of governance to illustrate the choices we face and consider the ethics of these models for the common good

  8. Nuclear Pore Proteins and Cancer

    PubMed Central

    Xu, Songli; Powers, Maureen A.

    2009-01-01

    Nucleocytoplasmic trafficking of macromolecules, a highly specific and tightly regulated process, occurs exclusively through the Nuclear Pore Complex. This immense structure is assembled from approximately 30 proteins, termed nucleoporins. Here we discuss the four nucleoporins that have been linked to cancers, either through elevated expression in tumors (Nup88) or through involvement in chromosomal translocations that encode chimeric fusion proteins (Tpr, Nup98, Nup214). In each case we consider the normal function of the nucleoporin and its translocation partners, as well as what is known about their mechanistic contributions to carcinogenesis, particularly in leukemias. Studies of nucleoporin-linked cancers have revealed novel mechanisms of oncogenesis and. in the future, should continue to expand our understanding of cancer biology. PMID:19577736

  9. Performance of Small Pore Microchannel Plates

    NASA Technical Reports Server (NTRS)

    Siegmund, O. H. W.; Gummin, M. A.; Ravinett, T.; Jelinsky, S. R.; Edgar, M.

    1995-01-01

    Small pore size microchannel plates (MCP's) are needed to satisfy the requirements for future high resolution small and large format detectors for astronomy. MCP's with pore sizes in the range 5 micron to 8 micron are now being manufactured, but they are of limited availability and are of small size. We have obtained sets of Galileo 8 micron and 6.5 micron MCP's, and Philips 6 micron and 7 micron pore MCP's, and compared them to our larger pore MCP Z stacks. We have tested back to back MCP stacks of four of these MCP's and achieved gains greater than 2 x 1O(exp 7) with pulse height distributions of less than 40% FWHM, and background rates of less than 0.3 events sec(exp -1) cm(exp -2). Local counting rates up to approx. 100 events/pore/sec have been attained with little drop of the MCP gain. The bare MCP quantum efficiencies are somewhat lower than those expected, however. Flat field images are characterized by an absence of MCP fixed pattern noise.

  10. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

    Quintero Noda, C.; Shimizu, T.; Ruiz Cobo, B.; Suematsu, Y.; Katsukawa, Y.; Ichimoto, K.

    2016-08-01

    Solar pores are active regions with large magnetic field strengths and apparent simple magnetic configurations. Their properties resemble the ones found for the sunspot umbra although pores do not show penumbra. Therefore, solar pores present themselves as an intriguing phenomenon that is not completely understood. We examine in this work a solar pore observed with Hinode/SP using two state of the art techniques. The first one is the spatial deconvolution of the spectropolarimetric data that allows removing the stray light contamination induced by the spatial point spread function of the telescope. The second one is the inversion of the Stokes profiles assuming local thermodynamic equilibrium that let us to infer the atmospheric physical parameters. After applying these techniques, we found that the spatial deconvolution method does not introduce artefacts, even at the edges of the magnetic structure, where large horizontal gradients are detected on the atmospheric parameters. Moreover, we also describe the physical properties of the magnetic structure at different heights finding that, in the inner part of the solar pore, the temperature is lower than outside, the magnetic field strength is larger than 2 kG and unipolar, and the line-of-sight velocity is almost null. At neighbouring pixels, we found low magnetic field strengths of same polarity and strong downward motions that only occur at the low photosphere, below the continuum optical depth log τ = -1. Finally, we studied the spatial relation between different atmospheric parameters at different heights corroborating the physical properties described before.

  11. Magnetic-resonance pore imaging of nonsymmetric microscopic pore shapes

    NASA Astrophysics Data System (ADS)

    Hertel, Stefan Andreas; Wang, Xindi; Hosking, Peter; Simpson, M. Cather; Hunter, Mark; Galvosas, Petrik

    2015-07-01

    Imaging of the microstructure of porous media such as biological tissue or porous solids is of high interest in health science and technology, engineering and material science. Magnetic resonance pore imaging (MRPI) is a recent technique based on nuclear magnetic resonance (NMR) which allows us to acquire images of the average pore shape in a given sample. Here we provide details on the experimental design, challenges, and requirements of MRPI, including its calibration procedures. Utilizing a laser-machined phantom sample, we present images of microscopic pores with a hemiequilateral triangular shape even in the presence of NMR relaxation effects at the pore walls. We therefore show that MRPI is applicable to porous samples without a priori knowledge about their pore shape and symmetry. Furthermore, we introduce "MRPI mapping," which combines MRPI with conventional magnetic resonance imaging (MRI). This enables one to resolve microscopic pore sizes and shapes spatially, thus expanding the application of MRPI to samples with heterogeneous distributions of pores.

  12. Effects of rupture complexity on local tsunami inundation: Implications for probabilistic tsunami hazard assessment

    NASA Astrophysics Data System (ADS)

    Müller, Christof; Power, William; Fraser, Stuart; Wang, Xiaoming

    2015-04-01

    We investigate the influence of earthquake source complexity on the extent of inundation caused by a resulting tsunami. We simulated 100 scenarios with sources on the Hikurangi subduction-interface in the vicinity of Hawke's Bay/Napier and Poverty Bay/Gisborne (New Zealand). For both target areas rupture complexity was found to have a first order effect on flow depth and inundation extent for the local tsunami sources investigated. The position of individual asperities in the slip distribution on the rupture interface control to some extent how severe inundation will be. However, predicting inundation extent in detail from investigating the distribution of slip on the rupture interface proves difficult. The distribution of inundation extent for one earthquake of given magnitude but different realisations of slip distribution is skewed. The extent of inundation predicted by a uniform distribution of slip on the rupture interface is roughly represented by the median of this distribution. Assuming uniform slip on the rupture interface therefore will underestimate the potential impact and extent of inundation. For example, simulation of an MW 8.7 to MW 8.8 earthquake with uniform slip reproduced the area potentially affected by inundation of an equivalent non-uniform slip event of MW 8.4 for Napier. The extent of inundation does not follow a simple monotonic relationship to the magnitude of the earthquake. Therefore de-aggregation, to establish the contribution of different sources with different slip distributions to the probabilistic hazard, cannot be performed based on magnitude considerations alone. We propose to use parameters of the tsunami wave field measured offshore as predictors for inundation severity to perform de-aggregation based on simulations with the linear wave equations.

  13. Speed and Complexity Characterize Attention Problems in Children with Localization-Related Epilepsy

    PubMed Central

    Berl, Madison; Terwilliger, Virginia; Scheller, Alexandra; Sepeta, Leigh; Walkowiak, Jenifer; Gaillard, William D.

    2015-01-01

    Summary Objective Children with epilepsy (EPI) have a higher rate of ADHD (28–70%) than typically developing (TD) children (5–10%); however, attention is multidimensional. Thus, we aimed to characterize the profile of attention difficulties in children with epilepsy. Methods Seventy-five children with localization-related epilepsy ages 6–16 and 75 age-matched controls were evaluated using multimodal, multidimensional measures of attention including direct performance and parent ratings of attention as well as intelligence testing. We assessed group differences across attention measures, determined if parent rating predicted performance on attention measures, and examined if epilepsy characteristics were associated with attention skills. Results The EPI group performed worse than the TD group on timed and complex attention aspects of attention (p<.05), while performance on simple visual and simple auditory attention tasks was comparable. Children with EPI were 12 times as likely as TD children to have clinically elevated symptoms of inattention as rated by parents, but ratings were a weak predictor of attention performance. Earlier age of onset was associated with slower motor speed (p<.01), but no other epilepsy-related clinical characteristics were associated with attention skills. Significance This study clarifies the nature of the attention problems in pediatric epilepsy, which may be under recognized. Children with EPI had difficulty with complex attention and rapid response, not simple attention. As such, they may not exhibit difficulty until later in primary school when demands increase. Parent report with standard ADHD screening tools may underdetect these higher order attention difficulties. Thus, monitoring through direct neuropsychological performance is recommended. PMID:25940056

  14. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

    Pohlmeier, Andreas; Haber-Pohlmeier, Sabina; Haber, Agnes; Sucre, Oscar; Stingaciu, Laura; Stapf, Siegfried; Blümich, Bernhard

    2010-05-01

    Within Cluster A, Partial Project A1, the pore space exploration by means of Nuclear Magnetic Resonance (NMR) plays a central role. NMR is especially convenient since it probes directly the state and dynamics of the substance of interest: water. First, NMR is applied as relaxometry, where the degree of saturation but also the pore geometry controls the NMR signature of natural porous systems. Examples are presented where soil samples from the Selhausen, Merzenhausen (silt loams), and Kaldenkirchen (sandy loam) test sites are investigated by means of Fast Field Cycling Relaxometry at different degrees of saturation. From the change of the relaxation time distributions with decreasing water content and by comparison with conventional water retention curves we conclude that the fraction of immobile water is characterized by T1 < 5 ms. Moreover, the dependence of the relaxation rate on magnetic field strength allows the identification of 2D diffusion at the interfaces as the mechanism which governs the relaxation process (Pohlmeier et al. 2009). T2 relaxation curves are frequently measured for the rapid characterization of soils by means of the CPMG echo train. Basically, they contain the same information about the pore systems like T1 curves, since mostly the overall relaxation is dominated by surface relaxivity and the surface/volume ratio of the pores. However, one must be aware that T2 relaxation is additionally affected by diffusion in internal gradients, and this can be overcome by using sufficiently short echo times and low magnetic fields (Stingaciu et al. 2009). Second, the logic continuation of conventional relaxation measurements is the 2-dimensional experiment, where prior to the final detection of the CPMG echo train an encoding period is applied. This can be T1-encoding by an inversion pulse, or T2 encoding by a sequence of 90 and 180° pulses. During the following evolution time the separately encoded signals can mix and this reveals information about

  15. Assessing the Stability of a Geologically Complex Slope Where Strong Dykes Locally Act as Reinforcement

    NASA Astrophysics Data System (ADS)

    Lee, S. G.; Hencher, S. R.

    2013-11-01

    This paper presents a case study of aspects of the design of large slope cuttings in complex geological conditions in South Korea. During the original cutting of the slopes to geometries prescribed by Korean standards for rock slopes, several translational slides occurred on daylighting bedding planes. From observation it was evident that away from the areas of distress, some parts of the slopes appeared to be relatively stable, apparently because of the strengthening influence of relatively strong and massive igneous dykes and sills through the sedimentary rock. This paper describes how the geological conditions were assessed and stability analysed, section-by-section, along the road. This was achieved using a form of the method of slices to account for those sections of potential failure surfaces where sliding could occur along bedding and others where failure would necessitate shear through the intrusive igneous rock. Results were checked using UDEC models of critical sections. Following these analyses, recommendations were made for localized additional preventive measures including anchors and drainage.

  16. Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning

    PubMed Central

    Levin, Michael

    2012-01-01

    Establishment of shape during embryonic development, and the maintenance of shape against injury or tumorigenesis, requires constant coordination of cell behaviors toward the patterning needs of the host organism. Molecular cell biology and genetics have made great strides in understanding the mechanisms that regulate cell function. However, generalized rational control of shape is still largely beyond our current capabilities. Significant instructive signals function at long range to provide positional information and other cues to regulate organism-wide systems properties like anatomical polarity and size control. Is complex morphogenesis best understood as the emergent property of local cell interactions, or as the outcome of a computational process that is guided by a physically-encoded map or template of the final goal state? Here I review recent data and molecular mechanisms relevant to morphogenetic fields: large-scale systems of physical properties that have been proposed to store patterning information during embryogenesis, regenerative repair, and cancer suppression that ultimately controls anatomy. Placing special emphasis on the role of endogenous bioelectric signals as an important component of the morphogenetic field, I speculate on novel approaches for the computational modeling and control of these fields with applications to synthetic biology, regenerative medicine, and evolutionary developmental biology. PMID:22542702

  17. N-terminal palmitoylation is required for Toxoplasma gondii HSP20 inner membrane complex localization.

    PubMed

    De Napoli, M G; de Miguel, N; Lebrun, M; Moreno, S N J; Angel, S O; Corvi, M M

    2013-06-01

    Toxoplasma gondii is an obligate intracellular parasite and the causative agent of toxoplasmosis. Protein palmitoylation is known to play roles in signal transduction and in enhancing the hydrophobicity of proteins thus contributing to their membrane association. Global inhibition of protein palmitoylation has been shown to affect T. gondii physiology and invasion of the host cell. However, the proteins affected by this modification have been understudied. This paper shows that the small heat shock protein 20 from T. gondii (TgHSP20) is synthesized as a mature protein in the cytosol and is palmitoylated in three cysteine residues. However, its localization at the inner membrane complex (IMC) is dependent only on N-terminal palmitoylation. Absence or incomplete N-terminal palmitoylation causes TgHSP20 to partially accumulate in a membranous structure. Interestingly, TgHSP20 palmitoylation is not responsible for its interaction with the daughter cells IMCs. Together, our data describe the importance of palmitoylation in protein targeting to the IMC in T. gondii. PMID:23485398

  18. N-terminal palmitoylation is required for Toxoplasma gondii HSP20 inner membrane complex localization

    PubMed Central

    De Napoli, MG; de Miguel, N; Lebrun, M; Moreno, SNJ; Angel, SO; Corvi, MM

    2013-01-01

    Toxoplasma gondii is an obligate intracellular parasite and the causative agent of toxoplasmosis. Protein palmitoylation is known to play roles in signal transduction and in enhancing the hydrophobicity of proteins thus contributing to their membrane association. Global inhibition of protein palmitoylation has been shown to affect T. gondii physiology and invasion of the host cell. However, the proteins affected by this modification have been understudied. This paper shows that the small heat shock protein 20 from T. gondii (TgHSP20) is synthesized as a mature protein in the cytosol and is palmitoylated in three cysteine residues. However, its localization at the inner membrane complex (IMC) is dependent only on N-terminal palmitoylation. Absence or incomplete N-terminal palmitoylation causes TgHSP20 to partially accumulate in a membranous structure. Interestingly, TgHSP20 palmitoylation is not responsible for its interaction with the daughter cells IMCs. Together, our data describe the importance of palmitoylation in protein targeting to the IMC in T. gondii. PMID:23485398

  19. N-terminal palmitoylation is required for Toxoplasma gondii HSP20 inner membrane complex localization.

    PubMed

    De Napoli, M G; de Miguel, N; Lebrun, M; Moreno, S N J; Angel, S O; Corvi, M M

    2013-06-01

    Toxoplasma gondii is an obligate intracellular parasite and the causative agent of toxoplasmosis. Protein palmitoylation is known to play roles in signal transduction and in enhancing the hydrophobicity of proteins thus contributing to their membrane association. Global inhibition of protein palmitoylation has been shown to affect T. gondii physiology and invasion of the host cell. However, the proteins affected by this modification have been understudied. This paper shows that the small heat shock protein 20 from T. gondii (TgHSP20) is synthesized as a mature protein in the cytosol and is palmitoylated in three cysteine residues. However, its localization at the inner membrane complex (IMC) is dependent only on N-terminal palmitoylation. Absence or incomplete N-terminal palmitoylation causes TgHSP20 to partially accumulate in a membranous structure. Interestingly, TgHSP20 palmitoylation is not responsible for its interaction with the daughter cells IMCs. Together, our data describe the importance of palmitoylation in protein targeting to the IMC in T. gondii.

  20. Ancestral major histocompatibility complex DRB genes beget conserved patterns of localized polymorphisms.

    PubMed Central

    Gaur, L K; Nepom, G T

    1996-01-01

    Genes within the major histocompatibility complex (MHC) are characterized by extensive polymorphism within species and also by a remarkable conservation of contemporary human allelic sequences in evolutionarily distant primates. Mechanisms proposed to account for strict nucleotide conservation in the context of highly variable genes include the suggestion that intergenic exchange generates repeated sets of MHC DRB polymorphisms [Gyllensten, U. B., Sundvall, M. & Erlich, H. A. (1991) Proc. Natl. Acad. Sci. USA 88, 3686-3690; Lundberg, A. S. & McDevitt, H. 0. (1992) Proc. Natl. Acad. Sci. USA 89, 6545-6549]. We analyzed over 50 primate MHC DRB sequences, and identified nucleotide elements within macaque and baboon DRB6-like sequences with deletions corresponding to specific exon 2 hypervariable regions, which encode a discrete alpha helical segment of the MHC antigen combining site. This precisely localized deletion provides direct evidence implicating segmental exchange of MHC-encoded DRB gene fragments as one of the evolutionary mechanisms both generating and maintaining MHC diversity. Intergenic exchange at this site may be fundamental to the diversification of immune protection in populations by permitting alteration in the specificity of the MHC that determines the repertoire of antigens bound. Images Fig. 2 PMID:8643583

  1. A single frequency component-based re-estimated MUSIC algorithm for impact localization on complex composite structures

    NASA Astrophysics Data System (ADS)

    Yuan, Shenfang; Bao, Qiao; Qiu, Lei; Zhong, Yongteng

    2015-10-01

    The growing use of composite materials on aircraft structures has attracted much attention for impact monitoring as a kind of structural health monitoring (SHM) method. Multiple signal classification (MUSIC)-based monitoring technology is a promising method because of its directional scanning ability and easy arrangement of the sensor array. However, for applications on real complex structures, some challenges still exist. The impact-induced elastic waves usually exhibit a wide-band performance, giving rise to the difficulty in obtaining the phase velocity directly. In addition, composite structures usually have obvious anisotropy, and the complex structural style of real aircrafts further enhances this performance, which greatly reduces the localization precision of the MUSIC-based method. To improve the MUSIC-based impact monitoring method, this paper first analyzes and demonstrates the influence of measurement precision of the phase velocity on the localization results of the MUSIC impact localization method. In order to improve the accuracy of the phase velocity measurement, a single frequency component extraction method is presented. Additionally, a single frequency component-based re-estimated MUSIC (SFCBR-MUSIC) algorithm is proposed to reduce the localization error caused by the anisotropy of the complex composite structure. The proposed method is verified on a real composite aircraft wing box, which has T-stiffeners and screw holes. Three typical categories of 41 impacts are monitored. Experimental results show that the SFCBR-MUSIC algorithm can localize impact on complex composite structures with an obviously improved accuracy.

  2. Local regeneration of dentin-pulp complex using controlled release of fgf-2 and naturally derived sponge-like scaffolds.

    PubMed

    Kitamura, Chiaki; Nishihara, Tatsuji; Terashita, Masamichi; Tabata, Yasuhiko; Washio, Ayako

    2012-01-01

    Restorative and endodontic procedures have been recently developed in an attempt to preserve the vitality of dental pulp after exposure to external stimuli, such as caries infection or traumatic injury. When damage to dental pulp is reversible, pulp wound healing can proceed, whereas irreversible damage induces pathological changes in dental pulp, eventually requiring its removal. Nonvital teeth lose their defensive abilities and become severely damaged, resulting in extraction. Development of regeneration therapy for the dentin-pulp complex is important to overcome limitations with presently available therapies. Three strategies to regenerate the dentin-pulp complex have been proposed; regeneration of the entire tooth, local regeneration of the dentin-pulp complex from amputated dental pulp, and regeneration of dental pulp from apical dental pulp or periapical tissues. In this paper, we focus on the local regeneration of the dentin-pulp complex by application of exogenous growth factors and scaffolds to amputated dental pulp.

  3. Pore architecture of nanoporous gold and titania by hydrogen thermoporometry

    NASA Astrophysics Data System (ADS)

    Johnston, L. T.; Biener, M. M.; Ye, J. C.; Baumann, T. F.; Kucheyev, S. O.

    2015-07-01

    Nanoporous gold (NPG) and materials derived from it by templating have complex pore architecture that determines their technologically relevant physical properties. Here, we apply high-resolution hydrogen thermoporometry to study the pore structure of NPG and NPG-derived titania nanofoam (TNF). Results reveal complex multimodal pore size distributions for NPG and TNF. The freezing-melting hysteresis is pronounced, with freezing and melting scans having entirely different shapes. Experiments involving partial freeze-melt cycles reveal the lack of direct correlation between individual freezing and melting peaks, pointing to phenomena that are beyond the Gibbs-Thomson formalism. The depression of the average freezing temperature scales linearly with the ratio of the internal surface area (measured by gas sorption) and the total pore volume derived from the density of monoliths. Thermoporometry yields total pore volumes in good agreement with those derived from monolith densities for both NPG and TNF.

  4. Pore dynamics in lipid membranes

    NASA Astrophysics Data System (ADS)

    Gozen, I.; Dommersnes, P.

    2014-09-01

    Transient circular pores can open in plasma membrane of cells due to mechanical stress, and failure to repair such pores lead to cell death. Similar pores in the form of defects also exist among smectic membranes, such as in myelin sheaths or mitochondrial membranes. The formation and growth of membrane defects are associated with diseases, for example multiple sclerosis. A deeper understanding of membrane pore dynamics can provide a more refined picture of membrane integrity-related disease development, and possibly also treatment options and strategies. Pore dynamics is also of great importance regarding healthcare applications such as drug delivery, gene or as recently been implied, cancer therapy. The dynamics of pores significantly differ in stacks which are confined in 2D compared to those in cells or vesicles. In this short review, we will summarize the dynamics of different types of pores that can be observed in biological membranes, which include circular transient, fusion and hemi-fusion pores. We will dedicate a section to floral and fractal pores which were discovered a few years ago and have highly peculiar characteristics. Finally, we will discuss the repair mechanisms of large area pores in conjunction with the current cell membrane repair hypotheses.

  5. Arabidopsis CML38, a Calcium Sensor That Localizes to Ribonucleoprotein Complexes under Hypoxia Stress1[OPEN

    PubMed Central

    McClintock, Carlee; Li, Tian

    2016-01-01

    During waterlogging and the associated oxygen deprivation stress, plants respond by the induction of adaptive programs, including the redirected expression of gene networks toward the synthesis of core hypoxia-response proteins. Among these core response proteins in Arabidopsis (Arabidopsis thaliana) is the calcium sensor CML38, a protein related to regulator of gene silencing calmodulin-like proteins (rgsCaMs). CML38 transcripts are up-regulated more than 300-fold in roots within 6 h of hypoxia treatment. Transfer DNA insertional mutants of CML38 show an enhanced sensitivity to hypoxia stress, with lowered survival and more severe inhibition of root and shoot growth. By using yellow fluorescent protein (YFP) translational fusions, CML38 protein was found to be localized to cytosolic granule structures similar in morphology to hypoxia-induced stress granules. Immunoprecipitation of CML38 from the roots of hypoxia-challenged transgenic plants harboring CML38pro::CML38:YFP followed by liquid chromatography-tandem mass spectrometry analysis revealed the presence of protein targets associated with messenger RNA ribonucleoprotein (mRNP) complexes including stress granules, which are known to accumulate as messenger RNA storage and triage centers during hypoxia. This finding is further supported by the colocalization of CML38 with the mRNP stress granule marker RNA Binding Protein 47 (RBP47) upon cotransfection of Nicotiana benthamiana leaves. Ruthenium Red treatment results in the loss of CML38 signal in cytosolic granules, suggesting that calcium is necessary for stress granule association. These results confirm that CML38 is a core hypoxia response calcium sensor protein and suggest that it serves as a potential calcium signaling target within stress granules and other mRNPs that accumulate during flooding stress responses. PMID:26634999

  6. Local difference measures between complex networks for dynamical system model evaluation.

    PubMed

    Lange, Stefan; Donges, Jonathan F; Volkholz, Jan; Kurths, Jürgen

    2015-01-01

    A faithful modeling of real-world dynamical systems necessitates model evaluation. A recent promising methodological approach to this problem has been based on complex networks, which in turn have proven useful for the characterization of dynamical systems. In this context, we introduce three local network difference measures and demonstrate their capabilities in the field of climate modeling, where these measures facilitate a spatially explicit model evaluation.Building on a recent study by Feldhoff et al. [8] we comparatively analyze statistical and dynamical regional climate simulations of the South American monsoon system [corrected]. types of climate networks representing different aspects of rainfall dynamics are constructed from the modeled precipitation space-time series. Specifically, we define simple graphs based on positive as well as negative rank correlations between rainfall anomaly time series at different locations, and such based on spatial synchronizations of extreme rain events. An evaluation against respective networks built from daily satellite data provided by the Tropical Rainfall Measuring Mission 3B42 V7 reveals far greater differences in model performance between network types for a fixed but arbitrary climate model than between climate models for a fixed but arbitrary network type. We identify two sources of uncertainty in this respect. Firstly, climate variability limits fidelity, particularly in the case of the extreme event network; and secondly, larger geographical link lengths render link misplacements more likely, most notably in the case of the anticorrelation network; both contributions are quantified using suitable ensembles of surrogate networks. Our model evaluation approach is applicable to any multidimensional dynamical system and especially our simple graph difference measures are highly versatile as the graphs to be compared may be constructed in whatever way required. Generalizations to directed as well as edge- and node

  7. Local Difference Measures between Complex Networks for Dynamical System Model Evaluation

    PubMed Central

    Lange, Stefan; Donges, Jonathan F.; Volkholz, Jan; Kurths, Jürgen

    2015-01-01

    A faithful modeling of real-world dynamical systems necessitates model evaluation. A recent promising methodological approach to this problem has been based on complex networks, which in turn have proven useful for the characterization of dynamical systems. In this context, we introduce three local network difference measures and demonstrate their capabilities in the field of climate modeling, where these measures facilitate a spatially explicit model evaluation. Building on a recent study by Feldhoff et al. [1] we comparatively analyze statistical and dynamical regional climate simulations of the South American monsoon system. Three types of climate networks representing different aspects of rainfall dynamics are constructed from the modeled precipitation space-time series. Specifically, we define simple graphs based on positive as well as negative rank correlations between rainfall anomaly time series at different locations, and such based on spatial synchronizations of extreme rain events. An evaluation against respective networks built from daily satellite data provided by the Tropical Rainfall Measuring Mission 3B42 V7 reveals far greater differences in model performance between network types for a fixed but arbitrary climate model than between climate models for a fixed but arbitrary network type. We identify two sources of uncertainty in this respect. Firstly, climate variability limits fidelity, particularly in the case of the extreme event network; and secondly, larger geographical link lengths render link misplacements more likely, most notably in the case of the anticorrelation network; both contributions are quantified using suitable ensembles of surrogate networks. Our model evaluation approach is applicable to any multidimensional dynamical system and especially our simple graph difference measures are highly versatile as the graphs to be compared may be constructed in whatever way required. Generalizations to directed as well as edge- and node

  8. Complexity of Language Ideologies in Transnational Movement: Korean "Jogi Yuhak" Families' Ambivalent Attitudes towards Local Varieties of English in Singapore

    ERIC Educational Resources Information Center

    Bae, So Hee

    2015-01-01

    This paper discusses the complex and competing language ideologies that Korean educational migrant families in Singapore hold about the normativity and legitimacy of English language varieties. During their educational migration in Singapore, Korean families show ambivalent attitudes toward the local variety of English in Singapore, Singlish.…

  9. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework.

