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Sample records for pore complex localization

  1. 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

  2. Localization of Pom121 to the inner nuclear membrane is required for an early step of interphase nuclear pore complex assembly

    PubMed Central

    Funakoshi, Tomoko; Clever, Michaela; Watanabe, Ai; Imamoto, Naoko

    2011-01-01

    The nuclear pore complex (NPC) is a large protein assembly that mediates molecular trafficking between the cytoplasm and the nucleus. NPCs assemble twice during the cell cycle in metazoans: postmitosis and during interphase. In this study, using small interfering RNA (siRNA) in conjunction with a cell fusion–based NPC assembly assay, we demonstrated that pore membrane protein (Pom)121, a vertebrate-specific integral membrane nucleoporin, is indispensable for an early step in interphase NPC assembly. Functional domain analysis of Pom121 showed that its nuclear localization signals, which bind to importin β via importin α and likely function with RanGTP, play an essential role in targeting Pom121 to the interphase NPC. Furthermore, a region of Pom121 that interacts with the inner nuclear membrane (INM) and lamin B receptor was found to be crucial for its NPC targeting. Based on these findings and on evidence that Pom121 localizes at the INM in the absence of a complete NPC structure, we propose that the nuclear migration of Pom121 and its subsequent interaction with INM proteins are required to initiate interphase NPC assembly. Our data also suggest, for the first time, the importance of the INM as a seeding site for “prepores” during interphase NPC assembly. PMID:21289085

  3. Nuclear pores. Architecture of the nuclear pore complex coat.

    PubMed

    Stuwe, Tobias; Correia, Ana R; Lin, Daniel H; Paduch, Marcin; Lu, Vincent T; Kossiakoff, Anthony A; Hoelz, André

    2015-03-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a reconstituted ~400-kilodalton coat nucleoporin complex (CNC) from Saccharomyces cerevisiae at a 7.4 angstrom resolution. The crystal structure revealed a curved Y-shaped architecture and the molecular details of the coat nucleoporin interactions forming the central "triskelion" of the Y. A structural comparison of the yeast CNC with an electron microscopy reconstruction of its human counterpart suggested the evolutionary conservation of the elucidated architecture. Moreover, 32 copies of the CNC crystal structure docked readily into a cryoelectron tomographic reconstruction of the fully assembled human NPC, thereby accounting for ~16 megadalton of its mass. PMID:25745173

  4. Viral Subversion of the Nuclear Pore Complex

    PubMed Central

    Le Sage, Valerie; Mouland, Andrew J.

    2013-01-01

    The nuclear pore complex (NPC) acts as a selective barrier between the nucleus and the cytoplasm and is responsible for mediating communication by regulating the transport of RNA and proteins. Numerous viral pathogens have evolved different mechanisms to hijack the NPC in order to regulate trafficking of viral proteins, genomes and even capsids into and out of the nucleus thus promoting virus replication. The present review examines the different strategies and the specific nucleoporins utilized during viral infections as a means of promoting their life cycle and inhibiting host viral defenses. PMID:23959328

  5. Interaction of local anesthetics with the K+ channel pore domain

    PubMed Central

    Gray, Noel W.; Zhorov, Boris S.; Moczydlowski, Edward G.

    2013-01-01

    Local anesthetics and related drugs block ionic currents of Na+, K+ and Ca2+ conducted across the cell membrane by voltage-dependent ion channels. Many of these drugs bind in the permeation pathway, occlude the pore and stop ion movement. However channel-blocking drugs have also been associated with decreased membrane stability of certain tetrameric K+ channels, similar to the destabilization of channel function observed at low extracellular K+ concentration. Such drug-dependent stability may result from electrostatic repulsion of K+ from the selectivity filter by a cationic drug molecule bound in the central cavity of the channel. In this study we used the pore domain of the KcsA K+ channel protein to test this hypothesis experimentally with a biochemical assay of tetramer stability and theoretically by computational simulation of local anesthetic docking to the central cavity. We find that two common local anesthetics, lidocaine and tetracaine, promote thermal dissociation of the KcsA tetramer in a K+-dependent fashion. Docking simulations of these drugs with open, open-inactivated and closed crystal structures of KcsA yield many energetically favorable drug-channel complexes characterized by nonbonded attraction to pore-lining residues and electrostatic repulsion of K+. The results suggest that binding of cationic drugs to the inner cavity can reduce tetramer stability of K+ channels. PMID:23545989

  6. 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. PMID:26416747

  7. 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. PMID:25146397

  8. 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.

  9. Purification of the Vertebrate Nuclear Pore Complex by Biochemical Criteria

    PubMed Central

    Miller, Brian R.; Forbes, Douglass J.

    2015-01-01

    The nuclear pore is a large and complex biological machine, mediating all signal-directed transport between the nucleus and the cytoplasm. The vertebrate pore has a mass of ~120 million daltons or 30 times the size of a ribosome. The large size of the pore, coupled to its tight integration in the nuclear lamina, has hampered the isolation of pore complexes from vertebrate sources. We have now developed a strategy for the purification of nuclear pores from in vitro assembled annulate lamellae (AL), a cytoplasmic mimic of the nuclear envelope that lacks a lamina, nuclear matrix, and chromatin-associated proteins. We find that purified pore complexes from annulate lamellae contain every nuclear pore protein tested. In addition, immunoblotting reveals the presence of soluble transport receptors and factors known to play important roles in the transport of macromolecules through the pore. While transport factors such as Ran and NTF2 show only transient interaction with the pores, a number of soluble transport receptors, including importin β, show a tight association with the purified pores. In summary, we report that we have purified the vertebrate pore by biochemical criteria; silver staining reveals ~40–50 distinct protein bands. PMID:11208084

  10. 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

  11. 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

  12. Assembly of nuclear pore complexes mediated by major vault protein.

    PubMed

    Vollmar, Friederike; Hacker, Christian; Zahedi, René-Peiman; Sickmann, Albert; Ewald, Andrea; Scheer, Ulrich; Dabauvalle, Marie-Christine

    2009-03-15

    During interphase growth of eukaryotic cells, nuclear pore complexes (NPCs) are continuously incorporated into the intact nuclear envelope (NE) by mechanisms that are largely unknown. De novo formation of NPCs involves local fusion events between the inner and outer nuclear membrane, formation of a transcisternal membranous channel of defined diameter and the coordinated assembly of hundreds of nucleoporins into the characteristic NPC structure. Here we have used a cell-free system based on Xenopus egg extract, which allows the experimental separation of nuclear-membrane assembly and NPC formation. Nuclei surrounded by a closed double nuclear membrane, but devoid of NPCs, were first reconstituted from chromatin and a specific membrane fraction. Insertion of NPCs into the preformed pore-free nuclei required cytosol containing soluble nucleoporins or nucleoporin subcomplexes and, quite unexpectedly, major vault protein (MVP). MVP is the main component of vaults, which are ubiquitous barrel-shaped particles of enigmatic function. Our results implicate MVP, and thus also vaults, in NPC biogenesis and provide a functional explanation for the association of a fraction of vaults with the NE and specifically with NPCs in intact cells. PMID:19240118

  13. Local membrane mechanics of pore-spanning bilayers.

    PubMed

    Mey, Ingo; Stephan, Milena; Schmitt, Eva K; Müller, Martin Michael; Ben Amar, Martine; Steinem, Claudia; Janshoff, Andreas

    2009-05-27

    The mechanical behavior of lipid bilayers spanning the pores of highly ordered porous silicon substrates was scrutinized by local indentation experiments as a function of surface functionalization, lipid composition, solvent content, indentation velocity, and pore radius. Solvent-containing nano black lipid membranes (nano-BLMs) as well as solvent-free pore-spanning bilayers were imaged by fluorescence and atomic force microscopy prior to force curve acquisition, which allows distinguishing between membrane-covered and uncovered pores. Force indentation curves on pore-spanning bilayers attached to functionalized hydrophobic porous silicon substrates reveal a predominately linear response that is mainly attributed to prestress in the membranes. This is in agreement with the observation that indentation leads to membrane lysis well below 5% area dilatation. However, membrane bending and lateral tension dominate over prestress and stretching if solvent-free supported membranes obtained from spreading giant liposomes on hydrophilic porous silicon are indented. An elastic regime diagram is presented that readily allows determining the dominant contribution to the mechanical response upon indentation as a function of load and pore radius. PMID:19453196

  14. HIV-1 remodels the nuclear pore complex

    PubMed Central

    Monette, Anne; Panté, Nelly

    2011-01-01

    Human immunodeficiency virus type 1 (HIV-1) commandeers host cell proteins and machineries for its replication. Our earlier work showed that HIV-1 induced the cytoplasmic retention of nucleocytoplasmic shuttling and ribonucleic acid (RNA)–binding proteins. This retention is dependent on nuclear export of the viral genomic RNA and on changes in the localization and expression level of the nucleoporin (Nup) p62 (Nup62). To further characterize the extent of perturbation induced by HIV-1, we performed proteomics analyses of nuclear envelopes (NEs) isolated from infected T cells. Infection induced extensive changes in the composition of the NE and its associated proteins, including a remarkable decrease in the abundance of Nups. Immunogold electron microscopy revealed the translocation of Nups into the cytoplasm. Nup62 was identified as a component of purified virus, and small interfering RNA depletion studies revealed an important role for this Nup in virus gene expression and infectivity. This detailed analysis highlights the profound effects on NE composition induced by HIV-1 infection, providing further evidence of the magnitude of viral control over the cell biology of its host. PMID:21576391

  15. Strain localization driven by co-seismic pore fluid pressurization

    NASA Astrophysics Data System (ADS)

    Rice, James; Platt, John; Brantut, Nicolas; Rudnicki, John

    2015-04-01

    The absence of a thermal anomaly associated with the San Andreas fault, and low driving stress resolved on it, suggest that such mature faults weaken dramatically during seismic slip. Thermal pressurization (TP) and thermal decomposition (TD) are two mechanisms to explain this co-seismic weakening. Both rely on elevated pore pressures in a fluid-saturated gouge, with TP achieving this through thermal expansion of native pore fluid and TD by releasing additional pore fluid (e.g., H2O or CO2) during a reaction. We use a one-dimensional model for a fluid-saturated gouge layer sheared between two undeforming half-spaces to study how TP (Rice et al., Platt et al., JGR-B, 2014) and TD (Platt et al., submitted JGR-B) drive seismic strain localization. A linear stability analysis is first used to predict the localized zone thickness for each of the weakening mechanisms. Using representative parameters for fault gouge we predict localized zone thicknesses of a few tens of microns, in line with laboratory (Kitajima et al., 2010) and field (Chester and Chester, 1998) observations. Next we use numerical simulations to study how the localized zone develops once nonlinear effects become important. These show that the final localized zone thickness is very similar to the linear stability prediction. In the simulations, the onset of localization accelerates fault weakening, making co-seismic strain localization an important consideration, apparently neglected in all current earthquake simulations. Finally we show how a secondary instability can lead to migration of the deforming zone across the gouge layer. This instability is driven by hydrothermal diffusion for TP, and by reactant depletion for TD. Our results show that migration must be taken into account when inferring the width of the deforming zone from field observations. Even when the zone of localized straining is only a few tens of microns wide, migration can lead to a final strain profile with a zone of roughly uniform

  16. Strain localization driven by co-seismic pore fluid pressurization

    NASA Astrophysics Data System (ADS)

    Platt, J. D.; Brantut, N.; Rice, J. R.; Rudnicki, J. W.

    2014-12-01

    The absence of a thermal anomaly associated with the San Andreas fault, and low driving stress resolved on it, suggest that such mature faults weaken dramatically during seismic slip. Thermal pressurization (TP) and thermal decomposition (TD) are two mechanisms to explain this co-seismic weakening. Both rely on elevated pore pressures in a fluid-saturated gouge, with TP achieving this through thermal expansion of native pore fluid and TD by releasing additional pore fluid (e.g., H2O or CO2) during a reaction. We use a one-dimensional model for a fluid-saturated gouge layer sheared between two undeforming half-spaces to study how TP (Rice et al., Platt et al., JGR-B, 2014) and TD (Platt et al., submitted JGR-B) drive seismic strain localization. A linear stability analysis is first used to predict the localized zone thickness for each of the weakening mechanisms. Using representative parameters for fault gouge we predict localized zone thicknesses of a few tens of microns, in line with laboratory (Kitajima et al., 2010) and field (Chester and Chester, 1998) observations. Next we use numerical simulations to study how the localized zone develops once nonlinear effects become important. These show that the final localized zone thickness is very similar to the linear stability prediction. In the simulations, the onset of localization accelerates fault weakening, making co-seismic strain localization an important consideration, apparently neglected in all current earthquake simulations. Finally we show how a secondary instability can lead to migration of the deforming zone across the gouge layer. This instability is driven by hydrothermal diffusion for TP, and by reactant depletion for TD. Our results show that migration must be taken into account when inferring the width of the deforming zone from field observations. Even when the zone of localized straining is only a few tens of microns wide, migration can lead to a final strain profile with a zone of roughly uniform

  17. The Nuclear Pore Complex as a Flexible and Dynamic Gate.

    PubMed

    Knockenhauer, Kevin E; Schwartz, Thomas U

    2016-03-10

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and serve as the primary transport gates for molecular exchange between nucleus and cytoplasm. Stripping the megadalton complex down to its most essential organizational elements, one can divide the NPC into scaffold components and the disordered elements attached to them that generate a selective barrier between compartments. These structural elements exhibit flexibility, which may hold a clue in understanding NPC assembly and function. Here we review the current status of NPC research with a focus on the functional implications of its structural and compositional heterogeneity. PMID:26967283

  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. Mitogen activated protein kinase at the nuclear pore complex

    PubMed Central

    Faustino, Randolph S; Maddaford, Thane G; Pierce, Grant N

    2011-01-01

    Abstract Mitogen activated protein (MAP) kinases control eukaryotic proliferation, and import of kinases into the nucleus through the nuclear pore complex (NPC) can influence gene expression to affect cellular growth, cell viability and homeostatic function. The NPC is a critical regulatory checkpoint for nucleocytoplasmic traffic that regulates gene expression and cell growth, and MAP kinases may be physically associated with the NPC to modulate transport. In the present study, highly enriched NPC fractions were isolated and investigated for associated kinases and/or activity. Endogenous kinase activity was identified within the NPC fraction, which phosphorylated a 30 kD nuclear pore protein. Phosphomodification of this nucleoporin, here termed Nup30, was inhibited by apigenin and PD-98059, two MAP kinase antagonists as well as with SB-202190, a pharmacological blocker of p38. Furthermore, high throughput profiling of enriched NPCs revealed constitutive presence of all members of the MAP kinase family, extracellular regulated kinases (ERK), p38 and Jun N-terminal kinase. The NPC thus contains a spectrum of associated MAP kinases that suggests an intimate role for ERK and p38 in regulation of nuclear pore function. PMID:20497490

  20. The Structure Inventory of the Nuclear Pore Complex.

    PubMed

    Schwartz, Thomas U

    2016-05-22

    The nuclear pore complex (NPC) is the principal gateway for molecular exchange between nucleus and cytoplasm across the nuclear envelope. Due to its sheer size of estimated 50-112MDa and its complex buildup from about 500-1000 individual proteins, it is a difficult object to study for structural biologists. Here, I review the extensive ensemble of high-resolution structures of the building blocks of the NPC. Concurrent with the increase in size and complexity, these latest, large structures and assemblies can now be used as the basis for hybrid approaches, primarily in combination with cryo-electron microscopic analysis, generating the first structure-based assembly models of the NPC. Going forward, the structures will be critically important for a detailed analysis of the NPC, including function, evolution, and assembly. PMID:27016207

  1. 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. PMID:26316600

  2. Architecture of the nuclear pore inner ring complex

    PubMed Central

    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

    2016-01-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kDa 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 hetero-trimer (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. PMID:26316600

  3. 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. PMID:26894898

  4. The Molecular Basis for Ca2+ Signalling by NAADP: Two-Pore Channels in a Complex?

    PubMed Central

    Marchant, Jonathan S.; Lin-Moshier, Yaping; Walseth, Timothy F.; Patel, Sandip

    2014-01-01

    NAADP is a potent Ca2+ mobilizing messenger in a variety of cells but its molecular mechanism of action is incompletely understood. Accumulating evidence indicates that the poorly characterized two-pore channels (TPCs) in animals are NAADP sensitive Ca2+-permeable channels. TPCs localize to the endo-lysosomal system but are functionally coupled to the better characterized endoplasmic reticulum Ca2+ channels to generate physiologically relevant complex Ca2+ signals. Whether TPCs directly bind NAADP is not clear. Here we discuss the idea based on recent studies that TPCs are the pore-forming subunits of a protein complex that includes tightly associated, low molecular weight NAADP-binding proteins. PMID:25309835

