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Sample records for pore complexes harbor

  1. Uncovering Nuclear Pore Complexity with Innovation

    PubMed Central

    Adams, Rebecca L.; Wente, Susan R.

    2013-01-01

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

  2. Active genes at the nuclear pore complex.

    PubMed

    Taddei, Angela

    2007-06-01

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

  3. The nuclear pore complex and nuclear transport.

    PubMed

    Wente, Susan R; Rout, Michael P

    2010-10-01

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

  4. 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.

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

    PubMed Central

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

    1999-01-01

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

  6. 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

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

    PubMed

    Bird, Sean P; Baker, Lane A

    2011-09-12

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

  8. Enriching the pore: Splendid complexity from humble origins

    PubMed Central

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

    2014-01-01

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

  9. 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.

  10. 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

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

    PubMed

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

    2015-01-01

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

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  15. Energetics of Transport through the Nuclear Pore Complex

    PubMed Central

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

    2016-01-01

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

  16. 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.

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

    PubMed Central

    1990-01-01

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

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

    PubMed

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

    2014-06-17

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

  19. Lumenal interactions in nuclear pore complex assembly and stability

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2015-03-23

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2010-01-01

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

  3. Primary Biliary Cirrhosis and the Nuclear Pore Complex

    PubMed Central

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

    2012-01-01

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

  4. 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

  5. Regulation of mRNA trafficking by nuclear pore complexes.

    PubMed

    Bonnet, Amandine; Palancade, Benoit

    2014-09-02

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

  6. 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

  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.

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

    PubMed Central

    1996-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  10. 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

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

    PubMed

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

    2014-07-01

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

  12. 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

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

    PubMed Central

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

    2014-01-01

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

  14. 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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

    1996-01-01

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

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

    PubMed

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

    2004-12-10

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

  19. 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.

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

    PubMed

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

    2015-11-03

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

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

    PubMed Central

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

    2013-01-01

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

  2. 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.

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2013-04-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. 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

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

    Breuer, Manuel; Ohkura, Hiroyuki

    2015-01-01

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

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

    PubMed Central

    Bickel, Thomas; Bruinsma, Robijn

    2002-01-01

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

  12. 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.

  13. 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

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

    PubMed Central

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Opferman, Michael G.

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

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

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Lesmes, David P.; Frye, Kevin M.

    2001-01-01

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

  18. 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

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

    PubMed

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

    2013-06-15

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

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

    PubMed

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

    2013-10-28

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

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

    2012-05-22

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

  3. 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.

  4. 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

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

    PubMed

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

    2009-09-16

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

  6. 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.

  7. 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

  8. 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.

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Xiao, F.; Yin, X.

    2015-12-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2007-02-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    2000-06-01

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

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

    PubMed

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

    2014-01-01

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

  16. 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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2002-02-18

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

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

    PubMed Central

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

    2016-01-01

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

  20. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    1999-10-12

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

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

    PubMed Central

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

    1999-01-01

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

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

    PubMed

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

    2016-05-01

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

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

    PubMed Central

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

    2012-01-01

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

  6. 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.

  7. 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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

    2013-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  11. 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.

  12. 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.

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

    PubMed

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

    2003-11-01

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

  14. 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.

  15. 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

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

    PubMed

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

    2007-01-01

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

  17. [Pearl Harbor.

    ERIC Educational Resources Information Center

    Johnson, Jennifer, Ed.

    1992-01-01

    This issue of "Loblolly Magazine" was written in observance of the 50th anniversary of the U.S. entrance into World War II. The publication features interviews conducted by East Texas high school students with Clarence Otterman, one of the few survivors of the crew of the USS Arizona, which was bombed during the attack on Pearl Harbor, and with a…

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

    PubMed

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

    1997-11-17

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

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

    PubMed

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

    2016-09-30

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

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

    PubMed

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

    2016-09-30

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

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

    PubMed Central

    Kampmann, Martin; Blobel, Günter

    2009-01-01

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

  2. 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

  3. 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

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

    SciTech Connect

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

    2012-07-25

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

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

    PubMed Central

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

    2011-01-01

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

  6. 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.

  7. 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.

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

    SciTech Connect

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

    2010-02-02

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

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

    PubMed

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

    2012-06-01

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

  10. 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

  11. 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.

  12. 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

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

    PubMed

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

    2004-05-01

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

  14. 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.

  15. 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

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

    PubMed Central

    1988-01-01

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

  17. 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.

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

    PubMed

    Jani, Divyang; Valkov, Eugene; Stewart, Murray

    2014-06-01

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

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

    PubMed

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

    2015-02-18

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

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

    PubMed Central

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

    1997-01-01

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

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-08-01

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

  3. 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

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

    PubMed

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

    1995-08-01

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

  5. 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

  6. A clonal complex 12 methicillin-resistant Staphylococcus aureus strain, West Australian MRSA-59, harbors a novel pseudo-SCCmec element.