    PubMed

    Brand, Sarah L; Fleming, Lora E; Wyatt, Katrina M

    2015-01-01

    Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics) that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW) framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change. PMID:26380358

  10. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework

    PubMed Central

    Brand, Sarah L.; Fleming, Lora E.; Wyatt, Katrina M.

    2015-01-01

    Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics) that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW) framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change. PMID:26380358

  11. Tailoring Healthy Workplace Interventions to Local Healthcare Settings: A Complexity Theory-Informed Workplace of Well-Being Framework.

    PubMed

    Brand, Sarah L; Fleming, Lora E; Wyatt, Katrina M

    2015-01-01

    Many healthy workplace interventions have been developed for healthcare settings to address the consistently low scores of healthcare professionals on assessments of mental and physical well-being. Complex healthcare settings present challenges for the scale-up and spread of successful interventions from one setting to another. Despite general agreement regarding the importance of the local setting in affecting intervention success across different settings, there is no consensus on what it is about a local setting that needs to be taken into account to design healthy workplace interventions appropriate for different local settings. Complexity theory principles were used to understand a workplace as a complex adaptive system and to create a framework of eight domains (system characteristics) that affect the emergence of system-level behaviour. This Workplace of Well-being (WoW) framework is responsive and adaptive to local settings and allows a shared understanding of the enablers and barriers to behaviour change by capturing local information for each of the eight domains. We use the results of applying the WoW framework to one workplace, a UK National Health Service ward, to describe the utility of this approach in informing design of setting-appropriate healthy workplace interventions that create workplaces conducive to healthy behaviour change.

  12. Local stability analysis of discrete-time, continuous-state, complex-valued recurrent neural networks with inner state feedback.

    PubMed

    Mostafa, Mohamad; Teich, Werner G; Lindner, Jürgen

    2014-04-01

    Recurrent neural networks (RNNs) are well known for their capability to minimize suitable cost functions without the need for a training phase. This is possible because they can be Lyapunov stable. Although the global stability analysis has attracted a lot of interest, local stability is desirable for specific applications. In this brief, we investigate the local asymptotical stability of two classes of discrete-time, continuous-state, complex-valued RNNs with parallel update and inner state feedback. We show that many already known results are special cases of the results obtained here. We also generalize some known results from the real-valued case to the complex-valued one. Finally, we investigate the stability in the presence of time-variant activation functions. Complex-valued activation functions in this brief are separable with respect to the real and imaginary parts.

  13. The dielectric properties of water within model transbilayer pores.

    PubMed Central

    Sansom, M S; Smith, G R; Adcock, C; Biggin, P C

    1997-01-01

    Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation. Images FIGURE 1 PMID:9370434

  14. Latent fingermark pore area reproducibility.

    PubMed

    Gupta, A; Buckley, K; Sutton, R

    2008-08-01

    The study of the reproducibility of friction ridge pore detail in fingermarks is a measure of their usefulness in personal identification. Pore area in latent prints developed using cyanoacrylate and ninhydrin were examined and measured by photomicrography using appropriate software tools. The data were analysed statistically and the results showed that pore area is not reproducible in developed latent prints, using either of the development techniques. The results add further support to the lack of reliability of pore area in personal identification. PMID:18617339

  15. The Arabidopsis Wave Complex: Mechanisms Of Localized Actin Polymerization And Growth

    SciTech Connect

    Daniel Szymanski

    2012-10-23

    The objective of this project was to discover the protein complexes and control mechanisms that determine the location of actin filament roadways in plant cells. Our work provided the first molecular description of protein complexes that are converted from inactive complexes to active actin filament nucleators in the cell. These discoveries provided a conceptual framework to control to roadways in plant cells that determine the location and delivery of plant metabolites and storage molecules that are relevant to the bioenergy economy.

  16. Open–closed switching of synthetic tubular pores

    PubMed Central

    Kim, Yongju; Kang, Jiheong; Shen, Bowen; Wang, Yanqiu; He, Ying; Lee, Myongsoo

    2015-01-01

    While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open–closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open–closed motion. PMID:26456695

  17. Calreticulin secures calcium-dependent nuclear pore competency required for cardiogenesis.

    PubMed

    Faustino, Randolph S; Behfar, Atta; Groenendyk, Jody; Wyles, Saranya P; Niederlander, Nicolas; Reyes, Santiago; Puceat, Michel; Michalak, Marek; Terzic, Andre; Perez-Terzic, Carmen

    2016-03-01

    Calreticulin deficiency causes myocardial developmental defects that culminate in an embryonic lethal phenotype. Recent studies have linked loss of this calcium binding chaperone to failure in myofibrillogenesis through an as yet undefined mechanism. The purpose of the present study was to identify cellular processes corrupted by calreticulin deficiency that precipitate dysregulation of cardiac myofibrillogenesis related to acquisition of cardiac phenotype. In an embryonic stem cell knockout model, calreticulin deficit (crt(-/-)) compromised nucleocytoplasmic transport of nuclear localization signal-dependent and independent pathways, disrupting nuclear import of the cardiac transcription factor MEF2C. The expression of nucleoporins and associated nuclear transport proteins in derived crt(-/-) cardiomyocytes revealed an abnormal nuclear pore complex (NPC) configuration. Altered protein content in crt(-/-) cells resulted in remodeled NPC architecture that caused decreased pore diameter and diminished probability of central channel occupancy versus wild type counterparts. Ionophore treatment of impaired calcium handling in crt(-/-) cells corrected nuclear pore microarchitecture and rescued nuclear import resulting in normalized myofibrillogenesis. Thus, calreticulin deficiency alters nuclear pore function and structure, impeding myofibrillogenesis in nascent cardiomyocytes through a calcium dependent mechanism. This essential role of calreticulin in nucleocytoplasmic communication competency ties its regulatory action with proficiency of cardiac myofibrillogenesis essential for proper cardiac development.

  18. A single subunit of a heterotrimeric CCAAT-binding complex carries a nuclear localization signal: piggy back transport of the pre-assembled complex to the nucleus.

    PubMed

    Steidl, Stefan; Tüncher, André; Goda, Hideya; Guder, Corina; Papadopoulou, Natalia; Kobayashi, Tetsuo; Tsukagoshi, Norihiro; Kato, Masashi; Brakhage, Axel A

    2004-09-10

    An unresolved question concerns the nuclear localization of the heterotrimeric CCAAT-binding complex, which is evolutionarily conserved in eukaryotic organisms including fungi, plants and mammals. All three subunits are necessary for DNA binding. In the filamentous fungus Aspergillus nidulans the corresponding complex was designated AnCF (A.nidulans CCAAT-binding factor). AnCF consists of the HapB, HapC and HapE subunits. Here, by using various green fluorescent protein constructs, a nuclear localization signal sequence (NLS) of the HapB protein was identified, outside of the evolutionarily conserved domain. HapB-EGFP was transported into the nucleus in both DeltahapC and DeltahapE strains, indicating that its NLS interacts with the import machinery independently of the other Hap subunits. In contrast, HapC-EGFP did not enter the nucleus in the absence of HapE or HapB. A similar finding was made for HapE-EGFP, which did not localize to the nucleus in the absence of HapC or HapB. Addition of the HapB-NLS to either HapC or HapE led to nuclear localization of the respective protein fusions, indicating that both HapC and HapE lack a functional NLS. Furthermore, these data strongly suggest that HapC and HapE have first to form a heterodimer and can be transported only as a heterodimer via the HapB protein into the nucleus. Therefore, the HapB subunit is the primary cargo for the import machinery, while HapC and HapE are transported to the nucleus only as a heterodimer and in complex with HapB via a piggy back mechanism. This enables the cell to provide equimolar concentrations of all subunits to the nucleus.

  19. Bypassing the need for subcellular localization of a polysaccharide export-anchor complex by overexpressing its protein subunits

    PubMed Central

    Javens, June; Wan, Zhe; Hardy, Gail G.; Brun, Yves V.

    2013-01-01

    Summary Subcellular protein localization is thought to promote protein-protein interaction by increasing the effective concentration and enabling spatial coordination and proper segregation of proteins. We found that protein overexpression allowed the assembly of a productive polysaccharide biosynthesis-export-anchoring complex in the absence of polar localization in Caulobacter crescentus. Polar localization of the holdfast export protein, HfsD, depends on the presence of the other export proteins, HfsA, and HfsB, and on the polar scaffold protein PodJ. The holdfast deficiency of hfsB and podJ mutants is suppressed by the overexpression of export proteins. Restored holdfasts are randomly positioned and co-localize with a holdfast anchor protein in these strains, indicating that functional complexes can form at non-polar sites. Therefore, overexpression of export proteins surpasses a concentration threshold necessary for holdfast synthesis. Restoration of holdfast synthesis at non-polar sites reduces surface adhesion, consistent with the need to spatially coordinate the holdfast synthesis machinery with the flagellum and pili. These strains lack the cell-specific segregation of the holdfast, resulting in the presence of holdfasts in motile daughter cells. Our results highlight the fact that multiple facets of subcellular localization can be coupled to improve the phenotypic outcome of a protein assembly. PMID:23714375

  20. A Visual Screen of Protein Localization during Sporulation Identifies New Components of Prospore Membrane-Associated Complexes in Budding Yeast

    PubMed Central

    Lam, Chien; Santore, Ethan; Lavoie, Elizabeth; Needleman, Leor; Fiacco, Nicholas; Kim, Carey

    2014-01-01

    During ascospore formation in Saccharomyces cerevisiae, the secretory pathway is reorganized to create new intracellular compartments, termed prospore membranes. Prospore membranes engulf the nuclei produced by the meiotic divisions, giving rise to individual spores. The shape and growth of prospore membranes are constrained by cytoskeletal structures, such as septin proteins, that associate with the membranes. Green fluorescent protein (GFP) fusions to various proteins that associate with septins at the bud neck during vegetative growth as well as to proteins encoded by genes that are transcriptionally induced during sporulation were examined for their cellular localization during prospore membrane growth. We report localizations for over 100 different GFP fusions, including over 30 proteins localized to the prospore membrane compartment. In particular, the screen identified IRC10 as a new component of the leading-edge protein complex (LEP), a ring structure localized to the lip of the prospore membrane. Localization of Irc10 to the leading edge is dependent on SSP1, but not ADY3. Loss of IRC10 caused no obvious phenotype, but an ady3 irc10 mutant was completely defective in sporulation and displayed prospore membrane morphologies similar to those of an ssp1 strain. These results reveal the architecture of the LEP and provide insight into the evolution of this membrane-organizing complex. PMID:24390141

  1. Local region statistics combining multi-parameter intensity fitting module for medical image segmentation with intensity inhomogeneity and complex composition

    NASA Astrophysics Data System (ADS)

    Zhao, Fan; Zhao, Jian; Zhao, Wenda; Qu, Feng; Sui, Long

    2016-08-01

    It is difficult to segment medical image with intensity inhomogeneity and complex composition, because most region-based modules relay on the intensity distributions. In this paper, we propose a novel method which uses local region statistics and multi-parameter intensity fitting as well. By replacing the original local region statistics with the novel local region statistics after bias field correction, the effect of intensity inhomogeneity can be eliminated. Then we devise a maximum likelihood energy function based on the distribution of each local region. Segmentation and bias field estimation can be jointly obtained by minimizing the proposed energy function. Furthermore, in order to characterize the features of each local region effectively, two parameters are used to fit the average intensity inside and outside of the counter, respectively. This can well handle the medical images with complex composition, such as larger gray difference even in the same region. Comparisons with several representative methods on synthetic and medical images demonstrate the superiority of the proposed method over other representative algorithms.

  2. Measuring Search Efficiency in Complex Visual Search Tasks: Global and Local Clutter

    ERIC Educational Resources Information Center

    Beck, Melissa R.; Lohrenz, Maura C.; Trafton, J. Gregory

    2010-01-01

    Set size and crowding affect search efficiency by limiting attention for recognition and attention against competition; however, these factors can be difficult to quantify in complex search tasks. The current experiments use a quantitative measure of the amount and variability of visual information (i.e., clutter) in highly complex stimuli (i.e.,…

  3. Environment, Complexity and Professional Training in Agriculture. "Turning Local Learning into Global Knowledge."

    ERIC Educational Resources Information Center

    Prevost, P.

    1994-01-01

    Training farmers to care for the environment must address the complex relationship between farming and the environment. The example of maize weeding in France demonstrates the process of decision making on a farm and the need for teaching about complexity and adopting a pragmatic approach to training. (SK)

  4. Subcellular localization of Regulator of G protein Signaling RGS7 complex in neurons and transfected cells

    PubMed Central

    Liapis, Evangelos; Sandiford, Simone; Wang, Qiang; Gaidosh, Gabriel; Motti, Dario; Levay, Konstantin; Slepak, Vladlen Z.

    2012-01-01

    The R7 family of regulators of G protein signaling (RGS) is involved in many functions of the nervous system. This family includes RGS6, RGS7, RGS9, and RGS11 gene products and is defined by the presence of the characteristic DEP, DHEX, GGL and RGS domains. Here, we examined the subcellular localization of RGS7, the most broadly expressed R7 member. Our immunofluorescence studies of retinal and dorsal root ganglion (DRG) neurons showed that RGS7 concentrated at the plasma membrane of cell bodies, in structures resembling lamellipodia or filopodia along the processes, and at the dendritic tips. At the plasma membrane of DRG neurons, RGS7 co-localized with its known binding partners R7BP, Gαo and Gαq. More than 50% of total RGS7-specific immunofluorescence was present in the cytoplasm, primarily within numerous small puncta that did not co-localize with R7BP. No specific RGS7 or R7BP immunoreactivity was detected in the nuclei. In transfected cell lines, ectopic RGS7 had both diffuse cytosolic and punctate localization patterns. RGS7 also localized in centrosomes. Structure-function analysis showed that the punctate localization was mediated by the DEP/DHEX domains, and centrosomal localization was dependent on the DHEX domain. PMID:22640015

  5. Subcellular localization of regulator of G protein signaling RGS7 complex in neurons and transfected cells.

    PubMed

    Liapis, Evangelos; Sandiford, Simone; Wang, Qiang; Gaidosh, Gabriel; Motti, Dario; Levay, Konstantin; Slepak, Vladlen Z

    2012-08-01

    The R7 family of regulators of G protein signaling (RGS) is involved in many functions of the nervous system. This family includes RGS6, RGS7, RGS9, and RGS11 gene products and is defined by the presence of the characteristic first found in Disheveled, Egl-10, Pleckstrin (DEP), DEP helical extension (DHEX), Gγ-like, and RGS domains. Herein, we examined the subcellular localization of RGS7, the most broadly expressed R7 member. Our immunofluorescence studies of retinal and dorsal root ganglion neurons showed that RGS7 concentrated at the plasma membrane of cell bodies, in structures resembling lamellipodia or filopodia along the processes, and at the dendritic tips. At the plasma membrane of dorsal root ganglia neurons, RGS7 co-localized with its known binding partners R7 RGS binding protein (R7BP), Gαo, and Gαq. More than 50% of total RGS7-specific immunofluorescence was present in the cytoplasm, primarily within numerous small puncta that did not co-localize with R7BP. No specific RGS7 or R7BP immunoreactivity was detected in the nuclei. In transfected cell lines, ectopic RGS7 had both diffuse cytosolic and punctate localization patterns. RGS7 also localized in centrosomes. Structure-function analysis showed that the punctate localization was mediated by the DEP/DHEX domains, and centrosomal localization was dependent on the DHEX domain.

  6. Characterizing 3-D flow velocity in evolving pore networks driven by CaCO3 precipitation and dissolution

    NASA Astrophysics Data System (ADS)

    Chojnicki, K. N.; Yoon, H.; Martinez, M. J.

    2015-12-01

    Understanding reactive flow in geomaterials is important for optimizing geologic carbon storage practices, such as using pore space efficiently. Flow paths can be complex in large degrees of geologic heterogeneities across scales. In addition, local heterogeneity can evolve as reactive transport processes alter the pore-scale morphology. For example, dissolved carbon dioxide may react with minerals in fractured rocks, confined aquifers, or faults, resulting in heterogeneous cementation (and/or dissolution) and evolving flow conditions. Both path and flow complexities are important and poorly characterized, making it difficult to determine their evolution with traditional 2-D transport models. Here we characterize the development of 3-D pore-scale flow with an evolving pore configuration due to calcium carbonate (CaCO3) precipitation and dissolution. A simple pattern of a microfluidic pore network is used initially and pore structures will become more complex due to precipitation and dissolution processes. At several stages of precipitation and dissolution, we directly visualize 3-D velocity vectors using micro particle image velocimetry and a laser scanning confocal microscope. Measured 3-D velocity vectors are then compared to 3-D simulated flow fields which will be used to simulate reactive transport. Our findings will highlight the importance of the 3-D flow dynamics and its impact on estimating reactive surface area over time. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Award Number DE-SC0001114.

  7. Robust and low complexity localization algorithm based on head-related impulse responses and interaural time difference.

    PubMed

    Wan, Xinwang; Liang, Juan

    2013-01-01

    This article introduces a biologically inspired localization algorithm using two microphones, for a mobile robot. The proposed algorithm has two steps. First, the coarse azimuth angle of the sound source is estimated by cross-correlation algorithm based on interaural time difference. Then, the accurate azimuth angle is obtained by cross-channel algorithm based on head-related impulse responses. The proposed algorithm has lower computational complexity compared to the cross-channel algorithm. Experimental results illustrate that the localization performance of the proposed algorithm is better than those of the cross-correlation and cross-channel algorithms. PMID:23298016

  8. Localization and Function of Pals1-associated Tight Junction Protein in Drosophila Is Regulated by Two Distinct Apical Complexes.

    PubMed

    Sen, Arnab; Sun, Rui; Krahn, Michael P

    2015-05-22

    The transmembrane protein Crumbs (Crb) and its intracellular adaptor protein Pals1 (Stardust, Sdt in Drosophila) play a crucial role in the establishment and maintenance of apical-basal polarity in epithelial cells in various organisms. In contrast, the multiple PDZ domain-containing protein Pals1-associated tight junction protein (PATJ), which has been described to form a complex with Crb/Sdt, is not essential for apical basal polarity or for the stability of the Crb/Sdt complex in the Drosophila epidermis. Here we show that, in the embryonic epidermis, Sdt is essential for the correct subcellular localization of PATJ in differentiated epithelial cells but not during cellularization. Consistently, the L27 domain of PATJ is crucial for the correct localization and function of the protein. Our data further indicate that the four PDZ domains of PATJ function, to a large extent, in redundancy, regulating the function of the protein. Interestingly, the PATJ-Sdt heterodimer is not only recruited to the apical cell-cell contacts by binding to Crb but depends on functional Bazooka (Baz). However, biochemical experiments show that PATJ associates with both complexes, the Baz-Sdt and the Crb-Sdt complex, in the mature epithelium of the embryonic epidermis, suggesting a role of these two complexes for the function of PATJ during the development of Drosophila.

  9. Localization and Function of Pals1-associated Tight Junction Protein in Drosophila Is Regulated by Two Distinct Apical Complexes*

    PubMed Central

    Sen, Arnab; Sun, Rui; Krahn, Michael P.

    2015-01-01

    The transmembrane protein Crumbs (Crb) and its intracellular adaptor protein Pals1 (Stardust, Sdt in Drosophila) play a crucial role in the establishment and maintenance of apical-basal polarity in epithelial cells in various organisms. In contrast, the multiple PDZ domain-containing protein Pals1-associated tight junction protein (PATJ), which has been described to form a complex with Crb/Sdt, is not essential for apical basal polarity or for the stability of the Crb/Sdt complex in the Drosophila epidermis. Here we show that, in the embryonic epidermis, Sdt is essential for the correct subcellular localization of PATJ in differentiated epithelial cells but not during cellularization. Consistently, the L27 domain of PATJ is crucial for the correct localization and function of the protein. Our data further indicate that the four PDZ domains of PATJ function, to a large extent, in redundancy, regulating the function of the protein. Interestingly, the PATJ-Sdt heterodimer is not only recruited to the apical cell-cell contacts by binding to Crb but depends on functional Bazooka (Baz). However, biochemical experiments show that PATJ associates with both complexes, the Baz-Sdt and the Crb-Sdt complex, in the mature epithelium of the embryonic epidermis, suggesting a role of these two complexes for the function of PATJ during the development of Drosophila. PMID:25847234

  10. Effect of pore pressure buildup on slowness of rupture propagation

    NASA Astrophysics Data System (ADS)

    Ougier-Simonin, A.; Zhu, W.

    2015-12-01

    Pore fluid pressure is known to play an important role in brittle fracture initiation and propagation, yet the underlying mechanisms remain unclear. We conducted triaxial experiments on saturated porous sandstones to investigate effects of pore pressure buildup on the slowness of shear rupture propagation at different confining pressures. At low to intermediate confinements, rocks fail by brittle faulting, and pore pressure buildup causes a reduction in rock's shear strength but does not induce measurable differences in slip behavior. When the confinement is high enough to prohibit dynamic faulting, rocks fail in the brittle-ductile transitional regime. In the transitional regime, pore pressure buildup promotes slip instability on an otherwise stably sliding fracture. Compared to those observed in the brittle regime, the slip rate, stress drop, and energy dissipated during rupture propagation with concurrent pore pressure buildup in the transitional regime are distinctively different. When decreasing confining pressure instead, the slip behavior resembles the ones of the brittle regime, emphasizing how the observed slowness is related to excess pore pressure beyond the effective pressure phenomenon. Analysis of the mechanical data using existing theoretical models confirms these observations. Quantitative microstructural analyses reveal that increasing pore pressure lessens the dilatancy hardening during failure, thus enhances slip along the localized zone in the transitional regime. Our experimental results suggest that pore pressure buildup induces slow slip in the transitional regime, and slip rates along a shear fracture may vary considerably depending on effective stress states.

  11. Sound source localization and speech understanding in complex listening environments by single-sided deaf listeners after cochlear implantation

    PubMed Central

    Zeitler, Daniel M.; Dorman, Michael F.; Natale, Sarah J.; Loiselle, Louise; Yost, William A.; Gifford, Rene H.