  5. Structure and gating of the nuclear pore complex

    PubMed Central

    Eibauer, Matthias; Pellanda, Mauro; Turgay, Yagmur; Dubrovsky, Anna; Wild, Annik; Medalia, Ohad

    2015-01-01

    Nuclear pore complexes (NPCs) perforate the nuclear envelope and allow the exchange of macromolecules between the nucleus and the cytoplasm. To acquire a deeper understanding of this transport mechanism, we analyse the structure of the NPC scaffold and permeability barrier, by reconstructing the Xenopus laevis oocyte NPC from native nuclear envelopes up to 20 Å resolution by cryo-electron tomography in conjunction with subtomogram averaging. In addition to resolving individual protein domains of the NPC constituents, we propose a model for the architecture of the molecular gate at its central channel. Furthermore, we compare and contrast this native NPC structure to one that exhibits reduced transport activity and unveil the spatial properties of the NPC gate. PMID:26112706

  6. Quantifying Nucleoporin Stoichiometry Inside Single Nuclear Pore Complexes In vivo

    PubMed Central

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

    2015-01-01

    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. PMID:25797490

  7. Single molecule atomic force microscopy of aerolysin pore complexes reveals unexpected star-shaped topography.

    PubMed

    He, Jianfeng; Wang, Jiabin; Hu, Jun; Sun, Jielin; Czajkowsky, Daniel Mark; Shao, Zhifeng

    2016-04-01

    Aerolysin is the paradigmatic member of a large family of toxins that convert from a water-soluble monomer/dimer into a membrane-spanning oligomeric pore. While there is x-ray crystallographic data of its water-soluble conformation, the most recent structural model of the membrane-inserted pore is based primarily on data of water-soluble tetradecamers of mutant protein, together with computational modeling ultimately performed in vacuum. Here we examine this pore model with atomic force microscopy (AFM) of membrane-associated wild-type complexes and all-atom molecular dynamics (MD) simulations in water. In striking contrast to a disc-shaped cap region predicted by the present model, the AFM images reveal a star-shaped complex, with a central ring surrounded by seven radial projections. Further, the MD simulations suggest that the locations of the receptor-binding (D1) domains in the present model are not correct. However, a modified model in which the D1 domains, rather than localized at fixed positions, adopt a wide range of configurations through fluctuations of an intervening linker is compatible with existing data. Thus our work not only demonstrates the importance of directly resolving such complexes in their native environment but also points to a dynamic receptor binding region, which may be critical for toxin assembly on the cell surface. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26537438

  8. 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

  9. 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

  10. Three-Dimensional pore space and strain localization distribution in Majella limestone.

    NASA Astrophysics Data System (ADS)

    Ji, Yuntao; Hall, Stephen; Baud, Patrick; Wond, Teng-fong

    2015-04-01

    Brittle-ductile transition in porous rock is a topic of importance in many geological applications. Traditionally pore space in rock is characterized using optical and scanning electron microscopes (SEM). Advances in 3-dimensional imaging techniques such as X-ray computed tomography (CT) and laser scanning confocal microscopy have furnished enhanced perspective on pore geometry complexity. In particular, X-ray CT has been used widely for characterizing porous clastic rocks such as sandstone, whose void space is dominated by relatively equant pores connected by throats that are sufficiently large for direct imaging by X-ray microCT. However, standard techniques for CT imaging are not directly applicable to a carbonate rock because of the geometric complexity of its pore space. In this study, we first characterized the pore structure in Majella limestone. MicroCT data was partitioned into three distinct domains: macropores, solid grains and an intermediate domain made up of voxels of solid embedded with micropores below the resolution. A morphological analysis of the microCT images shows that both the solid and intermediate domains in Majella limestone are interconnected as it has been previously reported in a less porous limestone. We however show that the macroporosity in Majella limestone is fundamentally different, in that it has a percolative backbone which may contribute to significant enhancement of its permeability. We then present the first application of 3D-volumetric Digital Image Correlation (DIC) to a very porous limestone. If images of a rock sample are acquired before and after deformation, then DIC can be used to infer the displacement and strain fields. In our study, four Majella limestone samples were triaxially compressed at confining pressures ranging from 5 MPa to 25 MPa and another under hydrostatic conditions up to 60 MPa. For each of these five samples, two CT images were acquired before and after the deformation. We then used the Tomo

  11. The transmembrane nucleoporin NDC1 is required for targeting of ALADIN to nuclear pore complexes

    SciTech Connect

    Yamazumi, Yusuke; Kamiya, Atsushi; Nishida, Ayumu; Nishihara, Ayako; Iemura, Shun-ichiro; Natsume, Tohru; Akiyama, Tetsu

    2009-11-06

    NDC1 is a transmembrane nucleoporin that is required for NPC assembly and nucleocytoplasmic transport. We show here that NDC1 directly interacts with the nucleoporin ALADIN, mutations of which are responsible for triple-A syndrome, and that this interaction is required for targeting of ALADIN to nuclear pore complexes (NPCs). Furthermore, we show that NDC1 is required for selective nuclear import. Our findings suggest that NDC1-mediated localization of ALADIN to NPCs is essential for selective nuclear protein import, and that abrogation of the interaction between ALADIN and NDC1 may be important for the development of triple-A syndrome.

  12. Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex

    PubMed Central

    Popken, Petra; Ghavami, Ali; Onck, Patrick R.; Poolman, Bert; Veenhoff, Liesbeth M.

    2015-01-01

    Nuclear pore complexes (NPCs) allow selective import and export while forming a barrier for untargeted proteins. Using fluorescence microscopy, we measured in vivo the permeability of the Saccharomyces cerevisiae NPC for multidomain proteins of different sizes and found that soluble proteins of 150 kDa and membrane proteins with an extralumenal domain of 90 kDa were still partly localized in the nucleus on a time scale of hours. The NPCs thus form only a weak barrier for the majority of yeast proteins, given their monomeric size. Using FGΔ-mutant strains, we showed that specific combinations of Nups, especially with Nup100, but not the total mass of FG-nups per pore, were important for forming the barrier. Models of the disordered phase of wild-type and mutant NPCs were generated using a one bead per amino acid molecular dynamics model. The permeability measurements correlated with the density predictions from coarse-grained molecular dynamics simulations in the center of the NPC. The combined in vivo and computational approach provides a framework for elucidating the structural and functional properties of the permeability barrier of nuclear pore complexes. PMID:25631821

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

    NASA Astrophysics Data System (ADS)

    Wang, Hsiu-Wen; Anovitz, Lawrence M.; Burg, Avihu; Cole, David R.; Allard, Lawrence F.; Jackson, Andrew J.; Stack, Andrew G.; Rother, Gernot

    2013-11-01

    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 low- and 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. 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.

  15. Characterization of pore structure and strain localization in Majella limestone by X-ray Computed Tomography and Digital Image Correlation

    NASA Astrophysics Data System (ADS)

    Ji, Y.; Hall, S.; Baud, P.; Wong, T.

    2013-12-01

    X-ray Computed Tomography (CT) and Digital Image Correlation (DIC) have been widely used for characterizing the pore structure and damage evolution in porous clastic rocks. In comparison, these 3D imaging techniques have not been used as widely in carbonate rocks. This paucity of 3D imaging arises primarily because carbonates have pore geometry that is significantly more complex than siliciclastics and consequently microCT imaging of the pore space is not straightforward. Hence most investigations of the pore structure and damage development in porous carbonate rocks have been done on 2D thin-sections, synthesizing observations on different scales using the optical microscope and SEM. In this study, we used two techniques for characterizing the pore structure and development of strain localization in Majella limestone of 31% porosity. The first technique allows us to extract 3D information from microCT data on the partitioning of porosity and pore size statistics in this limestone. Specifically the microCT image was partitioned into three distinct domains separated by two thresholds in the global histogram: macropores, solid grains and an intermediate domain (made up of voxels of solid embedded with micropores). Our morphological analysis of the microCT images shows that both the solid and intermediate domains are basically interconnected. Our new data underscore some of the 3D complexities of the macropores and implies that a dual porosity model is necessary for analyzing the mechanical behavior of porous carbonate rock. The second technique undertaken in this study is DIC analysis of the failure mode in relation to the brittle-ductile transition. With decrease in confinement, the failure mode of a porous rock undergoes a transition from delocalized compaction to brittle faulting. The damage associated with strain localization in Majella limestone is subtle and not easily resolvable under optical microscope or SEM. Our first application of 3D-volumetric DIC to a

  16. 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

  17. 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.

  18. Nuclear pore complex assembly studied with a biochemical assay for annulate lamellae formation.

    PubMed

    Meier, E; Miller, B R; Forbes, D J

    1995-06-01

    Formation of the nuclear pore is an intricate process involving membrane fusion and the ordered assembly of up to 1,000 pore proteins. As such, the study of pore assembly is not a simple one. Interestingly, annulate lamellae, a cytoplasmic organelle consisting of stacks of flattened membrane cisternae perforated by numerous pore complexes, have been found to form spontaneously in a reconstitution system derived from Xenopus egg extracts, as determined by electron microscopy (Dabauvalle et al., 1991). In this work, a biochemical assay for annulate lamellae (AL) formation was developed and used to study the mechanism of AL assembly in general and the assembly of individual nucleoporins into pore complexes in particular. Upon incubation of Xenopus egg cytosol and membrane vesicles, the nucleoporins nup58, nup60, nup97, nup153, and nup200 initially present in a disassembled form in the cytosol became associated with membranes and were pelletable. The association was time and temperature dependent and could be measured by immunoblotting. Thin-section electron microscopy as well as negative staining confirmed that annulate lamellae were forming coincident with the incorporation of pore proteins into membranes. Homogenization and subsequent flotation of the membrane fraction allowed us to separate a population of dense membranes, containing the integral membrane pore protein gp210 and all other nucleoporins tested, from the bulk of cellular membranes. Electron microscopy indicated that annulate lamellae were enriched in this dense, pore protein-containing fraction. GTP gamma S prevented incorporation of the soluble pore proteins into membranes. To address whether AL form in the absence of N-acetylglucosaminylated pore proteins, AL assembly was carried out in WGA-sepharose-depleted cytosol. Under these conditions, annulate lamellae formed but were altered in appearance. When the membrane fraction containing this altered AL was homogenized and subjected to flotation, the

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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

  4. An assay for clogging the ciliary pore complex distinguishes mechanisms of cytosolic and membrane protein entry

    PubMed Central

    Takao, Daisuke; Dishinger, John F; Kee, H Lynn; Pinskey, Justine M; Allen, Ben L; Verhey, Kristen J

    2014-01-01

    Summary As a cellular organelle, the cilium contains a unique protein composition [1, 2]. Entry of both membrane [3–5] and cytosolic components [6–8] is tightly regulated by gating mechanisms at the cilium base, however, the mechanistic details of ciliary gating are largely unknown. We previously proposed that entry of cytosolic components is regulated by mechanisms similar to those of nuclear transport and is dependent on nucleoporins (NUPs) which comprise a ciliary pore complex (CPC) [6, 9]. To investigate ciliary gating mechanisms, we developed a system to clog the pore by inhibiting NUP function via forced dimerization. We targeted NUP62, a component of the central channel of the nuclear pore complex (NPC) [10], for forced dimerization by tagging it with the homodimerizing Fv domain. As proof of principle, we show that forced dimerization of NUP62-Fv attenuated active transport of bovine serum albumin into the nuclear compartment and of the kinesin-2 motor KIF17 into the ciliary compartment. Using the pore clogging technique, we find that forced dimerization of NUP62 attenuated the gated entry of cytosolic proteins but did not affect entry of membrane proteins or diffusional entry of small cytosolic proteins. We propose a model in which active transport of cytosolic proteins into both nuclear and ciliary compartments requires functional NUPs of the central pore whereas lateral entry of membrane proteins utilizes a different mechanism that is likely specific to each organelle’s limiting membrane. PMID:25264252

  5. 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

  6. P granules extend the nuclear pore complex environment in the C. elegans germ line

    PubMed Central

    Updike, Dustin L.; Hachey, Stephanie J.; Kreher, Jeremy

    2011-01-01

    The immortal and totipotent properties of the germ line depend on determinants within the germ plasm. A common characteristic of germ plasm across phyla is the presence of germ granules, including P granules in Caenorhabditis elegans, which are typically associated with the nuclear periphery. In C. elegans, nuclear pore complex (NPC)–like FG repeat domains are found in the VASA-related P-granule proteins GLH-1, GLH-2, and GLH-4 and other P-granule components. We demonstrate that P granules, like NPCs, are held together by weak hydrophobic interactions and establish a size-exclusion barrier. Our analysis of intestine-expressed proteins revealed that GLH-1 and its FG domain are not sufficient to form granules, but require factors like PGL-1 to nucleate the localized concentration of GLH proteins. GLH-1 is necessary but not sufficient for the perinuclear location of granules in the intestine. Our results suggest that P granules extend the NPC environment in the germ line and provide insights into the roles of the PGL and GLH family proteins. PMID:21402789

  7. Disentangling the Complex Pore-Scale Dispersion Process in Natural Porous Media by Means of DNS

    NASA Astrophysics Data System (ADS)

    Medellin-Azuara, J.; Howitt, R. E.; MacEwan, D.; Lund, J. R.

    2014-12-01

    Over the recent past, important advances have been made in the area of micro-CT scanning of natural porous media. The acquired pore-space geometries enable detailed investigations of flow and transport via pore-scale direct numerical simulation (DNS). In this work, we utilize pore-scale DNS to investigate single-phase pore-scale dispersion. We focus on data stemming from beadpacks, Bentheimer sandstone, and Ketton and Estaillades carbonates. Our DNS results clearly show the transition from ballistic dispersion to the asymptotic Fickian regime (see figure a) at decimeter or meter scale depending on the medium type. We outline a universal Lagrangian model for tracer dispersion that is based on a low-dimensional parametrization of the complex three-dimensional motion of tracer particles (see figure b). We relate the process parameters to certain pore-geometry characteristics such as the tortuosity. Our model accurately captures the wide range of flow and transport dynamics observed in the samples considered. We establish the accuracy of the model by validating its limiting dispersion behavior, the resulting velocity statistics, and also, most challenging, snapshots of tracer plumes at travel times encompassing both ballistic and Fickian behavior.