    PubMed

    Monecke, Stefan; Coombs, Geoffrey W; Pearson, Julie; Hotzel, Helmut; Slickers, Peter; Ehricht, Ralf

    2015-11-01

    A West Australian methicillin-resistant Staphylococcus aureus strain (WA MRSA-59) was characterized by microarray and sequencing. Its pseudo-staphylococcal cassette chromosome mec (SCCmec) element comprised dcs, Q9XB68-dcs, mvaS-SCC, Q5HJW6, dru, ugpQ, ydeM, mecA-mecR-mecI, txbi mecI, tnp IS431, copA2-mco (copper resistance), ydhK, arsC-arsB-arsR (arsenic resistance), open reading frame PT43, and per-2. Recombinase genes, xylR (mecR2), and PSM-mec (phenol-soluble modulin) were absent. We suggest that mec complex A should be split into two subtypes. One harbors PSM-mec and xylR (mecR2). It is found in SCCmec types II, III, and VIII. The second subtype, described herein, is present in WA MRSA-59 and some coagulase-negative staphylococci.

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

    PubMed Central

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

    1998-01-01

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

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

    PubMed

    Kelich, Joseph M; Yang, Weidong

    2014-01-01

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

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

    SciTech Connect

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

    2012-10-23

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

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

    PubMed

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

    2015-05-01

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

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

    PubMed Central

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

    2012-01-01

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and cytoplasm. The yeast NPC is an eight-fold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins (Nups). Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal “FG” repeats containing a Gle2p-binding sequence motif (GLEBS motif) and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by Small Angle X-ray Scattering (SAXS). Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiaeNup145N, and human Nup98 are discussed. PMID:22544723

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

    PubMed

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

    2012-08-01

    The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of ~456 polypeptide chains contributed by ~30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal "FG" repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 Å resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed. PMID:22544723

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

    SciTech Connect

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

    2012-10-23

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

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

    PubMed Central

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

    2015-01-01

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

  15. 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.

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

    PubMed

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

    2004-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  18. 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.

  19. Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis

    PubMed Central

    Wei, Wen-Hua; Bowes, John; Plant, Darren; Viatte, Sebastien; Yarwood, Annie; Massey, Jonathan; Worthington, Jane; Eyre, Stephen

    2016-01-01

    Genotypic variability based genome-wide association studies (vGWASs) can identify potentially interacting loci without prior knowledge of the interacting factors. We report a two-stage approach to make vGWAS applicable to diseases: firstly using a mixed model approach to partition dichotomous phenotypes into additive risk and non-additive environmental residuals on the liability scale and secondly using the Levene’s (Brown-Forsythe) test to assess equality of the residual variances across genotype groups per marker. We found widespread significant (P < 2.5e-05) vGWAS signals within the major histocompatibility complex (MHC) across all three study cohorts of rheumatoid arthritis. We further identified 10 epistatic interactions between the vGWAS signals independent of the MHC additive effects, each with a weak effect but jointly explained 1.9% of phenotypic variance. PTPN22 was also identified in the discovery cohort but replicated in only one independent cohort. Combining the three cohorts boosted power of vGWAS and additionally identified TYK2 and ANKRD55. Both PTPN22 and TYK2 had evidence of interactions reported elsewhere. We conclude that vGWAS can help discover interacting loci for complex diseases but require large samples to find additional signals. PMID:27109064

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

    PubMed

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

    2008-11-01

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

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

    SciTech Connect

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

    2008-07-03

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

  2. Architecture of a Coat for the Nuclear Pore Membrane

    PubMed Central

    Hsia, Kuo-Chiang; Stavropoulos, Pete; Blobel, Günter; Hoelz, André

    2008-01-01

    SUMMARY The symmetric core of the nuclear pore complex can be considered schematically as a series of concentric cylinders. A peripheral cylinder coating the pore membrane contains the previously characterized, elongated heptamer that harbors Sec13-Nup145C in its middle section. Strikingly, Sec13-Nup145C crystallized as a hetero-octamer in two space groups. Oligomerization of Sec13-Nup145C was confirmed biochemically. Importantly, the numerous interacting surfaces in the hetero-octamer are evolutionarily highly conserved, further underlining the physiological relevance of the oligomerization. The hetero-octamer forms a slightly curved, yet rigid rod of sufficient length to span the entire height of the proposed membrane-adjacent cylinder. In concordance with the dimensions and symmetry of the nuclear pore complex core, we suggest that the cylinder is constructed of four anti-parallel rings, each ring being composed of eight heptamers arranged in a head-to-tail fashion. Our model proposes that the hetero-octamer would vertically traverse and connect the four stacked rings. PMID:18160040

  3. 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

  4. Evaluation of sediment contamination in Pearl Harbor. Final report

    SciTech Connect

    Grovhoug, J.G.