    2015-01-01

    Objective To assess improvements in sound source localization and speech understanding in complex listening environments following unilateral cochlear implantation for single-sided deafness (SSD). Study Design Non-randomized, open, prospective case series Setting Tertiary referral center Patients Nine subjects with a unilateral cochlear implant (CI) for SSD (SSD-CI) were tested. Reference groups for the task of sound source localization included young (n=45) and older (n=12) normal hearing (NH) subjects and 27 bilateral CI (BCI) subjects. Intervention Unilateral cochlear implantation Main outcome measures Sound source localization was tested with 13 loudspeakers in a 180 arc in front of the subject. Speech understanding was tested with the subject seated in an 8-loudspeaker sound system arrayed in a 360-degree pattern. Directionally appropriate noise, originally recorded in a restaurant, was played from each loudspeaker. Speech understanding in noise was tested using the Azbio sentence test and sound source localization quantified using root mean square error. Results All CI subjects showed poorer-than-normal sound source localization. SSD-CI subjects showed a bimodal distribution of scores - six subjects had scores near the mean of those obtained by BCI subjects, while three had scores just outside the 95th percentile of NH listeners. Speech understanding improved significantly in the restaurant environment when the signal was presented to the side of the CI. Conclusions Cochlear implantation for SSD can offer improved speech understanding in complex listening environments and improved sound source localization in both children and adults. On tasks of sound source localization, SSD-CI patients typically perform as well as BCI patients and, in some cases, achieve scores at the upper boundary of normal performance. PMID:26375967

  12. Effect of Radiotherapy Planning Complexity on Survival of Elderly Patients With Unresected Localized Lung Cancer

    SciTech Connect

    Park, Chang H.; Bonomi, Marcelo; Cesaretti, Jamie; Neugut, Alfred I.; Wisnivesky, Juan P.

    2011-11-01

    Purpose: To evaluate whether complex radiotherapy (RT) planning was associated with improved outcomes in a cohort of elderly patients with unresected Stage I-II non-small-cell lung cancer (NSCLC). Methods and Materials: Using the Surveillance, Epidemiology, and End Results registry linked to Medicare claims, we identified 1998 patients aged >65 years with histologically confirmed, unresected stage I-II NSCLC. Patients were classified into an intermediate or complex RT planning group using Medicare physician codes. To address potential selection bias, we used propensity score modeling. Survival of patients who received intermediate and complex simulation was compared using Cox regression models adjusting for propensity scores and in a stratified and matched analysis according to propensity scores. Results: Overall, 25% of patients received complex RT planning. Complex RT planning was associated with better overall (hazard ratio 0.84; 95% confidence interval, 0.75-0.95) and lung cancer-specific (hazard ratio 0.81; 95% confidence interval, 0.71-0.93) survival after controlling for propensity scores. Similarly, stratified and matched analyses showed better overall and lung cancer-specific survival of patients treated with complex RT planning. Conclusions: The use of complex RT planning is associated with improved survival among elderly patients with unresected Stage I-II NSCLC. These findings should be validated in prospective randomized controlled trials.

  13. Minority business bidding for local government contracts: the complexity of availability.

    PubMed

    Bangs, Ralph L; Murrell, Audrey; Constance-Huggins, Monique

    2007-01-01

    While minority-business enterprises (MBEs) have gained some access to local government contracts during the last three decades, these firms continue to receive a small share of local government contract spending relative to the number of available firms. Researchers have suggested two general explanations for the low representation of MBEs in contract awards: (1) lack of qualifications and capacity among MBEs, and (2) public and private discrimination against MBEs in contracting processes. This study on prime contract opportunities in a Northern central city and county with a large minority population finds that low bid rates greatly contribute to the low MBE shares of prime contracts and that bidding is reduced by both local government processes and characteristics of the firms. Some implications of these findings are that local governments need to: (1) monitor MBE shares of prime contract bids by size of contract and use share of bids as one measure of program and organizational effectiveness; (2) identify MBEs that are qualified for prime contracts and encourage and help interested firms to submit competitive bids; and (3) ensure that local government policies and practices do not diminish access to information about prime contract opportunities for qualified and interested minority firms. Another implication is that bidders lists should not be a primary basis for determining MBE availability, since many qualified and interested MBEs do not bid because of perceived barriers in local government.

  14. Pore Structure and the Low Frequency Permittivity of Sea Ice

    NASA Astrophysics Data System (ADS)

    O'Sadnick, M.; Ingham, M.; Eicken, H.

    2014-12-01

    Field and laboratory measurements of the dielectric permittivity of first-year sea ice both show that below a frequency of about 10 Hz the real part of the relative permittivity (ɛ') increases with decreasing frequency. Field measurements in Barrow, Alaska and McMurdo Sound suggest that this rise in low frequency ɛ' steepens as the ice warms, and is confined primarily to the upper 0.50m of the ice cover as it approaches maximum thickness. We propose that this behaviour may be related to membrane polarization occurring in the pore structure within the ice. With ice-liquid interfaces carrying a net charge, an electric double layer forms within the brine filled pores. Polarization occurs at grain boundaries, intragranular films and "necks" in the pore structure where the effective thickness of the double layer approaches the width of the pore resulting in differential transport of ions. This process is dependent on both the characteristic lengths and radii of pores relative to the length and radii of the "necks" or the geometry of inter/intragranular brine layers. By representing the measured dielectric permittivity in terms of a Cole-Cole model it is possible to show that the distribution of pore sizes evolves with temperature. Derived values of complex conductivity are also examined in relationship to the temporal evolution of pore geometry including smoothness of the pore-ice interface.

  15. Dynamic pore-pressure fluctuations in rapidly shearing granular materials

    USGS Publications Warehouse

    Iverson, R.M.; LaHusen, R.G.

    1989-01-01

    Results from two types of experiments show that intergranular pore pressures fluctuated dynamically during rapid, steady shear deformation of water-saturated granular materials. During some fluctuations, the pore water locally supported all normal and shear stresses, while grain-contact stresses transiently fell to zero. Fluctuations also propagated outward from the shear zone; this process modifies grain-contact stresses in adjacent areas and potentially instigates shear-zone growth.

  16. Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome–Mitochondria Interactions through the ERMES Complex

    PubMed Central

    Mattiazzi Ušaj, M.; Brložnik, M.; Kaferle, P.; Žitnik, M.; Wolinski, H.; Leitner, F.; Kohlwein, S.D.; Zupan, B.; Petrovič, U.

    2015-01-01

    Pex11 is a peroxin that regulates the number of peroxisomes in eukaryotic cells. Recently, it was found that a mutation in one of the three mammalian paralogs, PEX11β, results in a neurological disorder. The molecular function of Pex11, however, is not known. Saccharomyces cerevisiae Pex11 has been shown to recruit to peroxisomes the mitochondrial fission machinery, thus enabling proliferation of peroxisomes. This process is essential for efficient fatty acid β-oxidation. In this study, we used high-content microscopy on a genome-wide scale to determine the subcellular localization pattern of yeast Pex11 in all non-essential gene deletion mutants, as well as in temperature-sensitive essential gene mutants. Pex11 localization and morphology of peroxisomes was profoundly affected by mutations in 104 different genes that were functionally classified. A group of genes encompassing MDM10, MDM12 and MDM34 that encode the mitochondrial and cytosolic components of the ERMES complex was analyzed in greater detail. Deletion of these genes caused a specifically altered Pex11 localization pattern, whereas deletion of MMM1, the gene encoding the fourth, endoplasmic-reticulum-associated component of the complex, did not result in an altered Pex11 localization or peroxisome morphology phenotype. Moreover, we found that Pex11 and Mdm34 physically interact and that Pex11 plays a role in establishing the contact sites between peroxisomes and mitochondria through the ERMES complex. Based on these results, we propose that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11. PMID:25769804

  17. Genome-Wide Localization Study of Yeast Pex11 Identifies Peroxisome-Mitochondria Interactions through the ERMES Complex.

    PubMed

    Mattiazzi Ušaj, M; Brložnik, M; Kaferle, P; Žitnik, M; Wolinski, H; Leitner, F; Kohlwein, S D; Zupan, B; Petrovič, U

    2015-06-01

    Pex11 is a peroxin that regulates the number of peroxisomes in eukaryotic cells. Recently, it was found that a mutation in one of the three mammalian paralogs, PEX11β, results in a neurological disorder. The molecular function of Pex11, however, is not known. Saccharomyces cerevisiae Pex11 has been shown to recruit to peroxisomes the mitochondrial fission machinery, thus enabling proliferation of peroxisomes. This process is essential for efficient fatty acid β-oxidation. In this study, we used high-content microscopy on a genome-wide scale to determine the subcellular localization pattern of yeast Pex11 in all non-essential gene deletion mutants, as well as in temperature-sensitive essential gene mutants. Pex11 localization and morphology of peroxisomes was profoundly affected by mutations in 104 different genes that were functionally classified. A group of genes encompassing MDM10, MDM12 and MDM34 that encode the mitochondrial and cytosolic components of the ERMES complex was analyzed in greater detail. Deletion of these genes caused a specifically altered Pex11 localization pattern, whereas deletion of MMM1, the gene encoding the fourth, endoplasmic-reticulum-associated component of the complex, did not result in an altered Pex11 localization or peroxisome morphology phenotype. Moreover, we found that Pex11 and Mdm34 physically interact and that Pex11 plays a role in establishing the contact sites between peroxisomes and mitochondria through the ERMES complex. Based on these results, we propose that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11.

  18. DNA Ends Alter the Molecular Composition and Localization of Ku Multicomponent Complexes*

    PubMed Central

    Adelmant, Guillaume; Calkins, Anne S.; Garg, Brijesh K.; Card, Joseph D.; Askenazi, Manor; Miron, Alex; Sobhian, Bijan; Zhang, Yi; Nakatani, Yoshihiro; Silver, Pamela A.; Iglehart, J. Dirk; Marto, Jarrod A.; Lazaro, Jean-Bernard

    2012-01-01

    The Ku heterodimer plays an essential role in non-homologous end-joining and other cellular processes including transcription, telomere maintenance and apoptosis. While the function of Ku is regulated through its association with other proteins and nucleic acids, the specific composition of these macromolecular complexes and their dynamic response to endogenous and exogenous cellular stimuli are not well understood. Here we use quantitative proteomics to define the composition of Ku multicomponent complexes and demonstrate that they are dramatically altered in response to UV radiation. Subsequent biochemical assays revealed that the presence of DNA ends leads to the substitution of RNA-binding proteins with DNA and chromatin associated factors to create a macromolecular complex poised for DNA repair. We observed that dynamic remodeling of the Ku complex coincided with exit of Ku and other DNA repair proteins from the nucleolus. Microinjection of sheared DNA into live cells as a mimetic for double strand breaks confirmed these findings in vivo. PMID:22535209

  19. Changes in the localization of the Saccharomyces cerevisiae anaphase-promoting complex upon microtubule depolymerization and spindle checkpoint activation.

    PubMed Central

    Melloy, Patricia G; Holloway, Sandra L

    2004-01-01

    The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase in the ubiquitin-mediated proteolysis pathway (UMP). To understand how the APC/C was targeted to its substrates, we performed a detailed analysis of one of the APC/C components, Cdc23p. In live cells, Cdc23-GFP localized to punctate nuclear spots surrounded by homogenous nuclear signal throughout the cell cycle. These punctate spots colocalized with two outer kinetochore proteins, Slk19p and Okp1p, but not with the spindle pole body protein, Spc42p. In late anaphase, the Cdc23-GFP was also visualized along the length of the mitotic spindle. We hypothesized that spindle checkpoint activation may affect the APC/C nuclear spot localization. Localization of Cdc23-GFP was disrupted upon nocodazole treatment in the kinetochore mutant okp1-5 and in the cdc20-1 mutant. Cdc23-GFP nuclear spot localization was not affected in the ndc10-1 mutant, which is defective in spindle checkpoint function. Additional studies using a mad2Delta strain revealed a microtubule dependency of Cdc23-GFP spot localization, whether or not the checkpoint response was activated. On the basis of these data, we conclude that Cdc23p localization was dependent on microtubules and was affected by specific types of kinetochore disruption. PMID:15280225

  20. The Cauchy Problem in Local Spaces for the Complex Ginzburg-Landau EquationII. Contraction Methods

    NASA Astrophysics Data System (ADS)

    Ginibre, J.; Velo, G.

    We continue the study of the initial value problem for the complex Ginzburg-Landau equation (with a > 0, b > 0, g>= 0) in initiated in a previous paper [I]. We treat the case where the initial data and the solutions belong to local uniform spaces, more precisely to spaces of functions satisfying local regularity conditions and uniform bounds in local norms, but no decay conditions (or arbitrarily weak decay conditions) at infinity in . In [I] we used compactness methods and an extended version of recent local estimates [3] and proved in particular the existence of solutions globally defined in time with local regularity of the initial data corresponding to the spaces Lr for r>= 2 or H1. Here we treat the same problem by contraction methods. This allows us in particular to prove that the solutions obtained in [I] are unique under suitable subcriticality conditions, and to obtain for them additional regularity properties and uniform bounds. The method extends some of those previously applied to the nonlinear heat equation in global spaces to the framework of local uniform spaces.

  1. The effect of brain lesions on sound localization in complex acoustic environments.

    PubMed

    Zündorf, Ida C; Karnath, Hans-Otto; Lewald, Jörg

    2014-05-01

    Localizing sound sources of interest in cluttered acoustic environments--as in the 'cocktail-party' situation--is one of the most demanding challenges to the human auditory system in everyday life. In this study, stroke patients' ability to localize acoustic targets in a single-source and in a multi-source setup in the free sound field were directly compared. Subsequent voxel-based lesion-behaviour mapping analyses were computed to uncover the brain areas associated with a deficit in localization in the presence of multiple distracter sound sources rather than localization of individually presented sound sources. Analyses revealed a fundamental role of the right planum temporale in this task. The results from the left hemisphere were less straightforward, but suggested an involvement of inferior frontal and pre- and postcentral areas. These areas appear to be particularly involved in the spectrotemporal analyses crucial for effective segregation of multiple sound streams from various locations, beyond the currently known network for localization of isolated sound sources in otherwise silent surroundings.

  2. Polo kinase regulates the localization and activity of the chromosomal passenger complex in meiosis and mitosis in Drosophila melanogaster.

    PubMed

    Carmena, Mar; Lombardia, Miguel Ortiz; Ogawa, Hiromi; Earnshaw, William C

    2014-11-01

    Cell cycle progression is regulated by members of the cyclin-dependent kinase (CDK), Polo and Aurora families of protein kinases. The levels of expression and localization of the key regulatory kinases are themselves subject to very tight control. There is increasing evidence that crosstalk between the mitotic kinases provides for an additional level of regulation. We have previously shown that Aurora B activates Polo kinase at the centromere in mitosis, and that the interaction between Polo and the chromosomal passenger complex (CPC) component INCENP is essential in this activation. In this report, we show that Polo kinase is required for the correct localization and activity of the CPC in meiosis and mitosis. Study of the phenotype of different polo allele combinations compared to the effect of chemical inhibition revealed significant differences in the localization and activity of the CPC in diploid tissues. Our results shed new light on the mechanisms that control the activity of Aurora B in meiosis and mitosis.

  3. The influence of electric field on the global and local reactivity descriptors: reactivity and stability of weakly bonded complexes.

    PubMed

    Kar, Rahul; Chandrakumar, K R S; Pal, Sourav

    2007-01-18

    The response of the global and local reactivity density-based descriptors (chemical potential, hardness, softness, Fukui function, and local softness) in the presence of external electric field has been studied for some of the simple prototype molecular systems. In addition to the analysis on the reactivity of these systems, the influence of the electric field on the interaction energy of the complexes formed by these systems has also been studied using the recently proposed semiquantitative model based on the local hard-soft acid-base principle. By using the inverse relationship between the global hardness and softness parameters, a simple relationship is obtained for the variation of hardness in terms of the Fukui function under the external electric field. It is shown that the increase in the hardness values for a particular system in the presence of external field does not necessarily imply that the reactivity of the system would be deactivated or vice versa. PMID:17214475

  4. Zinc(II)-Thiosemicarbazone Complexes Are Localized to the Lysosomal Compartment Where They Transmetallate with Copper Ions to Induce Cytotoxicity.

    PubMed

    Stacy, Alexandra E; Palanimuthu, Duraippandi; Bernhardt, Paul V; Kalinowski, Danuta S; Jansson, Patric J; Richardson, Des R

    2016-05-26

    As the di-2-pyridylketone thiosemicarbazone (DpT) and 2-acetylpyridine thiosemicarbazone (ApT) series show potent antitumor activity in vitro and in vivo, we synthesized their fluorescent zinc(II) complexes to assess their intracellular distribution. The Zn(II) complexes generally showed significantly greater cytotoxicity than the thiosemicarbazones alone in several tumor cell-types. Notably, specific structure-activity relationships demonstrated the importance of the di-2-pyridyl pharmacophore in their activity. Confocal fluorescence imaging and live cell microscopy showed that the Zn(II) complex of our lead compound, di-2-pyridylketone 4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC), which is scheduled to enter clinical trials, was localized to lysosomes. Under lysosomal conditions, the Zn(II) complexes were shown to transmetallate with copper ions, leading to redox-active copper complexes that induced lysosomal membrane permeabilization (LMP) and cytotoxicity. This is the first study to demonstrate direct lysosomal targeting of our novel Zn(II)-thiosemicarbazone complexes that mediate their activity via transmetalation with copper ions and LMP. PMID:27023111

  5. Vaginal inserts based on chitosan and carboxymethylcellulose complexes for local delivery of chlorhexidine: preparation, characterization and antimicrobial activity.

    PubMed

    Bigucci, Federica; Abruzzo, Angela; Vitali, Beatrice; Saladini, Bruno; Cerchiara, Teresa; Gallucci, Maria Caterina; Luppi, Barbara

    2015-01-30

    The aim of this work was to prepare vaginal inserts based on chitosan/carboxymethylcellulose polyelectrolyte complexes for local delivery of chlorhexidine digluconate. Complexes were prepared with different chitosan/carboxymethylcellulose molar ratios at a pH value close to pKa interval of the polymers and were characterized in terms of physico-chemical properties, complexation yield and drug loading. Then complexes were used to prepare inserts as vaginal dosage forms and their physical handling, morphology, water-uptake ability and drug release properties as well as antimicrobial activity toward Candida albicans and Escherichia coli were evaluated. Results confirmed the ionic interaction between chitosan and carboxymethylcellulose and the influence of the charge amount on the complexation yield. Complexes were characterized by high values of drug loading and showed increasing water-uptake ability with the increase of carboxymethylcellulose amount. The selection of appropriate chitosan/carboxymethylcellulose molar ratios allowed to obtain cone-like shaped solid inserts, easy to handle and able to hydrate releasing the drug over time. Finally, the formulated inserts showed antimicrobial activity against common pathogens responsible for vaginal infections.

  6. Cloning, characterization and sub-cellular localization of gamma subunit of T-complex protein-1 (chaperonin) from Leishmania donovani.

    PubMed

    Bhaskar; Kumari, Neeti; Goyal, Neena

    2012-12-01

    T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1γ), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1γ of Leishmania donovani (LdTCP1γ), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1γ revealed the presence of all the characteristic features of TCP1γ. However, leishmanial TCP1γ represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1γ exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1γ as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1γ was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1γ with actin suggests that, this gene may have a role in maintaining the structural dynamics of cytoskeleton of parasite. PMID:23137535

  7. The emplacement of the granitic Las Tazas complex, northern Chile: the relationship between local and regional strain

    NASA Astrophysics Data System (ADS)

    Wilson, Jeff; Grocott, John

    1999-11-01

    The Coastal batholith of northern Chile grew under transtensional-extensional conditions that prevailed along the Andean margin during the Mesozoic. The batholith hosts the Atacama Fault Zone, a major arc-parallel fault system which was characterised by sinistral transtensional shearing during the Early Cretaceous. The Las Tazas complex is a composite granitoid intrusion that was emplaced syntectonically along the Atacama Fault Zone at ˜130 Ma. Syntectonic emplacement is indicated by a consistent kinematic history between the complex and its wall rocks, together with synchronous crystallisation and shearing ages. In contrast to regional patterns, the Las Tazas complex was emplaced during a local change from vertical east-side-down to dextral transcurrent displacement along the fault zone. During intrusion, strain was partitioned between non-coaxial simple shearing within country-rock mylonites and a flattening strain across the crystallising complex. This combination indicates that the pluton was emplaced under temporary transpressive conditions that were localised around the pluton, probably induced by magma emplacement. Such a difference between local and regional strain suggests that emplacement-related structures should only be related to regional strain-states with great care.

  8. Local Stress Control of Spatiotemporal Ordering of Colloidal Crystals in Complex Flows

    NASA Astrophysics Data System (ADS)

    Shereda, Laura T.; Larson, Ronald G.; Solomon, Michael J.

    2008-07-01

    We show that spin coating, an unsteady, nonuniform shear flow, produces spatiotemporal variation in the crystal order of concentrated colloidal dispersions that is a universal function of the local reduced critical stress and the macroscopic strain. The dependence of the crystal quality of model poly(methyl methacrylate) colloids on radial and axial position, spin speed, and particle size is quantified by confocal microscopy. The coupling of flow-induced crystallization with the centrifugally driven spin coating flow determines local crystal quality without a priori knowledge of the suspension rheology.

  9. Designed membrane channels and pores.

    PubMed

    Bayley, H

    1999-02-01

    Advances in the synthesis and assembly of designed membrane channels and pores include addressable template-assisted synthetic protein (TASP) syntheses of helix bundles, the production of a new class of nanotubes and the ability to purify hetero-oligomeric pores. Channels and pores with altered functional properties and with built-in triggers and switches have been prepared. Progress in applications has been greatest in sensor technology, where sensor elements based on ligand activation, channel selectivity and channel block have been made. Structural information about natural membrane proteins is emerging to inspire new designs.

  10. Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

    SciTech Connect

    Hankel, Marlies E-mail: j.n.l.connor@manchester.ac.uk; Connor, J. N. L. E-mail: j.n.l.connor@manchester.ac.uk

    2015-07-15

    A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact that accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S({sup 1}D) + HD → SH + D, S({sup 1}D) + DH → SD + H, N({sup 2}D) +H{sub 2} → NH + H, and H{sup +} + D{sub 2} → HD + D{sup +}. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H{sub 2} → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.

  11. Scale parameter-estimating method for adaptive fingerprint pore extraction model

    NASA Astrophysics Data System (ADS)

    Yi, Yao; Cao, Liangcai; Guo, Wei; Luo, Yaping; He, Qingsheng; Jin, Guofan

    2011-11-01

    Sweat pores and other level 3 features have been proven to provide more discriminatory information about fingerprint characteristics, which is useful for personal identification especially in law enforcement applications. With the advent of high resolution (>=1000 ppi) fingerprint scanning equipment, sweat pores are attracting increasing attention in automatic fingerprint identification system (AFIS), where the extraction of pores is a critical step. This paper presents a scale parameter-estimating method in filtering-based pore extraction procedure. Pores are manually extracted from a 1000 ppi grey-level fingerprint image. The size and orientation of each detected pore are extracted together with local ridge width and orientation. The quantitative relation between the pore parameters (size and orientation) and local image parameters (ridge width and orientation) is statistically obtained. The pores are extracted by filtering fingerprint image with the new pore model, whose parameters are determined by local image parameters and the statistically established relation. Experiments conducted on high resolution fingerprints indicate that the new pore model gives good performance in pore extraction.

  12. Cellular localization of GDNF and its GFRalpha1/RET receptor complex in the developing pancreas of cat

    PubMed Central

    Lucini, C; Maruccio, L; Facello, B; Cocchia, N; Tortora, G; Castaldo, L

    2008-01-01

    Glial cell line-derived neurotrophic factor (GDNF) acts through RET receptor tyrosine kinase and its co-receptor GFRalpha1. In an effort to better understand the possible biological contribution of the GDNF and GFRalpha1/RET complex in pancreatic development, in this study we report the cellular localization of these proteins in the pancreas of domestic cat embryos and fetuses by immunocytochemical methods. In early embryos, GDNF, GFRalpha and RET immunoreactivity (IR) was localized in closely intermingled cells. GDNF and RET immunoreactive cells displayed chromogranin (an endocrine marker) and PGP 9.5 (a neuronal marker) IR, respectively. GFRalpha IR was present in both a few GDNF/chromogranin and RET/PGP 9.5 immunoreactive cells. In elderly fetuses, GDNF and GFRalpha IR were co-localized in glucagon cells and RET IR was detected in few neurons and never co-localized with GFRalpha or GDNF IR. In early embryos, the presence of GDNF IR in chromogranin immunoreactive cells and GFRalpha1/RET complex IR in PGP9.5 immunoreactive cells seems to suggest a paracrine action of GDNF contained in endocrine cell precursors on neuronal cell precursors expressing its receptor complex. The presence in different cell populations of RET and its co-receptor GFRalpha1 IR could be due to independent signaling of GRFalpha1. Thus, the co-presence of GDNF and GFRalpha1 in chromogranin and glucagon cells could lead to the hypothesis that GDNF can act in an autocrinal manner. In fetuses, RET IR was detected only in intrapancreatic ganglia. Because of the lack of GFRalpha1 IR in pancreatic innervation, RET receptor could be activated by other GFR alphas and ligands of GDNF family. In conclusion, these findings suggest that in differently aged embryos and fetuses the GDNF signal is differently mediated by RET and GFRalpha1. PMID:19014364

  13. Machine learning framework for analysis of transport through complex networks in porous, granular media: A focus on permeability.