  8. Surveillance of nuclear pore complex assembly by ESCRT-III/Vps4

    PubMed Central

    Webster, Brant M.; Colombi, Paolo; Jäger, Jens; Lusk, C. Patrick

    2014-01-01

    SUMMARY The maintenance of nuclear compartmentalization by the nuclear envelope and nuclear pore complexes (NPCs) is essential for cell function; loss of compartmentalization is associated with cancers, laminopathies and aging. We uncovered a pathway that surveils NPC assembly intermediates to promote the formation of functional NPCs. Surveillance is mediated by Heh2, a member of the LEM (Lap2-emerin-MAN1) family of integral inner nuclear membrane proteins, which binds to an early NPC assembly intermediate, but not to mature NPCs. Heh2 recruits the Endosomal Sorting Complex Required for Transport (ESCRT) – III subunit Snf7 and the AAA-ATPase Vps4 to destabilize and clear defective NPC assembly intermediates. When surveillance or clearance is compromised, malformed NPCs accumulate in a Storage of Improperly assembled Nuclear Pore Complexes compartment, or SINC. The SINC is retained in old mothers to prevent loss of daughter lifespan, highlighting a continuum of mechanisms to ensure nuclear compartmentalization. PMID:25303532

  9. The TOM core complex: the general protein import pore of the outer membrane of mitochondria.

    PubMed

    Ahting, U; Thun, C; Hegerl, R; Typke, D; Nargang, F E; Neupert, W; Nussberger, S

    1999-11-29

    Translocation of nuclear-encoded preproteins across the outer membrane of mitochondria is mediated by the multicomponent transmembrane TOM complex. We have isolated the TOM core complex of Neurospora crassa by removing the receptors Tom70 and Tom20 from the isolated TOM holo complex by treatment with the detergent dodecyl maltoside. It consists of Tom40, Tom22, and the small Tom components, Tom6 and Tom7. This core complex was also purified directly from mitochondria after solubilization with dodecyl maltoside. The TOM core complex has the characteristics of the general insertion pore; it contains high-conductance channels and binds preprotein in a targeting sequence-dependent manner. It forms a double ring structure that, in contrast to the holo complex, lacks the third density seen in the latter particles. Three-dimensional reconstruction by electron tomography exhibits two open pores traversing the complex with a diameter of approximately 2.1 nm and a height of approximately 7 nm. Tom40 is the key structural element of the TOM core complex. PMID:10579717

  10. Characterization of pore structure and strain localization in Majella limestone by X-ray computed tomography and digital image correlation

    NASA Astrophysics Data System (ADS)

    Ji, Yuntao; Hall, Stephen A.; Baud, Patrick; Wong, Teng-fong

    2015-02-01

    Standard techniques for computed tomography imaging are not directly applicable to a carbonate rock because of the geometric complexity of its pore space. In this study, we first characterized the pore structure in Majella limestone with 30 per cent porosity. Microtomography data acquired on this rock was partitioned into three distinct domains: macropores, solid grains, and an intermediate domain made up of voxels of solid embedded with micropores below the resolution. A morphological analysis of the microtomography images shows that in Majella limestone both the solid and intermediate domains are interconnected in a manner similar to that reported previously in a less porous limestone. We however show that the macroporosity in Majella limestone is fundamentally different, in that it has a percolative backbone which may contribute significantly to its permeability. We then applied for the first time 3-D-volumetric digital image correlation (DIC) to characterize the mode of mechanical failure in this limestone. Samples were triaxially deformed over a wide range of confining pressures. Tomography imaging was performed on these samples before and after deformation. Inelastic compaction was observed at all tested pressures associated with both brittle and ductile behaviors. Our DIC analysis reveals the structure of compacting shear bands in Majella limestone deformed in the transitional regime. It also indicates an increase of geometric complexity with increasing confinement-from a planar shear band, to a curvilinear band, and ultimately to a diffuse multiplicity of bands, before shear localization is inhibited as the failure mode completes the transition to delocalized cataclastic flow.

  11. 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.

  12. The nuclear pore complex--structure and function at a glance.

    PubMed

    Kabachinski, Greg; Schwartz, Thomas U

    2015-02-01

    Nuclear pore complexes (NPCs) are indispensable for cell function and are at the center of several human diseases. NPCs provide access to the nucleus and regulate the transport of proteins and RNA across the nuclear envelope. They are aqueous channels generated from a complex network of evolutionarily conserved proteins known as nucleporins. In this Cell Science at a Glance article and the accompanying poster, we discuss how transport between the nucleoplasm and the cytoplasm is regulated, what we currently know about the structure of individual nucleoporins and the assembled NPC, and how the cell regulates assembly and disassembly of such a massive structure. Our aim is to provide a general overview on what we currently know about the nuclear pore and point out directions of research this area is heading to. PMID:26046137

  13. Saccharomyces cerevisiae Porin Pore Forms Complexes with Mitochondrial Outer Membrane Proteins Om14p and Om45p

    PubMed Central

    Lauffer, Susann; Mäbert, Katrin; Czupalla, Cornelia; Pursche, Theresia; Hoflack, Bernard; Rödel, Gerhard; Krause-Buchholz, Udo

    2012-01-01

    Numerous transport processes occur between the two mitochondrial (mt) membranes due to the diverse functions and metabolic processes of the mt organelle. The metabolite and ion transport through the mt outer membrane (OM) is widely assumed to be mediated by the porin pore, whereas in the mt inner membrane (IM) specific carriers are responsible for transport processes. Here, we provide evidence by means of Blue Native (BN)-PAGE analysis, co-immunoprecipitation, and tandem affinity purification that the two mt OM proteins Om14p and Om45p associate with the porin pore. Porin molecules seem to assemble independently to build the core unit. A subpopulation of these core units interacts with Om14p and Om45p. With preparative tandem affinity purification followed by MS analysis, we could identify interaction partners of this OM complex, which are mainly localized within the mt IM and function as carriers for diverse molecules. We propose a model for the role of the two OM proteins in addressing the porin pore to bind to specific channels in the mt IM to facilitate transport of metabolites. PMID:22461620

  14. Zero-Mode Waveguide detection of biomolecules transport through artificial nanopores and nuclear pore complexes

    NASA Astrophysics Data System (ADS)

    Auger, Thomas; Auvray, Loic; Montel, Fabien

    We have developed a novel single molecule optical observation method using a custom Zero-Mode Waveguide setup to study the translocation of biopolymers through artificial and biological nanopores. Our work focuses on two aspects. First we monitored the flow driven injection of DNA molecules through solid state nanopores and showed that DNA starts translocating over a flow threshold independent of the pore radius, the DNA concentration and length. We demonstrate that the translocation is controlled by an energy barrier as proposed by the de Gennes - Brochard suction model. The height of the energy barrier can be modulated by functionalizing the nanopores with PEG-Thiols. More recently we adapted our setup to the study of transport through the nuclear pore complex (NPC) using extracted nuclear membranes from Xenopus Laevis oocytes. We aim at probing the conformation of unstructured proteins - the FG-Nucleoporins - crowding the central channel of the NPC by monitoring the free diffusion of small Dextran molecules (3kDa). We have been able to estimate the radius of the central pore of the NPC. We want to study the effects of transporter molecules, which have a high affinity for the FG-Nups, on the central pore size and correlate it to the conformation of FG-Nups.

  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. Structure Determination of the Nuclear Pore Complex with Three-Dimensional Cryo electron Microscopy.

    PubMed

    von Appen, Alexander; Beck, Martin

    2016-05-22

    Determining the structure of the nuclear pore complex (NPC) imposes an enormous challenge due to its size, intricate composition and membrane-embedded nature. In vertebrates, about 1000 protein building blocks assemble into a 110-MDa complex that fuses the inner and outer membranes of a cell's nucleus. Here, we review the recent progress in understanding the in situ architecture of the NPC with a specific focus on approaches using three-dimensional cryo electron microscopy. We discuss technological benefits and limitations and give an outlook toward obtaining a high-resolution structure of the NPC. PMID:26791760

  17. 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

  18. Components of the Arabidopsis nuclear pore complex play multiple diverse roles in control of plant growth

    PubMed Central

    Parry, Geraint

    2014-01-01

    The nuclear pore complex (NPC) is a multisubunit protein conglomerate that facilitates movement of RNA and protein between the nucleus and cytoplasm. Relatively little is known regarding the influence of the Arabidopsis NPC on growth and development. Seedling development, flowering time, nuclear morphology, mRNA accumulation, and gene expression changes in Arabidopsis nucleoporin mutants were investigated. Nuclear export of mRNA is differentially affected in plants with defects in nucleoporins that lie in different NPC subcomplexes. This study reveals differences in the manner by which nucleoporins alter molecular and plant growth phenotypes, suggesting that nuclear pore subcomplexes play distinct roles in nuclear transport and reveal a possible feedback relationship between the expression of genes involved in nuclear transport. PMID:25165147

  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. 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

  1. 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

  2. Reorganization of Nuclear Pore Complexes and the Lamina in Late-Stage Parvovirus Infection.

    PubMed

    Mäntylä, Elina; Niskanen, Einari A; Ihalainen, Teemu O; Vihinen-Ranta, Maija

    2015-11-01

    Canine parvovirus (CPV) infection induces reorganization of nuclear structures. Our studies indicated that late-stage infection induces accumulation of nuclear pore complexes (NPCs) and lamin B1 concomitantly with a decrease of lamin A/C levels on the apical side of the nucleus. Newly formed CPV capsids are located in close proximity to NPCs on the apical side. These results suggest that parvoviruses cause apical enrichment of NPCs and reorganization of nuclear lamina, presumably to facilitate the late-stage infection. PMID:26311881

  3. Reorganization of Nuclear Pore Complexes and the Lamina in Late-Stage Parvovirus Infection

    PubMed Central

    Mäntylä, Elina; Niskanen, Einari A.; Ihalainen, Teemu O.

    2015-01-01

    Canine parvovirus (CPV) infection induces reorganization of nuclear structures. Our studies indicated that late-stage infection induces accumulation of nuclear pore complexes (NPCs) and lamin B1 concomitantly with a decrease of lamin A/C levels on the apical side of the nucleus. Newly formed CPV capsids are located in close proximity to NPCs on the apical side. These results suggest that parvoviruses cause apical enrichment of NPCs and reorganization of nuclear lamina, presumably to facilitate the late-stage infection. PMID:26311881

  4. 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

  5. Intracellular distribution of an integral nuclear pore membrane protein fused to green fluorescent protein--localization of a targeting domain.

    PubMed

    Söderqvist, H; Imreh, G; Kihlmark, M; Linnman, C; Ringertz, N; Hallberg, E

    1997-12-15

    The 121-kDa pore membrane protein (POM121) is a bitopic integral membrane protein specifically located in the pore membrane domain of the nuclear envelope with its short N-terminal tail exposed on the luminal side and its major C-terminal portion adjoining the nuclear pore complex. In order to locate a signal for targeting of POM121 to the nuclear pores, we overexpressed selected regions of POM121 alone or fused to the green fluorescent protein (GFP) in transiently transfected COS-1 cells or in a stably transfected neuroblastoma cell line. Microscopic analysis of the GFP fluorescence or immunostaining was used to determine the intracellular distribution of the overexpressed proteins. The endofluorescent GFP tag had no effect on the distribution of POM121, since the chimerical POM121-GFP fusion protein was correctly targeted to the nuclear pores of both COS-1 cells and neuroblastoma cells. Based on the differentiated intracellular sorting of the POM121 variants, we conclude that the first 128 amino acids of POM121 contains signals for targeting to the continuous endoplasmic reticulum/nuclear envelope membrane system but not specifically to the nuclear pores and that a specific nuclear pore targeting signal is located between amino acids 129 and 618 in the endoplasmically exposed portion of POM121. PMID:9461306

  6. 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

  7. Nuclear pore complex proteins mark the implantation window in human endometrium

    PubMed Central

    Guffanti, Elisa; Kittur, Nupur; Brodt, Z. Nilly; Polotsky, Alex J.; Kuokkanen, Satu M.; Heller, Debra S.; Young, Steven L.; Santoro, Nanette; Meier, U. Thomas

    2009-01-01

    Summary Nucleolar channel systems (NCSs) are membranous organelles appearing transiently in the epithelial cell nuclei of postovulatory human endometrium. Their characterization and use as markers for a healthy receptive endometrium have been limited because they are only identifiable by electron microscopy. Here we describe the light microscopic detection of NCSs using immunofluorescence. Specifically, the monoclonal nuclear pore complex antibody 414 shows that NCSs are present in about half of all human endometrial epithelial cells but not in any other cell type, tissue or species. Most nuclei contain only a single NCS of uniform 1 μm diameter indicating a tightly controlled organelle. The composition of NCSs is as unique as their structure; they contain only a subset each of the proteins of nuclear pore complexes, inner nuclear membrane, nuclear lamina and endoplasmic reticulum. Validation of our robust NCS detection method on 95 endometrial biopsies defines a 6-day window, days 19-24 (±1) of an idealized 28 day cycle, wherein NCSs occur. Therefore, NCSs precede and overlap with the implantation window and serve as potential markers of uterine receptivity. The immunodetection assay, combined with the hitherto underappreciated prevalence of NCSs, now enables simple screening and further molecular and functional dissection. PMID:18505792

  8. 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.

  9. Structure–function mapping of a heptameric module in the nuclear pore complex

    PubMed Central

    Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; Diaz-Avalos, Ruben; Velazquez-Muriel, Javier; Franke, Josef D.; Williams, Rosemary; Stokes, David L.; Chait, Brian T.

    2012-01-01

    The nuclear pore complex (NPC) is a multiprotein assembly that serves as the sole mediator of nucleocytoplasmic exchange in eukaryotic cells. In this paper, we use an integrative approach to determine the structure of an essential component of the yeast NPC, the ∼600-kD heptameric Nup84 complex, to a precision of ∼1.5 nm. The configuration of the subunit structures was determined by satisfaction of spatial restraints derived from a diverse set of negative-stain electron microscopy and protein domain–mapping data. Phenotypic data were mapped onto the complex, allowing us to identify regions that stabilize the NPC’s interaction with the nuclear envelope membrane and connect the complex to the rest of the NPC. Our data allow us to suggest how the Nup84 complex is assembled into the NPC and propose a scenario for the evolution of the Nup84 complex through a series of gene duplication and loss events. This work demonstrates that integrative approaches based on low-resolution data of sufficient quality can generate functionally informative structures at intermediate resolution. PMID:22331846

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

    PubMed

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

    2016-01-18

    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

  11. 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

  12. 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.

  13. Comparative Genomic Evidence for a Complete Nuclear Pore Complex in the Last Eukaryotic Common Ancestor

    PubMed Central

    Neumann, Nadja; Lundin, Daniel; Poole, Anthony M.

    2010-01-01

    Background The Nuclear Pore Complex (NPC) facilitates molecular trafficking between nucleus and cytoplasm and is an integral feature of the eukaryote cell. It exhibits eight-fold rotational symmetry and is comprised of approximately 30 nucleoporins (Nups) in different stoichiometries. Nups are broadly conserved between yeast, vertebrates and plants, but few have been identified among other major eukaryotic groups. Methodology/Principal Findings We screened for Nups across 60 eukaryote genomes and report that 19 Nups (spanning all major protein subcomplexes) are found in all eukaryote supergroups represented in our study (Opisthokonts, Amoebozoa, Viridiplantae, Chromalveolates and Excavates). Based on parsimony, between 23 and 26 of 31 Nups can be placed in LECA. Notably, they include central components of the anchoring system (Ndc1 and Gp210) indicating that the anchoring system did not evolve by convergence, as has previously been suggested. These results significantly extend earlier results and, importantly, unambiguously place a fully-fledged NPC in LECA. We also test the proposal that transmembrane Pom proteins in vertebrates and yeasts may account for their variant forms of mitosis (open mitoses in vertebrates, closed among yeasts). The distribution of homologues of vertebrate Pom121 and yeast Pom152 is not consistent with this suggestion, but the distribution of fungal Pom34 fits a scenario wherein it was integral to the evolution of closed mitosis in ascomycetes. We also report an updated screen for vesicle coating complexes, which share a common evolutionary origin with Nups, and can be traced back to LECA. Surprisingly, we find only three supergroup-level differences (one gain and two losses) between the constituents of COPI, COPII and Clathrin complexes. Conclusions/Significance Our results indicate that all major protein subcomplexes in the Nuclear Pore Complex are traceable to the Last Eukaryotic Common Ancestor (LECA). In contrast to previous screens

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Disordered proteins are an interesting class of unfolded protein biopolymers which are functionally versatile. Their sequences are unconstrained by a sequence-structure relationship, and allow for a wide range of chemical and physical polymer properties. The Nuclear Pore Complex (NPC) contains over one hundred of such proteins (FG nups), which collectively function to regulate the exchange of all materials between the nucleus and cytoplasm. We perform coarse grained simulations of both individual FG nups and grafted rings of nups mimicking the in vivo geometry of the NPC, supplemented with polymer brush modeling. Our results indicate that different regions or ``blocks'' of an individual FG nup can have distinctly different forms of disorder, and that this property appears to be a conserved feature across eukarya. Furthermore, this block structure at the individual protein level is critical to the formation of a unique higher-order polymer brush architecture. Because the interactions between FG nups 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.