    1992-06-01

    Pearl Harbor demonstrates remarkable resilience to natural and human-induced contaminant stresses. A review of more than fifty harbor-specific data sets reveals a complex contamination and recovery history. Siltation is a major contaminant pathway in Pearl Harbor. Dredging operations, which are necessary due to high siltation rates, reduce contaminant loading by periodically removing the upper harbor sediment layers. The response of test organisms during sediment toxicity and bioaccumulation studies showed negligible effects from sediment toxicity. The environmental quality at an offshore dredge disposal site for the harbor is not measurable affected. Urban runoff via storm drains and tributaries is an important nonpoint source of contaminant exposure to the Pearl Harbor ecosystem. Most contaminants experience extensive physical, chemical, and biological, modification after entering the harbor environment. Certain contaminants, including PCBs, petroleum hydrocarbons, and silver, were reported at sufficiently elevated sediment concentrations to warrant environmental concern in some harbor regions and may warrant further evaluation. The overall sediment quality in Pearl Harbor, however, is less degraded than that of many U.S. mainland coastal harbors. Further detailed study of the abundance and distribution of important marine resources in Pearl Harbor is recommended.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-11-01

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

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

    PubMed

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

    2014-11-01

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

  8. 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.

  9. 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.

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

    PubMed Central

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

    2008-01-01

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

  11. 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

  12. 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

  13. 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

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

    PubMed

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

    2016-08-15

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

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

    PubMed

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

    2007-08-15

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

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

    PubMed

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

    2015-02-15

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

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

    SciTech Connect

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

    2007-07-15

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

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

    PubMed

    Paul, Biplab; Montpetit, Ben

    2016-09-01

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed Central

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

    1997-01-01

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

  1. 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

  2. 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.

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

    PubMed

    Rajanala, Kalpana; Nandicoori, Vinay Kumar

    2012-01-01

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

  4. Port and Harbor Security

    SciTech Connect

    Saito, T; Guthmuller, H; DeWeert, M

    2004-12-15

    Port and Harbor Security is a daunting task to which optics and photonics offers significant solutions. We are pleased to report that the 2005 Defense and Security Symposium (DSS, Orlando, FL) will include reports on active and passive photonic systems operating from both airborne and subsurface platforms. In addition to imaging techniques, there are various photonic applications, such as total internal reflection fluorescence (TIRF), which can be used to ''sniff'' for traces of explosives or contaminants in marine. These non-imaging technologies are beyond the scope of this article, but will also be represented at DSS 2005. We encourage colleagues to join our technical group to help us to make our ports and harbors safer and more secure.

  5. Contaminant levels in Herring (Larus argentatus) and Great Black-backed Gull (Larus marinus) eggs from colonies in the New York harbor complex between 2012 and 2013.

    PubMed

    Burger, Joanna; Elbin, Susan

    2015-03-01

    Birds living in coastal areas are exposed to severe storms and tidal flooding during the nesting season, but also to contaminants that move up the food chain from the water column and sediment to their prey items. We examine metals in Herring Gull (Larus argentatus) and Great Black-backed Gull (Larus marinus) eggs collected from the New York/New Jersey harbor estuary in 2012 and in 2013 to determine if there were significant yearly differences in metal levels. We test the null hypothesis that there were no significant yearly differences in metal levels. We investigate whether there were consistent differences in metals from 2012 to 2013 that might suggest a storm-related effect because Superstorm Sandy landed in New Jersey in October 2012 with high winds and extensive flooding, and view this research as exploratory. Except for arsenic, there were significant inter-year variations in the mean levels for all colonies combined for Herring Gull, and for lead, mercury and selenium for Great Black-backed Gulls. All metal levels in 2013 were less than in 2012, except for lead. These differences were present for individual colonies as well. Metal levels varied significantly among islands for Herring Gulls in both years (except for cadmium in 2013). No one colony had the highest levels of all metals for Herring Gulls. A long term data set on mercury levels in Herring Gulls indicated that the differences between 2012 and 2013 were greater than usual. Several different factors could account for these differences, and these are discussed.