    PubMed

    van der Linden, Joost H; Narsilio, Guillermo A; Tordesillas, Antoinette

    2016-08-01

    We present a data-driven framework to study the relationship between fluid flow at the macroscale and the internal pore structure, across the micro- and mesoscales, in porous, granular media. Sphere packings with varying particle size distribution and confining pressure are generated using the discrete element method. For each sample, a finite element analysis of the fluid flow is performed to compute the permeability. We construct a pore network and a particle contact network to quantify the connectivity of the pores and particles across the mesoscopic spatial scales. Machine learning techniques for feature selection are employed to identify sets of microstructural properties and multiscale complex network features that optimally characterize permeability. We find a linear correlation (in log-log scale) between permeability and the average closeness centrality of the weighted pore network. With the pore network links weighted by the local conductance, the average closeness centrality represents a multiscale measure of efficiency of flow through the pore network in terms of the mean geodesic distance (or shortest path) between all pore bodies in the pore network. Specifically, this study objectively quantifies a hypothesized link between high permeability and efficient shortest paths that thread through relatively large pore bodies connected to each other by high conductance pore throats, embodying connectivity and pore structure. PMID:27627377

  14. Machine learning framework for analysis of transport through complex networks in porous, granular media: A focus on permeability

    NASA Astrophysics Data System (ADS)

    van der Linden, Joost H.; Narsilio, Guillermo A.; Tordesillas, Antoinette

    2016-08-01

    We present a data-driven framework to study the relationship between fluid flow at the macroscale and the internal pore structure, across the micro- and mesoscales, in porous, granular media. Sphere packings with varying particle size distribution and confining pressure are generated using the discrete element method. For each sample, a finite element analysis of the fluid flow is performed to compute the permeability. We construct a pore network and a particle contact network to quantify the connectivity of the pores and particles across the mesoscopic spatial scales. Machine learning techniques for feature selection are employed to identify sets of microstructural properties and multiscale complex network features that optimally characterize permeability. We find a linear correlation (in log-log scale) between permeability and the average closeness centrality of the weighted pore network. With the pore network links weighted by the local conductance, the average closeness centrality represents a multiscale measure of efficiency of flow through the pore network in terms of the mean geodesic distance (or shortest path) between all pore bodies in the pore network. Specifically, this study objectively quantifies a hypothesized link between high permeability and efficient shortest paths that thread through relatively large pore bodies connected to each other by high conductance pore throats, embodying connectivity and pore structure.

  15. Triggered pore-forming agents

    DOEpatents

    Bayley, Hagan; Walker, Barbara J.; Chang, Chung-yu; Niblack, Brett; Panchal, Rekha

    1998-01-01

    An inactive pore-forming agent which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell.

  16. Metal structures with parallel pores

    NASA Technical Reports Server (NTRS)

    Sherfey, J. M.

    1976-01-01

    Four methods of fabricating metal plates having uniformly sized parallel pores are studied: elongate bundle, wind and sinter, extrude and sinter, and corrugate stack. Such plates are suitable for electrodes for electrochemical and fuel cells.

  17. DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes.

    PubMed

    Dougherty, Gerard W; Loges, Niki T; Klinkenbusch, Judith A; Olbrich, Heike; Pennekamp, Petra; Menchen, Tabea; Raidt, Johanna; Wallmeier, Julia; Werner, Claudius; Westermann, Cordula; Ruckert, Christian; Mirra, Virginia; Hjeij, Rim; Memari, Yasin; Durbin, Richard; Kolb-Kokocinski, Anja; Praveen, Kavita; Kashef, Mohammad A; Kashef, Sara; Eghtedari, Fardin; Häffner, Karsten; Valmari, Pekka; Baktai, György; Aviram, Micha; Bentur, Lea; Amirav, Israel; Davis, Erica E; Katsanis, Nicholas; Brueckner, Martina; Shaposhnykov, Artem; Pigino, Gaia; Dworniczak, Bernd; Omran, Heymut

    2016-08-01

    Primary ciliary dyskinesia (PCD) is a recessively inherited disease that leads to chronic respiratory disorders owing to impaired mucociliary clearance. Conventional transmission electron microscopy (TEM) is a diagnostic standard to identify ultrastructural defects in respiratory cilia but is not useful in approximately 30% of PCD cases, which have normal ciliary ultrastructure. DNAH11 mutations are a common cause of PCD with normal ciliary ultrastructure and hyperkinetic ciliary beating, but its pathophysiology remains poorly understood. We therefore characterized DNAH11 in human respiratory cilia by immunofluorescence microscopy (IFM) in the context of PCD. We used whole-exome and targeted next-generation sequence analysis as well as Sanger sequencing to identify and confirm eight novel loss-of-function DNAH11 mutations. We designed and validated a monoclonal antibody specific to DNAH11 and performed high-resolution IFM of both control and PCD-affected human respiratory cells, as well as samples from green fluorescent protein (GFP)-left-right dynein mice, to determine the ciliary localization of DNAH11. IFM analysis demonstrated native DNAH11 localization in only the proximal region of wild-type human respiratory cilia and loss of DNAH11 in individuals with PCD with certain loss-of-function DNAH11 mutations. GFP-left-right dynein mice confirmed proximal DNAH11 localization in tracheal cilia. DNAH11 retained proximal localization in respiratory cilia of individuals with PCD with distinct ultrastructural defects, such as the absence of outer dynein arms (ODAs). TEM tomography detected a partial reduction of ODAs in DNAH11-deficient cilia. DNAH11 mutations result in a subtle ODA defect in only the proximal region of respiratory cilia, which is detectable by IFM and TEM tomography.

  18. DNAH11 Localization in the Proximal Region of Respiratory Cilia Defines Distinct Outer Dynein Arm Complexes.

    PubMed

    Dougherty, Gerard W; Loges, Niki T; Klinkenbusch, Judith A; Olbrich, Heike; Pennekamp, Petra; Menchen, Tabea; Raidt, Johanna; Wallmeier, Julia; Werner, Claudius; Westermann, Cordula; Ruckert, Christian; Mirra, Virginia; Hjeij, Rim; Memari, Yasin; Durbin, Richard; Kolb-Kokocinski, Anja; Praveen, Kavita; Kashef, Mohammad A; Kashef, Sara; Eghtedari, Fardin; Häffner, Karsten; Valmari, Pekka; Baktai, György; Aviram, Micha; Bentur, Lea; Amirav, Israel; Davis, Erica E; Katsanis, Nicholas; Brueckner, Martina; Shaposhnykov, Artem; Pigino, Gaia; Dworniczak, Bernd; Omran, Heymut

    2016-08-01

    Primary ciliary dyskinesia (PCD) is a recessively inherited disease that leads to chronic respiratory disorders owing to impaired mucociliary clearance. Conventional transmission electron microscopy (TEM) is a diagnostic standard to identify ultrastructural defects in respiratory cilia but is not useful in approximately 30% of PCD cases, which have normal ciliary ultrastructure. DNAH11 mutations are a common cause of PCD with normal ciliary ultrastructure and hyperkinetic ciliary beating, but its pathophysiology remains poorly understood. We therefore characterized DNAH11 in human respiratory cilia by immunofluorescence microscopy (IFM) in the context of PCD. We used whole-exome and targeted next-generation sequence analysis as well as Sanger sequencing to identify and confirm eight novel loss-of-function DNAH11 mutations. We designed and validated a monoclonal antibody specific to DNAH11 and performed high-resolution IFM of both control and PCD-affected human respiratory cells, as well as samples from green fluorescent protein (GFP)-left-right dynein mice, to determine the ciliary localization of DNAH11. IFM analysis demonstrated native DNAH11 localization in only the proximal region of wild-type human respiratory cilia and loss of DNAH11 in individuals with PCD with certain loss-of-function DNAH11 mutations. GFP-left-right dynein mice confirmed proximal DNAH11 localization in tracheal cilia. DNAH11 retained proximal localization in respiratory cilia of individuals with PCD with distinct ultrastructural defects, such as the absence of outer dynein arms (ODAs). TEM tomography detected a partial reduction of ODAs in DNAH11-deficient cilia. DNAH11 mutations result in a subtle ODA defect in only the proximal region of respiratory cilia, which is detectable by IFM and TEM tomography. PMID:26909801

  19. Similarity index based on local paths for link prediction of complex networks.

    PubMed

    Lü, Linyuan; Jin, Ci-Hang; Zhou, Tao

    2009-10-01

    Predictions of missing links of incomplete networks, such as protein-protein interaction networks or very likely but not yet existent links in evolutionary networks like friendship networks in web society, can be considered as a guideline for further experiments or valuable information for web users. In this paper, we present a local path index to estimate the likelihood of the existence of a link between two nodes. We propose a network model with controllable density and noise strength in generating links, as well as collect data of six real networks. Extensive numerical simulations on both modeled networks and real networks demonstrated the high effectiveness and efficiency of the local path index compared with two well-known and widely used indices: the common neighbors and the Katz index. Indeed, the local path index provides competitively accurate predictions as the Katz index while requires much less CPU time and memory space than the Katz index, which is therefore a strong candidate for potential practical applications in data mining of huge-size networks.

  20. Nocturnal Low-Level Jet in a Mountain Basin Complex. I. Evolution and Effects on Local Flows

    SciTech Connect

    Banta, Robert M.; Darby, Lisa S.; Fast, Jerome D.; Pinto, James O.; Whiteman, Charles D.; Shaw, William J.; Orr, Brad W.

    2004-10-01

    A Doppler lidar deployed to the center of the Great Salt Lake (GSL) basin during the Vertical Transport and Mixing Experiment (VTMX) in October 2000 found a diurnal cycle of the along-basin winds with northerly, up-basin flow during the day and a southerly, down-basin low-level jet at night. The emphasis of VTMX was on stable atmospheric processes in the cold-air pool that formed in the basin at night. During the night the jet was fully formed as it entered the GSL basin from the south. Thus it was a feature of the complex string of basins draining into the Great Salt Lake, which included at least the Utah Lake basin to the south. The timing of the evening reversal to down-basin flow was sensitive to the larger-scale north-south pressure gradient imposed on the basin complex. On nights when the pressure gradient was not too strong, local drainage flow (slope flows and canyon outflow) was well developed along the Wasatch Range to the east and coexisted with the basin jet. The coexistence of these two types of flow generated localized regions of convergence and divergence, in which regions of vertical motions and transport were focused. Mesoscale numerical simulations captured these features and indicated that updrafts on the order of 5 cm/s could persist in these localized convergence zones, contributing to vertical displacement of air masses within the basin cold pool.

  1. Nocturnal Low-Level Jet in a Mountain Basin Complex. Part I: Evolution and Effects on Local Flows.

    NASA Astrophysics Data System (ADS)

    Banta, Robert M.; Darby, Lisa S.; Fast, Jerome D.; Pinto, James O.; Whiteman, C. David; Shaw, William J.; Orr, Brad W.

    2004-10-01

    A Doppler lidar deployed to the center of the Great Salt Lake (GSL) basin during the Vertical Transport and Mixing (VTMX) field campaign in October 2000 found a diurnal cycle of the along-basin winds with northerly up-basin flow during the day and a southerly down-basin low-level jet at night. The emphasis of VTMX was on stable atmospheric processes in the cold-air pool that formed in the basin at night. During the night the jet was fully formed as it entered the GSL basin from the south. Thus, it was a feature of the complex string of basins draining toward the Great Salt Lake, which included at least the Utah Lake basin to the south. The timing of the evening reversal to down-basin flow was sensitive to the larger-scale north south pressure gradient imposed on the basin complex. On nights when the pressure gradient was not too strong, local drainage flow (slope flows and canyon outflow) was well developed along the Wasatch Range to the east and coexisted with the basin jet. The coexistence of these two types of flow generated localized regions of convergence and divergence, in which regions of vertical motion and transport were focused. Mesoscale numerical simulations captured these features and indicated that updrafts on the order of 5 cm s-1 could persist in these localized convergence zones, contributing to vertical displacement of air masses within the basin cold pool.


  2. Optical Coherence Tomography Noise Reduction Using Anisotropic Local Bivariate Gaussian Mixture Prior in 3D Complex Wavelet Domain

    PubMed Central

    Sonka, Milan; Abramoff, Michael D.

    2013-01-01

    In this paper, MMSE estimator is employed for noise-free 3D OCT data recovery in 3D complex wavelet domain. Since the proposed distribution for noise-free data plays a key role in the performance of MMSE estimator, a priori distribution for the pdf of noise-free 3D complex wavelet coefficients is proposed which is able to model the main statistical properties of wavelets. We model the coefficients with a mixture of two bivariate Gaussian pdfs with local parameters which are able to capture the heavy-tailed property and inter- and intrascale dependencies of coefficients. In addition, based on the special structure of OCT images, we use an anisotropic windowing procedure for local parameters estimation that results in visual quality improvement. On this base, several OCT despeckling algorithms are obtained based on using Gaussian/two-sided Rayleigh noise distribution and homomorphic/nonhomomorphic model. In order to evaluate the performance of the proposed algorithm, we use 156 selected ROIs from 650 × 512 × 128 OCT dataset in the presence of wet AMD pathology. Our simulations show that the best MMSE estimator using local bivariate mixture prior is for the nonhomomorphic model in the presence of Gaussian noise which results in an improvement of 7.8 ± 1.7 in CNR. PMID:24222760

  3. Localized structures in complex plasmas in the presence of a magnetic field

    NASA Astrophysics Data System (ADS)

    Dongmo Tsopgue, P.; Mohamadou, A.; Kourakis, I.; Kofane, Timoleon C.; Tanga, J. P.

    2016-04-01

    In this work, the general framework in which fits our investigation is that of modeling the dynamics of dust grains therein dusty plasma (complex plasma) in the presence of electromagnetic fields. The generalized discrete complex Ginzburg-Landau equation (DCGLE) is thus obtained to model discrete dynamical structure in dusty plasma with Epstein friction. In the collisionless limit, the equation reduces to the modified discrete nonlinear Schrödinger equation (MDNLSE). The modulational instability phenomenon is studied and we present the criterion of instability in both cases and it is shown that high values of damping extend the instability region. Equations thus obtained highlight the presence of soliton-like excitation in dusty plasma. We studied the generation of soliton in a dusty plasma taking in account the effects of interaction between dust grains and theirs neighbours. Numerical simulations are carried out to show the validity of analytical approach.

  4. Detection of Mycobacterium tuberculosis complex by PCR in fresh cheese from local markets in Hidalgo, Mexico.

    PubMed

    Pereira-Suárez, Ana Laura; Estrada-Chávez, Yessica; Zúñiga-Estrada, Armidá; Lopez-Rincón, Gonzálo; Hernández, David Ulises Miranda; Padilla-Ramírez, Francisco Javier; Estrada-Chávez, Ciro

    2014-05-01

    The objective of this study was to identify the presence of Mycobacterium tuberculosis complex bacterial DNA in samples extracted from fresh cheeses; 95 samples of fresh cheese were obtained from municipal markets in the state of Hidalgo, in central Mexico, and were analyzed in triplicate. The exogenous control for the amplification was the mitochondrial gene for cytochrome b (cyt-b). M. tuberculosis complex DNA was detected by nested-PCR amplification of a fragment of the mpb70 gene in six samples, four of which were obtained from regions with enzootic bovine tuberculosis. These results suggest that cheeses prepared with raw milk contaminated with M. bovis are being sold and consumed by humans, which may cause tuberculosis.

  5. Detection of Mycobacterium tuberculosis complex by PCR in fresh cheese from local markets in Hidalgo, Mexico.

    PubMed

    Pereira-Suárez, Ana Laura; Estrada-Chávez, Yessica; Zúñiga-Estrada, Armidá; Lopez-Rincón, Gonzálo; Hernández, David Ulises Miranda; Padilla-Ramírez, Francisco Javier; Estrada-Chávez, Ciro

    2014-05-01

    The objective of this study was to identify the presence of Mycobacterium tuberculosis complex bacterial DNA in samples extracted from fresh cheeses; 95 samples of fresh cheese were obtained from municipal markets in the state of Hidalgo, in central Mexico, and were analyzed in triplicate. The exogenous control for the amplification was the mitochondrial gene for cytochrome b (cyt-b). M. tuberculosis complex DNA was detected by nested-PCR amplification of a fragment of the mpb70 gene in six samples, four of which were obtained from regions with enzootic bovine tuberculosis. These results suggest that cheeses prepared with raw milk contaminated with M. bovis are being sold and consumed by humans, which may cause tuberculosis. PMID:24780344

  6. Impact of the Kohn-Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes.

    PubMed

    Duignan, Thomas J; Autschbach, Jochen

    2016-07-12

    The extent of ligand to metal donation bonding and mixing of 4f (and 5d) orbitals with ligand orbitals is studied by Kohn-Sham (KS) calculations for LaX3 (X = F, Cl, Br, I), GdX3, and LuX3 model complexes, CeCl6(2-), YbCp3, and selected lanthanide complexes with larger ligands. The KS delocalization error (DE) is quantified via the curvature of the energy for noninteger electron numbers. The extent of donation bonding and 4f-ligand mixing correlates well with the DE. For Lu complexes, the DE also correlates with the extent of mixing of ligand and 4f orbitals in the canonical molecular orbitals (MOs). However, the localized set of MOs and population analyses indicate that the closed 4f shell is localized. Attempts to create situations where mixing of 4f and ligand orbitals occurs due to a degeneracy of fragment orbitals were unsuccessful. For La(III) and, in particular, for Ce(IV), Hartree-Fock, KS, and coupled cluster singles and doubles calculations are in agreement in that excess 4f populations arise from ligand donation, along with donation into the 5d shell. Likewise, KS calculations for all systems with incompletely filled 4f shells, even those with "optimally tuned" functionals affording a small DE, produce varying degrees of excess 4f populations which may be only partially attributed to 5d polarization.

  7. Impact of the Kohn-Sham Delocalization Error on the 4f Shell Localization and Population in Lanthanide Complexes.

    PubMed

    Duignan, Thomas J; Autschbach, Jochen

    2016-07-12

    The extent of ligand to metal donation bonding and mixing of 4f (and 5d) orbitals with ligand orbitals is studied by Kohn-Sham (KS) calculations for LaX3 (X = F, Cl, Br, I), GdX3, and LuX3 model complexes, CeCl6(2-), YbCp3, and selected lanthanide complexes with larger ligands. The KS delocalization error (DE) is quantified via the curvature of the energy for noninteger electron numbers. The extent of donation bonding and 4f-ligand mixing correlates well with the DE. For Lu complexes, the DE also correlates with the extent of mixing of ligand and 4f orbitals in the canonical molecular orbitals (MOs). However, the localized set of MOs and population analyses indicate that the closed 4f shell is localized. Attempts to create situations where mixing of 4f and ligand orbitals occurs due to a degeneracy of fragment orbitals were unsuccessful. For La(III) and, in particular, for Ce(IV), Hartree-Fock, KS, and coupled cluster singles and doubles calculations are in agreement in that excess 4f populations arise from ligand donation, along with donation into the 5d shell. Likewise, KS calculations for all systems with incompletely filled 4f shells, even those with "optimally tuned" functionals affording a small DE, produce varying degrees of excess 4f populations which may be only partially attributed to 5d polarization. PMID:27224494

  8. Endoplasmic Reticulum-Localized Iridium(III) Complexes as Efficient Photodynamic Therapy Agents via Protein Modifications.

    PubMed

    Nam, Jung Seung; Kang, Myeong-Gyun; Kang, Juhye; Park, Sun-Young; Lee, Shin Jung C; Kim, Hyun-Tak; Seo, Jeong Kon; Kwon, Oh-Hoon; Lim, Mi Hee; Rhee, Hyun-Woo; Kwon, Tae-Hyuk

    2016-08-31

    Protein inactivation by reactive oxygen species (ROS) such as singlet oxygen ((1)O2) and superoxide radical (O2(•-)) is considered to trigger cell death pathways associated with protein dysfunction; however, the detailed mechanisms and direct involvement in photodynamic therapy (PDT) have not been revealed. Herein, we report Ir(III) complexes designed for ROS generation through a rational strategy to investigate protein modifications by ROS. The Ir(III) complexes are effective as PDT agents at low concentrations with low-energy irradiation (≤ 1 J cm(-2)) because of the relatively high (1)O2 quantum yield (> 0.78), even with two-photon activation. Furthermore, two types of protein modifications (protein oxidation and photo-cross-linking) involved in PDT were characterized by mass spectrometry. These modifications were generated primarily in the endoplasmic reticulum and mitochondria, producing a significant effect for cancer cell death. Consequently, we present a plausible biologically applicable PDT modality that utilizes rationally designed photoactivatable Ir(III) complexes. PMID:27494510

  9. Intracellular disassembly and localization of a new P123-PEI-R13/DNA complex.

    PubMed

    Zhu, Manman; Liu, Kehai; Zhu, Qing; Chen, Shunsheng; Lv, Hui; Zhao, Wenfang; Mao, Yuan; Hu, Jing

    2014-01-01

    The appropriate location and release of target gene is necessary for gene therapy. In our previous paper, a gene vector named P123-PEI-R13 has been successfully synthesized, and the physical characteristics and cellular trafficking of nanoparticle P123-PEI-R13/DNA has been explored explicitly, but little was known about its disassembly within cells. In order to investigate its intracellular disassembly, P123-PEI-R13/DNA complex was exposed to the different competitors (RNA, DNA, proteins) or different conditions of pH and osmolarity, DNA release was determined by gel electrophoresis. Meanwhile, confocal laser technology was used to locate the complex in cells. The results revealed that DNA, RNA and osmolarity could affect the stability of the complex obviously, especially RNA which exist in nucleus. In addition, the speed of DNA release decreased as the weight ratio of polymer increased. Images got by a confocal fluorescence microscope confirmed that after cell uptake, P123-PEI-R13 could translocate DNA into nucleus.

  10. Transport pathways within percolating pore space networks of granular materials

    NASA Astrophysics Data System (ADS)

    Vo, Kevin; Walker, David M.; Tordesillas, Antoinette

    2013-06-01

    Granular media can be regarded as a mixture of two components: grains and the material filling the voids or pores between the grains. Pore properties give rise to a range of applications such as modelling ground water flow, carbon capture and sequestration. The grains within a dense granular material respond to deformation (e.g., shearing or compression) by rearranging to create local zones of compression and zones of dilatation (i.e., regions of high pore space). Descriptions of the deformation are typically focused on analysis of the solid skeleton via topology of physical contact networks of grains but an alternative perspective is to consider network representations of the evolving anisotropic pore space. We demonstrate how to construct pore space networks that express the local size of voids about a grain through network edge weights. We investigate sectors of the loading history when a percolating giant component of the pore space network exists. At these states the grains are in a configuration more prone to the efficient transport of material (e.g., fluid flow, mineral/gas deposits). These pathways can be found through examination of the weighted shortest paths percolating the boundaries of the material. In particular, network weights biased towards large void space results in efficient percolating pathways traversing the shear band in the direction of principal stress within a 2D granular assembly subject to high strains.

  11. Localized numerical impulse solutions in diffuse neural networks modeled by the complex fractional Ginzburg-Landau equation

    NASA Astrophysics Data System (ADS)

    Mvogo, Alain; Tambue, Antoine; Ben-Bolie, Germain H.; Kofané, Timoléon C.

    2016-10-01

    We investigate localized wave solutions in a network of Hindmarsh-Rose neural model taking into account the long-range diffusive couplings. We show by a specific analytical technique that the model equations in the infrared limit (wave number k → 0) can be governed by the complex fractional Ginzburg-Landau (CFGL) equation. According to the stiffness of the system, we propose both the semi and the linearly implicit Riesz fractional finite-difference schemes to solve efficiently the CFGL equation. The obtained fractional numerical solutions for the nerve impulse reveal localized short impulse properties. We also show the equivalence between the continuous CFGL and the discrete Hindmarsh-Rose models for relatively large network.

  12. Sphingosine kinase 2 is a chikungunya virus host factor co-localized with the viral replication complex.

    PubMed

    Reid, St Patrick; Tritsch, Sarah R; Kota, Krishna; Chiang, Chih-Yuan; Dong, Lian; Kenny, Tara; Brueggemann, Ernest E; Ward, Michael D; Cazares, Lisa H; Bavari, Sina

    2015-10-01

    Chikungunya virus (CHIKV) is a re-emerging alphavirus which causes severe and prolonged arthralgic febrile illness. The recent global spread of the virus and lack of approved therapeutic options makes it imperative to gain greater insight into the molecular mechanisms underlying CHIKV pathogenesis, in particular host factors recruited by the virus. In the current study, we identify sphingosine kinase 2 (SK2) as a CHIKV host factor co-localized with the viral replication complex (VRC) during infection. SK2 was demonstrated to co-localize with viral RNA and nonstructural proteins. Targeted impairment of SK2 expression or function significantly inhibited CHIKV infection. Furthermore, affinity purification-mass spectrometry studies revealed that SK2 associates with a number of proteins involved in cellular gene expression specifically during viral infection, suggesting a role in replication. Collectively these results identify SK2 as a novel CHIKV host factor.