  16. 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

  17. From hypothesis to mechanism: uncovering nuclear pore complex links to gene expression.

    PubMed

    Burns, Laura T; Wente, Susan R

    2014-06-01

    The gene gating hypothesis put forth by Blobel in 1985 was an alluring proposal outlining functions for the nuclear pore complex (NPC) in transcription and nuclear architecture. Over the past several decades, collective studies have unveiled a full catalog of nucleoporins (Nups) that comprise the NPC, structural arrangements of Nups in the nuclear pore, and mechanisms of nucleocytoplasmic transport. With this foundation, investigations of the gene gating hypothesis have now become possible. Studies of several model organisms provide credence for Nup functions in transcription, mRNA export, and genome organization. Surprisingly, Nups are not only involved in transcriptional events that occur at the nuclear periphery, but there are also novel roles for dynamic Nups within the nucleoplasmic compartment. Several tenants of the original gene gating hypothesis have yet to be addressed. Knowledge of whether the NPC impacts the organization of the genome to control subsets of genes is limited, and the cooperating molecular machinery or specific genomic anchoring sequences are not fully resolved. This minireview summarizes the current evidence for gene gating in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mammalian model systems. These examples highlight new and unpredicted mechanisms for Nup impacts on transcription and questions that are left to be explored. PMID:24615017

  18. Effect of pore sizes on catalytic activities of arenetricarbonyl metal complexes constructed within Zr-based MOFs.

    PubMed

    Saito, Masakazu; Toyao, Takashi; Ueda, Kozo; Kamegawa, Takashi; Horiuchi, Yu; Matsuoka, Masaya

    2013-07-14

    Arenetricarbonyl metal complexes ([-phM(CO)3-] and [-biphM(CO)3-]; ph = phenylene, biph = biphenylene, M = Mo, Cr) constructed within Zr-based MOFs act as highly active and selective catalysts for epoxidation of cyclooctene. Catalytic activities of these complexes are enhanced with increasing the pore sizes of Zr-based MOFs. PMID:23694976

  19. Modern tools to study nuclear pore complexes and nucleocytoplasmic transport in Caenorhabditis elegans.

    PubMed

    Askjaer, Peter; Galy, Vincent; Meister, Peter

    2014-01-01

    The nematode Caenorhabditis elegans is characterized by many features that make it highly attractive to study nuclear pore complexes (NPCs) and nucleocytoplasmic transport. NPC composition and structure are highly conserved in nematodes and being amenable to a variety of genetic manipulations, key aspects of nuclear envelope dynamics can be observed in great details during breakdown, reassembly, and interphase. In this chapter, we provide an overview of some of the most relevant modern techniques that allow researchers unfamiliar with C. elegans to embark on studies of nucleoporins in an intact organism through its development from zygote to aging adult. We focus on methods relevant to generate loss-of-function phenotypes and their analysis by advanced microscopy. Extensive references to available reagents, such as mutants, transgenic strains, and antibodies are equally useful to scientists with or without prior C. elegans or nucleoporin experience. PMID:24857735

  20. 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. PMID:27273515

  1. Super-resolution 3D tomography of interactions and competition in the nuclear pore complex.

    PubMed

    Ma, Jiong; Goryaynov, Alexander; Yang, Weidong

    2016-03-01

    A selective barrier formed by intrinsically disordered Phe-Gly (FG) nucleoporins (Nups) allows transport receptor (TR)-facilitated translocation of signal-dependent cargos through the nuclear pore complexes (NPCs) of eukaryotic cells. However, the configuration of the FG-Nup barrier and its interactions with multiple TRs in native NPCs remain obscure. Here, we mapped the interaction sites of various TRs or FG segments within the FG-Nup barrier by using high-speed super-resolution microscopy and used these sites to reconstruct the three-dimensional tomography of the native barrier in the NPC. We found that each TR possesses a unique interaction zone within the FG-Nup barrier and that two major TRs, importin β1 and Crm1, outcompete other TRs in binding FG Nups. Moreover, TRs may alter the tomography of the FG-Nup barrier and affect one another's pathways under circumstances of heavy competition. PMID:26878241

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

    PubMed

    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. PMID:27198189

  3. 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

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

    PubMed

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

    2016-02-01

    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

  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. PMID:23202855

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

    PubMed Central

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

    2013-01-01

    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. PMID:23202855

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

    2016-01-01

    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. Yeast Integral Membrane Proteins Apq12, Brl1, and Brr6 Form a Complex Important for Regulation of Membrane Homeostasis and Nuclear Pore Complex Biogenesis

    PubMed Central

    Lone, Museer A.; Atkinson, Aaron E.; Hodge, Christine A.; Cottier, Stéphanie; Martínez-Montañés, Fernando; Maithel, Shelley; Mène-Saffrané, Laurent

    2015-01-01

    Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical properties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during interphase in all eukaryotes. Here we report on the role of the essential nuclear envelope/endoplasmic reticulum (NE/ER) protein Brl1 in regulating the membrane composition of the NE/ER. We show that Brl1 and two other proteins characterized previously—Brr6, which is closely related to Brl1, and Apq12—function together and are required for lipid homeostasis. All three transmembrane proteins are localized to the NE and can be coprecipitated. As has been shown for mutations affecting Brr6 and Apq12, mutations in Brl1 lead to defects in lipid metabolism, increased sensitivity to drugs that inhibit enzymes involved in lipid synthesis, and strong genetic interactions with mutations affecting lipid metabolism. Mutations affecting Brl1 or Brr6 or the absence of Apq12 leads to hyperfluid membranes, because mutant cells are hypersensitive to agents that increase membrane fluidity. We suggest that the defects in nuclear pore complex biogenesis and mRNA export seen in these mutants are consequences of defects in maintaining the biophysical properties of the NE. PMID:26432634

  14. Yeast Integral Membrane Proteins Apq12, Brl1, and Brr6 Form a Complex Important for Regulation of Membrane Homeostasis and Nuclear Pore Complex Biogenesis.

    PubMed

    Lone, Museer A; Atkinson, Aaron E; Hodge, Christine A; Cottier, Stéphanie; Martínez-Montañés, Fernando; Maithel, Shelley; Mène-Saffrané, Laurent; Cole, Charles N; Schneiter, Roger

    2015-12-01

    Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical properties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during interphase in all eukaryotes. Here we report on the role of the essential nuclear envelope/endoplasmic reticulum (NE/ER) protein Brl1 in regulating the membrane composition of the NE/ER. We show that Brl1 and two other proteins characterized previously-Brr6, which is closely related to Brl1, and Apq12-function together and are required for lipid homeostasis. All three transmembrane proteins are localized to the NE and can be coprecipitated. As has been shown for mutations affecting Brr6 and Apq12, mutations in Brl1 lead to defects in lipid metabolism, increased sensitivity to drugs that inhibit enzymes involved in lipid synthesis, and strong genetic interactions with mutations affecting lipid metabolism. Mutations affecting Brl1 or Brr6 or the absence of Apq12 leads to hyperfluid membranes, because mutant cells are hypersensitive to agents that increase membrane fluidity. We suggest that the defects in nuclear pore complex biogenesis and mRNA export seen in these mutants are consequences of defects in maintaining the biophysical properties of the NE. PMID:26432634

  15. 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

  16. 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

  17. 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

  18. Physical modeling of the conformation of the unfolded proteins of the Nuclear Pore Complex

    NASA Astrophysics Data System (ADS)

    Zilman, Anton; Opferman, Michael; Coalson, Rob; Jasnow, David

    2013-03-01

    Nuclear Pore Complex (NPC) is a biological ``nano-machine'' that controls the macromolecular transport between the cell nucleus and the cytoplasm. NPC functions without direct input of metabolic energy and without transitions of the gate from a ``closed'' to an ``open'' state during transport. The key and unique aspect of transport is the interaction of the transported molecules with the unfolded, natively unstructured proteins that cover the lumen of the NPC. Recently, the NPC inspired creation of artificial bio-mimetic for nano-technology applications. Although several models have been proposed, it is still not clear how the passage of the transport factors is coupled to the conformational dynamics of the unfolded proteins within the NPC. Morphology changes in assemblies of the unfolded proteins induced by the transport factors have been investigated experimentally in vitro. I will present a coarse-grained theoretical and simulation framework that mimics the interactions of unfolded proteins with nano-sized transport factors. The simple physical model predicts morphology changes that explain the recent puzzling experimental results and suggests possible new modes of transport through the NPC. It also provides insights into the physics of the behavior of unfolded proteins.

  19. Plant nuclear pore complex proteins are modified by novel oligosaccharides with terminal N-acetylglucosamine.

    PubMed Central

    Heese-Peck, A; Cole, R N; Borkhsenious, O N; Hart, G W; Raikhel, N V

    1995-01-01

    Only a few nuclear pore complex (NPC) proteins, mainly in vertebrates and yeast but none in plants, have been well characterized. As an initial step to identify plant NPC proteins, we examined whether NPC proteins from tobacco are modified by N-acetylglucosamine (GlcNAc). Using wheat germ agglutinin, a lectin that binds specifically to GlcNAc in plants, specific labeling was often found associated with or adjacent to NPCs. Nuclear proteins containing GlcNAc can be partially extracted by 0.5 M salt, as shown by a wheat germ agglutinin blot assay, and at least eight extracted proteins were modified by terminal GlcNAc, as determined by in vitro galactosyltransferase assays. Sugar analysis indicated that the plant glycans with terminal GlcNAc differ from the single O-linked GlcNAc of vertebrate NPC proteins in that they consist of oligosaccharides that are larger in size than five GlcNAc residues. Most of these appear to be bound to proteins via a hydroxyl group. This novel oligosaccharide modification may convey properties to the plant NPC that are different from those of vertebrate NPCs. PMID:8589629

  20. SUMO-Dependent Relocalization of Eroded Telomeres to Nuclear Pore Complexes Controls Telomere Recombination.

    PubMed

    Churikov, Dmitri; Charifi, Ferose; Eckert-Boulet, Nadine; Silva, Sonia; Simon, Marie-Noelle; Lisby, Michael; Géli, Vincent

    2016-05-10

    In budding yeast, inactivation of telomerase and ensuing telomere erosion cause relocalization of telomeres to nuclear pore complexes (NPCs). However, neither the mechanism of such relocalization nor its significance are understood. We report that proteins bound to eroded telomeres are recognized by the SUMO (small ubiquitin-like modifier)-targeted ubiquitin ligase (STUbL) Slx5-Slx8 and become increasingly SUMOylated. Recruitment of Slx5-Slx8 to eroded telomeres facilitates telomere relocalization to NPCs and type II telomere recombination, a counterpart of mammalian alternative lengthening of telomeres (ALT). Moreover, artificial tethering of a telomere to a NPC promotes type II telomere recombination but cannot bypass the lack of Slx5-Slx8 in this process. Together, our results indicate that SUMOylation positively contributes to telomere relocalization to the NPC, where poly-SUMOylated proteins that accumulated over time have to be removed. We propose that STUbL-dependent relocalization of telomeres to NPCs constitutes a pathway in which excessively SUMOylated proteins are removed from "congested" intermediates to ensure unconventional recombination. PMID:27134164

  1. Global motions of the nuclear pore complex: insights from elastic network models.

    PubMed

    Lezon, Timothy R; Sali, Andrej; Bahar, Ivet

    2009-09-01

    The nuclear pore complex (NPC) is the gate to the nucleus. Recent determination of the configuration of proteins in the yeast NPC at approximately 5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models. We investigate these large-scale motions by using an extended elastic network model (ENM) formalism applied to several coarse-grained representations of the NPC. Two types of collective motions (global modes) are predicted by the ENMs to be intrinsically favored by the NPC architecture: global bending and extension/contraction from circular to elliptical shapes. These motions are shown to be robust against tested variations in the representation of the NPC, and are largely captured by a simple model of a toroid with axially varying mass density. We demonstrate that spoke multiplicity significantly affects the accessible number of symmetric low-energy modes of motion; the NPC-like toroidal structures composed of 8 spokes have access to highly cooperative symmetric motions that are inaccessible to toroids composed of 7 or 9 spokes. The analysis reveals modes of motion that may facilitate macromolecular transport through the NPC, consistent with previous experimental observations. PMID:19730674

  2. 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

  3. 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

  4. 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.

  5. 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

  6. Double complexes and local cochain projections

    PubMed Central

    Falk, Richard S; Winther, Ragnar

    2015-01-01

    The construction of projection operators, which commute with the exterior derivative and at the same time are bounded in the proper Sobolev spaces, represents a key tool in the recent stability analysis of finite element exterior calculus. These so-called bounded cochain projections have been constructed by combining a smoothing operator and the unbounded canonical projections defined by the degrees of freedom. However, an undesired property of these bounded projections is that, in contrast to the canonical projections, they are nonlocal. The purpose of this article is to discuss a recent alternative construction of bounded cochain projections, which also are local. A key tool for the new construction is the structure of a double complex, resembling the Čech-de Rham double complex of algebraic topology. © 2014 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 31: 541–551, 2015 PMID:25914441

  7. Photoactivated Localization Microscopy (PALM) of Adhesion Complexes

    PubMed Central

    White, Helen; Betzig, Eric

    2013-01-01

    Key to understanding a protein’s biological function is the accurate determination of its spatial distribution inside a cell. Although fluorescent protein markers allow the targeting of specific proteins with molecular precision, much of this information is lost when the resultant fusion proteins are imaged with conventional, diffraction-limited optics. In response, several imaging modalities that are capable of resolution below the diffraction limit (~200 nm) have emerged. Here, both single- and dual-color superresolution imaging of biological structures using photoactivated localization microscopy (PALM) are described. The examples discussed focus on adhesion complexes: dense, protein-filled assemblies that form at the interface between cells and their substrata. A particular emphasis is placed on the instrumentation and photoactivatable fluorescent protein (PA-FP) tags necessary to achieve PALM images at ~20 nm resolution in 5 to 30 min in fixed cells. PMID:19085989

  8. Modified localized attack on complex network

    NASA Astrophysics Data System (ADS)

    Dong, Gaogao; Du, Ruijin; Hao, Huifang; Tian, Lixin

    2016-01-01

    Since a shell structure contains a wealth of information, it is not only very important for understanding the transport properties of the network, but also essential to identify influential spreaders in complex networks. Nodes within each shell can be classified into two categories: protected nodes and unprotected nodes. In this paper, we propose a generalization of the localized attack, modified localized attack, which means that when a randomly chosen node (root node) is under attack, protected nodes will not be removed, but unprotected nodes in the nearest shells will fail. We numerically and analytically study the system robustness under this attack by taking an Erdös-Rényi (ER) network, a regular random (RR) network and a scale-free (SF) network as examples. Moreover, a fraction of nodes belonging to giant component S and a critical threshold q c , where S approaches to zero, are given. The result implies that increasing connection density has been found to be useful to significantly improve network robustness.

  9. 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

  10. Structure of a pore-blocking toxin in complex with a eukaryotic voltage-dependent K+ channel

    PubMed Central

    Banerjee, Anirban; Lee, Alice; Campbell, Ernest; MacKinnon, Roderick

    2013-01-01

    Pore-blocking toxins inhibit voltage-dependent K+ channels (Kv channels) by plugging the ion-conduction pathway. We have solved the crystal structure of paddle chimera, a Kv channel in complex with charybdotoxin (CTX), a pore-blocking toxin. The toxin binds to the extracellular pore entryway without producing discernable alteration of the selectivity filter structure and is oriented to project its Lys27 into the pore. The most extracellular K+ binding site (S1) is devoid of K+ electron-density when wild-type CTX is bound, but K+ density is present to some extent in a Lys27Met mutant. In crystals with Cs+ replacing K+, S1 electron-density is present even in the presence of Lys27, a finding compatible with the differential effects of Cs+ vs K+ on CTX affinity for the channel. Together, these results show that CTX binds to a K+ channel in a lock and key manner and interacts directly with conducting ions inside the selectivity filter. DOI: http://dx.doi.org/10.7554/eLife.00594.001 PMID:23705070

  11. Nucleoporin FG Domains Facilitate mRNP Remodeling at the Cytoplasmic Face of the Nuclear Pore Complex

    PubMed Central

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

    2014-01-01

    Directional export of messenger RNA (mRNA) protein particles (mRNPs) through nuclear pore complexes (NPCs) requires multiple factors. In Saccharomyces cerevisiae, the NPC proteins Nup159 and Nup42 are asymmetrically localized to the cytoplasmic face and have distinct functional domains: a phenylalanine-glycine (FG) repeat domain that docks mRNP transport receptors and domains that bind the DEAD-box ATPase Dbp5 and its activating cofactor Gle1, respectively. We speculated that the Nup42 and Nup159 FG domains play a role in positioning mRNPs for the terminal mRNP-remodeling steps carried out by Dbp5. Here we find that deletion (Δ) of both the Nup42 and Nup159 FG domains results in a cold-sensitive poly(A)+ mRNA export defect. The nup42ΔFG nup159ΔFG mutant also has synthetic lethal genetic interactions with dbp5 and gle1 mutants. RNA cross-linking experiments further indicate that the nup42ΔFG nup159ΔFG mutant has a reduced capacity for mRNP remodeling during export. To further analyze the role of these FG domains, we replaced the Nup159 or Nup42 FG domains with FG domains from other Nups. These FG “swaps” demonstrate that only certain FG domains are functional at the NPC cytoplasmic face. Strikingly, fusing the Nup42 FG domain to the carboxy-terminus of Gle1 bypasses the need for the endogenous Nup42 FG domain, highlighting the importance of proximal positioning for these factors. We conclude that the Nup42 and Nup159 FG domains target the mRNP to Gle1 and Dbp5 for mRNP remodeling at the NPC. Moreover, these results provide key evidence that character and context play a direct role in FG domain function and mRNA export. PMID:24931410

  12. Nuclear Import of the Retrotransposon Tf1 Is Governed by a Nuclear Localization Signal That Possesses a Unique Requirement for the FXFG Nuclear Pore Factor Nup124p

    PubMed Central

    Dang, Van-Dinh; Levin, Henry L.