  6. Contaminant levels in Herring (Larus argentatus) and Great Black-backed Gull (Larus marinus) eggs from colonies in the New York harbor complex between 2012 and 2013

    PubMed Central

    Elbin, Susan

    2014-01-01

    Birds living in coastal areas are exposed to severe storms and tidal flooding during the nesting season, but also to contaminants that move up the food chain from the water column and sediment to their prey items. We examine metals in Herring Gull (Larus argentatus) and Great Black-backed Gull (Larus marinus) eggs collected from the New York/New Jersey harbor estuary in 2012 and in 2013 to determine if there were significant yearly differences in metal levels. We test the null hypothesis that there were no significant yearly differences in metal levels. We investigate whether there were consistent differences in metals from 2012 to 2013 that might suggest a storm-related effect because Superstorm Sandy landed in New Jersey in October 2012 with high winds and extensive flooding, and view this research as exploratory. Except for arsenic, there were significant inter-year variations in the mean levels for all colonies combined for Herring Gull, and for lead, mercury and selenium for Great Black-backed Gulls. All metal levels in 2013 were less than in 2012, except for lead. These differences were present for individual colonies as well. Metal levels varied significantly among islands for Herring Gulls in both years (except for cadmium in 2013). No one colony had the highest levels of all metals for Herring Gulls. A long term data set on mercury levels in Herring Gulls indicated that the differences between 2012 and 2013 were greater than usual. Several different factors could account for these differences, and these are discussed. PMID:25471353

  7. 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

  8. 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

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

    PubMed

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

    2012-09-15

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

  10. 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

  11. 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

  12. MRSA Clonal Complex 22 Strains Harboring Toxic Shock Syndrome Toxin (TSST-1) Are Endemic in the Primary Hospital in Gaza, Palestine

    PubMed Central

    Chen, Liang; Abdelateef, Nahed; Elamreen, Farid Abu; Ginocchio, Christine C.; Pierard, Denis; Becker, Karsten; Kreiswirth, Barry N.

    2015-01-01

    Background Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen in both community and healthcare-related settings worldwide. Current knowledge regarding the epidemiology of S. aureus and MRSA in Gaza is based on a single community-based carriage study. Here we describe a cross-sectional analysis of 215 clinical isolates collected from Al-Shifa Hospital in Gaza during 2008 and 2012. Methods All isolates were characterized by spa typing, SCCmec typing, and detection of genes encoding Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST-1). Representative genotypes were also subjected to multilocus sequence typing (MLST). Antibiotic susceptibility testing was performed using VITEK2 and MicroScan. Results MRSA represented 56.3% of all S. aureus strains, and increased in frequency from 2008 (54.8%) to 2012 (58.4%). Aside from beta-lactams, resistance was observed to tetracycline, erythromycin, clindamycin, gentamicin, and fluoroquinolones. Molecular typing identified 35 spa types representing 17 MLST clonal complexes (CC), with spa 998 (Ridom t223, CC22) and spa 70 (Ridom t044, CC80) being the most prevalent. SCCmec types I, III, IV, V and VI were identified among MRSA isolates, while type II was not detected. PVL genes (lukF/S-PV) were detected in 40.0% of all isolates, while the TSST-1 gene (tst) was detected in 27.4% of all isolates, with surprisingly high frequency within CC22 (70.4%). Both PVL and TSST-1 genes were found in several isolates from 2012. Conclusions Molecular typing of clinical isolates from Gaza hospitals revealed unusually high prevalence of TSST-1 genes among CC22 MRSA, which is noteworthy given a recent community study describing widespread carriage of a CC22 MRSA clone known as the ‘Gaza strain’. While the latter did not address TSST-1, tst-positive spa 998 (Ridom t223) has been detected in several neighboring countries, and described as endemic in an Italian NICU, suggesting international spread of a

  13. Safe harbor: protecting ports with shipboard fuel cells.

    PubMed

    Taylor, David A

    2006-04-01

    With five of the largest harbors in the United States, California is beginning to take steps to manage the large amounts of pollution generated by these bustling centers of transport and commerce. One option for reducing diesel emissions is the use of fuel cells, which run cleaner than diesel and other internal combustion engines. Other technologies being explored by harbor officials are diesel-electric hybrid and gas turbine locomotives for moving freight within port complexes. PMID:16581531

  14. Safe harbor: protecting ports with shipboard fuel cells.

    PubMed

    Taylor, David A

    2006-04-01

    With five of the largest harbors in the United States, California is beginning to take steps to manage the large amounts of pollution generated by these bustling centers of transport and commerce. One option for reducing diesel emissions is the use of fuel cells, which run cleaner than diesel and other internal combustion engines. Other technologies being explored by harbor officials are diesel-electric hybrid and gas turbine locomotives for moving freight within port complexes.

  15. 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

  16. 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.