  13. [Comparative effectiveness study of local antioxidants in complex treatment of chronic periodontal disease].

    PubMed

    Butiugin, I A; Kornilova, N V; Abramov, O V

    2013-01-01

    Prospective, placebo-control, randomized blind study was carried out on the clinical effectiveness of the local administration of 1% emoxipine solution, 1,5% reamberin solution and 5% mexidol solution in patients with chronic periodontitis (CP). It was determined that all medications under study cause the decrease of simplified oral hygienic index by Green and Vermillion (OHI-S, Green J.C., Vermillion J.R., 1969), papillary-marginal-alveolar index (РМА, Parma C., 1960), papillary bleeding index (PBI, Saxer U.P., Muhlemann M.R., 1975) and increase the sialometry index in the case of CP. The best clinical effect was achieved by the local administration of reamberin, which turned out to be the only medication among those under study to lower the content of lipid peroxidation products in the mixed saliva, to decrease the periodontal index (PI, Russel A., 1956) and to result in the concomitant increase of life satisfaction index in patients with chronic periodontitis.

  14. Tactile localization training for pain, sensory disturbance, and distorted body image: a case study of complex regional pain syndrome.

    PubMed

    Osumi, Michihiro; Okuno, Hiroyuki; Nishigami, Tomohiko; Ueta, Kozo; Morioka, Shu

    2015-01-01

    This report presents a case of complex regional pain syndrome. The patient presented with severe pain, sensory disturbance, and distorted body image at the site of initial injury and other body sites. Tactile localization training (TLT) at only the site of initial injury decreased severe pain at the site of initial injury and the secondary affected sites, whereas TLT at secondary affected sites had no effect. These results highlighted the importance of assessing changes in patients' pain processes to determine the part of the body where TLT should be applied.

  15. Bacterial secretins form constitutively open pores akin to general porins.

    PubMed

    Disconzi, Elena; Guilvout, Ingrid; Chami, Mohamed; Masi, Muriel; Huysmans, Gerard H M; Pugsley, Anthony P; Bayan, Nicolas

    2014-01-01

    Proteins called secretins form large multimeric complexes that are essential for macromolecular transit across the outer membrane of Gram-negative bacteria. Evidence suggests that the channels formed by some secretin complexes are not tightly closed, but their permeability properties have not been well characterized. Here, we used cell-free synthesis coupled with spontaneous insertion into liposomes to investigate the permeability of the secretin PulD. Leakage assays using preloaded liposomes indicated that PulD allows the efflux of small fluorescent molecules with a permeation cutoff similar to that of general porins. Other secretins were also found to form similar pores. To define the polypeptide region involved in determining the pore size, we analyzed a collection of PulD variants and studied the roles of gates 1 and 2, which were previously reported to affect the pore size of filamentous phage f1 secretin pIV, in assembly and pore formation. Liposome leakage and a novel in vivo assay showed that replacement of the conserved proline residue at position 443 in PulD by leucine increased the apparent size of the pore. The in vitro approach described here could be used to study the pore properties of membrane proteins whose production in vivo is toxic.

  16. Bacterial Secretins Form Constitutively Open Pores Akin to General Porins

    PubMed Central

    Disconzi, Elena; Guilvout, Ingrid; Chami, Mohamed; Masi, Muriel; Huysmans, Gerard H. M.; Pugsley, Anthony P.

    2014-01-01

    Proteins called secretins form large multimeric complexes that are essential for macromolecular transit across the outer membrane of Gram-negative bacteria. Evidence suggests that the channels formed by some secretin complexes are not tightly closed, but their permeability properties have not been well characterized. Here, we used cell-free synthesis coupled with spontaneous insertion into liposomes to investigate the permeability of the secretin PulD. Leakage assays using preloaded liposomes indicated that PulD allows the efflux of small fluorescent molecules with a permeation cutoff similar to that of general porins. Other secretins were also found to form similar pores. To define the polypeptide region involved in determining the pore size, we analyzed a collection of PulD variants and studied the roles of gates 1 and 2, which were previously reported to affect the pore size of filamentous phage f1 secretin pIV, in assembly and pore formation. Liposome leakage and a novel in vivo assay showed that replacement of the conserved proline residue at position 443 in PulD by leucine increased the apparent size of the pore. The in vitro approach described here could be used to study the pore properties of membrane proteins whose production in vivo is toxic. PMID:24142256

  17. Modeling permeability evolution by precipitation and dissolution: from a single-pore channel to heterogeneous multi-pore systems

    NASA Astrophysics Data System (ADS)

    Silin, D.; Molins, S.

    2011-12-01

    Permeability modification by mineral precipitation or dissolution can significantly affect injection well performance in a bioremediation project. Well clogging may occur due to massive mineral deposition on the pore walls near the wellbore. Although the size of a cleanup site can be measured in hundreds of meters or even kilometers, the underlying geochemical and hydrologic processes in individual pores eventually define where and how fast the permeability will decline. Therefore, it is important to understand these pore-scale mechanisms in order to reduce the hindering effect of pore clogging and develop efficient well treatment procedures when its injectivity drops below the minimal-tolerance level. Additionally, model-based permeability-porosity correlations for pore space evolution caused by precipitation or dissolution are needed for realistic reservoir-scale numerical simulations. To gain insights into the pore-scale mechanisms of permeability modification by mineral precipitation and dissolution, we have developed a model describing the dynamic coupling between flow and reactive transport. The model relies on a sequential approach where alternating finite-volume multicomponent reactive transport and flow simulations evaluate the local precipitation-dissolution rates, update the pore space geometry from the mass balance considerations, the re-compute the flow field on the updated sample model. Segmented three dimensional micro-tomography images of the sediment, the chemical composition of the fluid, and the mineral composition of the rock are the input data for simulations. Some model details were reported at previous AGU meetings. We validate the model against a single-pore calcite dissolution experiment. Building on this problem, we use the model to evaluate the precipitation-dissolution patterns for a range of flow rates. We then simulate multi-pore systems to qualitatively reproduce the pattern of precipitation observed in experiments. For that purpose

  18. The perforin pore facilitates the delivery of cationic cargos.

    PubMed

    Stewart, Sarah E; Kondos, Stephanie C; Matthews, Antony Y; D'Angelo, Michael E; Dunstone, Michelle A; Whisstock, James C; Trapani, Joseph A; Bird, Phillip I

    2014-03-28

    Cytotoxic lymphocytes eliminate virally infected or neoplastic cells through the action of cytotoxic proteases (granzymes). The pore-forming protein perforin is essential for delivery of granzymes into the cytoplasm of target cells; however the mechanism of this delivery is incompletely understood. Perforin contains a membrane attack complex/perforin (MACPF) domain and oligomerizes to form an aqueous pore in the plasma membrane; therefore the simplest (and best supported) model suggests that granzymes passively diffuse through the perforin pore into the cytoplasm of the target cell. Here we demonstrate that perforin preferentially delivers cationic molecules while anionic and neutral cargoes are delivered inefficiently. Furthermore, another distantly related pore-forming MACPF protein, pleurotolysin (from the oyster mushroom), also favors the delivery of cationic molecules, and efficiently delivers human granzyme B. We propose that this facilitated diffusion is due to conserved features of oligomerized MACPF proteins, which may include an anionic lumen. PMID:24558045

  19. Conservation laws, radiative decay rates, and excited state localization in organometallic complexes with strong spin-orbit coupling.

    PubMed

    Powell, B J

    2015-01-01

    There is longstanding fundamental interest in 6-fold coordinated d(6) (t(2g)(6)) transition metal complexes such as [Ru(bpy)3](2+) and Ir(ppy)3, particularly their phosphorescence. This interest has increased with the growing realisation that many of these complexes have potential uses in applications including photovoltaics, imaging, sensing, and light-emitting diodes. In order to design new complexes with properties tailored for specific applications a detailed understanding of the low-energy excited states, particularly the lowest energy triplet state, T1, is required. Here we describe a model of pseudo-octahedral complexes based on a pseudo-angular momentum representation and show that the predictions of this model are in excellent agreement with experiment - even when the deviations from octahedral symmetry are large. This model gives a natural explanation of zero-field splitting of T1 and of the relative radiative rates of the three sublevels in terms of the conservation of time-reversal parity and total angular momentum modulo two. We show that the broad parameter regime consistent with the experimental data implies significant localization of the excited state. PMID:26123864

  20. Conservation laws, radiative decay rates, and excited state localization in organometallic complexes with strong spin-orbit coupling.

    PubMed

    Powell, B J

    2015-06-30

    There is longstanding fundamental interest in 6-fold coordinated d(6) (t(2g)(6)) transition metal complexes such as [Ru(bpy)3](2+) and Ir(ppy)3, particularly their phosphorescence. This interest has increased with the growing realisation that many of these complexes have potential uses in applications including photovoltaics, imaging, sensing, and light-emitting diodes. In order to design new complexes with properties tailored for specific applications a detailed understanding of the low-energy excited states, particularly the lowest energy triplet state, T1, is required. Here we describe a model of pseudo-octahedral complexes based on a pseudo-angular momentum representation and show that the predictions of this model are in excellent agreement with experiment - even when the deviations from octahedral symmetry are large. This model gives a natural explanation of zero-field splitting of T1 and of the relative radiative rates of the three sublevels in terms of the conservation of time-reversal parity and total angular momentum modulo two. We show that the broad parameter regime consistent with the experimental data implies significant localization of the excited state.

  1. Cloning, characterization and sub-cellular localization of gamma subunit of T-complex protein-1 (chaperonin) from Leishmania donovani

    SciTech Connect

    Bhaskar,; Kumari, Neeti; Goyal, Neena

    2012-12-07

    Highlights: Black-Right-Pointing-Pointer The study presents cloning and characterization of TCP1{gamma} gene from L. donovani. Black-Right-Pointing-Pointer TCP1{gamma} is a subunit of T-complex protein-1 (TCP1), a chaperonin class of protein. Black-Right-Pointing-Pointer LdTCP{gamma} exhibited differential expression in different stages of promastigotes. Black-Right-Pointing-Pointer LdTCP{gamma} co-localized with actin, a cytoskeleton protein. Black-Right-Pointing-Pointer The data suggests that this gene may have a role in differentiation/biogenesis. Black-Right-Pointing-Pointer First report on this chapronin in Leishmania. -- Abstract: T-complex protein-1 (TCP1) complex, a chaperonin class of protein, ubiquitous in all genera of life, is involved in intracellular assembly and folding of various proteins. The gamma subunit of TCP1 complex (TCP1{gamma}), plays a pivotal role in the folding and assembly of cytoskeleton protein(s) as an individual or complexed with other subunits. Here, we report for the first time cloning, characterization and expression of the TCP1{gamma} of Leishmania donovani (LdTCP1{gamma}), the causative agent of Indian Kala-azar. Primary sequence analysis of LdTCP1{gamma} revealed the presence of all the characteristic features of TCP1{gamma}. However, leishmanial TCP1{gamma} represents a distinct kinetoplastid group, clustered in a separate branch of the phylogenic tree. LdTCP1{gamma} exhibited differential expression in different stages of promastigotes. The non-dividing stationary phase promastigotes exhibited 2.5-fold less expression of LdTCP1{gamma} as compared to rapidly dividing log phase parasites. The sub-cellular distribution of LdTCP1{gamma} was studied in log phase promastigotes by employing indirect immunofluorescence microscopy. The protein was present not only in cytoplasm but it was also localized in nucleus, peri-nuclear region, flagella, flagellar pocket and apical region. Co-localization of LdTCP1{gamma} with actin suggests

  2. Low-complexity atlas-based prostate segmentation by combining global, regional, and local metrics

    SciTech Connect

    Xie, Qiuliang; Ruan, Dan

    2014-04-15

    Purpose: To improve the efficiency of atlas-based segmentation without compromising accuracy, and to demonstrate the validity of the proposed method on MRI-based prostate segmentation application. Methods: Accurate and efficient automatic structure segmentation is an important task in medical image processing. Atlas-based methods, as the state-of-the-art, provide good segmentation at the cost of a large number of computationally intensive nonrigid registrations, for anatomical sites/structures that are subject to deformation. In this study, the authors propose to utilize a combination of global, regional, and local metrics to improve the accuracy yet significantly reduce the number of required nonrigid registrations. The authors first perform an affine registration to minimize the global mean squared error (gMSE) to coarsely align each atlas image to the target. Subsequently, atarget-specific regional MSE (rMSE), demonstrated to be a good surrogate for dice similarity coefficient (DSC), is used to select a relevant subset from the training atlas. Only within this subset are nonrigid registrations performed between the training images and the target image, to minimize a weighted combination of gMSE and rMSE. Finally, structure labels are propagated from the selected training samples to the target via the estimated deformation fields, and label fusion is performed based on a weighted combination of rMSE and local MSE (lMSE) discrepancy, with proper total-variation-based spatial regularization. Results: The proposed method was applied to a public database of 30 prostate MR images with expert-segmented structures. The authors’ method, utilizing only eight nonrigid registrations, achieved a performance with a median/mean DSC of over 0.87/0.86, outperforming the state-of-the-art full-fledged atlas-based segmentation approach of which the median/mean DSC was 0.84/0.82 when applying to their data set. Conclusions: The proposed method requires a fixed number of nonrigid

  3. Differential localization of SNARE complex proteins SNAP-25, syntaxin, and VAMP during development of the mammalian retina.

    PubMed

    Greenlee, M H; Roosevelt, C B; Sakaguchi, D S

    2001-02-12

    SNARE complex proteins have critical functions during regulated vesicular release of neurotransmitter. In addition, they play critical roles during neurite outgrowth and synaptogenesis. Although it is clear that the function of any one SNARE complex protein during release of neurotransmitter is dependent on its association with other members of the complex, it is less certain whether their function during development and differentiation is dependent on interaction with one another. Previously, we have observed transient high levels of SNARE complex protein SNAP-25 in developing cholinergic amacrine cells (West Greenlee et al. [1998] J Comp Neurol 394:374-385). In addition, we detected, high levels of SNAP-25 in developing and mature photoreceptors. To better understand the functional significance of these high levels of SNAP-25 expression, we used immunocytochemistry to examine the developmental expression of the three members of the SNARE complex, SNAP-25, Syntaxin, and vesicle associated membrane protein (VAMP/also Synaptobrevin). Our results demonstrate that the high levels of SNAP-25 in cholinergic amacrine cells and photoreceptors are not accompanied by the same relatively high levels of other SNARE complex proteins. These results suggest that high levels of SNAP-25 in specific cell types may function independently of association with Syntaxin and VAMP. In this analysis, we characterized the changing patterns of immunoreactivity for the three SNARE complex proteins during the development and differentiation of the mammalian retina. We have compared the pattern of expression of the core SNARE complex proteins in the Brazilian opossum, Monodelphis domestica, and in the rat and found common patterns of expression between these diverse mammalian species. We observed temporal differences in the onset of immunoreactivity between these three proteins, and differences in their localization within synaptic layers in the developing and mature mammalian retina. This

  4. Proximate humid and dry regions in Jupiter's atmosphere indicate complex local meteorology.

    PubMed

    Roos-Serote, M; Vasavada, A R; Kamp, L; Drossart, P; Irwin, P; Nixon, C; Carlson, R W

    2000-05-11

    Models of Jupiter's formation and structure predict that its atmosphere is enriched in oxygen, relative to the Sun, and that consequently water clouds should be present globally near the 5-bar pressure level. Past attempts to confirm these predictions have led to contradictory results; in particular, the Galileo probe revealed a very dry atmosphere at the entry site, with no significant clouds at depths exceeding the 2-bar level. Although the entry site was known to be relatively cloud-free, the contrast between the observed local dryness and the expected global wetness was surprising. Here we analyse near-infrared (around 5 microm) observations of Jupiter, a spectral region that can reveal the water vapour abundance and vertical cloud structure in the troposphere. We find that humid and extremely dry regions exist in close proximity, and that some humid regions are spatially correlated with bright convective clouds extending from the deep water clouds to the visible atmosphere.

  5. k-core percolation on complex networks: Comparing random, localized, and targeted attacks.

    PubMed

    Yuan, Xin; Dai, Yang; Stanley, H Eugene; Havlin, Shlomo

    2016-06-01

    The type of malicious attack inflicting on networks greatly influences their stability under ordinary percolation in which a node fails when it becomes disconnected from the giant component. Here we study its generalization, k-core percolation, in which a node fails when it loses connection to a threshold k number of neighbors. We study and compare analytically and by numerical simulations of k-core percolation the stability of networks under random attacks (RA), localized attacks (LA) and targeted attacks (TA), respectively. By mapping a network under LA or TA into an equivalent network under RA, we find that in both single and interdependent networks, TA exerts the greatest damage to the core structure of a network. We also find that for Erdős-Rényi (ER) networks, LA and RA exert equal damage to the core structure, whereas for scale-free (SF) networks, LA exerts much more damage than RA does to the core structure. PMID:27415275

  6. Quantification of the global and local complexity of the epithelial-connective tissue interface of normal, dysplastic, and neoplastic oral mucosae using digital imaging.

    PubMed

    Abu Eid, Rasha; Landini, Gabriel

    2003-01-01

    This study aimed at quantifying the complexity of the epithelial-connective tissue interface (ECTI) in human normal mucosa, premalignant, and malignant lesions using fractal geometry. Two approaches were used to describe the complexity of 377 oral mucosa ECTI profiles. The box counting method was used to estimate their global fractal dimension, while local fractal dimensions were estimated using the mass radius relation at various local scales. The ECTI complexity significantly increased from normal through premalignant to malignant profiles in both global and local (over 283 microm) scales. Normal mucosa samples from different sites of the oral cavity also had different degrees of global complexity. Fractal geometry is a useful morphological marker of tissue complexity changes taking place during epithelial malignancy and premalignancy, and we propose it as a quantitative marker of epithelial complexity. PMID:14521264

  7. Localization of disinhibition-dementia-parkinsonism-amyotrophy complex to 17q21-22.

    PubMed Central

    Wilhelmsen, K. C.; Lynch, T.; Pavlou, E.; Higgins, M.; Nygaard, T. G.

    1994-01-01

    Disinhibition-dementia-parkinsonism-amyotrophy complex (DDPAC) is defined by familial adult-onset behavioral disturbance, followed by frontal lobe dementia, parkinsonism, and amyotrophy in variable proportions. A genetic etiology of DDPAC was suspected because of the familial clustering in family Mo, despite their wide geographic distribution. We have mapped the DDPAC locus to a 12-cM (sex averaged) region between D17S800 and D17S787 on chromosome 17q21-22. The basis for the variability of the clinical findings and pathology in DDPAC is unknown but suggests that the DDPAC locus should be screened as a candidate locus in family studies of conditions with behavioral abnormalities and neurological degeneration. PMID:7977375

  8. Localization of disinhibition-dementia-parkinsonism-amyotrophy complex to 17q21-22

    SciTech Connect

    Wilhelmsen, K.C.; Lynch, T.; Pavlou, E.; Higgins, M.; Nygaard, T.G.

    1994-12-01

    Disinhibition-dementia-parkinsonism-amyotrophy complex (DDPAC) is defined by familial adult-onset behavioral disturbance, followed by frontal lobe dementia, parkinsonism, and amyotrophy in variable proportions. A genetic etiology of DDPAC was suspected because of the familial clustering in family Mo, despite their wide geographic distribution. We have mapped the DDPAC locus to a 12-cM (sex averaged) region between D17S800 and D17S787 on chromosome 17q21-22. The basis for the variability of the clinical findings and pathology in DDPAC is unknown but suggests that the DDPAC locus should be screened as a candidate locus in family studies of conditions with behavioral abnormalities and neurological degeneration.

  9. The F0F1 ATP Synthase Complex Localizes to Membrane Rafts in Gonadotrope Cells.

    PubMed

    Allen-Worthington, Krystal; Xie, Jianjun; Brown, Jessica L; Edmunson, Alexa M; Dowling, Abigail; Navratil, Amy M; Scavelli, Kurt; Yoon, Hojean; Kim, Do-Geun; Bynoe, Margaret S; Clarke, Iain; Roberson, Mark S

    2016-09-01

    Fertility in mammals requires appropriate communication within the hypothalamic-pituitary-gonadal axis and the GnRH receptor (GnRHR) is a central conduit for this communication. The GnRHR resides in discrete membrane rafts and raft occupancy is required for signaling by GnRH. The present studies use immunoprecipitation and mass spectrometry to define peptides present within the raft associated with the GnRHR and flotillin-1, a key raft marker. These studies revealed peptides from the F0F1 ATP synthase complex. The catalytic subunits of the F1 domain were validated by immunoprecipitation, flow cytometry, and cell surface biotinylation studies demonstrating that this complex was present at the plasma membrane associated with the GnRHR. The F1 catalytic domain faces the extracellular space and catalyzes ATP synthesis when presented with ADP in normal mouse pituitary explants and a gonadotrope cell line. Steady-state extracellular ATP accumulation was blunted by coadministration of inhibitory factor 1, limiting inorganic phosphate in the media, and by chronic stimulation of the GnRHR. Steady-state extracellular ATP accumulation was enhanced by pharmacological inhibition of ecto-nucleoside triphosphate diphosphohydrolases. Kisspeptin administration induced coincident GnRH and ATP release from the median eminence into the hypophyseal-portal vasculature in ovariectomized sheep. Elevated levels of extracellular ATP augmented GnRH-induced secretion of LH from pituitary cells in primary culture, which was blocked in media containing low inorganic phosphate supporting the importance of extracellular ATP levels to gonadotrope cell function. These studies indicate that gonadotropes have intrinsic ability to metabolize ATP in the extracellular space and extracellular ATP may serve as a modulator of GnRH-induced LH secretion. PMID:27482602

  10. The F0F1 ATP Synthase Complex Localizes to Membrane Rafts in Gonadotrope Cells.

    PubMed

    Allen-Worthington, Krystal; Xie, Jianjun; Brown, Jessica L; Edmunson, Alexa M; Dowling, Abigail; Navratil, Amy M; Scavelli, Kurt; Yoon, Hojean; Kim, Do-Geun; Bynoe, Margaret S; Clarke, Iain; Roberson, Mark S

    2016-09-01

    Fertility in mammals requires appropriate communication within the hypothalamic-pituitary-gonadal axis and the GnRH receptor (GnRHR) is a central conduit for this communication. The GnRHR resides in discrete membrane rafts and raft occupancy is required for signaling by GnRH. The present studies use immunoprecipitation and mass spectrometry to define peptides present within the raft associated with the GnRHR and flotillin-1, a key raft marker. These studies revealed peptides from the F0F1 ATP synthase complex. The catalytic subunits of the F1 domain were validated by immunoprecipitation, flow cytometry, and cell surface biotinylation studies demonstrating that this complex was present at the plasma membrane associated with the GnRHR. The F1 catalytic domain faces the extracellular space and catalyzes ATP synthesis when presented with ADP in normal mouse pituitary explants and a gonadotrope cell line. Steady-state extracellular ATP accumulation was blunted by coadministration of inhibitory factor 1, limiting inorganic phosphate in the media, and by chronic stimulation of the GnRHR. Steady-state extracellular ATP accumulation was enhanced by pharmacological inhibition of ecto-nucleoside triphosphate diphosphohydrolases. Kisspeptin administration induced coincident GnRH and ATP release from the median eminence into the hypophyseal-portal vasculature in ovariectomized sheep. Elevated levels of extracellular ATP augmented GnRH-induced secretion of LH from pituitary cells in primary culture, which was blocked in media containing low inorganic phosphate supporting the importance of extracellular ATP levels to gonadotrope cell function. These studies indicate that gonadotropes have intrinsic ability to metabolize ATP in the extracellular space and extracellular ATP may serve as a modulator of GnRH-induced LH secretion.

  11. Determination of local optical response functions of nanostructures with increasing complexity by using single and coupled Lorentzian oscillator models

    NASA Astrophysics Data System (ADS)

    Aeschlimann, Martin; Brixner, Tobias; Fischer, Alexander; Hensen, Matthias; Huber, Bernhard; Kilbane, Deirdre; Kramer, Christian; Pfeiffer, Walter; Piecuch, Martin; Thielen, Philip

    2016-07-01

    We reconstruct the optical response of nanostructures of increasing complexity by fitting interferometric time-resolved photoemission electron microscopy (PEEM) data from an ultrashort (21 fs) laser excitation source with different harmonic oscillator-based models. Due to its high spatial resolution of ~40 nm, PEEM is a true near-field imaging system and enables in normal incidence mode a mapping of plasmon polaritons and an intuitive interpretation of the plasmonic behaviour. Using an actively stabilized Mach-Zehnder interferometer, we record two-pulse correlation signals with 50 as time resolution that contain information about the temporal plasmon polariton evolution. Spectral amplitude and phase of excited plasmon polaritons are extracted from the recorded phase-resolved interferometric two-pulse correlation traces. We show that the optical response of a plasmon polariton generated at a gold nanoparticle can be reconstructed from the interferometric two-pulse correlation signal using a single harmonic oscillator model. In contrast, for a corrugated silver surface, a system with increased plasmonic complexity, in general an unambiguous reconstruction of the local optical response based on coupled and uncoupled harmonic oscillators, fails. Whereas for certain local responses different models can be discriminated, this is impossible for other positions. Multidimensional spectroscopy offers a possibility to overcome this limitation.