    2000-01-01

    Retroviruses, such as human immunodeficiency virus, that infect nondividing cells generate integration precursors that must cross the nuclear envelope to reach the host genome. As a model for retroviruses, we investigated the nuclear entry of Tf1, a long-terminal-repeat-containing retrotransposon of the fission yeast Schizosaccharomyces pombe. Because the nuclear envelope of yeasts remains intact throughout the cell cycle, components of Tf1 must be transported through the envelope before integration can occur. The nuclear localization of the Gag protein of Tf1 is different from that of other proteins tested in that it has a specific requirement for the FXFG nuclear pore factor, Nup124p. Using extensive mutagenesis, we found that Gag contained three nuclear localization signals (NLSs) which, when included individually in a heterologous protein, were sufficient to direct nuclear import. In the context of the intact transposon, mutations in the NLS that mapped to the first 10 amino acid residues of Gag significantly impaired Tf1 retrotransposition and abolished nuclear localization of Gag. Interestingly, this NLS activity in the heterologous protein was specifically dependent upon the presence of Nup124p. Deletion analysis of heterologous proteins revealed the surprising result that the residues in Gag with the NLS activity were independent from the residues that conveyed the requirement for Nup124p. In fact, a fragment of Gag that lacked NLS activity, residues 10 to 30, when fused to a heterologous protein, was sufficient to cause the classical NLS of simian virus 40 to require Nup124p for nuclear import. Within the context of the current understanding of nuclear import, these results represent the novel case of a short amino acid sequence that specifies the need for a particular nuclear pore complex protein. PMID:11003674

  13. 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

  14. 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

  15. Extracellular ATP dissociates nonmuscle myosin from P2X(7) complex: this dissociation regulates P2X(7) pore formation.

    PubMed

    Gu, Ben J; Rathsam, Catherine; Stokes, Leanne; McGeachie, Andrew B; Wiley, James S

    2009-08-01

    The P2X(7) receptor is a ligand-gated cation channel that is highly expressed on monocyte-macrophages and that mediates the pro-inflammatory effects of extracellular ATP. Dilation of the P2X(7) channel and massive K(+) efflux follows initial channel opening, but the mechanism of secondary pore formation is unclear. The proteins associated with P2X(7) were isolated by using anti-P2X(7) monoclonal antibody-coated Dynabeads from both interferon-gamma plus LPS-stimulated monocytic THP-1 cells and P2X(7)-transfected HEK-293 cells. Two nonmuscle myosins, NMMHC-IIA and myosin Va, were found to associate with P2X(7) in THP-1 cells and HEK-293 cells, respectively. Activation of the P2X(7) receptor by ATP caused dissociation of P2X(7) from nonmuscle myosin in both cell types. The interaction of P2X(7) and NMMHC-IIA molecules was confirmed by fluorescent life time measurements and fluorescent resonance of energy transfer-based time-resolved flow cytometry assay. Reducing the expression of NMMHC-IIA or myosin Va by small interfering RNA or short hairpin RNA led to a significant increase of P2X(7) pore function without any increase in surface expression or ion channel function of P2X(7) receptors. S-l-blebbistatin, a specific inhibitor of NMMHC-IIA ATPase, inhibited both ATP-induced ethidium uptake and ATP-induced dissociation of P2X(7)-NMMHC-IIA complex. In both cell types nonmuscle myosin closely interacts with P2X(7) and is dissociated from the complex by extracellular ATP. Dissociation of this anchoring protein may be required for the transition of P2X(7) channel to a pore. PMID:19494237

  16. 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. PMID:27147058

  17. The Nuclear Pore Complex Function of Sec13 Protein Is Required for Cell Survival during Retinal Development*

    PubMed Central

    Niu, Xubo; Hong, Jian; Zheng, Xiaofeng; Melville, David B.; Knapik, Ela W.; Meng, Anming; Peng, Jinrong

    2014-01-01

    Sec13 is a dual function protein, being a core component of both the COPII coat, which mediates protein trafficking from the endoplasmic reticulum to the Golgi apparatus, and the nuclear pore complex (NPC), which facilitates nucleo-cytoplasmic traffic. Here, we present a genetic model to differentiate the roles of these two functions of Sec13 in vivo. We report that sec13sq198 mutant embryos develop small eyes that exhibit disrupted retinal lamination and that the mutant retina contains an excessive number of apoptotic cells. Surprisingly, we found that loss of COPII function by oligonucleotide-mediated gene knockdown of sec31a and sec31b or brefeldin A treatment did not disrupt retinal lamination, although it did result in digestive organ defects similar to those seen in sec13sq198, suggesting that the digestive organ defects observed in sec13sq198 are due to loss of COPII function, whereas the retinal lamination defects are due to loss of the NPC function. We showed that the retinal cells of sec13sq198 failed to form proper nuclear pores, leading to a nuclear accumulation of total mRNA and abnormal activation of the p53-dependent apoptosis pathway, causing the retinal defect in sec13sq198. Furthermore, we found that a mutant lacking Nup107, a key NPC-specific component, phenocopied the retinal lamination phenotype as observed in sec13sq198. Our results demonstrate a requirement for the nuclear pore function of Sec13 in development of the retina and provide the first genetic evidence to differentiate the contributions of the NPC and the COPII functions of Sec13 during organogenesis. PMID:24627485

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

    PubMed Central

    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

  19. 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

  20. 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

    2016-01-01

    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

  1. 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

  2. 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.

  3. 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

  4. PARTICLE SIZE SEGREGATION DURING HAND PACKING OF COARSE GRANULAR MATERIALS AND IMPACTS ON LOCAL PORE-SCALE STRUCTURE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soils and sediments consist of granular particles with an intricate network of pores in between. The structure and orientation of these pores will determine how the material transports fluids and contaminants. A common practice in soil science to simplify experiments and to achieve a homogeneous med...

  5. 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

  6. Community detection using local neighborhood in complex networks

    NASA Astrophysics Data System (ADS)

    Eustace, Justine; Wang, Xingyuan; Cui, Yaozu

    2015-10-01

    It is common to characterize community structure in complex networks using local neighborhood. Existing related methods fail to estimate the accurate number of nodes present in each community in the network. In this paper a community detection algorithm using local community neighborhood ratio function is proposed. The proposed algorithm predicts vertex association to a specific community using visited node overlapped neighbors. In the beginning, the algorithm detects local communities; then through iterations and local neighborhood ratio function, final communities are detected by merging close related local communities. Analysis of simulation results on real and artificial networks shows the proposed algorithm detects well defined communities in both networks by wide margin.

  7. The Three Fungal Transmembrane Nuclear Pore Complex Proteins of Aspergillus nidulans Are Dispensable in the Presence of an Intact An-Nup84-120 Complex

    PubMed Central

    Liu, Hui-Lin; De Souza, Colin P.C.; Osmani, Aysha H.

    2009-01-01

    In Aspergillus nidulans nuclear pore complexes (NPCs) undergo partial mitotic disassembly such that 12 NPC proteins (Nups) form a core structure anchored across the nuclear envelope (NE). To investigate how the NPC core is maintained, we affinity purified the major core An-Nup84-120 complex and identified two new fungal Nups, An-Nup37 and An-ELYS, previously thought to be vertebrate specific. During mitosis the An-Nup84-120 complex locates to the NE and spindle pole bodies but, unlike vertebrate cells, does not concentrate at kinetochores. We find that mutants lacking individual An-Nup84-120 components are sensitive to the membrane destabilizer benzyl alcohol (BA) and high temperature. Although such mutants display no defects in mitotic spindle formation, they undergo mitotic specific disassembly of the NPC core and transient aggregation of the mitotic NE, suggesting the An-Nup84-120 complex might function with membrane. Supporting this, we show cells devoid of all known fungal transmembrane Nups (An-Ndc1, An-Pom152, and An-Pom34) are viable but that An-ndc1 deletion combined with deletion of individual An-Nup84-120 components is either lethal or causes sensitivity to treatments expected to destabilize membrane. Therefore, the An-Nup84-120 complex performs roles, perhaps at the NPC membrane as proposed previously, that become essential without the An-Ndc1 transmembrane Nup. PMID:19019988

  8. 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

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

    PubMed

    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

  10. Molecular Basis for the Anchoring of Proto-Oncoprotein Nup98 to the Cytoplasmic Face of the Nuclear Pore Complex

    PubMed Central

    Stuwe, Tobias T.; von Borzyskowski, Lennart Schada; Davenport, Andrew M.; Hoelz, André

    2014-01-01

    The cytoplasmic filament nucleoporins of the nuclear pore complex (NPC) are critically involved in nuclear export and remodeling of mRNA ribonucleoprotein particles and are associated with various human malignancies. Here, we report the crystal structure of the Nup98 C-terminal autoproteolytic domain, frequently missing from leukemogenic forms of the protein, in complex with the N-terminal domain of Nup82 and the C-terminal tail fragment of Nup159. The Nup82 β propeller serves as a non-cooperative binding platform for both binding partners. Interaction of Nup98 with Nup82 occurs through a reciprocal exchange of loop structures. Strikingly, the same Nup98 groove promiscuously interacts with Nup82 and Nup96 in a mutually excusive fashion. Simultaneous disruption of both Nup82 interactions in yeast causes severe defects in mRNA export, while the severing of a single interaction is tolerated. Thus, the cytoplasmic filament network of the NPC is robust, consistent with its essential function in nucleocytoplasmic transport. PMID:22480613

  11. 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

  12. Biallelic Mutations in Nuclear Pore Complex Subunit NUP107 Cause Early-Childhood-Onset Steroid-Resistant Nephrotic Syndrome

    PubMed Central

    Miyake, Noriko; Tsukaguchi, Hiroyasu; Koshimizu, Eriko; Shono, Akemi; Matsunaga, Satoko; Shiina, Masaaki; Mimura, Yasuhiro; Imamura, Shintaro; Hirose, Tomonori; Okudela, Koji; Nozu, Kandai; Akioka, Yuko; Hattori, Motoshi; Yoshikawa, Norishige; Kitamura, Akiko; Cheong, Hae Il; Kagami, Shoji; Yamashita, Michiaki; Fujita, Atsushi; Miyatake, Satoko; Tsurusaki, Yoshinori; Nakashima, Mitsuko; Saitsu, Hirotomo; Ohashi, Kenichi; Imamoto, Naoko; Ryo, Akihide; Ogata, Kazuhiro; Iijima, Kazumoto; Matsumoto, Naomichi

    2015-01-01

    The nuclear pore complex (NPC) is a huge protein complex embedded in the nuclear envelope. It has central functions in nucleocytoplasmic transport, nuclear framework, and gene regulation. Nucleoporin 107 kDa (NUP107) is a component of the NPC central scaffold and is an essential protein in all eukaryotic cells. Here, we report on biallelic NUP107 mutations in nine affected individuals who are from five unrelated families and show early-onset steroid-resistant nephrotic syndrome (SRNS). These individuals have pathologically focal segmental glomerulosclerosis, a condition that leads to end-stage renal disease with high frequency. NUP107 is ubiquitously expressed, including in glomerular podocytes. Three of four NUP107 mutations detected in the affected individuals hamper NUP107 binding to NUP133 (nucleoporin 133 kDa) and NUP107 incorporation into NPCs in vitro. Zebrafish with nup107 knockdown generated by morpholino oligonucleotides displayed hypoplastic glomerulus structures and abnormal podocyte foot processes, thereby mimicking the pathological changes seen in the kidneys of the SRNS individuals with NUP107 mutations. Considering the unique properties of the podocyte (highly differentiated foot-process architecture and slit membrane and the inability to regenerate), we propose a “podocyte-injury model” as the pathomechanism for SRNS due to biallelic NUP107 mutations. PMID:26411495

  13. BGLF4 Kinase Modulates the Structure and Transport Preference of the Nuclear Pore Complex To Facilitate Nuclear Import of Epstein-Barr Virus Lytic Proteins

    PubMed Central

    Chang, Chou-Wei; Lee, Chung-Pei; Su, Mei-Tzu; Tsai, Ching-Hwa

    2014-01-01

    ABSTRACT BGLF4 kinase, the only Ser/Thr protein kinase encoded by the Epstein-Barr virus (EBV) genome, phosphorylates multiple viral and cellular substrates to optimize the cellular environment for viral DNA replication and the nuclear egress of nucleocapsids. Previously, we found that nuclear targeting of BGLF4 is through direct interaction with the FG repeat-containing nucleoporins (FG-Nups) Nup62 and Nup153 independently of cytosolic transport factors. Here, we investigated the regulatory effects of BGLF4 on the structure and biological functions of the nuclear pore complex (NPC). In EBV-positive NA cells, the distribution of FG-Nups was modified during EBV reactivation. In transfected cells, BGLF4 changed the staining pattern of Nup62 and Nup153 in a kinase activity-dependent manner. Detection with anti-phospho-Ser/Thr-Pro MPM-2 antibody demonstrated that BGLF4 induced the phosphorylation of Nup62 and Nup153. The nuclear targeting of importin β was attenuated in the presence of BGLF4, leading to inhibition of canonical nuclear localization signal (NLS)-mediated nuclear import. An in vitro nuclear import assay revealed that BGLF4 induced the nuclear import of larger molecules. Notably, we found that BGLF4 promoted the nuclear import of several non-NLS-containing EBV proteins, including the viral DNA-replicating enzymes BSLF1, BBLF2/3, and BBLF4 and the major capsid protein (VCA), in cotransfected cells. The data presented here suggest that BGLF4 interferes with the normal functions of Nup62 and Nup153 and preferentially helps the nuclear import of viral proteins for viral DNA replication and assembly. In addition, the nuclear import-promoting activity was found in cells expressing the BGLF4 homologs of another two gammaherpesviruses but not those from alpha- and betaherpesviruses. IMPORTANCE During lytic replication, many EBV genome-encoded proteins need to be transported into the nucleus, not only for viral DNA replication but also for the assembly of

  14. Local Activity Principle:. the Cause of Complexity and Symmetry Breaking

    NASA Astrophysics Data System (ADS)

    Mainzer, Klaus

    2013-01-01

    The principle of local activity is precisely the missing concept to explain the emergence of complex patterns in a homogeneous medium. Leon O. Chua discovered and defined this principle in the theory of nonlinear electronic circuits in a mathematically rigorous way. The local principle can be generalized and proven at least for the class of nonlinear reaction-diffusion systems in physics, chemistry, biology and brain research. Recently, it was realized by memristors for nanoelectronic device applications in technical brains. In general, the emergence of complex patterns and structures is explained by symmetry breaking in homogeneous media. The principle of local activity is the cause of symmetry breaking in homogeneous media. We argue that the principle of local activity is really fundamental in science and can even be identified in quantum cosmology as symmetry breaking of local gauge symmetries generating the complexity of matter and forces in our universe. Finally, we consider applications in economic, financial, and social systems with the emergence of equilibrium states, symmetry breaking at critical points of phase transitions and risky acting at the edge of chaos. In any case, the driving causes of symmetry breaking and the emergence of complexity are locally active elements, cells, units, or agents.

  15. 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.

  16. 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

  17. 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. PMID:25788697

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. Interaction graph mining for protein complexes using local clique merging.

    PubMed

    Li, Xiao-Li; Tan, Soon-Heng; Foo, Chuan-Sheng; Ng, See-Kiong

    2005-01-01

    While recent technological advances have made available large datasets of experimentally-detected pairwise protein-protein interactions, there is still a lack of experimentally-determined protein complex data. To make up for this lack of protein complex data, we explore the mining of existing protein interaction graphs for protein complexes. This paper proposes a novel graph mining algorithm to detect the dense neighborhoods (highly connected regions) in an interaction graph which may correspond to protein complexes. Our algorithm first locates local cliques for each graph vertex (protein) and then merge the detected local cliques according to their affinity to form maximal dense regions. We present experimental results with yeast protein interaction data to demonstrate the effectiveness of our proposed method. Compared with other existing techniques, our predicted complexes can match or overlap significantly better with the known protein complexes in the MIPS benchmark database. Novel protein complexes were also predicted to help biologists in their search for new protein complexes. PMID:16901108

  4. 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.