  17. Environment-dependent distribution of the sediment nifH-harboring microbiota in the Northern South China Sea.

    PubMed

    Dang, Hongyue; Yang, Jinying; Li, Jing; Luan, Xiwu; Zhang, Yunbo; Gu, Guizhou; Xue, Rongrong; Zong, Mingyue; Klotz, Martin G

    2013-01-01

    The South China Sea (SCS), the largest marginal sea in the Western Pacific Ocean, is a huge oligotrophic water body with very limited influx of nitrogenous nutrients. This suggests that sediment microbial N(2) fixation plays an important role in the production of bioavailable nitrogen. To test the molecular underpinning of this hypothesis, the diversity, abundance, biogeographical distribution, and community structure of the sediment diazotrophic microbiota were investigated at 12 sampling sites, including estuarine, coastal, offshore, deep-sea, and methane hydrate reservoirs or their prospective areas by targeting nifH and some other functional biomarker genes. Diverse and novel nifH sequences were obtained, significantly extending the evolutionary complexity of extant nifH genes. Statistical analyses indicate that sediment in situ temperature is the most significant environmental factor influencing the abundance, community structure, and spatial distribution of the sediment nifH-harboring microbial assemblages in the northern SCS (nSCS). The significantly positive correlation of the sediment pore water NH(4)(+) concentration with the nifH gene abundance suggests that the nSCS sediment nifH-harboring microbiota is active in N(2) fixation and NH(4)(+) production. Several other environmental factors, including sediment pore water PO(4)(3-) concentration, sediment organic carbon, nitrogen and phosphorus levels, etc., are also important in influencing the community structure, spatial distribution, or abundance of the nifH-harboring microbial assemblages. We also confirmed that the nifH genes encoded by archaeal diazotrophs in the ANME-2c subgroup occur exclusively in the deep-sea methane seep areas, providing for the possibility to develop ANME-2c nifH genes as a diagnostic tool for deep-sea methane hydrate reservoir discovery.

  18. Geoscience rediscovers Phoenicia's buried harbors

    NASA Astrophysics Data System (ADS)

    Marriner, Nick; Morhange, Christophe; Doumet-Serhal, Claude; Carbonel, Pierre

    2006-01-01

    After centuries of archaeological debate, the harbors of Phoenicia's two most important city states, Tyre and Sidon, have been rediscovered, and including new geoarcheological results reveal how, where, and when they evolved after their Bronze Age foundations. The early ports lie beneath their present urban centers, and we have indentified four harbor phases. (1) During the Bronze Age, Tyre and Sidon were characterized by semi-open marine coves that served as protoharbors. (2) Biostratigraphic and lithostratigraphic data indicate the presence of early artificial basins after the first millennium B.C. (3) The harbors reached their apogees during the Greco-Roman and Byzantine periods. (4) Silting up and coastal progradation led to burial of the medieval basins, lost until now.

  19. Velocities in Solar Pores

    NASA Astrophysics Data System (ADS)

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

    1996-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Asakuma, Yusuke; Yamamoto, Tsuyoshi

    2016-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Or, D.; Moebius, F.

    2014-12-01

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

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

    PubMed

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

    2012-07-01

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

  3. 75 FR 78601 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-16

    ... Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS... Seeber/Claiborne Avenue) ] vertical lift bridge across the Inner Harbor Navigational Canal, mile 0.9... (Judge Seeber/ Claiborne Avenue) vertical lift bridge across the Inner Harbor Navigational Canal, mile...

  4. 76 FR 8653 - Drawbridge Operation Regulation; Gulf Intracoastal Waterway, New Orleans Harbor, Inner Harbor...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-15

    ... Orleans Harbor, Inner Harbor Navigation Canal, New Orleans, Orleans Parish, LA AGENCY: Coast Guard, DHS... Seeber/Claiborne Avenue) vertical lift bridge across the Inner Harbor Navigational Canal, mile 0.9, (Gulf... across the Inner Harbor Navigational Canal, mile 0.9, (GIWW mile 6.7 EHL). The bridge provides 40 feet...

  5. Visualization of enzyme activities inside earthworm pores

    NASA Astrophysics Data System (ADS)

    Hoang, Duyen; Razavi, Bahar S.

    2015-04-01

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

  6. Tributyltin contamination and imposex in Alaska harbors.

    PubMed

    Tallmon, David A

    2012-02-01

    We quantified imposex in file dogwinkles (Nucella lima) and tributyltin (TBT) contamination in bay mussels (Mytilus trossulus) from 10 harbors and nearby control sites throughout Alaska. We found evidence of TBT contamination in mussels from four harbors (29-54 ng TBT/g wet tissue wt). Two of these harbors now show reduced TBT contamination relative to levels found in 1987. We were able to find and collect dogwinkles from seven sites. Of these, all three dogwinkle samples from harbor sites exhibited imposex, with 36%-87.5% females affected per site. In total, six of the 10 harbors had some evidence of TBT contamination.

  7. 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.

  8. The Arabidopsis Nuclear Pore and Nuclear Envelope

    PubMed Central

    Meier, Iris; Brkljacic, Jelena

    2010-01-01

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

  9. The pore space scramble

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  10. 33 CFR 125.15 - Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., and port and harbor areas, including vessels and harbor craft therein. 125.15 Section 125.15....15 Access to waterfront facilities, and port and harbor areas, including vessels and harbor craft....09 to those waterfront facilities, and port and harbor areas, including vessels and harbor...