  12. Efficient Unstructured Cartesian/Immersed-Boundary Method with Local Mesh Refinement to Simulate Flows in Complex 3D Geometries

    NASA Astrophysics Data System (ADS)

    de Zelicourt, Diane; Ge, Liang; Sotiropoulos, Fotis; Yoganathan, Ajit

    2008-11-01

    Image-guided computational fluid dynamics has recently gained attention as a tool for predicting the outcome of different surgical scenarios. Cartesian Immersed-Boundary methods constitute an attractive option to tackle the complexity of real-life anatomies. However, when such methods are applied to the branching, multi-vessel configurations typically encountered in cardiovascular anatomies the majority of the grid nodes of the background Cartesian mesh end up lying outside the computational domain, increasing the memory and computational overhead without enhancing the numerical resolution in the region of interest. To remedy this situation, the method presented here superimposes local mesh refinement onto an unstructured Cartesian grid formulation. A baseline unstructured Cartesian mesh is generated by eliminating all nodes that reside in the exterior of the flow domain from the grid structure, and is locally refined in the vicinity of the immersed-boundary. The potential of the method is demonstrated by carrying out systematic mesh refinement studies for internal flow problems ranging in complexity from a 90 deg pipe bend to an actual, patient-specific anatomy reconstructed from magnetic resonance.

  13. ECG criteria for localizing the pulmonary vein origin of spontaneous atrial premature complexes: validation using intracardiac recordings.

    PubMed

    Rajawat, Yadavendra S; Gerstenfeld, Edward P; Patel, Vickas V; Dixit, Sanjay; Callans, David J; Marchlinski, Francis E

    2004-02-01

    We have shown that pacemapping from each of the pulmonary veins reveals unique surface ECG characteristics. However, application of these criteria to spontaneous atrial premature complexes is often difficult because of obscuration by the prior T wave. We hypothesized that the pulmonary vein of origin of spontaneous atrial premature complexes can be determined by measuring characteristics of the P wave whether or not the P wave was superimposed on the prior T wave. We analyzed 58 spontaneous atrial premature complexes of known pulmonary vein origin in 30 patients referred for atrial fibrillation ablation. The origin of all the atrial premature complexes was documented by detailed, intracardiac multipolar catheter mapping. Based on previous work, the criteria for distinguishing right-sided from left-sided pulmonary vein origin of atrial premature complex includes: (1) P wave duration < 120 ms; (2) P wave amplitude in lead I > 0.05 mV; and (3) P wave amplitude in leads II/III > 1.25. The criteria to separate superior from inferior pulmonary veins included the sum of the P wave amplitude in all the inferior leads greater than 0.3 mV. The combination of the P wave duration < 120 ms and the ratio of the P wave amplitude in leads II/III > 1.25, distinguished right-sided from left-sided pulmonary vein origin of spontaneous atrial premature complexes with a sensitivity of 82% and specificity of 100%. The sum of the P wave amplitude in leads II, III, and aVF > 0.3 mV distinguished superior from inferior pulmonary vein of origin with a sensitivity of 39% and specificity of 73%. The pulmonary vein origin of spontaneous atrial premature complexes can often be localized using careful quantitative analysis of the surface ECG despite superimposition of the P wave upon the T wave. Separation of right-sided from left-sided pulmonary vein origin of spontaneous atrial premature complexes can be determined with good specificity and sensitivity, while the ability to distinguish inferior

  14. Reactive Transport in Porous Media: Pore-scale Mass Exchange between Aqueous Phase and Biofilms

    NASA Astrophysics Data System (ADS)

    Hassanizadeh, S.; Qin, C.

    2013-12-01

    In the presence of water and necessary nutrients, biofilms can grow on soil grain surfaces. They occupy void pore spaces blocking water flow. As a result, some hydrodynamic properties of porous media like porosity and permeability will be reduced. This ultimately leads to a condition known as bioclogging. Also, biofilms can degrade certain compounds. So, the features of bioclogging and biodegradation in porous media with biofilms have given rise to a broad range of environmental and engineering applications, such as bioremediation, biobarriers, microbial enhanced oil recovery, and protection of steel corrosion. To date, a number of macroscale and pore-scale models for describing biodegradation in porous media with biofilms are available in the literature. At the macro scale, to simplify numerical implementation, a ';one-equation' model is normally preferred. In this approach, only the solute concentration in aqueous phase is modeled associated with the consumption of solute in biofilms. Because the solute concentration in biofilms is different from that in aqueous phase, an effectiveness factor may be used in Monod kinetics for relating reaction rate within biofilms to the solute concentration in aqueous phase. Notice that this approach has its validity domains like local equilibrium and reaction-rate limited consumption. Another approach to modeling biodegradation is referred to as a ';two-equation' model, in which one needs to simultaneously track the solute concentrations in both aqueous phase and biofilms. In addition, the two concentrations may be related by a first-order kinetic mass exchange model. This first-rate exchange model is normally represented by a constant mas exchange coefficient multiplied by the concentration difference in the two domains. Here, one may question if complex advection-diffusion-reaction processes can be represented just by a constant mass exchange coefficient. In addition, the kinetic model of mass exchange between aqueous phase

  15. The RSC complex localizes to coding sequences to regulate Pol II and histone occupancy.

    PubMed

    Spain, Marla M; Ansari, Suraiya A; Pathak, Rakesh; Palumbo, Michael J; Morse, Randall H; Govind, Chhabi K

    2014-12-01

    ATP-dependent chromatin remodelers regulate chromatin structure during multiple stages of transcription. We report that RSC, an essential chromatin remodeler, is recruited to the open reading frames (ORFs) of actively transcribed genes genome wide, suggesting a role for RSC in regulating transcription elongation. Consistent with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced upon depletion of the RSC catalytic subunit Sth1. RSC inactivation also reduced histone H3 occupancy across transcribed regions. Remarkably, the strongest effects on Pol II and H3 occupancy were confined to the genes displaying the greatest RSC ORF enrichment. Additionally, RSC recruitment to the ORF requires the activities of the SAGA and NuA4 HAT complexes and is aided by the activities of the Pol II CTD Ser2 kinases Bur1 and Ctk1. Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in maintaining chromatin structure over transcribed regions.

  16. The relationship between structure and function in locally observed complex networks

    NASA Astrophysics Data System (ADS)

    Comin, Cesar H.; Viana, Matheus P.; Costa, Luciano da F.

    2013-01-01

    Recently, studies looking at the small scale interactions taking place in complex networks have started to unveil the wealth of interactions that occur between groups of nodes. Such findings make the claim for a new systematic methodology to quantify, at node level, how dynamics are influenced (or differentiated) by the structure of the underlying system. Here we define a new measure that, based on the dynamical characteristics obtained for a large set of initial conditions, compares the dynamical behavior of the nodes present in the system. Through this measure, we find that the geographic and Barabási-Albert models have a high capacity for generating networks that exhibit groups of nodes with distinct dynamics compared to the rest of the network. The application of our methodology is illustrated with respect to two real systems. In the first we use the neuronal network of the nematode Caenorhabditis elegans to show that the interneurons of the ventral cord of the nematode present a very large dynamical differentiation when compared to the rest of the network. The second application concerns the SIS epidemic model on an airport network, where we quantify how different the distribution of infection times of high and low degree nodes can be, when compared to the expected value for the network.

  17. Dynamic Localization of Electronic Excitation in Photosynthetic Complexes Revealed with Chiral Two-Dimensional Spectroscopy

    PubMed Central

    Fidler, Andrew F.; Singh, Ved P.; Long, Phillip D.; Dahlberg, Peter D.; Engel, Gregory S.

    2014-01-01

    Time-resolved ultrafast optical probes of chiral dynamics provide a new window allowing us to explore how interactions with such structured environments drive electronic dynamics. Incorporating optical activity into time-resolved spectroscopies has proven challenging due to the small signal and large achiral background. Here, we demonstrate that two-dimensional electronic spectroscopy can be adapted to detect chiral signals and that these signals reveal how excitations delocalize and contract following excitation. We dynamically probe the evolution of chiral electronic structure in the light harvesting complex 2 of purple bacteria following photoexcitation by creating a chiral two-dimensional mapping. The dynamics of the chiral two-dimensional signal directly reports on changes in the degree of delocalization of the excitonic state following photoexcitation. The mechanism of energy transfer in this system may enhance transfer probability due to the coherent coupling among chromophores while suppressing fluorescence that arises from populating delocalized states. This generally applicable spectroscopy will provide an incisive tool to probe ultrafast transient molecular fluctuations that are obscured in non-chiral experiments. PMID:24504144

  18. Dynamic localization of electronic excitation in photosynthetic complexes revealed with chiral two-dimensional spectroscopy.

    PubMed

    Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

    2014-01-01

    Time-resolved ultrafast optical probes of chiral dynamics provide a new window allowing us to explore how interactions with such structured environments drive electronic dynamics. Incorporating optical activity into time-resolved spectroscopies has proven challenging because of the small signal and large achiral background. Here we demonstrate that two-dimensional electronic spectroscopy can be adapted to detect chiral signals and that these signals reveal how excitations delocalize and contract following excitation. We dynamically probe the evolution of chiral electronic structure in the light-harvesting complex 2 of purple bacteria following photoexcitation by creating a chiral two-dimensional mapping. The dynamics of the chiral two-dimensional signal directly reports on changes in the degree of delocalization of the excitonic states following photoexcitation. The mechanism of energy transfer in this system may enhance transfer probability because of the coherent coupling among chromophores while suppressing fluorescence that arises from populating delocalized states. This generally applicable spectroscopy will provide an incisive tool to probe ultrafast transient molecular fluctuations that are obscured in non-chiral experiments. PMID:24504144

  19. Pore network model of electrokinetic transport through charged porous media

    NASA Astrophysics Data System (ADS)

    Obliger, Amaël; Jardat, Marie; Coelho, Daniel; Bekri, Samir; Rotenberg, Benjamin

    2014-04-01

    We introduce a method for the numerical determination of the steady-state response of complex charged porous media to pressure, salt concentration, and electric potential gradients. The macroscopic fluxes of solvent, salt, and charge are computed within the framework of the Pore Network Model (PNM), which describes the pore structure of the samples as networks of pores connected to each other by channels. The PNM approach is used to capture the couplings between solvent and ionic flows which arise from the charge of the solid surfaces. For the microscopic transport coefficients on the channel scale, we take a simple analytical form obtained previously by solving the Poisson-Nernst-Planck and Stokes equations in a cylindrical channel. These transport coefficients are upscaled for a given network by imposing conservation laws for each pores, in the presence of macroscopic gradients across the sample. The complex pore structure of the material is captured by the distribution of channel diameters. We investigate the combined effects of this complex geometry, the surface charge, and the salt concentration on the macroscopic transport coefficients. The upscaled numerical model preserves the Onsager relations between the latter, as expected. The calculated macroscopic coefficients behave qualitatively as their microscopic counterparts, except for the permeability and the electro-osmotic coupling coefficient when the electrokinetic effects are strong. Quantitatively, the electrokinetic couplings increase the difference between the macroscopic coefficients and the corresponding ones for a single channel of average diameter.

  20. Pro-apoptotic Bax molecules densely populate the edges of membrane pores

    PubMed Central

    Kuwana, Tomomi; Olson, Norman H.; Kiosses, William B.; Peters, Bjoern; Newmeyer, Donald D.

    2016-01-01

    How the pro-apoptotic Bax protein permeabilizes the mitochondrial outer membrane is not fully understood. Previously, using cryo-electron microscopy (cryo-EM), we showed that activated Bax forms large, growing pores. Whether formed in liposomes or in mitochondrial outer membranes, Bax-induced pores exhibit the same morphology, with negative curvature flanking the edges and with no visible protein structure protruding from the membranes. Here we used cryo-EM to show that gold-labeled Bax molecules, after activation by Bid, became localized strictly at pore edges. This argues that Bax acts at short range to deform the membrane. Also, Bax molecules populated the walls of both small and large pores at the same density, implying that Bax is continuously recruited to the pores as they widen. Moreover, because all Bax molecules became oligomerized after membrane insertion, we infer that Bax oligomers are present at pore edges. We suggest that oligomerization may promote pore enlargement. PMID:27255832

  1. Polo kinase regulates the localization and activity of the chromosomal passenger complex in meiosis and mitosis in Drosophila melanogaster

    PubMed Central

    Carmena, Mar; Lombardia, Miguel Ortiz; Ogawa, Hiromi; Earnshaw, William C.

    2014-01-01

    Cell cycle progression is regulated by members of the cyclin-dependent kinase (CDK), Polo and Aurora families of protein kinases. The levels of expression and localization of the key regulatory kinases are themselves subject to very tight control. There is increasing evidence that crosstalk between the mitotic kinases provides for an additional level of regulation. We have previously shown that Aurora B activates Polo kinase at the centromere in mitosis, and that the interaction between Polo and the chromosomal passenger complex (CPC) component INCENP is essential in this activation. In this report, we show that Polo kinase is required for the correct localization and activity of the CPC in meiosis and mitosis. Study of the phenotype of different polo allele combinations compared to the effect of chemical inhibition revealed significant differences in the localization and activity of the CPC in diploid tissues. Our results shed new light on the mechanisms that control the activity of Aurora B in meiosis and mitosis. PMID:25376909

  2. Formation of conical fractures in sedimentary basins: Experiments involving pore fluids and implications for sandstone intrusion mechanisms

    NASA Astrophysics Data System (ADS)

    Mourgues, R.; Bureau, D.; Bodet, L.; Gay, A.; Gressier, J. B.

    2012-01-01

    Large sand intrusions often exhibit conical morphologies analogous to magmatic intrusions such as saucer-shaped or cup-shaped sills. Whereas some physical processes may be similar, we show with scaled experiments that the formation of conical sand intrusions may be favoured by the pore-pressure gradients prevailing in the host rock before sand injection. Our experiments involve injecting air into a permeable and cohesive analogue material to produce hydraulic fractures while controlling the pore pressure field. We control the state of overpressure in the overburden by applying homogeneous basal pore pressure, and then adding a second local pore pressure field by injecting air via a central injector to initiate hydraulic fractures near the injection point. In experiments involving small vertical effective stresses (small overburden, or high pore fluid overpressure), the fracturing pressure ( λfract) is supralithostatic and two dipping fractures are initiated at the injection point forming a conical structure. From theoretical considerations, we predict that high values of λfract are due to strong cohesion or high pore fluid overpressure distributed in the overburden. Such conditions are favoured by the pore pressure/stress coupling induced by both pore pressure fields. The dips of cones can be accounted for elastic-stress rotation occurring around the source. Contrary to magmatic chamber models, the aqueous fluid overpressure developed in a parent sandbody (and prevailing before the formation of injectites) may diffuse into the surrounding overburden, thus favouring stress rotation and the formation of inclined sheets far from the parent source. For experiments involving higher vertical effective stresses (thick overburden or low pore fluid overpressure), the fracturing pressure is lower than the lithostatic stress, and a single fracture is opened in mode I which then grows vertically. At a critical depth, the fracture separates into two dilatant branches forming

  3. Local cytokine changes in complex regional pain syndrome type I (CRPS I) resolve after 6 months.

    PubMed

    Lenz, Melanie; Uçeyler, Nurcan; Frettlöh, Jule; Höffken, Oliver; Krumova, Elena K; Lissek, Silke; Reinersmann, Annika; Sommer, Claudia; Stude, Philipp; Waaga-Gasser, Ana M; Tegenthoff, Martin; Maier, Christoph

    2013-10-01

    There is evidence that inflammatory processes are involved in at least the early phase of complex regional pain syndrome (CRPS). We compared a panel of pro- and antiinflammatory cytokines in skin blister fluids and serum from patients with CRPS and patients with upper-limb pain of other origin (non-CRPS) in the early stage (< 1 year) and after 6 months of pain treatment. Blister fluid was collected from the affected and contralateral nonaffected side. We used a multiplex-10 bead array cytokine assay and Luminex technology to measure protein concentrations of the cytokines interleukin-1 receptor antagonist (IL-1RA), IL-2, IL-6, IL-8, IL-10, IL-12p40, and tumor necrosis factor-alpha (TNF-α) and the chemokines eotaxin, monocyte chemotactic protein-1 (MCP-1), and macrophage inflammatory protein-1β (MIP-1β). We found bilaterally increased proinflammatory TNF-α and MIP-1β and decreased antiinflammatory IL-1RA protein levels in CRPS patients compared to non-CRPS patients. Neither group showed side differences. After 6 months under analgesic treatment, protein levels of all measured cytokines in CRPS patients, except for IL-6, significantly changed bilaterally to the level of non-CRPS patients. These changes were not related to treatment outcome. In serum, only IL-8, TNF-α, eotaxin, MCP-1, and MIP-1β were detectable without intergroup differences. Blister fluid of CRPS patients showed a bilateral proinflammatory cytokine profile. This profile seems to be relevant only at the early stage of CRPS. Almost all measured cytokine levels were comparable to those of non-CRPS patients after 6 months of analgesic treatment and were not related to treatment outcome.

  4. Triggered pore-forming agents

    DOEpatents

    Bayley, H.; Walker, B.J.; Chang, C.Y.; Niblack, B.; Panchal, R.

    1998-07-07

    An inactive pore-forming agent is revealed which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell. 30 figs.

  5. Membrane pores induced by magainin

    SciTech Connect

    Ludtke, S.J.; He, Ke; Heller, W.T.

    1996-10-29

    Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data. 33 refs., 5 figs.

  6. Pore-scale simulations of drainage in granular materials: Finite size effects and the representative elementary volume

    NASA Astrophysics Data System (ADS)

    Yuan, Chao; Chareyre, Bruno; Darve, Félix

    2016-09-01

    A pore-scale model is introduced for two-phase flow in dense packings of polydisperse spheres. The model is developed as a component of a more general hydromechanical coupling framework based on the discrete element method, which will be elaborated in future papers and will apply to various processes of interest in soil science, in geomechanics and in oil and gas production. Here the emphasis is on the generation of a network of pores mapping the void space between spherical grains, and the definition of local criteria governing the primary drainage process. The pore space is decomposed by Regular Triangulation, from which a set of pores connected by throats are identified. A local entry capillary pressure is evaluated for each throat, based on the balance of capillary pressure and surface tension at equilibrium. The model reflects the possible entrapment of disconnected patches of the receding wetting phase. It is validated by a comparison with drainage experiments. In the last part of the paper, a series of simulations are reported to illustrate size and boundary effects, key questions when studying small samples made of spherical particles be it in simulations or experiments. Repeated tests on samples of different sizes give evolution of water content which are not only scattered but also strongly biased for small sample sizes. More than 20,000 spheres are needed to reduce the bias on saturation below 0.02. Additional statistics are generated by subsampling a large sample of 64,000 spheres. They suggest that the minimal sampling volume for evaluating saturation is one hundred times greater that the sampling volume needed for measuring porosity with the same accuracy. This requirement in terms of sample size induces a need for efficient computer codes. The method described herein has a low algorithmic complexity in order to satisfy this requirement. It will be well suited to further developments toward coupled flow-deformation problems in which evolution of the

  7. 3D nuclear architecture reveals coupled cell cycle dynamics of chromatin and nuclear pores in the malaria parasite Plasmodium falciparum.

    PubMed

    Weiner, Allon; Dahan-Pasternak, Noa; Shimoni, Eyal; Shinder, Vera; von Huth, Palle; Elbaum, Michael; Dzikowski, Ron

    2011-07-01

    The deadliest form of human malaria is caused by the protozoan parasite Plasmodium falciparum. The complex life cycle of this parasite is associated with tight transcriptional regulation of gene expression. Nuclear positioning and chromatin dynamics may play an important role in regulating P. falciparum virulence genes. We have applied an emerging technique of electron microscopy to construct a 3D model of the parasite nucleus at distinct stages of development within the infected red blood cell. We have followed the distribution of nuclear pores and chromatin throughout the intra-erythrocytic cycle, and have found a striking coupling between the distributions of nuclear pores and chromatin organization. Pore dynamics involve clustering, biogenesis, and division among daughter cells, while chromatin undergoes stage-dependent changes in packaging. Dramatic changes in heterochromatin distribution coincide with a previously identified transition in gene expression and nucleosome positioning during the mid-to-late schizont phase. We also found a correlation between euchromatin positioning at the nuclear envelope and the local distribution of nuclear pores, as well as a dynamic nuclear polarity during schizogony. These results suggest that cyclic patterns in gene expression during parasite development correlate with gross changes in cellular and nuclear architecture.

  8. Strain localization in granodiorite mylonites: a microstructural and electron backscatter diffraction (EBSD) study of the South Mountains core complex, Arizona

    NASA Astrophysics Data System (ADS)

    Greenberg, R. M.; Miranda, E.

    2009-12-01

    The quantification of strain localization in detachment fault shear zones is essential to the study of continental core complex development and permits insight into continental crust rheology during extension. We present a microstructural and EBSD study of naturally deformed shear zone rocks from the footwall of the South Mountains, Arizona, core complex to interpret the deformation mechanisms that lead to strain localization along the detachment fault. The footwall of the South Mountains core complex is dominated by a Miocene composite pluton that exhibits Miocene extensional mylonitic fabrics associated with the structural development of the core complex. The composite pluton is composed of granodiorite, granite, and quartzolite, but the granodiorite is the most voluminous of the intrusive units. The detachment fault shear zone is developed within the granodiorite and quartzolite intrusive units. We conducted a microstructural and EBSD study of the Tertiary South Mountains granodiorite and quartzolite mylonites to determine the deformation mechanisms that promote strain localization. We hypothesize that the strength of quartz strongly influences strain localization in the naturally deformed granodiorite mylonites and quartzolite mylonites. The five samples were collected on an up-structure traverse through the ~60 meter thick mylonitic shear zone towards the interpreted detachment fault surface. Microstructural observation of quartz grains reveals the presence of elongate ‘ribbon grains’ with subgrain development along the rims of these grains, and irregular and sinuous sutured grain boundaries. We interpret these microstructures as evidence of Regimes 2 and 3 dynamic recrystallization. In contrast, the plagioclase feldspar and potassium feldspar crystals are microfractured with limited development of bulging grain boundaries on the rims of the feldspar grains, which we interpret as evidence of Regime 1 dynamic recrystallization. Up the traverse in the

  9. Overexpression and Nucleolar Localization of γ-Tubulin Small Complex Proteins GCP2 and GCP3 in Glioblastoma.

    PubMed

    Dráberová, Eduarda; D'Agostino, Luca; Caracciolo, Valentina; Sládková, Vladimíra; Sulimenko, Tetyana; Sulimenko, Vadym; Sobol, Margaryta; Maounis, Nicoletta F; Tzelepis, Elias; Mahera, Eleni; Křen, Leoš; Legido, Agustin; Giordano, Antonio; Mörk, Sverre; Hozák, Pavel; Dráber, Pavel; Katsetos, Christos D

    2015-07-01

    The expression, cellular distribution, and subcellular sorting of the microtubule (MT)-nucleating γ-tubulin small complex (γTuSC) proteins, GCP2 and GCP3, were studied in human glioblastoma cell lines and in clinical tissue samples representing all histologic grades of adult diffuse astrocytic gliomas (n = 54). Quantitative real-time polymerase chain reaction revealed a significant increase in the expression of GCP2 and GCP3 transcripts in glioblastoma cells versus normal human astrocytes; these were associated with higher amounts of both γTuSC proteins. GCP2 and GCP3 were concentrated in the centrosomes in interphase glioblastoma cells, but punctate and diffuse localizations were also detected in the cytosol and nuclei/nucleoli. Nucleolar localization was fixation dependent. GCP2 and GCP3 formed complexes with γ-tubulin in the nucleoli as confirmed by reciprocal immunoprecipitation experiments and immunoelectron microscopy. GCP2 and GCP3 depletion caused accumulation of cells in G2/M and mitotic delay but did not affect nucleolar integrity. Overexpression of GCP2 antagonized the inhibitory effect of the CDK5 regulatory subunit-associated tumor suppressor protein 3 (C53) on DNA damage G2/M checkpoint activity. Tumor cell GCP2 and GCP3 immunoreactivity was significantly increased over that in normal brains in glioblastoma samples; it was also associated with microvascular proliferation. These findings suggest that γTuSC protein dysregulation in glioblastomas may be linked to altered transcriptional checkpoint activity or interaction with signaling pathways associated with a malignant phenotype. PMID:26079448

  10. Saturation fluorimetry of complex organic compounds with a high local concentration of fluorophores (by the example of phytoplankton)

    SciTech Connect

    Maslov, D V; Ostroumov, E E; Fadeev, V V

    2006-02-28

    Saturation of fluorescence of complex organic compounds with a high local concentration of fluorescing molecules (fluorophores), when singlet-singlet annihilation makes a noticeable contribution to saturation, is considered. The fluorescence saturation curve is obtained analytically for the case of a rectangular temporal and spatial distribution of photons in a laser pulse. It is shown that the fluorescence saturation curve depends on the parameter {Phi}{sub 0}, which is proportional to the concentration of fluorescing molecules, and on the parameters A, B, and {alpha} describing the influence of singlet-singlet annihilation, bleaching of an optically thin layer, and nonstationarity of excitation, respectively. The fluorescence saturation curves are studied experimentally for compounds with a high local concentration of fluorescing molecules such as molecules of a monoculture of diatomic alga Thalassiosira weissflogii. The experimental fluorescence saturation curves are well described by the obtained analytic expression. The values of the parameter {Phi}{sub 0}, proportional to the concentration of chlorophyll a, and the parameter A (for the first time) are obtained from the alga fluorescence saturation curves. (laser applications and other topics in quantum electronics)

  11. Chaos and localization in the wave functions of complex atoms Nd I, Pm I, and Sm I

    SciTech Connect

    Angom, Dilip; Kota, V.K.B.