  5. Phenotypic complexity and local variations in neutral degree.

    PubMed

    Lehre, Per Kristian; Haddow, Pauline C

    2007-02-01

    Neutrality is important in natural, molecular and artificial evolution. This work studies how local neutral degree varies over the genospace in a simple class of Lindenmayer-systems, and investigates whether this variation relates to Lempel-Ziv complexity of the phenotype. PMID:17188803

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. Dominant-negative mutants of importin-beta block multiple pathways of import and export through the nuclear pore complex.

    PubMed Central

    Kutay, U; Izaurralde, E; Bischoff, F R; Mattaj, I W; Görlich, D

    1997-01-01

    Nuclear protein import proceeds through the nuclear pore complex (NPC). Importin-beta mediates translocation via direct interaction with NPC components and carries importin-alpha with the NLS substrate from the cytoplasm into the nucleus. The import reaction is terminated by the direct binding of nuclear RanGTP to importin-beta which dissociates the importin heterodimer. Here, we analyse the sites of interaction on importin-beta for its multiple partners. Ran and importin-alpha respectively require residues 1-364 and 331-876 of importin-beta for binding. Thus, RanGTP-mediated release of importin-alpha from importin-beta is likely to be an active displacement rather than due to simple competition between Ran and importin-alpha for a common binding site. Importin-beta has at least two non-overlapping sites of interaction with the NPC, which could potentially be used sequentially during translocation. Our data also suggest that termination of import involves a transient release of importin-beta from the NPC. Importin-beta fragments which bind to the NPC, but not to Ran, resist this release mechanism. As would be predicted from this, these importin-beta mutants are very efficient inhibitors of NLS-dependent protein import. Surprisingly, however, they also inhibit M9 signal-mediated nuclear import as well as nuclear export of mRNA, U snRNA, and the NES-containing Rev protein. This suggests that mediators of these various transport events share binding sites on the NPC and/or that mechanisms exist to coordinate translocation through the NPC via different nucleocytoplasmic transport pathways. PMID:9135132

  11. 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.

  12. Local degree blocking model for link prediction in complex networks.

    PubMed

    Liu, Zhen; Dong, Weike; Fu, Yan

    2015-01-01

    Recovering and reconstructing networks by accurately identifying missing and unreliable links is a vital task in the domain of network analysis and mining. In this article, by studying a specific local structure, namely, a degree block having a node and its all immediate neighbors, we find it contains important statistical features of link formation for complex networks. We therefore propose a parameter-free local blocking (LB) predictor to quantitatively detect link formation in given networks via local link density calculations. The promising experimental results performed on six real-world networks suggest that the new index can outperform other traditional local similarity-based methods on most of tested networks. After further analyzing the scores' correlations between LB and two other methods, we find that LB index simultaneously captures the features of both PA index and short-path-based index, which empirically verifies that LB index is a multiple-mechanism-driven link predictor. PMID:25637926

  13. 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.

  14. 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

  15. Modelling multiphase dynamics during infiltration using a pore network model

    NASA Astrophysics Data System (ADS)

    Tzavaras, Jannis; Arns, Ji-Youns; Max, Koehne; Hans-Joerg, Vogel

    2013-04-01

    We present an implementation of water infiltration into a pore network model where the local water pressures is continuously updated during the transient process. The network geometry is designed to represent structured soil which is different from simple granular porous media in some respect: Pores are more elongated and less isometric and the pore size distribution is much wider and structured hierarchically. To reproduce these properties, the classical concept of pore-bodies and throats is replaced by direct measurements of pore topology and the pores below the minimal pore size of the network model are represented by a continuous network of water saturated micro pores. The latter ensures that the water phase is always continuous which affects the propagation of the water potential during infiltration. The network model is based on cylindrical pores and considers capillary and gravitational forces. The propagation of interfaces is calculated for each time step by repeatedly solving the complete set of linear equation arising from Kirchhoff's law based on mass balance at each node of the network. This is done using the public domain package ITPack. The successive overrelaxation (SOR) and the Jacobi conjugate gradient (JCG) method proved to be more robust and faster than other solvers tested for the complex topology. The model accounts for entrapped air which is assumed to be incompressible. We present first results demonstrating the impact of external forcing (i.e infiltration rate) and pore topology on the dynamics of water-gas interfaces, the volume of entrapped air and hysteresis.

  16. Complex interactions among residues within pore region determine the K+ dependence of a KAT1-type potassium channel AmKAT1.

    PubMed

    Yang, Guangzhe; Sentenac, Hervé; Véry, Anne-Aliénor; Su, Yanhua

    2015-08-01

    KAT1-type channels mediate K(+) influx into guard cells that enables stomatal opening. In this study, a KAT1-type channel AmKAT1 was cloned from the xerophyte Ammopiptanthus mongolicus. In contrast to most KAT1-type channels, its activation is strongly dependent on external K(+) concentration, so it can be used as a model to explore the mechanism for the K(+) -dependent gating of KAT1-type channels. Domain swapping between AmKAT1 and KAT1 reveals that the S5-pore-S6 region controls the K(+) dependence of AmKAT1, and residue substitutions show that multiple residues within the S5-Pore linker and Pore are involved in its K(+) -dependent gating. Importantly, complex interactions occur among these residues, and it is these interactions that determine its K(+) dependence. Finally, we analyzed the potential mechanism for the K(+) dependence of AmKAT1, which could originate from the requirement of K(+) occupancy in the selectivity filter to maintain its conductive conformation. These results provide new insights into the molecular basis of the K(+) -dependent gating of KAT1-type channels. PMID:26032087

  17. Biogenesis of porin of the outer mitochondrial membrane involves an import pathway via receptors and the general import pore of the TOM complex.

    PubMed

    Krimmer, T; Rapaport, D; Ryan, M T; Meisinger, C; Kassenbrock, C K; Blachly-Dyson, E; Forte, M; Douglas, M G; Neupert, W; Nargang, F E; Pfanner, N

    2001-01-22

    Porin, also termed the voltage-dependent anion channel, is the most abundant protein of the mitochondrial outer membrane. The process of import and assembly of the protein is known to be dependent on the surface receptor Tom20, but the requirement for other mitochondrial proteins remains controversial. We have used mitochondria from Neurospora crassa and Saccharomyces cerevisiae to analyze the import pathway of porin. Import of porin into isolated mitochondria in which the outer membrane has been opened is inhibited despite similar levels of Tom20 as in intact mitochondria. A matrix-destined precursor and the porin precursor compete for the same translocation sites in both normal mitochondria and mitochondria whose surface receptors have been removed, suggesting that both precursors utilize the general import pore. Using an assay established to monitor the assembly of in vitro-imported porin into preexisting porin complexes we have shown that besides Tom20, the biogenesis of porin depends on the central receptor Tom22, as well as Tom5 and Tom7 of the general import pore complex (translocase of the outer mitochondrial membrane [TOM] core complex). The characterization of two new mutant alleles of the essential pore protein Tom40 demonstrates that the import of porin also requires a functional Tom40. Moreover, the porin precursor can be cross-linked to Tom20, Tom22, and Tom40 on its import pathway. We conclude that import of porin does not proceed through the action of Tom20 alone, but requires an intact outer membrane and involves at least four more subunits of the TOM machinery, including the general import pore. PMID:11266446

  18. 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

  19. 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

  20. Composition and Localization of Treponema denticola Outer Membrane Complexes

    PubMed Central

    Godovikova, Valentina; Goetting-Minesky, M. Paula; Fenno, J. Christopher

    2011-01-01

    The Treponema denticola outer membrane lipoprotein-protease complex (dentilisin) contributes to periodontal disease by degrading extracellular matrix components and disrupting intercellular host signaling pathways. We recently demonstrated that prcB, located upstream of and cotranscribed with prcA and prtP, encodes a 22-kDa lipoprotein that interacts with PrtP and is required for its activity. Here we further characterize products of the protease locus and their roles in expression, formation, and localization of outer membrane complexes. PrcB migrates in native gels as part of a >400-kDa complex that includes PrtP and PrcA, as well as the major outer sheath protein Msp. PrcB is detectable as a minor constituent of the purified active protease complex, which was previously reported to consist of only PrtP and auxiliary polypeptides PrcA1 and PrcA2. Though it lacks the canonical ribosome binding site present upstream of both prcA and prtP, PrcB is present at levels similar to those of PrtP in whole-cell extracts. Immunofluorescence microscopy demonstrated cell surface exposure of the mature forms of PrtP, PrcA1, PrcB, and Msp. The 16-kDa N-terminal acylated fragment of PrtP (predicted to be released during activation of PrtP) was present in cell extracts but was detected neither in the purified active protease complex nor on the cell surface. PrcA2, detectable on the surface of Msp-deficient cells but not that of wild-type cells, coimmunoprecipitated with Msp. Our results indicate that PrcB is a component of the outer membrane lipoprotein protease complex and that Msp and PrcA2 interaction may mediate formation of a very-high-molecular-weight outer membrane complex. PMID:21986628

  1. Anderson localization in metamaterials and other complex media (Review Article)

    NASA Astrophysics Data System (ADS)

    Gredeskul, Sergey A.; Kivshar, Yuri S.; Asatryan, Ara A.; Bliokh, Konstantin Y.; Bliokh, Yuri P.; Freilikher, Valentin D.; Shadrivov, Ilya V.

    2012-07-01

    This is a review of some recent (mostly ours) results on Anderson localization of light and electron waves in complex disordered systems, including: (i) left-handed metamaterials, (ii) magnetoactive optical structures, (iii) graphene superlattices, and (iv) nonlinear dielectric media. First, we demonstrate that left-handed metamaterials can significantly suppress localization of light and lead to an anomalously enhanced transmission. This suppression is essential at the long-wavelength limit in the case of normal incidence, at specific angles of oblique incidence (Brewster anomaly), and in vicinity of zero-ɛ or zero-μ frequencies for dispersive metamaterials. Remarkably, in disordered samples comprised of alternating normal and left-handed metamaterials, the reciprocal Lyapunov exponent and reciprocal transmittance increment can differ from each other. Second, we study magnetoactive multilayered structures, which exhibit nonreciprocal localization of light depending on the direction of propagation and on polarization. At resonant frequencies or realizations such nonreciprocity results in effectively unidirectional transport of light. Third, we discuss the analogy between wave propagation through multilayered samples with metamaterials and charge transport in graphene, which provides a simple physical explanation of unusual conductive properties of disordered graphene superlatices. We predict disorder-induced resonance of the transmission coefficient at oblique incidence of Dirac quasiparticles. Finally, we demonstrate that an interplay of nonlinearity and disorder in dielectric media can lead to bistability of individual localized states excited inside the medium at resonant frequencies. This results in nonreciprocity of wave transmission and unidirectional transport of light.

  2. Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

    PubMed Central

    Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

    2014-01-01

    Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

  3. 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.

  4. 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

  5. Complexity and Approximation of a Geometric Local Robot Assignment Problem

    NASA Astrophysics Data System (ADS)

    Bonorden, Olaf; Degener, Bastian; Kempkes, Barbara; Pietrzyk, Peter

    We introduce a geometric multi-robot assignment problem. Robots positioned in a Euclidean space have to be assigned to treasures in such a way that their joint strength is sufficient to unearth a treasure with a given weight. The robots have a limited range and thus can only be assigned to treasures in their proximity. The objective is to unearth as many treasures as possible. We investigate the complexity of several variants of this problem and show whether they are in {mathcal P} or are mathcal{ NP}-complete. Furthermore, we provide a distributed and local constant-factor approximation algorithm using constant-factor resource augmentation for the two-dimensional setting with {mathcal O}(log^*n) communication rounds.

  6. 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

  7. 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.

  8. 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.

  9. Localization and visual verification of a complex minke whale vocalization.

    PubMed

    Gedamke, J; Costa, D P; Dunstan, A

    2001-06-01

    A recently described population of minke whales (Balaenoptera acutorostrata) offered a unique opportunity to study its acoustic behavior. The often-inquisitive dwarf minke whale is seen on the Great Barrier Reef nearly coincident with its suspected calving and breeding seasons. During drifting encounters with whales, a towed hydrophone array was used to record sounds for subsequent localization of sound sources. Shipboard and in-water observers linked these sounds to the closely circling minke whale. A complex and stereotyped sound sequence, the "star-wars" (SW) vocalization, was recorded during a series of visual and acoustic observations. The SW vocalization spanned a wide frequency range (50 Hz-9.4 kHz) and was composed of distinct and stereotypically repeated units with both amplitude and frequency-modulated components. Broadband source levels between 150 and 165 dB re 1 microPa at 1 m were calculated. Passive acoustic studies can utilize this distinct vocalization to help determine the behavior, distribution, and movements of this animal. While the SW vocalization's function remains unknown, the regularly repeated and complex sound sequence was common in low latitude, winter month aggregations of minke whales. At this early stage, the SW vocalization appears similar to the songs of other whale species and has characteristics consistent with those of reproductive advertisement displays. PMID:11425146

  10. 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.

  11. Nup358/RanBP2 Attaches to the Nuclear Pore Complex via Association with Nup88 and Nup214/CAN and Plays a Supporting Role in CRM1-Mediated Nuclear Protein Export

    PubMed Central

    Bernad, Rafael; van der Velde, Hella; Fornerod, Maarten; Pickersgill, Helen

    2004-01-01

    Nuclear pore complexes (NPCs) traverse the nuclear envelope (NE), providing a channel through which nucleocytoplasmic transport occurs. Nup358/RanBP2, Nup214/CAN, and Nup88 are components of the cytoplasmic face of the NPC. Here we show that Nup88 localizes midway between Nup358 and Nup214 and physically interacts with them. RNA interference of either Nup88 or Nup214 in human cells caused a strong reduction of Nup358 at the NE. Nup88 and Nup214 showed an interdependence at the NPC and were not affected by the absence of Nup358. These data indicate that Nup88 and Nup214 mediate the attachment of Nup358 to the NPC. We show that localization of the export receptor CRM1 at the cytoplasmic face of the NE is Nup358 dependent and represents its empty state. Also, removal of Nup358 causes a distinct reduction in nuclear export signal-dependent nuclear export. We propose that Nup358 provides both a platform for rapid disassembly of CRM1 export complexes and a binding site for empty CRM1 recycling into the nucleus. PMID:14993277

  12. Solvation-Driven Charge Transfer and Localization in Metal Complexes

    PubMed Central

    2016-01-01

    Conspectus 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

  13. Beamlet Imaging and Local Inversion for Complex Structures

    NASA Astrophysics Data System (ADS)

    Wu, R.; Luo, M.; Chen, L.

    2003-12-01

    Beamlet decomposition of wavefields is defined as wavelet transform applied to wavefield along spatial axes. Beamlets has both spatial and directional localization satisfying the Heisenberg uncertainty principle. We have used both Gabor-Daubechies frame and local-cosine basis for the decomposition. The theory of local perturbations and wave propagators in beamlet domain has been developed. In this presentation we will summarize the theory and method of beamlet propagation and imaging, and show the 2D and 3D imaging (prestack depth migration) results for SEG/EAGE salt models. The high-resolution and high quality images demonstrate the excellent performance and wide-angle capacity of beamlet imaging. Based on beamlet imaging in angle-domain, a method of local AVA (amplitude versus angle) and local inversion is proposed to estimate the medium parameters near a local discontinuity (reflector). The local image matrices derived during the amplitude-preserving imaging process can be reduced to common refection-angle image (CRAI) gathers and common dip-angle image (CDAI) gathers. CDAI gathers can be used to determine the dip-angle of the reflector and CRAI gathers are then used for local AVA analysis. In the target area, local inversion can be conducted based on local AVA and velocity analyses. Preliminary numerical tests of local AVA analysis will be shown to demonstrate the feasibility of the approach.

  14. 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. PMID:19047048

  15. 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

  16. The transient pore formed by homologous terminal complement complexes functions as a bidirectional route for the transport of autocrine and paracrine signals across human cell membranes.

    PubMed Central

    Acosta, J. A.; Benzaquen, L. R.; Goldstein, D. J.; Tosteson, M. T.; Halperin, J. A.