  11. Nuclear Pore Proteins and Cancer

    PubMed Central

    Xu, Songli; Powers, Maureen A.

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Hertel, Stefan Andreas; Wang, Xindi; Hosking, Peter; Simpson, M. Cather; Hunter, Mark; Galvosas, Petrik

    2015-07-01

    Imaging of the microstructure of porous media such as biological tissue or porous solids is of high interest in health science and technology, engineering and material science. Magnetic resonance pore imaging (MRPI) is a recent technique based on nuclear magnetic resonance (NMR) which allows us to acquire images of the average pore shape in a given sample. Here we provide details on the experimental design, challenges, and requirements of MRPI, including its calibration procedures. Utilizing a laser-machined phantom sample, we present images of microscopic pores with a hemiequilateral triangular shape even in the presence of NMR relaxation effects at the pore walls. We therefore show that MRPI is applicable to porous samples without a priori knowledge about their pore shape and symmetry. Furthermore, we introduce "MRPI mapping," which combines MRPI with conventional magnetic resonance imaging (MRI). This enables one to resolve microscopic pore sizes and shapes spatially, thus expanding the application of MRPI to samples with heterogeneous distributions of pores.

  13. Head capsule deformities in midge larvae exposed to Burlington Harbor (Lake Champlain) sediments -- field and laboratory investigations

    SciTech Connect

    Lester, D.; Williams, A.; McIntosh, A.; Lacey, R.

    1994-12-31

    Investigations of sediment associated contaminants in Burlington Harbor indicated the harbor contains elevated levels of a number of pollutants. Lead, silver, mercury and total PAH levels exceed NOAA`s ER-M at numerous sites in the harbor. Benzo(a)pyrene concentrations (ranging from 0.055 to 6.64 ug/g (dry wt.)) exceed the ER-M at a number of sites. Pyrene, phenanthrene, fluoranthene, chrysene, anthracene and fluorene also exceed the ER-M at a number of stations within the harbor. Despite these relatively high levels of contaminants found in harbor sediments, solid phase and pore water exposures with Ceriodaphnia dubia indicate acute toxicity at only a limited number of sites. Examination of midge larvae populations from the harbor, however, indicates a high rate of head capsule deformities at some sites. Preliminary work which exposed laboratory cultures of Chironomus tentans to harbor sediment induced a 17% incidence in deformities in the F{sub 1} generation, a 50% incidence in the F{sub 2} generation and a 75% in the F{sub 3} generation. The incidence of deformities decreased substantially when F{sub 3} generation organisms were reared in clean substrate. Laboratory cultures of C. tentans are being exposed to sediments from various harbor sites for determination of head capsule deformity induction. In addition, several generations of larvae will be reared in sediment to determine the overall impacts on survival and whether deformities increase in subsequent generations.

  14. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

    Pohlmeier, Andreas; Haber-Pohlmeier, Sabina; Haber, Agnes; Sucre, Oscar; Stingaciu, Laura; Stapf, Siegfried; Blümich, Bernhard

    2010-05-01

    Within Cluster A, Partial Project A1, the pore space exploration by means of Nuclear Magnetic Resonance (NMR) plays a central role. NMR is especially convenient since it probes directly the state and dynamics of the substance of interest: water. First, NMR is applied as relaxometry, where the degree of saturation but also the pore geometry controls the NMR signature of natural porous systems. Examples are presented where soil samples from the Selhausen, Merzenhausen (silt loams), and Kaldenkirchen (sandy loam) test sites are investigated by means of Fast Field Cycling Relaxometry at different degrees of saturation. From the change of the relaxation time distributions with decreasing water content and by comparison with conventional water retention curves we conclude that the fraction of immobile water is characterized by T1 < 5 ms. Moreover, the dependence of the relaxation rate on magnetic field strength allows the identification of 2D diffusion at the interfaces as the mechanism which governs the relaxation process (Pohlmeier et al. 2009). T2 relaxation curves are frequently measured for the rapid characterization of soils by means of the CPMG echo train. Basically, they contain the same information about the pore systems like T1 curves, since mostly the overall relaxation is dominated by surface relaxivity and the surface/volume ratio of the pores. However, one must be aware that T2 relaxation is additionally affected by diffusion in internal gradients, and this can be overcome by using sufficiently short echo times and low magnetic fields (Stingaciu et al. 2009). Second, the logic continuation of conventional relaxation measurements is the 2-dimensional experiment, where prior to the final detection of the CPMG echo train an encoding period is applied. This can be T1-encoding by an inversion pulse, or T2 encoding by a sequence of 90 and 180° pulses. During the following evolution time the separately encoded signals can mix and this reveals information about

  15. Pore architecture of nanoporous gold and titania by hydrogen thermoporometry

    NASA Astrophysics Data System (ADS)

    Johnston, L. T.; Biener, M. M.; Ye, J. C.; Baumann, T. F.; Kucheyev, S. O.