    2005-04-01

    Wave functions of complex lanthanide atoms Nd I, Pm I, and Sm I, obtained via multiconfiguration Dirac-Fock method, are analyzed for density of states in terms of partial densities, strength functions [F{sub k}(E)], number of principal components [{xi}{sub 2}(E)], and occupancies ({sup E}) of single-particle orbits using embedded Gaussian orthogonal ensemble of one plus two-body random matrix ensembles [EGOE(1+2)]. It is seen that density of states are in general multi-modal, F{sub k}(E)'s exhibit variations as function of the basis states energy and {xi}{sub 2}(E)'s show structures arising from localized states. The sources of these departures from EGOE(1+2) are investigated by examining the partial densities, correlations between F{sub k}(E), {xi}{sub 2}(E), and {sup E} and also by studying the structure of the Hamiltonian matrices. These studies point out the operation of EGOE(1+2) but at the same time suggest that weak admixing between well separated configurations should be incorporated into EGOE(1+2) for more quantitative description of chaos and localization in Nd I, Pm I, and Sm I.

  12. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.

    PubMed

    Shan, Hong; Wang, Zihao; Zhang, Fa; Xiong, Yong; Yin, Chang-Cheng; Sun, Fei

    2016-01-01

    Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.

  13. Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function.

    PubMed

    Tan, William; Schauder, Curtis; Naryshkina, Tatyana; Minakhina, Svetlana; Steward, Ruth

    2016-02-15

    Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in neurological and reproductive developmental defects in humans and flies. FMRP (Fragile-X Mental Retardation Protein) is a nucleo-cytoplasmic shuttling protein, involved in mRNA silencing and translational repression. Both Zfrp8 and Fmr1 have essential functions in the Drosophila ovary. In this study, we identified FMRP, Nufip (Nuclear Fragile-X Mental Retardation Protein-interacting Protein) and Tral (Trailer Hitch) as components of a Zfrp8 protein complex. We show that Zfrp8 is required in the nucleus, and controls localization of FMRP in the cytoplasm. In addition, we demonstrate that Zfrp8 genetically interacts with Fmr1 and tral in an antagonistic manner. Zfrp8 and FMRP both control heterochromatin packaging, also in opposite ways. We propose that Zfrp8 functions as a chaperone, controlling protein complexes involved in RNA processing in the nucleus.

  14. Assembly of a β2-adrenergic receptor—GluR1 signalling complex for localized cAMP signalling

    PubMed Central

    Joiner, Mei-ling A; Lisé, Marie-France; Yuen, Eunice Y; Kam, Angel Y F; Zhang, Mingxu; Hall, Duane D; Malik, Zulfiqar A; Qian, Hai; Chen, Yucui; Ulrich, Jason D; Burette, Alain C; Weinberg, Richard J; Law, Ping-Yee; El-Husseini, Alaa; Yan, Zhen; Hell, Johannes W

    2010-01-01

    Central noradrenergic signalling mediates arousal and facilitates learning through unknown molecular mechanisms. Here, we show that the β2-adrenergic receptor (β2AR), the trimeric Gs protein, adenylyl cyclase, and PKA form a signalling complex with the AMPA-type glutamate receptor subunit GluR1, which is linked to the β2AR through stargazin and PSD-95 and their homologues. Only GluR1 associated with the β2AR is phosphorylated by PKA on β2AR stimulation. Peptides that interfere with the β2AR–GluR1 association prevent this phosphorylation of GluR1. This phosphorylation increases GluR1 surface expression at postsynaptic sites and amplitudes of EPSCs and mEPSCs in prefrontal cortex slices. Assembly of all proteins involved in the classic β2AR–cAMP cascade into a supramolecular signalling complex and thus allows highly localized and selective regulation of one of its major target proteins. PMID:19942860

  15. Zfrp8 forms a complex with fragile-X mental retardation protein and regulates its localization and function.

    PubMed

    Tan, William; Schauder, Curtis; Naryshkina, Tatyana; Minakhina, Svetlana; Steward, Ruth

    2016-02-15

    Fragile-X syndrome is the most commonly inherited cause of autism and mental disabilities. The Fmr1 (Fragile-X Mental Retardation 1) gene is essential in humans and Drosophila for the maintenance of neural stem cells, and Fmr1 loss results in neurological and reproductive developmental defects in humans and flies. FMRP (Fragile-X Mental Retardation Protein) is a nucleo-cytoplasmic shuttling protein, involved in mRNA silencing and translational repression. Both Zfrp8 and Fmr1 have essential functions in the Drosophila ovary. In this study, we identified FMRP, Nufip (Nuclear Fragile-X Mental Retardation Protein-interacting Protein) and Tral (Trailer Hitch) as components of a Zfrp8 protein complex. We show that Zfrp8 is required in the nucleus, and controls localization of FMRP in the cytoplasm. In addition, we demonstrate that Zfrp8 genetically interacts with Fmr1 and tral in an antagonistic manner. Zfrp8 and FMRP both control heterochromatin packaging, also in opposite ways. We propose that Zfrp8 functions as a chaperone, controlling protein complexes involved in RNA processing in the nucleus. PMID:26772998

  16. Local Pathways in Coherent Electron Transport through Iron Porphyrin Complexes: A Challenge for First-Principles Transport Calculations

    SciTech Connect

    Herrmann, C.; Solomon, G.C.; Ratner, Mark A.

    2010-12-09

    We investigate the coherent electron transport properties of a selection of iron porphyrin complexes in their low-spin and high-spin states, binding the system to metallic electrodes with three different substitution patterns. We use a study of the local transmission through the complexes and their molecular orbitals to show the role of the various components of the molecular structure in mediating electron transport. While there are energies where the metal center and the axial ligands participate in transport, in the off-resonant energy range, these components simply form a scaffold, and the transport is dominated by transmission through the porphyrin macrocyle alone. This is still true when going from the low-spin to the high-spin state, except that now, an additional iron-centered MO contributes to transport in the formerly off-resonant region. It is found that while the choice of the exchange-correlation functional can strongly influence the quantitative results, our qualitative conclusions hold irrespective of the functional employed.

  17. Molecular characterization of dissolved organic matter in pore water of continental shelf sediments

    NASA Astrophysics Data System (ADS)

    Schmidt, Frauke; Elvert, Marcus; Koch, Boris P.; Witt, Matthias; Hinrichs, Kai-Uwe

    2009-06-01

    Dissolved organic matter (DOM) in sediment pore water is a complex molecular mixture reflecting various sources and biogeochemical processes. In order to constrain those sources and processes, molecular variations of pore water DOM in surface sediments from the NW Iberian shelf were analyzed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and compared to river and marine water column DOM. Weighted average molecular element ratios of oxygen to carbon ((O/C) wa) and hydrogen to carbon ((H/C) wa) provided general information about DOM sources. DOM in local rivers was more oxygenated ((O/C) wa 0.52) and contained less hydrogen ((H/C) wa 1.15) than marine pore water DOM (mean (O/C) wa 0.50, mean (H/C) wa 1.26). The relative abundance of specific compound groups, such as highly oxygenated aromatic compounds or nitrogen-bearing compounds with low H/C ratios, correspond to a high concentration of lignin phenols (160 μg/g sediment dry weight) and a high TOC/TN ratio (13.3) in the sedimentary organic matter and were therefore assigned to terrestrial sources. The lower degree of unsaturation and a higher relative abundance of nitrogen-bearing compounds in the pore water DOM reflected microbial activity within the sediment. One sampling site on the shelf with a high sediment accumulation, and a humic-rich river sample showed a wide range of sulfur compounds in the DOM, accompanied by a higher abundance of lipid biomarkers for sulfate-reducing bacteria, probably indicating early diagenetic sulfurization of organic matter.

  18. How Could SNARE Proteins Open a Fusion Pore?

    PubMed Central

    Fang, Qinghua

    2014-01-01

    The SNARE (Soluble NSF Attachment protein REceptor) complex, which in mammalian neurosecretory cells is composed of the proteins synaptobrevin 2 (also called VAMP2), syntaxin, and SNAP-25, plays a key role in vesicle fusion. In this review, we discuss the hypothesis that, in neurosecretory cells, fusion pore formation is directly accomplished by a conformational change in the SNARE complex via movement of the transmembrane domains. PMID:24985331

  19. Assembly of the nuclear pore: biochemically distinct steps revealed with NEM, GTP gamma S, and BAPTA

    PubMed Central

    1996-01-01

    A key event in nuclear formation is the assembly of functional nuclear pores. We have used a nuclear reconstitution system derived from Xenopus eggs to examine the process of nuclear pore assembly in vitro. With this system, we have identified three reagents which interfere with nuclear pore assembly, NEM, GTP gamma S, and the Ca++ chelator, BAPTA. These reagents have allowed us to determine that the assembly of a nuclear pore requires the prior assembly of a double nuclear membrane. Inhibition of nuclear vesicle fusion by pretreatment of the membrane vesicle fraction with NEM blocks pore complex assembly. In contrast, NEM treatment of already fused double nuclear membranes does not block pore assembly. This indicates that NEM inhibits a single step in pore assembly--the initial fusion of vesicles required to form a double nuclear membrane. The presence of GTP gamma S blocks pore assembly at two distinct steps, first by preventing fusion between nuclear vesicles, and second by blocking a step in pore assembly that occurs on already fused double nuclear membranes. Interestingly, when the Ca2+ chelator BAPTA is added to a nuclear assembly reaction, it only transiently blocks nuclear vesicle fusion, but completely blocks nuclear pore assembly. This results in the formation of a nucleus surrounded by a double nuclear membrane, but devoid of nuclear pores. To order the positions at which GTP gamma S and BAPTA interfere with pore assembly, a novel anchored nuclear assembly assay was developed. This assay revealed that the BAPTA-sensitive step in pore assembly occurs after the second GTP gamma S-sensitive step. Thus, through use of an in vitro nuclear reconstitution system, it has been possible to biochemically define and order multiple steps in nuclear pore assembly. PMID:8567730

  20. DESIGN INFORMATION ON FINE PORE AERATION SYSTEMS

    EPA Science Inventory

    Field studies were conducted over several years at municipal wastewater treatment plants employing line pore diffused aeration systems. These studies were designed to produce reliable information on the performance and operational requirements of fine pore devices under process ...

  1. Primary structure analysis of an integral membrane glycoprotein of the nuclear pore

    PubMed Central

    1989-01-01

    The complete primary structure of an integral membrane glycoprotein of the nuclear pore was deduced from the cDNA sequence. The cDNA encodes a polypeptide of 204,205 D containing a 25-residue-long signal sequence, two hydrophobic segments that could function as transmembrane segments, and 13 potential N-linked oligosaccharide addition sites. Endoglycosidase H reduces the molecular mass by approximately 9 kD suggesting that not all of these 13 sites are used. We discuss possible models for the topology of this protein in the pore membrane as well as a possible role in the formation of pores and pore complexes. PMID:2738089

  2. Viruses Challenge Selectivity Barrier of Nuclear Pores

    PubMed Central

    Labokha, Aksana A.; Fassati, Ariberto

    2013-01-01

    Exchange between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs) embedded in the double membrane of the nuclear envelope. NPC permeability barrier restricts the entry of inert molecules larger than 5 nm in diameter but allows facilitated entry of selected cargos, whose size can reach up to 39 nm. The translocation of large molecules is facilitated by nuclear transport receptors (NTRs) that have affinity to proteins of NPC permeability barrier. Viruses that enter the nucleus replicate evolved strategies to overcome this barrier. In this review, we will discuss the functional principles of NPC barrier and nuclear transport machinery, as well as the various strategies viruses use to cross the selective barrier of NPCs. PMID:24084236

  3. Antimicrobial Peptides in Toroidal and Cylindrical Pores

    PubMed Central

    Mihajlovic, Maja

    2010-01-01

    Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize biological membranes. Their mechanism of action is still not well understood. Here we investigate the preference of alamethicin and melittin for pores of different shapes, using molecular dynamics (MD) simulations of the peptides in pre-formed toroidal and cylindrical pores. When an alamethicin hexamer is initially embedded in a cylindrical pore, at the end of the simulation the pore remains cylindrical or closes if glutamines in the N-termini are not located within the pore. On the other hand, when a melittin tetramer is embedded in toroidal pore or in a cylindrical pore, at the end of the simulation the pore is lined both with peptides and lipid headgroups, and, thus, can be classified as a toroidal pore. These observations agree with the prevailing views that alamethicin forms barrel-stave pores whereas melittin forms toroidal pores. Both alamethicin and melittin form amphiphilic helices in the presence of membranes, but their net charge differs; at pH ~7, the net charge of alamethicin is −1 whereas that of melittin is +5. This gives rise to stronger electrostatic interactions of melittin with membranes than those of alamethicin. The melittin tetramer interacts more strongly with lipids in the toroidal pore than in the cylindrical one, due to more favorable electrostatic interactions. PMID:20403332

  4. SCAM analysis of Panx1 suggests a peculiar pore structure.

    PubMed

    Wang, Junjie; Dahl, Gerhard

    2010-11-01

    Vertebrates express two families of gap junction proteins: the well-characterized connexins and the pannexins. In contrast to connexins, pannexins do not appear to form gap junction channels but instead function as unpaired membrane channels. Pannexins have no sequence homology to connexins but are distantly related to the invertebrate gap junction proteins, innexins. Despite the sequence diversity, pannexins and connexins form channels with similar permeability properties and exhibit similar membrane topology, with two extracellular loops, four transmembrane (TM) segments, and cytoplasmic localization of amino and carboxy termini. To test whether the similarities extend to the pore structure of the channels, pannexin 1 (Panx1) was subjected to analysis with the substituted cysteine accessibility method (SCAM). The thiol reagents maleimidobutyryl-biocytin and 2-trimethylammonioethyl-methanethiosulfonate reacted with several cysteines positioned in the external portion of the first TM segment (TM1) and the first extracellular loop. These data suggest that portions of TM1 and the first extracellular loop line the outer part of the pore of Panx1 channels. In this aspect, the pore structures of Panx1 and connexin channels are similar. However, although the inner part of the pore is lined by amino-terminal amino acids in connexin channels, thiol modification was detected in carboxyterminal amino acids in Panx1 channels by SCAM analysis. Thus, it appears that the inner portion of the pores of Panx1 and connexin channels may be distinct.

  5. Impacts of simulated drought on pore water chemistry of peatlands.

    PubMed

    Juckers, Myra; Watmough, Shaun A

    2014-01-01

    Northern peatlands are increasingly threatened by climate change and industrial activities. This study examined the impact of simulated droughts on pore water chemistry at six peatlands in Sudbury, Ontario, that differ in copper (Cu), nickel (Ni) and cobalt (Co) contamination, including a site that had been previously limed. All sites responded similarly to simulated drought: pore water pH declined significantly following the 30 day drought and the decline was greater following the 60 day drought treatment. The decline in pore water pH was due to increasing sulphate concentrations, whereas nitrate increased more in the 60 day drought treatment. Decreases in pH were accompanied by large increases in Ni and Co that greatly exceeded provincial water quality guidelines. In contrast, dissolved organic carbon (DOC) concentrations decreased significantly following drought, along with concentrations of Cu and Al, which are strongly complexed by organic acids.

  6. Complex rupture process of the March 19, 2013, Rudna mine (Poland) seismic event - local and regional view

    NASA Astrophysics Data System (ADS)

    Rudzinski, Lukasz; Cesca, Simone; Lizurek, Grzegorz

    2015-04-01

    On March 19th, 2013 a strong shallow induced seismic event struck a mining panel in the room-and-pillar Rudna copper mine, SE Poland. The event caused important damages at the mining tunnel and trapped 19 miners, which were safely rescued few hour later. Despite mining induced seismicity is frequent at this mine, the March 19 event was unusual because of its larger magnitude, its occurrence far from the mining stopes, and because it was accompanied by a strong hazardous rockburst. The mining inspections following the event verified the occurrence of a rockfall with tunnel floor uplift, but also recognized the presence of a faulting structure at the hypocentral location. The availability of three monitoring networks, including local and regional data, short-period and broadband seismometers, as well as surface and in-mine installation, give an optimal set up to determine rupture parameters and compare the performance and results from different installations. We perform waveform and spectral based analysis to infer source properties, with a particular interest to the determination of the rupture processes, using different moment tensor inversion techniques. Our results are surprisingly different, ranging from a dominant thrust mechanism, resolved at closest distances, to a collapse-type rupture, resolved at regional distances. We proof that a complex rupture model is needed to explain all observations and justify these discrepancies. The final scenario indicates that the rupture nucleated as a weaker thrust mechanism, along a pre-existing weakened surface, and continued in a more energetic collapse event. The local surface LUMINEOS network has the potential to resolve both subevents, but not using a standard moment tensor decomposition. We propose here a new moment tensor decomposition and an alternative moment tensor fitting procedure, which can be used to analyze the moment tensor of collapse sources.

  7. Superposed local and regional paleostresses: Fault-slip analysis of Neogene extensional faulting near coeval caldera complexes, Yucca Flat, Nevada

    SciTech Connect

    Minor, S.A.

    1995-06-10

    Numerous reduced stress tensors are computed by multiple inversions of 906 temporally and spatially partitioned fault-slip data from the Yucca Flat region in the southwest Nevada volcanic field to constrain the Neogene paleostress and faulting history and to investigate how the regional tectonic stress field was affected by local caldera magmatism. Perturbed, shallow (<400 m), pre-11 Ma paleostress configurations, determined west and northwest of present (post-11 Ma) Yucca Flat basin, existed during mild extensional faulting and are attributed to superposition of transient caldera-magmatic stresses on the regional stress field. A brief ({approximately} 0.5 m.y.) change to a strike-slip stress state occurred at about 13 Ma and was accompanied by small-offset, quasi-conjugate strike-slip faulting. This stress state was most distinct, relative to a normalslip state, near calderas where stress solutions and fault relations indicate closer affinities to a reverse-slip state. Inferred 11.6-11.45 Ma paleostress tensors indicate radial tension associated with either initial caldera collapse or local post-collapse topographic modification of the stress field. Post-11 Ma normal-slip stress tensors are associated with normal- and oblique-slip faults that accommodated subsidence and eastward extension of Yucca Flat basin away from the caldera complexes. These tensors do not indicate stress modifications due to residual caldera-related effects and thus were used to infer post-11 Ma regional stress changes. The stress field has rotated as much as 65{degrees} clockwise since 11 Ma during extensional development of Yucca Flat basin, with most of the rotation and extension occurring before about 8.5 Ma. Results suggest that shallow magmatism and caldera development can strongly alter extensional tectonic stress fields, fault patterns, and slip directions in the uppermost crust out to distances of roughly two magma chamber radii away from a magma body. 59 refs., 11 figs., 2 tabs.

  8. Strongly-local reductions and the complexity/efficient approximability of algebra and optimization on abstract algebraic structures

    SciTech Connect

    Hunt, H. B.; Marathe, M. V.; Stearns, R. E.

    2001-01-01

    We demonstrate how the concepts of algebraic representability and strongly-local reductions developed here and in [HSM00] can be used to characterize the computational complexity/efficient approximability of a number of basic problems and their variants, on various abstract algebraic structures F. These problems include the following: (1) A1gebra:Determine the solvability, unique solvability, number of solutions, etc., of a system of equations on F. Determine the equivalence of two formulas or straight-line programs on F. 2. 0ptimization:Let {epsilon} > 0. (a) Determine the maximum number of simultaneously satisfiable equations in a system of equations on F; or approximate this number within a multiplicative factor of n{sup {epsilon}}. (b) Determine the maximum value of an objective function subject to satisfiable algebraically expressed constraints on F; or approximate this maximum value within a multiplicative factor of n{sup {epsilon}}. (c) Given a formula or straight-line program, find a minimum size equivalent formula or straightline program; or find an equivalent formula or straight-line program of size {le} f (minimum). Both finite and infinite algebraic structures are considered. These finite structures include all finite nondegenerate lattices and all finite rings or semi-rings with a nonzero element idempotent under multiplication (e.g. all non-degenerate finite unitary rings or semi-rings); and these infinite structures include the natural numbers, integers, real numbers, various algebras on these structures, all ordered rings, many cancellative semi-rings, and all infinite lattices with two elements a,b such that a is covered by b. Our results significantly extend a number of results by Ladner [La89], Condon, et. al. [CF+93], Khanna, et.al [KSW97], Cr951 and Zuckerman [Zu93] on the complexity and approximbaility of combinatorial problems.

  9. Assembling the puzzle: Oligomerization of α-pore forming proteins in membranes☆

    PubMed Central

    García-Sáez, Ana J.

    2016-01-01

    Pore forming proteins (PFPs) share the ability of creating pores that allow the passage of ions, proteins or other constituents through a wide variety of target membranes, ranging from bacteria to humans. They often cause cell death, as pore formation disrupts the membrane permeability barrier required for maintaining cell homeostasis. The organization into supramolecular complexes or oligomers that pierce the membrane is a common feature of PFPs. However, the molecular pathway of self-assembly and pore opening remains unclear. Here, we review the most recent discoveries in the mechanism of membrane oligomerization and pore formation of a subset of PFPs, the α-PFPs, whose pore-forming domains are formed by helical segments. Only now we are starting to grasp the molecular details of their function, mainly thanks to the introduction of single molecule microscopy and nanoscopy techniques. PMID:26375417

  10. Integrated landslide monitoring: rainfalls, pore water pressures and surface movements

    NASA Astrophysics Data System (ADS)

    Berti, M.; Casula, G.; Elmi, C.; Fabris, M.; Ghirotti, M.; Loddo, F.; Mora, P.; Pesci, A.; Simoni, A.

    2003-04-01

    Rainfall-induced landslides involving clay-rich soils are widely represented in the Apennines. They cover up to 30% of the slopes forming the relief constituted by chaotic clayey units and are typically subject to repeated reactivations of the movement which are often triggered by a series of discrete failures located in the upper part (headscarp). Failures and movement can then propagate downslope and reactivate the whole landslide deposit which displays a typical elongated body, limited depth and a fan-shaped toe as a result of successive slow earth-flow like movements. An experimental monitoring programme was designed and is currently operating on the Rocca Pitigliana landslide whose characteristics well represent the above described type of movements. Its last parossistic movement date back to 1999 and, since then, remedial works were realized on behalf of local authorities. They basically consist of surficial and deep drainage works located on the landslide body. Experimental activities focus on the main headscarp whose morphology and sub-surface water circulation scheme were unaffected by the interventions. The monitoring approach includes measuring rainfalls and pore-pressure responses in both saturated and unsaturated soils. Surficial movements are continuously measured by means of GPS permanent stations and by wire extensometers which allow real time control of headscarp activity. Main aim of the monitoring activities is to provide experimental data, which can be used to test various existing hydrologic models and to identify triggering conditions. Since the ‘70s, many hydrologic models have been proposed to describe the pore water pressure distribution within the soil and its response to precipitation. The topic has recently drawn growing attention because of the recognized importance in landslide triggering but still experimental data are very much needed in order to obtain and validate capable predicting tools. This is mostly due to the multiple and

  11. Pore formation by Cry toxins.

    PubMed

    Soberón, Mario; Pardo, Liliana; Muñóz-Garay, Carlos; Sánchez, Jorge; Gómez, Isabel; Porta, Helena; Bravo, Alejandra

    2010-01-01

    Bacillus thuringiensis (Bt) bacteria produce insecticidal Cry and Cyt proteins used in the biological control of different insect pests. In this review, we will focus on the 3d-Cry toxins that represent the biggest group of Cry proteins and also on Cyt toxins. The 3d-Cry toxins are pore-forming toxins that induce cell death by forming ionic pores into the membrane of the midgut epithelial cells in their target insect. The initial steps in the mode of action include ingestion of the protoxin, activation by midgut proteases to produce the toxin fragment and the interaction with the primary cadherin receptor. The interaction of the monomeric CrylA toxin with the cadherin receptor promotes an extra proteolytic cleavage, where helix alpha-1 of domain I is eliminated and the toxin oligomerization is induced, forming a structure of 250 kDa. The oligomeric structure binds to a secondary receptor, aminopeptidase N or alkaline phosphatase. The secondary receptor drives the toxin into detergent resistant membrane microdomains formingpores that cause osmotic shock, burst of the midgut cells and insect death. Regarding to Cyt toxins, these proteins have a synergistic effect on the toxicity of some Cry toxins. Cyt proteins are also proteolytic activated in the midgut lumen of their target, they bind to some phospholipids present in the mosquito midgut cells. The proposed mechanism of synergism between Cry and Cyt toxins is that Cyt1Aa function as a receptor for Cry toxins. The Cyt1A inserts into midgut epithelium membrane and exposes protein regions that are recognized by Cry11Aa. It was demonstrated that this interaction facilitates the oligomerization of Cry11Aa and also its pore formation activity.