    1996-01-01

    BACKGROUND: We have previously shown that the membrane attack complex (MAC) of complement stimulates cell proliferation and that insertion of homologous MAC into the membranes of endothelial cells results in the release of potent mitogens, including basic fibroblast growth factor (bFGF). The mechanism of secretion of bFGF and other polypeptides devoid of signal peptides, such as interleukin 1 (IL-1) is still an open problem in cell biology. We have hypothesized that the homologous MAC pore itself could constitute a transient route for the diffusion of biologically active macromolecules in and out of the target cells. MATERIALS AND METHODS: Human red blood cell ghosts and artificial lipid vesicles were loaded with labeled growth factors, cytokines and IgG, and exposed to homologous MAC. The release of the 125I-macromolecules was followed as a function of time. The incorporation of labeled polypeptides and fluorescent dextran (MW: 10,000) was measured in MAC-impacted human red blood cells and human umbilical endothelial cells (HUVEC), respectively. RESULTS: Homologous MAC insertion into HUVEC resulted in the massive uptake of 10-kD dextran and induced the release of bFGF, in the absence of any measurable lysis. Red blood cell ghosts preloaded with bFGF, IL-1 beta, and the alpha-chain of interferon-gamma (IFN-gamma) released the polypeptides upon MAC insertion, but they did not release preloaded IgG. MAC-impacted ghosts took up radioactive IFN-gamma from the extracellular medium. Vesicles loaded with IL-I released the polypeptide when exposed to MAC. CONCLUSIONS: The homologous MAC pore in its nonlytic form allows for the export of cytosolic proteins devoid of signal peptides that are not secreted through the classical endoplasmic reticulum/Golgi exocytotic pathways. Our results suggest that the release, and perhaps the uptake, of biologically active macromolecules through the homologous MAC pore is a novel biological function of the complement system in mammals

  17. 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

  18. Effect of the ostreolysin A/pleurotolysin B pore-forming complex on intracellular Ca2+ activity in the vascular smooth muscle cell line A10.

    PubMed

    Vrecl, Milka; Babnik, Monika; Sepčić, Kristina; Žužek, Monika C; Maček, Peter; Diacci, Uroš; Frangež, Robert

    2015-12-01

    Ostreolysin A/pleurotolysin B (OlyA/PlyB) is a binary pore-forming protein complex that produces a rapid cardiorespiratory arrest. Increased tonus of the coronary vascular wall produced by OlyA/PlyB may lead to ischemia, arrhythmias, the hypoxic injury of cardiomyocytes and cardiotoxicity. We evaluated the effects of OlyA/PlyB in cultured vascular smooth muscle A10 cells. Fluorometric measurements using the Ca(2+) indicator Fluo-4 AM and Fura-2 AM revealed that nanomolar concentrations of OlyA/PlyB increased the intracellular Ca(2+) activity [Ca(2+)]i in A10 cells. This effect was absent in a Ca(2+)-free medium, indicating that OlyA/PlyB-induced [Ca(2+)]i increase was dependent on Ca(2+) influx into cells. The increase in [Ca(2+)]i by OlyA/PlyB was partially prevented by: i) the calcium channel blockers verapamil and La(3+), ii) the inhibitor of the sodium-calcium exchanger (NCX) benzamil, and iii) the iso-osmotic replacement of NaCl by sucrose. The pre-treatment of cells with the Ca(2+)-ATPase inhibitor thapsigargin reduced the [Ca(2+)]i increase evoked by OlyA/PlyB, whereas the plasma membrane depolarization with high K(+) in the medium did not prevent OlyA/PlyB-induced [Ca(2+)]i. In summary, our data could suggest that the OlyA/PlyB-induced increase in [Ca(2+)]i is due to an influx of Ca(2+) through a variety of co-existing plasma membrane Ca(2+)-permeable channels, Ca(2+) entry through non-selective ion permeable pores formed de novo by OlyA/PlyB in the plasma membrane and calcium-induced intracellular Ca(2+) release, altogether leading to disturbed Ca(2+) homeostasis in A10 cells. PMID:26320834

  19. 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

  20. 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

  1. Starting with Complex Primitives Pays Off: Complicate Locally, Simplify Globally

    ERIC Educational Resources Information Center

    Joshi, Aravind K.

    2004-01-01

    In setting up a formal system to specify a grammar formalism, the conventional (mathematical) wisdom is to start with primitives (basic primitive structures) as simple as possible, and then introduce various operations for constructing more complex structures. An alternate approach is to start with complex (more complicated) primitives, which…

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  4. 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. PMID:26902741

  5. 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

  6. 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

  7. Structure of local interactions in complex financial dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  8. 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.

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

    DOE PAGESBeta

    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

  10. Curcumin Pretreatment Prevents Potassium Dichromate-Induced Hepatotoxicity, Oxidative Stress, Decreased Respiratory Complex I Activity, and Membrane Permeability Transition Pore Opening

    PubMed Central

    García-Niño, Wylly Ramsés; Tapia, Edilia; Zazueta, Cecilia; Zatarain-Barrón, Zyanya Lucía; Hernández-Pando, Rogelio; Vega-García, Claudia Cecilia; Pedraza-Chaverrí, José

    2013-01-01

    Curcumin is a polyphenol derived from turmeric with recognized antioxidant properties. Hexavalent chromium is an environmental toxic and carcinogen compound that induces oxidative stress. The objective of this study was to evaluate the potential protective effect of curcumin on the hepatic damage generated by potassium dichromate (K2Cr2O7) in rats. Animals were pretreated daily by 9-10 days with curcumin (400 mg/kg b.w.) before the injection of a single intraperitoneal of K2Cr2O7 (15 mg/kg b.w.). Groups of animals were sacrificed 24 and 48 h later. K2Cr2O7-induced damage to the liver was evident by histological alterations and increase in the liver weight and in the activity of alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, and alkaline phosphatase in plasma. In addition, K2Cr2O7 induced oxidative damage in liver and isolated mitochondria, which was evident by the increase in the content of malondialdehyde and protein carbonyl and decrease in the glutathione content and in the activity of several antioxidant enzymes. Moreover, K2Cr2O7 induced decrease in mitochondrial oxygen consumption, in the activity of respiratory complex I, and permeability transition pore opening. All the above-mentioned alterations were prevented by curcumin pretreatment. The beneficial effects of curcumin against K2Cr2O7-induced liver oxidative damage were associated with prevention of mitochondrial dysfunction. PMID:23956771

  11. The cellular uptake and localization of non-emissive iridium(III) complexes as cellular reaction-based luminescence probes.

    PubMed

    Li, Chunyan; Liu, Yi; Wu, Yongquan; Sun, Yun; Li, Fuyou

    2013-01-01

    Improvement of cellular uptake and subcellular resolution remains a major obstacle in the successful and broad application of cellular optical probes. In this context, we design and synthesize seven non-emissive cyclometalated iridium(III) solvent complexes [Ir(CˆN)(2)(solv)(2)](+)L(-) (LIr2-LIr8, in which CˆN = 2-phenylpyridine (ppy) or its derivative; solv = DMSO, H(2)O or CH(3)CN; L(-) = PF(6)(-) or OTf(-)) applicable in live cell imaging to facilitate selective visualization of cellular structures. Based on the above variations (including different counter ions, solvent ligands, and CˆN ligands), structure-activity relationship analyses reveal a number of clear correlations: (1) variations in counter anions and solvent ligands of iridium(III) complexes do not affect cellular imaging behavior, and (2) length of the side carbon chain in CˆN ligands has significant effects on cellular uptake and localization/accumulation of iridium complexes in living cells. Moreover, investigation of the uptake mechanism via low-temperature and metabolism inhibitor assays reveal that [Ir(4-Meppy)(2)(CH(3)CN)(2)](+)OTf(-) (LIr5) with 2-phenylpyridine derivative with side-chain of methyl group at the 4-position as CˆN ligand permeates the outer and nuclear membranes of living cells through an energy-dependent, non-endocytic entry pathway, and translocation of the complex from the cell periphery towards the perinuclear region possibly occurs through a microtubule-dependent transport pathway. Nuclear pore complexes (NPCs) appear to selectively control the transport of iridium(III) complexes between the cytoplasm and nucleus. A generalization of trends in behavior and structure-activity relationships is presented, which should provide further insights into the design and optimization of future probes. PMID:23131533

  12. Local and global responses in complex gene regulation networks

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Masa; Selvarajoo, Kumar; Piras, Vincent; Tomita, Masaru; Giuliani, Alessandro

    2009-04-01

    An exacerbated sensitivity to apparently minor stimuli and a general resilience of the entire system stay together side-by-side in biological systems. This apparent paradox can be explained by the consideration of biological systems as very strongly interconnected network systems. Some nodes of these networks, thanks to their peculiar location in the network architecture, are responsible for the sensitivity aspects, while the large degree of interconnection is at the basis of the resilience properties of the system. One relevant feature of the high degree of connectivity of gene regulation networks is the emergence of collective ordered phenomena influencing the entire genome and not only a specific portion of transcripts. The great majority of existing gene regulation models give the impression of purely local ‘hard-wired’ mechanisms disregarding the emergence of global ordered behavior encompassing thousands of genes while the general, genome wide, aspects are less known. Here we address, on a data analysis perspective, the discrimination between local and global scale regulations, this goal was achieved by means of the examination of two biological systems: innate immune response in macrophages and oscillating growth dynamics in yeast. Our aim was to reconcile the ‘hard-wired’ local view of gene regulation with a global continuous and scalable one borrowed from statistical physics. This reconciliation is based on the network paradigm in which the local ‘hard-wired’ activities correspond to the activation of specific crucial nodes in the regulation network, while the scalable continuous responses can be equated to the collective oscillations of the network after a perturbation.

  13. Commercial Complexity and Local and Global Involvement in Programs: Effects on Viewer Responses.

    ERIC Educational Resources Information Center

    Oberman, Heiko; Thorson, Esther

    A study investigated the effects of local (momentary) and global (whole program) involvement in program context and the effects of message complexity on the retention of television commercials. Sixteen commercials, categorized as simple video/simple audio through complex video/complex audio were edited into two globally high- and two globally…

  14. 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

  15. Assembly and localization of Toll-like receptor signalling complexes.

    PubMed

    Gay, Nicholas J; Symmons, Martyn F; Gangloff, Monique; Bryant, Clare E

    2014-08-01

    Signal transduction by the Toll-like receptors (TLRs) is central to host defence against many pathogenic microorganisms and also underlies a large burden of human disease. Thus, the mechanisms and regulation of signalling by TLRs are of considerable interest. In this Review, we discuss the molecular basis for the recognition of pathogen-associated molecular patterns, the nature of the protein complexes that mediate signalling, and the way in which signals are regulated and integrated at the level of allosteric assembly, post-translational modification and subcellular trafficking of the components of the signalling complexes. These fundamental molecular mechanisms determine whether the signalling output leads to a protective immune response or to serious pathologies such as sepsis. A detailed understanding of these processes at the molecular level provides a rational framework for the development of new drugs that can specifically target pathological rather than protective signalling in inflammatory and autoimmune disease. PMID:25060580

  16. Does Extension Play a Role in Ionian Tectonics? Potential Effects of Preexisting Bounding Faults, Local Brittle Failure, and Sulfur Pore Pressure on Crustal Stresses

    NASA Astrophysics Data System (ADS)

    McKinnon, William B.; Kirchoff, M.; Bland, M.

    2013-10-01

    The majority of mountains observed on Io are tectonic, upthrusted blocks. Their formation is generally thought to be related to Io’s heat-pipe volcanism, crustal subsidence, and accompanying lateral confinement. In previous work, we demonstrated that compressional thermal stresses from sustained local or regional shut down of Io’s heat-pipe volcanism could also play a vital role in mountain formation, and help explain the anticorrelation between Io’s mountains and volcanic centers [Kirchoff and McKinnon 2009, Formation of mountains on Io: Variable volcanism and thermal stresses, Icarus 201, 598-614; Kirchoff et al. 2011, Global distribution of volcanoes and mountains on Io: Control by asthenospheric heating and implications for mountain formation, Earth Planet. Sci. Lett. 301, 22-30]. Here we refine our previous model by using an “unconfined” horizontal boundary condition (zero average lateral stress), including brittle failure (crustal plasticity), and adding sulfur to our rheological model. The unconfined horizontal boundary condition accounts for stresses released on preexisting, more distant faults; including crustal plasticity allows us to more realistically represent stresses that would exceed the brittle failure limit otherwise, and addition of sulfur to the model composition of Io’s crust further improves the rheological model of the crust. Heated and melted at depth, liquid sulfur creates pore pressure in the lower crust and profoundly reduces the brittle failure limit. Including these modifications when the volcanic eruption rate decreases introduces a region of tensional failure in the upper crust and increases the size of the region in compressional failure in the lower crust. Finite element models show that increasing compression at depth imparts substantial bending stresses, which can drive surface faulting and block rotation. Such conditions further facilitate mountain formation at the surface, and highlight the difference between Io

  17. 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

  18. 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

  19. 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

  20. 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

  1. Pore Velocity Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

    Devary, J. L.; Doctor, P. G.

    1982-08-01

    Geostatistical data analysis techniques were used to stochastically model the spatial variability of groundwater pore velocity in a potential waste repository site. Kriging algorithms were applied to Hanford Reservation data to estimate hydraulic conductivities, hydraulic head gradients, and pore velocities. A first-order Taylor series expansion for pore velocity was used to statistically combine hydraulic conductivity, hydraulic head gradient, and effective porosity surfaces and uncertainties to characterize the pore velocity uncertainty. Use of these techniques permits the estimation of pore velocity uncertainties when pore velocity measurements do not exist. Large pore velocity estimation uncertainties were found to be located in the region where the hydraulic head gradient relative uncertainty was maximal.

  2. Nonlinear viscoelasticity and shear localization at complex fluid interfaces.

    PubMed

    Erni, Philipp; Parker, Alan

    2012-05-22

    Foams and emulsions are often exposed to strong external fields, resulting in large interface deformations far beyond the linear viscoelastic regime. Here, we investigate the nonlinear and transient interfacial rheology of adsorption layers in large-amplitude oscillatory shear flow. As a prototypical material forming soft-solid-type interfacial adsorption layers, we use Acacia gum (i.e., gum arabic), a protein/polysaccharide hybrid. We quantify its nonlinear flow properties at the oil/water interface using a biconical disk interfacial rheometer and analyze the nonlinear stress response under forced strain oscillations. From the resulting Lissajous curves, we access quantitative measures recently introduced for nonlinear viscoelasticity, including the intracycle moduli for both the maximum and zero strains and the degree of plastic energy dissipation upon interfacial yielding. We demonstrate using in situ flow visualization that the onset of nonlinear viscoelasticity coincides with shear localization at the interface. Finally, we address the nonperiodic character of this flow transition using an experimental procedure based on opposing stress pulses, allowing us to extract additional interfacial properties such as the critical interfacial stress upon yielding and the permanent deformation. PMID:22563849

  3. Localization of vanadyl complexes in polyaromatic structures of oils

    SciTech Connect

    Gal`tsev, V.E.; Grinberg, O.Ya.; Ratov, A.N.; Nemirovskaya, G.B.; Emel`yanova, A.S. |

    1994-01-01

    Many studies on vanadium in oils have been conducted to date. Among them, there have been some attempts made to elucidate the mobility of the formed associates of VC with the asphaltene molecules. Thus, the peak intensities were determined in the superposition of two vanadyl spectra of the {open_quotes}fixed{close_quotes} and {open_quotes}rapidly rotating{close_quotes} vanadyl complexes. The VC ligand transformations were studied under various conditions. The interaction between the VC and asphaltene molecules was deduced from these results. However, it should be pointed out that the study of VC rotating mobility is not enough to make definite conclusions. The authors chose to follow a different method. It involved the determination of spin relaxation times for the asphaltene paramagnetic centers. The authors succeeded in revealing new correlations between the VC and PC concentrations in the chosen series of oils with different vanadium content. The character of interaction between VC and asphaltene molecules was demonstrated by experiment using the observed distinctions in the relaxation characteristics in the series of the oil samples. The series of oils from the fields of the northern cluster, and the Fillipov group of the Ul`yanovsk oblast`, characterized by an irregularly high vanadium concentration, and its southern cluster of oil fields with less vanadium content were chosen for this study.