    2015-07-01

    Nanoporous gold (NPG) and materials derived from it by templating have complex pore architecture that determines their technologically relevant physical properties. Here, we apply high-resolution hydrogen thermoporometry to study the pore structure of NPG and NPG-derived titania nanofoam (TNF). Results reveal complex multimodal pore size distributions for NPG and TNF. The freezing-melting hysteresis is pronounced, with freezing and melting scans having entirely different shapes. Experiments involving partial freeze-melt cycles reveal the lack of direct correlation between individual freezing and melting peaks, pointing to phenomena that are beyond the Gibbs-Thomson formalism. The depression of the average freezing temperature scales linearly with the ratio of the internal surface area (measured by gas sorption) and the total pore volume derived from the density of monoliths. Thermoporometry yields total pore volumes in good agreement with those derived from monolith densities for both NPG and TNF.

  16. Numerical modeling of Waianae Harbor

    SciTech Connect

    Mader, C.L.; Lucas, S.

    1985-01-01

    The Waianae harbor problem is an example of the use of numerical modeling techniques available at JTRE of the University of Hawaii to assist in the evaluation of oceanographic fluid dynamic flow problems. The numerical techniques are available to assist in the modeling of many problems of interest to the Hawaii Ocean Experiment. One application that has received considerable effort is the formation, propagation, and run-up of tsunami waves. The interaction of tsunami waves with the island chain is an important problem that needs more study. The models can be used to study storm surge interaction with the Hawaii islands and current and circulation around and through the islands. It is important that the modeling not be limited to the usual nonlinear shallow-water models, since they are inappropriate for many of the problems of interest to the Hawaii Ocean Experiment. 6 references, 5 figures.

  17. 33 CFR 100.109 - Winter Harbor Lobster Boat Race, Winter Harbor, ME.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Winter Harbor Lobster Boat Race, Winter Harbor, ME. 100.109 Section 100.109 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF... Lobster Boat Race, Winter Harbor, ME. (a) Regulated area. The regulated area includes all waters of...

  18. Pore dynamics in lipid membranes

    NASA Astrophysics Data System (ADS)

    Gozen, I.; Dommersnes, P.

    2014-09-01

    Transient circular pores can open in plasma membrane of cells due to mechanical stress, and failure to repair such pores lead to cell death. Similar pores in the form of defects also exist among smectic membranes, such as in myelin sheaths or mitochondrial membranes. The formation and growth of membrane defects are associated with diseases, for example multiple sclerosis. A deeper understanding of membrane pore dynamics can provide a more refined picture of membrane integrity-related disease development, and possibly also treatment options and strategies. Pore dynamics is also of great importance regarding healthcare applications such as drug delivery, gene or as recently been implied, cancer therapy. The dynamics of pores significantly differ in stacks which are confined in 2D compared to those in cells or vesicles. In this short review, we will summarize the dynamics of different types of pores that can be observed in biological membranes, which include circular transient, fusion and hemi-fusion pores. We will dedicate a section to floral and fractal pores which were discovered a few years ago and have highly peculiar characteristics. Finally, we will discuss the repair mechanisms of large area pores in conjunction with the current cell membrane repair hypotheses.

  19. 33 CFR 117.549 - Cambridge Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cambridge Harbor. 117.549 Section... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of the S342 bridge, mile 0.1 at Cambridge, shall open on signal from 6 a.m. to 8 p.m.; except that, from...

  20. 16 CFR 312.10 - Safe harbors.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Safe harbors. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S ONLINE PRIVACY PROTECTION RULE § 312.10 Safe harbors. (a) In general. An operator will be deemed to be...

  1. 33 CFR 117.811 - Tonawanda Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Tonawanda Harbor. 117.811 Section 117.811 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New York § 117.811 Tonawanda Harbor. The draw of...

  2. 33 CFR 117.1061 - Tacoma Harbor.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Tacoma Harbor. 117.1061 Section 117.1061 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Washington § 117.1061 Tacoma Harbor. (a) When...

  3. 33 CFR 117.1061 - Tacoma Harbor.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Tacoma Harbor. 117.1061 Section 117.1061 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Washington § 117.1061 Tacoma Harbor. (a) When...

  4. 33 CFR 117.1061 - Tacoma Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Tacoma Harbor. 117.1061 Section 117.1061 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Washington § 117.1061 Tacoma Harbor. (a) When...

  5. 33 CFR 117.1061 - Tacoma Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Tacoma Harbor. 117.1061 Section 117.1061 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Washington § 117.1061 Tacoma Harbor. (a) When...