  12. Sediment Transport, Complex Topography, and Hydrokinetic Turbines: Bedform Dynamics, Local Scour, and the Effect on Turbine Performance.

    NASA Astrophysics Data System (ADS)

    Guala, M.; Hill, C.; Kozarek, J. L.; Sotiropoulos, F.

    2015-12-01

    Multi-scale experiments on the interactions between axial-flow marine hydrokinetic (MHK) turbines, sediment transport and complex channel topography were performed at St. Anthony Falls Laboratory (SAFL), University of Minnesota. Model axial-flow three-bladed turbines (rotor diameters, dT = 0.15m and 0.5m) were installed in open channel flumes with both erodible and non-erodible substrates. In erodible channels, device-induced local scour was monitored over several hydraulic conditions (clear water vs. live bedload transport) and material sizes. Synchronous velocity, bed elevation and turbine performance measurements provide an indication into the effect channel topography has on device performance. A novel data acquisition imaging system provided methods for monitoring the dynamics of bedform transport as they approached and migrated past an operating axial-flow turbine. Experiments were also performed in a realistic meandering outdoor research channel with active sediment transport to investigate MHK turbine interactions with bedform migration and turbulent flow in asymmetric channels, providing new insight into turbine-sediment interactions and turbine wake behavior in curving channels. Results provide the foundation for investigating advanced turbine control strategies for optimal power production in non-stationary environments, while also providing robust data for computational model validation enabling further investigations into the interactions between energy conversion devices and the physical environment.

  13. The mitochondrial permeability transition pore and its role in cell death.

    PubMed Central

    Crompton, M

    1999-01-01

    This article reviews the involvement of the mitochondrial permeability transition pore in necrotic and apoptotic cell death. The pore is formed from a complex of the voltage-dependent anion channel (VDAC), the adenine nucleotide translocase and cyclophilin-D (CyP-D) at contact sites between the mitochondrial outer and inner membranes. In vitro, under pseudopathological conditions of oxidative stress, relatively high Ca2+ and low ATP, the complex flickers into an open-pore state allowing free diffusion of low-Mr solutes across the inner membrane. These conditions correspond to those that unfold during tissue ischaemia and reperfusion, suggesting that pore opening may be an important factor in the pathogenesis of necrotic cell death following ischaemia/reperfusion. Evidence that the pore does open during ischaemia/reperfusion is discussed. There are also strong indications that the VDAC-adenine nucleotide translocase-CyP-D complex can recruit a number of other proteins, including Bax, and that the complex is utilized in some capacity during apoptosis. The apoptotic pathway is amplified by the release of apoptogenic proteins from the mitochondrial intermembrane space, including cytochrome c, apoptosis-inducing factor and some procaspases. Current evidence that the pore complex is involved in outer-membrane rupture and release of these proteins during programmed cell death is reviewed, along with indications that transient pore opening may provoke 'accidental' apoptosis. PMID:10393078

  14. Mammalian actin-related protein 2/3 complex localizes to regions of lamellipodial protrusion and is composed of evolutionarily conserved proteins.

    PubMed Central

    Machesky, L M; Reeves, E; Wientjes, F; Mattheyse, F J; Grogan, A; Totty, N F; Burlingame, A L; Hsuan, J J; Segal, A W

    1997-01-01

    Human neutrophils contain a complex of proteins similar to the actin-related protein 2/3 (Arp2/3) complex of Acanthamoeba. We have obtained peptide sequence information for each member of the putative seven-protein complex previously described for Acanthamoeba and human platelets. From the peptide sequences we have identified cDNA species encoding three novel proteins in this complex. We find that in addition to Arp2 and Arp3, this complex contains a relative of the human (Suppressor of Profilin) SOP2Hs protein and four previously unknown proteins. These proteins localize in the cytoplasm of fibroblasts that lack lamellipodia, but are enriched in lamellipodia on stimulation with serum or platelet-derived growth factor. We propose a conserved and dynamic role for this complex in the organization of the actin cytoskeleton. PMID:9359840

  15. Novel biometrics based on nose pore recognition

    NASA Astrophysics Data System (ADS)

    Song, Shangling; Ohnuma, Kazuhiko; Liu, Zhi; Mei, Liangmo; Kawada, Akira; Monma, Tomoyuki

    2009-05-01

    We present a new member of the biometrics family-i.e., nose pores-which uses particularly interesting properties of nose pores as a basis for noninvasive biometric assessment. The pore distribution on the nose is stable and easily inspected. More important, nose pore distribution features are distinguishable between different persons. Thus, these features can be used for personal identification. However, little work has been done on nose pores as a biometric identifier. We have developed an end-to-end recognition system based on nose pore features. We also made use of a database of nose pore images obtained over a long period to examine the performance of nose pores as a biometric identifier. This research showed that the nose pore is a promising candidate for biometric identification and deserves further research. The experimental results based on the unique nose pores database demonstrated that nose pores can give an 88.07% correct recognition rate for biometric identification, which showed this biometric identifier's feasibility and effectiveness.

  16. Diffusive resistance of avian eggshell pores.

    PubMed

    Tøien, O; Paganelli, C V; Rahn, H; Johnson, R R

    1988-12-01

    Resistance to gas diffusion through the avian eggshell resides in the microscopic pores which penetrate the shell. We calculated the resistance to water vapor diffusion of individual pores in the shells of 23 species of avian eggs, based on measurements of pore dimensions taken from drawings of 321 pore casts published by Tyler (1962, 1964, 1965) and Tyler and Simkiss (1959). Diffusive resistances were calculated from Fick's first law, using a 100-segment model of each pore. In addition, we added 2 series resistances, calculated from Stefan's law, to account for boundary layer resistances at the inner and outer pore apertures. Convective resistances for the same 100-segment model were computed from Poiseuille's law. A special, symmetrically branching model is presented for the diffusive resistance of the branched pores of ostrich eggshells, based on the drawings of Tyler and Simkiss (1959). The total aperture resistance was less than 6.2% of total pore resistance, while the outside aperture effect was on average only 1.5%. The calculated average pore conductance for all species was 5.4 micrograms (day Torr)-1, about three times higher than the average value of 1.6 micrograms (day Torr)-1 obtained by dividing measured shell conductance by the number of pores (Ar and Rahn, 1985). A possible explanation for this discrepancy is advanced. However, it is to be noted that in spite of the discrepancy, both calculated and functional values of pore conductance appear to be independent of egg mass.

  17. Glycosylation of the nuclear pore

    PubMed Central

    Li, Bin; Kohler, Jennifer J.

    2014-01-01

    The O-linked β-N-acetylglucosamine (O-GlcNAc) post-translational modification was first discovered thirty years ago and is highly concentrated in the nuclear pore. In the years since the discovery of this single sugar modification, substantial progress has been made in understanding the biochemistry of O-GlcNAc and its regulation. Nonetheless, O-GlcNAc modification of proteins continues to be overlooked, due in large part to the lack of reliable methods available for its detection. Recently, a new crop of immunological and chemical detection reagents has changed the research landscape. Using these tools, approximately 1000 O-GlcNAc-modified proteins have been identified. While other forms of glycosylation are typically associated with extracellular proteins, O-GlcNAc is abundant on nuclear and cytoplasmic proteins. In particular, phenylalanine-glycine (FG) nucleoporins (NUPs) are heavily O-GlcNAc-modified. Recent experiments are beginning to provide insight into the functional implications of O-GlcNAc modification on certain proteins, but its role in the nuclear pore has remained enigmatic. However, tantalizing new results suggest that O-GlcNAc may play roles in regulating nucleocytoplasmic transport. PMID:24423194

  18. A thermodynamic approach to Alamethicin pore formation

    PubMed Central

    Rahaman, Asif; Lazaridis, Themis

    2013-01-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11 Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6 Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8 Å pore and the octamer in an 11 Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted “barrel-stave” model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself. PMID:24071593

  19. Passive permeability and effective pore size of HeLa cell nuclear membranes.

    PubMed

    Samudram, Arunkarthick; Mangalassery, Bijeesh M; Kowshik, Meenal; Patincharath, Nandakumar; Varier, Geetha K

    2016-09-01

    Nuclear pore complexes in the nuclear membrane act as the sole gateway of transport of molecules from the cytoplasm to the nucleus and vice versa. Studies on biomolecular transport through nuclear membranes provide vital data on the nuclear pore complexes. In this work, we use fluorescein isothiocyanate-labeled dextran molecules as a model system and study the passive nuclear import of biomolecules through nuclear pore complexes in digitonin-permeabilized HeLa cells. Experiments are carried out under transient conditions in the time lapse imaging scheme using an in-house constructed confocal laser scanning microscope. Transport rates of dextran molecules having molecular weights of 4-70 kDa corresponding to Stokes radius of 1.4-6 nm are determined. Analyzing the permeability of the nuclear membrane for different sizes the effective pore radius of HeLa cell nuclear membrane is determined to be 5.3 nm, much larger than the value reported earlier using proteins as probe molecules. The range of values reported for the nuclear pore radius suggest that they may not be rigid structures and it is quite probable that the effective pore size of nuclear pore complexes is critically dependent on the probe molecules and on the environmental factors.

  20. Localization of Burkholderia cepacia Complex Bacteria in Cystic Fibrosis Lungs and Interactions with Pseudomonas aeruginosa in Hypoxic Mucus

    PubMed Central

    Abdullah, Lubna H.; Perlmutt, Olivia S.; Albert, Daniel; Davis, C. William; Arnold, Roland R.; Yankaskas, James R.; Gilligan, Peter; Neubauer, Heiner; Randell, Scott H.; Boucher, Richard C.

    2014-01-01

    The localization of Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) lungs, alone or during coinfection with Pseudomonas aeruginosa, is poorly understood. We performed immunohistochemistry for Bcc and P. aeruginosa bacteria on 21 coinfected or singly infected CF lungs obtained at transplantation or autopsy. Parallel in vitro experiments examined the growth of two Bcc species, Burkholderia cenocepacia and Burkholderia multivorans, in environments similar to those occupied by P. aeruginosa in the CF lung. Bcc bacteria were predominantly identified in the CF lung as single cells or small clusters within phagocytes and mucus but not as “biofilm-like structures.” In contrast, P. aeruginosa was identified in biofilm-like masses, but densities appeared to be reduced during coinfection with Bcc bacteria. Based on chemical analyses of CF and non-CF respiratory secretions, a test medium was defined to study Bcc growth and interactions with P. aeruginosa in an environment mimicking the CF lung. When test medium was supplemented with alternative electron acceptors under anaerobic conditions, B. cenocepacia and B. multivorans used fermentation rather than anaerobic respiration to gain energy, consistent with the identification of fermentation products by high-performance liquid chromatography (HPLC). Both Bcc species also expressed mucinases that produced carbon sources from mucins for growth. In the presence of P. aeruginosa in vitro, both Bcc species grew anaerobically but not aerobically. We propose that Bcc bacteria (i) invade a P. aeruginosa-infected CF lung when the airway lumen is anaerobic, (ii) inhibit P. aeruginosa biofilm-like growth, and (iii) expand the host bacterial niche from mucus to also include macrophages. PMID:25156735

  1. Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water

    SciTech Connect

    Harrach, Michael F. Klameth, Felix; Drossel, Barbara; Vogel, Michael

    2015-01-21

    We perform molecular dynamics simulations to observe the structure and dynamics of SPC/E water in amorphous silica pores and amorphous ice pores with radii slightly larger than 10 Å. In addition to atomically rough pores, we construct completely smooth pores such that the potential felt at a given distance from the pore wall is an averaged atomic potential. As compared to rough walls, smooth walls induce stronger distortions of water structure for both silica and ice confinements. On the other hand, unlike the smooth pores, the rough pores strongly slow down water dynamics at the pore wall. The slowdown vanishes when reducing the atomic charges in the wall, i.e., when varying the hydroaffinity, while keeping the surface topology, indicating that it is not a geometric effect. Rather, it is due to the fact that the wall atoms provide a static energy landscape along the surface, e.g., fixed anchor-points for hydrogen bonds, to which the water molecules need to adapt, blocking channels for structural rearrangement. In the smooth pores, water dynamics can be faster than in the bulk liquid not only at the pore wall but also in the pore center. Changes in the tetrahedral order rather than in the local density are identified as the main cause for this change of the dynamical behavior in the center of smooth pores.

  2. A New FE Modeling Method for Isothermal Local Loading Process of Large-scale Complex Titanium Alloy Components Based on DEFORM-3D

    SciTech Connect

    Zhang Dawei; Yang He; Sun Zhichao; Fan Xiaoguang

    2010-06-15

    Isothermal local loading process provides a new way to form large-scale complex titanium alloy components. The forming process is characterized by an extreme size (large scale in global and compared small size in regional), multi-parameter effects, and complicated loading path. To establish a reasonable finite element model is one of the key problems urgently to be solved in the research and development of isothermal local loading forming process of large-scale complex titanium alloy components. In this paper, a new finite element model of the isothermal local loading process is developed under the DEFORM-3D environment based on the solution of some key techniques. The modeling method has the following features: (1) different meshing techniques are used in different loading areas and the number of meshed elements is determined according to the deformation characteristic in different local loading steps in order to improve computational efficiency; (2) the accurate magnitude of the friction factor under titanium alloy hot forming (isothermal forming) condition is adopted instead of the typical value for lubricated hot forming processes; (3) different FEM solvers are chosen at different stages according to the loading characteristic and the contact state; (4) in contrast to the local component model, a full 3D component is modeled to simulate the process. The 3D-FE model is validated by experimental data of a large-scale bulkhead forming under isothermal local loading. The model can describe the quantitative relationships between the forming conditions and the forming results. The results of the present study may provide a basis for studying the local deformation mechanism, selecting the reasonable parameters, optimizing the die design and the process control in isothermal local loading process of large-scale complex titanium alloy components.

  3. A New FE Modeling Method for Isothermal Local Loading Process of Large-scale Complex Titanium Alloy Components Based on DEFORM-3D

    NASA Astrophysics Data System (ADS)

    Zhang, Dawei; Yang, He; Sun, Zhichao; Fan, Xiaoguang

    2010-06-01

    Isothermal local loading process provides a new way to form large-scale complex titanium alloy components. The forming process is characterized by an extreme size (large scale in global and compared small size in regional), multi-parameter effects, and complicated loading path. To establish a reasonable finite element model is one of the key problems urgently to be solved in the research and development of isothermal local loading forming process of large-scale complex titanium alloy components. In this paper, a new finite element model of the isothermal local loading process is developed under the DEFORM-3D environment based on the solution of some key techniques. The modeling method has the following features: (1) different meshing techniques are used in different loading areas and the number of meshed elements is determined according to the deformation characteristic in different local loading steps in order to improve computational efficiency; (2) the accurate magnitude of the friction factor under titanium alloy hot forming (isothermal forming) condition is adopted instead of the typical value for lubricated hot forming processes; (3) different FEM solvers are chosen at different stages according to the loading characteristic and the contact state; (4) in contrast to the local component model, a full 3D component is modeled to simulate the process. The 3D-FE model is validated by experimental data of a large-scale bulkhead forming under isothermal local loading. The model can describe the quantitative relationships between the forming conditions and the forming results. The results of the present study may provide a basis for studying the local deformation mechanism, selecting the reasonable parameters, optimizing the die design and the process control in isothermal local loading process of large-scale complex titanium alloy components.

  4. Permeability characteristics of cell-membrane pores induced by ostreolysin A/pleurotolysin B, binary pore-forming proteins from the oyster mushroom.

    PubMed

    Schlumberger, Sébastien; Kristan, Katarina Črnigoj; Ota, Katja; Frangež, Robert; Molgό, Jordi; Sepčić, Kristina; Benoit, Evelyne; Maček, Peter

    2014-01-01

    Proteins from the oyster mushroom, 15 kDa ostreolysin A (OlyA), and 59 kDa pleurotolysin B (PlyB) with a membrane attack complex/perforin (MACPF) domain, damage cell membranes as a binary cytolytic pore-forming complex. Measurements of single-channel conductance and transmembrane macroscopic current reveal that OlyA/PlyB form non-selective ion-conducting pores with broad, skewed conductance distributions in N18 neuroblastoma and CHO-K1 cell membranes. Polyethylene-glycol 8000 (hydrodynamic radius of 3.78 nm) provides almost complete osmotic protection against haemolysis, which strongly suggests a colloid-osmotic type of erythrocyte lysis. Our data indicate that OlyA/PlyB form transmembrane pores of varied sizes, as other pore-forming proteins with a MACPF domain. PMID:24211835

  5. Permeability characteristics of cell-membrane pores induced by ostreolysin A/pleurotolysin B, binary pore-forming proteins from the oyster mushroom.

    PubMed

    Schlumberger, Sébastien; Kristan, Katarina Črnigoj; Ota, Katja; Frangež, Robert; Molgό, Jordi; Sepčić, Kristina; Benoit, Evelyne; Maček, Peter

    2014-01-01

    Proteins from the oyster mushroom, 15 kDa ostreolysin A (OlyA), and 59 kDa pleurotolysin B (PlyB) with a membrane attack complex/perforin (MACPF) domain, damage cell membranes as a binary cytolytic pore-forming complex. Measurements of single-channel conductance and transmembrane macroscopic current reveal that OlyA/PlyB form non-selective ion-conducting pores with broad, skewed conductance distributions in N18 neuroblastoma and CHO-K1 cell membranes. Polyethylene-glycol 8000 (hydrodynamic radius of 3.78 nm) provides almost complete osmotic protection against haemolysis, which strongly suggests a colloid-osmotic type of erythrocyte lysis. Our data indicate that OlyA/PlyB form transmembrane pores of varied sizes, as other pore-forming proteins with a MACPF domain.

  6. Pore-water chemistry explains zinc phytotoxicity in soil.

    PubMed

    Kader, Mohammed; Lamb, Dane T; Correll, Ray; Megharaj, Mallavarapu; Naidu, Ravi

    2015-12-01

    Zinc (Zn) is a widespread soil contaminant arising from a numerous anthropogenic sources. However, adequately predicting toxicity of Zn to ecological receptors remains difficult due to the complexity of soil characteristics. In this study, we examined solid-solution partitioning using pore-water data and toxicity of Zn to cucumber (Cucumis sativus L.) in spiked soils. Pore-water effective concentration (ECx, x=10%, 20% and 50% reduction) values were negatively related to pH, indicating lower Zn pore water concentration were needed to cause phytotoxicity at high pH soils. Total dissolved zinc (Znpw) and free zinc (Zn(2+)) in soil-pore water successfully described 78% and 80.3% of the variation in relative growth (%) in the full dataset. When the complete data set was used (10 soils), the estimated EC50pw was 450 and 79.2 µM for Znpw and Zn(2+), respectively. Total added Zn, soil pore water pH (pHpw) and dissolve organic carbon (DOC) were the best predictors of Znpw and Zn(2+) in pore-water. The EC10 (total loading) values ranged from 179 to 5214 mg/kg, depending on soil type. Only pH measurements in soil were related to ECx total Zn data. The strongest relationship to ECx overall was pHca, although pHw and pHpw were in general related to Zn ECx. Similarly, when a solution-only model was used to predict Zn in shoot, DOC was negatively related to Zn in shoot, indicating a reduction in uptake/ translocation of Zn from solution with increasing DOC.

  7. [The transformation of liquid crystal complexes in biological body fluids during local laser stimulation of the healing process in an experimental suppurative wound].

    PubMed

    Mints, R I; Skopinov, S A; Iakovleva, S V; Lisienko, V M; Drobinina, O V

    1989-01-01

    It was established that localized exposure of an inflammatory focus to laser radiation causes, besides the well-known effect on biochemical activity, structural photophysical reorganization of the liquid crystalline complexes not only in the irradiated tissues but also in parts of the organism situated at a distance from the exposed area.

  8. Modeling pore collapse and chemical reactions in shock-loaded HMX crystals

    NASA Astrophysics Data System (ADS)

    Austin, R. A.; Barton, N. R.; Howard, W. M.; Fried, L. E.

    2014-05-01

    The localization of deformation in shock-loaded crystals of high explosive material leads to the formation of hot spots, which, if hot enough, initiate chemical reactions. The collapse of microscopic pores contained within a crystal is one such process that localizes energy and generates hot spots. Given the difficulty of resolving the details of pore collapse in shock compression experiments, it is useful to study the problem using direct numerical simulation. In this work, we focus on simulating the shock-induced closure of a single pore in crystalline β-HMX using a multiphysics finite element code. To address coupled thermal-mechanical-chemical responses, the model incorporates a crystal-mechanics-based description of thermoelasto-viscoplasticity, the crystal melting behavior, and transformation kinetics for a single-step decomposition reaction. The model is applied to stress wave amplitudes of up to 11 GPa to study the details of pore collapse, energy localization, and the early stages of reaction initiation.

  9. Open-pore polyurethane product

    DOEpatents

    Jefferson, R.T.; Salyer, I.O.

    1974-02-17

    The method is described of producing an open-pore polyurethane foam having a porosity of at least 50% and a density of 0.1 to 0.5 g per cu cm, and which consists of coherent spherical particles of less than 10 mu diam separated by interconnected interstices. It is useful as a filter and oil absorbent. The product is admirably adapted to scavenging of crude oil from the surface of seawater by preferential wicking. The oil-soaked product may then be compressed to recover the oil or burned for disposal. The crosslinked polyurethane structures are remarkably solvent and heat-resistance as compared with known thermoplastic structures. Because of their relative inertness, they are useful filters for gasoline and other hydrocarbon compounds. (7 claims)

  10. Fine structures at pore boundary

    NASA Astrophysics Data System (ADS)

    Bharti, L.; Quintero Noda, C.; Joshi, C.; Rakesh, S.; Pandya, A.

    2016-10-01

    We present high resolution observations of fine structures at pore boundaries. The inner part of granules towards umbra show dark striations which evolve into a filamentary structure with dark core and `Y' shape at the head of the filaments. These filaments migrate into the umbra similar to penumbral filaments. These filaments show higher temperature, lower magnetic field strength and more inclined field compared to the background umbra. The optical depth stratification of physical quantities suggests their similarity with penumbral filaments. However, line-of-sight velocity pattern is different from penumbral filaments where they show downflows in the deeper layers of the atmosphere while the higher layers show upflows. These observations show filamentation in a simple magnetic configuration.

  11. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert.

  12. Non-local formulation for multiscale flow in porous media

    NASA Astrophysics Data System (ADS)

    Delgoshaie, Amir H.; Meyer, Daniel W.; Jenny, Patrick; Tchelepi, Hamdi A.

    2015-12-01

    The multiscale nature of geological formations is reflected in the flow and transport behaviors of the pore fluids. For example, multiple pathways between different locations in the porous medium are usually present. The topology, length, and strength of these flow paths can vary significantly, and the total flow at a given location can be the result of contributions from a wide range of pathways between the points of interest. We use a high-resolution pore network of a natural porous formation as an example of the multiscale connectivity of the pore space. A single continuum model can capture the contributions from all the flow paths properly only if the control volume (computational cell) is much larger than the longest pathway. However, depending on the densities and lengths of these long pathways, choosing the appropriate size of the control volume that allows for a single continuum description of the properties, such as conductivity and transmissibility, may conflict with the desire to resolve the flow field properly. To capture the effects of the multiscale pathways on the flow, a non-local continuum model is described. The model can represent non-local effects, for which Darcy's law is not valid. In the limit where the longest connections are much smaller than the size of the control volume, the model is consistent with Darcy's law. The non-local model is used to describe the flow in complex pore networks. The pressure distributions obtained from the non-local model are compared with pore-network flow simulations, and the results are in excellent agreement. Importantly, such multiscale flow behaviors cannot be represented using the local Darcy law.

  13. Analysis of solute diffusion across the C5b-9 membrane lesion of complement: evidence that individual C5b-9 complexes do not function as discrete, uniform pores.

    PubMed

    Sims, P J; Lauf, P K

    1980-12-01

    We have investigated the diffusion of radiolabeled nonelectrolytes across the membranes of resealed erythrocyte ghosts that had been treated with the terminal complement components C5b-9 and i