  4. 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

  5. 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

  6. Pest control experiments show benefits of complexity at landscape and local scales.

    PubMed

    Chaplin-Kramer, Rebecca; Kremen, Claire

    2012-10-01

    Farms benefit from pest control services provided by nature, but management of these services requires an understanding of how habitat complexity within and around the farm impacts the relationship between agricultural pests and their enemies. Using cage experiments, this study measures the effect of habitat complexity across scales on pest suppression of the cabbage aphid Brevicoryne brassicae in broccoli. Our results reveal that proportional reduction of pest density increases with complexity both at the landscape scale (measured by natural habitat cover in the 1 km around the farm) and at the local scale (plant diversity). While high local complexity can compensate for low complexity at landscape scales and vice versa, a delay in natural enemy arrival to locally complex sites in simple landscapes may compromise the enemies' ability to provide adequate control. Local complexity in simplified landscapes may only provide adequate top-down pest control in cooler microclimates with relatively low aphid colonization rates. Even so, strong natural enemy function can be overwhelmed by high rates of pest reproduction or colonization from nearby source habitat. PMID:23210310

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

    DOE PAGESBeta

    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

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

    DOE PAGESBeta

    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

  9. 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

  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. Incomplete pneumolysin oligomers form membrane pores.

    PubMed

    Sonnen, Andreas F-P; Plitzko, Jürgen M; Gilbert, Robert J C

    2014-01-01

    Pneumolysin is a member of the cholesterol-dependent cytolysin (CDC) family of pore-forming proteins that are produced as water-soluble monomers or dimers, bind to target membranes and oligomerize into large ring-shaped assemblies comprising approximately 40 subunits and approximately 30 nm across. This pre-pore assembly then refolds to punch a large hole in the lipid bilayer. However, in addition to forming large pores, pneumolysin and other CDCs form smaller lesions characterized by low electrical conductance. Owing to the observation of arc-like (rather than full-ring) oligomers by electron microscopy, it has been hypothesized that smaller oligomers explain smaller functional pores. To investigate whether this is the case, we performed cryo-electron tomography of pneumolysin oligomers on model lipid membranes. We then used sub-tomogram classification and averaging to determine representative membrane-bound low-resolution structures and identified pre-pores versus pores by the presence of membrane within the oligomeric curve. We found pre-pore and pore forms of both complete (ring) and incomplete (arc) oligomers and conclude that arc-shaped oligomeric assemblies of pneumolysin can form pores. As the CDCs are evolutionarily related to the membrane attack complex/perforin family of proteins, which also form variably sized pores, our findings are of relevance to that class of proteins as well. PMID:24759615

  12. 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.

  13. Direct Numerical Simulation of Pore-Scale Flow in a Bead Pack: Comparison with Magnetic Resonance Imaging Observations

    SciTech Connect

    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 error 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.

  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 reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.

    PubMed

    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

  16. 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

  17. Emergent complexity matching in interpersonal coordination: Local dynamics and global variability.

    PubMed

    Fine, Justin M; Likens, Aaron D; Amazeen, Eric L; Amazeen, Polemnia G

    2015-06-01

    Rhythmic coordination with stimuli and other people's movements containing variable or unpredictable fluctuations might involve distinct processes: detecting the fluctuation structure and tuning to or matching the structure's temporal complexity. This framework predicts that global tuning and local parameter adjustments (e.g., position, velocity or phase) can operate independently during coordination (Marmelat & Delignières, 2012). Alternatively, we propose that complexity matching is a result of local phase adjustments during coordination (Delignières & Marmelat, 2014; Torre, Varlet, & Marmelat, 2013). The current study examined this relationship in a rhythmic interpersonal coordination task. Dyads coordinated swinging pendulums that differed in their uncoupled frequencies (detuning). We predicted that frequency detuning would require increased local corrections to maintain the intended phase pattern (in phase). This was expected to yield a relative phase shift accompanied by a change in period complexity and matching. Experimental data and numerical modeling of the pendulum dynamics confirmed our predictions. Increased relative phase shifts occurred simultaneously with increased dissociation between individuals' movement period complexity. This provided evidence that global complexity matching is intricately linked to local movement adjustments and is not a distinct coordination mechanism. These findings are considered with respect to dynamical and computational approaches to interpersonal coordination. PMID:25798782

  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. PMID:25961729

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

    NASA Astrophysics Data System (ADS)

    Bouch, Gabriel D.

    In a very general class of one-dimensional quantum spin systems, the infinite volume limit of the complex-time evolution of a local observable is an entire analytic function of the time variable and obeys a locality principle. This result has recently been used to prove a number of important results in statistical mechanics. In dimensions greater than one, although it has not been expected that the infinite volume limit of the complex-time evolution of a general local observable will be entire analytic, nothing rigorous has been established concerning the breakdown of analyticity or the nature of the singularities, if they exist. In this work we begin by presenting a possible approach to proving locality bounds for the complex-time dynamics of a general class of quantum spin systems in any dimension. Then we specifically apply this approach to the one-dimensional case, and establish entire analyticity of the dynamics as a corollary. In dimensions greater than one, ideas related to the much studied Eden growth process suggest that a similar locality result will also hold. In particular, we establish an upper bound on the expected perimeter of lattice animals grown according to an Eden growth process, and note that a similar upper bound on a closely related average perimeter would lead to a locality result in the plane. Finally, and perhaps unexpectedly, we demonstrate through a specific construction that such a locality result does not hold in general and that the infinite volume limit of the complex-time dynamics can blow up a finite distance along the imaginary-time axis.

  2. Exploring thermal spray gray alumina coating pore network architecture by combining stereological protocols and impedance electrochemical spectroscopy

    NASA Astrophysics Data System (ADS)

    Antou, G.; Montavon, G.; Hlawka, F.; Cornet, A.; Coddet, C.

    2006-12-01

    Complex multiscale pore network architecture characterized by multimodal pore size distribution and connectivity develops during the manufacture of ceramic thermal spray coatings from intra- and interlamellar cracks generated when each lamella spreads and solidifies to globular pores resulting from lamella stacking defects. This network significantly affects the coating properties and their in-service behaviors. De Hoff stereological analysis permits quantification of the three-dimensional (3D) distribution of spheroids (i.e., pores) from the determination of their two-dimensional (2D) distribution estimated by image analysis when analyzing the coating structure from a polished plane. Electrochemical impedance spectroscopy electrochemically examines a material surface by frequency variable current and potential and analyzes the complex impedance. When a coating covers the material surface, the electrolyte percolates through the more or less connected pore network to locally passivate the substrate. The resistive and capacitive characteristics of the equivalent electrical circuit will depend upon the connected pore network architecture. Both protocols were implemented to quantify thermal spray coating structures. Al2O3-13TiO2 coatings were atmospherically plasma sprayed using several sets of power parameters, are current intensity, plasma gas total flow rate, and plasma gas composition in order to determine their effects on pore network architecture. Particle characteristics upon impact, especially their related dimensionless numbers, such as Reynolds, Weber, and Sommerfeld criteria, were also determined. Analyses permitted identification of (a) the major effects of power parameters upon pore architecture and (b) the related formation mechanisms.

  3. A Low Complexity System Based on Multiple Weighted Decision Trees for Indoor Localization

    PubMed Central

    Sánchez-Rodríguez, David; Hernández-Morera, Pablo; Quinteiro, José Ma.; Alonso-González, Itziar

    2015-01-01

    Indoor position estimation has become an attractive research topic due to growing interest in location-aware services. Nevertheless, satisfying solutions have not been found with the considerations of both accuracy and system complexity. From the perspective of lightweight mobile devices, they are extremely important characteristics, because both the processor power and energy availability are limited. Hence, an indoor localization system with high computational complexity can cause complete battery drain within a few hours. In our research, we use a data mining technique named boosting to develop a localization system based on multiple weighted decision trees to predict the device location, since it has high accuracy and low computational complexity. The localization system is built using a dataset from sensor fusion, which combines the strength of radio signals from different wireless local area network access points and device orientation information from a digital compass built-in mobile device, so that extra sensors are unnecessary. Experimental results indicate that the proposed system leads to substantial improvements on computational complexity over the widely-used traditional fingerprinting methods, and it has a better accuracy than they have. PMID:26110413

  4. A Low Complexity System Based on Multiple Weighted Decision Trees for Indoor Localization.

    PubMed

    Sánchez-Rodríguez, David; Hernández-Morera, Pablo; Quinteiro, José Ma; Alonso-González, Itziar

    2015-01-01

    Indoor position estimation has become an attractive research topic due to growing interest in location-aware services. Nevertheless, satisfying solutions have not been found with the considerations of both accuracy and system complexity. From the perspective of lightweight mobile devices, they are extremely important characteristics, because both the processor power and energy availability are limited. Hence, an indoor localization system with high computational complexity can cause complete battery drain within a few hours. In our research, we use a data mining technique named boosting to develop a localization system based on multiple weighted decision trees to predict the device location, since it has high accuracy and low computational complexity. The localization system is built using a dataset from sensor fusion, which combines the strength of radio signals from different wireless local area network access points and device orientation information from a digital compass built-in mobile device, so that extra sensors are unnecessary. Experimental results indicate that the proposed system leads to substantial improvements on computational complexity over the widely-used traditional fingerprinting methods, and it has a better accuracy than they have. PMID:26110413

  5. Spatial co-localization of multi-enzymes by inorganic nanocrystal-protein complexes.

    PubMed

    Li, Zhixian; Zhang, Yifei; Su, Yechao; Ouyang, Pingkai; Ge, Jun; Liu, Zheng

    2014-10-25

    We report a simple precipitation method for the construction of spatially co-localized multi-enzyme systems based on inorganic nanocrystal-protein complexes. A spatially controlled multi-enzyme system exhibits enhanced overall catalytic performance, allowing for sensitive detection of glucose in solution. PMID:25192430

  6. 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.

  7. 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...

  8. 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…

  9. 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

  10. Local Solvent Acidities in β-Cyclodextrin Complexes with PRODAN Derivatives

    PubMed Central

    Naughton, Hannah R.; Abelt, Christopher J.

    2013-01-01

    The local solvent acidities (SA scale) of six 6-carbonyl-2-aminonaphthalene derivatives as β-cyclodextrin complexes in water are determined through fluorescence quenching. The local polarities (ETN scale) are determined through the shift of the emission center-of-mass. The apparent SA values reflect the solvent structure surrounding the guest’s carbonyl group, whereas the apparent ETN values reveal the net polarity of the entire guest molecule. Comparison of these values affords greater insight into the structures of the host-guest complexes. Derivatives 1 and 5 show unusually large acidities indicative of highly exposed carbonyl groups. The remaining compounds give emission intensities pointing to shielded carbonyl groups. In this study PRODAN and its derivatives are functioning as dual channel sensors of their local environment. PMID:23473052

  11. 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.

  12. 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

  13. 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

  14. Complex frequencies and field distributions of localized surface plasmon modes in graphene-coated subwavelength wires

    NASA Astrophysics Data System (ADS)

    Cuevas, Mauro; Riso, Máximo A.; Depine, Ricardo A.

    2016-04-01

    In this work we study the modal characteristics of localized surface plasmons in graphene-coated, circular cross-section wires. Localized surface plasmons are represented in terms of cylindrical multipole partial waves characterized by discrete, complex frequencies that depend on the size of the wire and can be dynamically tuned via a gate voltage. We consider both intrinsically nonplasmonic wires and intrinsically plasmonic wires. In the first case the localized surface plasmons are introduced by the graphene coating, whereas in the second case the localized eigenmodes of the graphene coating are expected to hybridize those already existing in the bare wire. We show that the approach presented here, valid for particle sizes where the retardation effects can be significant, is in good agreement with analytical expressions obtained in the limit when particle size is very small compared to the wavelength of the eigenmode and with results indirectly determined from scattering cross-section spectra.

  15. 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.

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

    PubMed

    Ikeda, Maaya Z; Jeon, Sung David; Cowell, Rosemary A; Remage-Healey, Luke

    2015-06-24

    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

  17. 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.

  18. Adaptive local complexity controlled data hiding method considering the human visual sensitivity

    NASA Astrophysics Data System (ADS)

    Ho, L.-H.; Lai, S.-L.; Chung, Y.-K.

    2012-12-01

    This paper proposes a human visual system based data hiding method with the consideration of the local complexity in images. It is known that human vision is more sensitive to the changes in smooth area than that of complex area, we embed less data into blocks with low complexity and embed more data into blocks with rich texture. We use the modified diamond encoding (MDE) as the embedding technique, and employ a sophisticated pixel pair adjustment process to maintain the complexity consistency of blocks before and after embedding data bits. Since the proposed method is robust to LSB-based steganalysis, it is more secure than other existing methods using the LSB replacement as their embedding technique. The experimental results revealed that the proposed method not only offers a better embedding performance, but is also secure under the attack of the LSB based steganalysis tools.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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. .

  4. Neuronal nitric-oxide synthase localization mediated by a ternary complex with synapsin and CAPON

    PubMed Central

    Jaffrey, Samie R.; Benfenati, Fabio; Snowman, Adele M.; Czernik, Andrew J.; Snyder, Solomon H.

    2002-01-01

    The specificity of the reactions of nitric oxide (NO) with its neuronal targets is determined in part by the precise localizations of neuronal NO synthase (nNOS) within the cell. The targeting of nNOS is mediated by adapter proteins that interact with its PDZ domain. Here, we show that the nNOS adapter protein, CAPON, interacts with synapsins I, II, and III through an N-terminal phosphotyrosine-binding domain interaction, which leads to a ternary complex comprising nNOS, CAPON, and synapsin I. The significance of this ternary complex is demonstrated by changes in subcellular localization of nNOS in mice harboring genomic deletions of both synapsin I and synapsin II. These results suggest a mechanism for specific actions of NO at presynaptic sites. PMID:11867766

  5. Asymmetric collapse in biomimetic complex coacervates revealed by local polymer and water dynamics.

    PubMed

    Ortony, Julia H; Hwang, Dong Soo; Franck, John M; Waite, J Herbert; Han, Songi

    2013-05-13

    Complex coacervation is a phenomenon characterized by the association of oppositely charged polyelectrolytes into micrometer-scale liquid condensates. This process is the purported first step in the formation of underwater adhesives by sessile marine organisms, as well as the process harnessed for the formation of new synthetic and protein-based contemporary materials. Efforts to understand the physical nature of complex coacervates are important for developing robust adhesives, injectable materials, or novel drug delivery vehicles for biomedical applications; however, their internal fluidity necessitates the use of in situ characterization strategies of their local dynamic properties, capabilities not offered by conventional techniques such as X-ray scattering, microscopy, or bulk rheological measurements. Herein, we employ the novel magnetic resonance technique Overhauser dynamic nuclear polarization enhanced nuclear magnetic resonance (DNP), together with electron paramagnetic resonance (EPR) line shape analysis, to concurrently quantify local molecular and hydration dynamics, with species- and site-specificity. We observe striking differences in the structure and dynamics of the protein-based biomimetic complex coacervates from their synthetic analogues, which is an asymmetric collapse of the polyelectrolyte constituents. From this study we suggest charge heterogeneity within a given polyelectrolyte chain to be an important parameter by which the internal structure of complex coacervates may be tuned. Acquiring molecular-level insight to the internal structure and dynamics of dynamic polymer complexes in water through the in situ characterization of site- and species-specific local polymer and hydration dynamics should be a promising general approach that has not been widely employed for materials characterization. PMID:23540713

  6. Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

    PubMed

    Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

    2008-11-15

    Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions. PMID:18491388

  7. 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

  8. Precipitation in pores: A geochemical frontier

    DOE PAGESBeta

    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

  9. Nonlinear transport of soft droplets in pore networks

    NASA Astrophysics Data System (ADS)

    Vernerey, Franck; Benet Cerda, Eduard; Koo, Kanghyeon

    A large number of biological and technological processes depend on the transport of soft colloidal particles through porous media; this includes the transport and separation of cells, viruses or drugs through tissues, membranes and microfluidic devices. In these systems, the interactions between soft particles, background fluid and the surrounding pore space yield complex, nonlinear behaviors such as non-Darcy flows, localization and jamming. We devise a computational strategy to investigate the transport of non-wetting and deformable water droplets in a microfluidic device made of a random distribution of cylindrical obstacles. We first derive scaling laws for the entry of the droplet in a single pore and discuss the role of surface tension, contact angle and size in this process. This information is then used to study the transport of multiple droplets in an obstacle network. We find that when the droplet size is close to the pore size, fluid flow and droplet trafficking strongly interact, leading to local redistributions in pressure fields, intermittent clogging and jamming. Importantly, it is found that the overall droplet and fluid transport display three different scaling regimes depending on the forcing pressure, and that these regimes can be related to droplet properties.

  10. 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