  6. 33 CFR 117.1061 - Tacoma Harbor.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Tacoma Harbor. 117.1061 Section 117.1061 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Washington § 117.1061 Tacoma Harbor. (a) When...

  7. 33 CFR 117.549 - Cambridge Harbor.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Cambridge Harbor. 117.549 Section 117.549 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of...

  8. 33 CFR 117.549 - Cambridge Harbor.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Cambridge Harbor. 117.549 Section 117.549 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of...

  9. 33 CFR 117.549 - Cambridge Harbor.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Cambridge Harbor. 117.549 Section 117.549 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of...

  10. 33 CFR 117.549 - Cambridge Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Cambridge Harbor. 117.549 Section 117.549 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of...

  11. A smart ROV solution for ship hull and harbor inspection

    NASA Astrophysics Data System (ADS)

    Reed, Scott; Wood, Jon; Vazquez, Jose; Mignotte, Pierre-Yves; Privat, Benjamin

    2010-04-01

    Hull and harbor infrastructure inspections are frequently performed manually and involve quite a bit of risk and human and monetary resources. In any kind of threat and resource constrained environment, this involves unacceptable levels of risk and cost. Modern Remotely Operated Vehicles are highly refined machines that provide features and capabilities previously unavailable. Operations once carried out by divers can now be carried out more quickly, efficiently and safely by smart enabled ROVs. ROVs are rapidly deployable and capable of continuous, reliable operations in adverse conditions. They also provide a stable platform on which multiple sensors may be mounted and utilized to meet the harbor inspection problem. Automated Control software provides ROV's and their pilots with the capability to inspect complex, constrained environments such as those found in a harbor region. This application and the user interface allow the ROV to automatically conduct complex maneuvers relative to the area being inspected and relieves the training requirements and work load for the pilot, allowing he or she to focus on the primary task of survey, inspection and looking for possible threats (such as IEDs, Limpet Mines, signs of sabotage, etc). Real-time sensor processing tools can be integrated into the smart ROV solution to assist the operator. Automatic Target Recognition (ATR) algorithms are used to search through the sensor data collected by the ROV in real time. These algorithms provide immediate feedback on possible threats and notify the operator of regions that may require manual verification. Sensor data (sonar or video) is also mosaiced, providing the operator with real-time situational awareness and a coverage map of the hull or seafloor. Detected objects may also be placed in the context of the large scale characteristics of the hull (or bottom or pilings) and localized. Within the complex areas such as the harbor pier pilings and the running gear of the ship, real

  12. Modeling tidal exchange and dispersion in Boston Harbor

    USGS Publications Warehouse

    Signell, Richard P.; Butman, Bradford

    1992-01-01

    Tidal dispersion and the horizontal exchange of water between Boston Harbor and the surrounding ocean are examined with a high-resolution (200 m) depth-averaged numerical model. The strongly varying bathymetry and coastline geometry of the harbor generate complex spatial patterns in the modeled tidal currents which are verified by shipboard acoustic Doppler surveys. Lagrangian exchange experiments demonstrate that tidal currents rapidly exchange and mix material near the inlets of the harbor due to asymmetry in the ebb/flood response. This tidal mixing zone extends roughly a tidal excursion from the inlets and plays an important role in the overall flushing of the harbor. Because the tides can only efficiently mix material in this limited region, however, harbor flushing must be considered a two step process: rapid exchange in the tidal mixing zone, followed by flushing of the tidal mixing zone by nontidal residual currents. Estimates of embayment flushing based on tidal calculations alone therefore can significantly overestimate the flushing time that would be expected under typical environmental conditions. Particle-release simulations from point sources also demonstrate that while the tides efficiently exchange material in the vicinity of the inlets, the exact nature of dispersion from point sources is extremely sensitive to the timing and location of the release, and the distribution of particles is streaky and patchlike. This suggests that high-resolution modeling of dispersion from point sources in these regions must be performed explicitly and cannot be parameterized as a plume with Gaussian-spreading in a larger scale flow field.

  13. Latent fingermark pore area reproducibility.

    PubMed

    Gupta, A; Buckley, K; Sutton, R

    2008-08-01

    The study of the reproducibility of friction ridge pore detail in fingermarks is a measure of their usefulness in personal identification. Pore area in latent prints developed using cyanoacrylate and ninhydrin were examined and measured by photomicrography using appropriate software tools. The data were analysed statistically and the results showed that pore area is not reproducible in developed latent prints, using either of the development techniques. The results add further support to the lack of reliability of pore area in personal identification. PMID:18617339

  14. 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

  15. Open–closed switching of synthetic tubular pores

    PubMed Central

    Kim, Yongju; Kang, Jiheong; Shen, Bowen; Wang, Yanqiu; He, Ying; Lee, Myongsoo

    2015-01-01

    While encouraging progress has been made on switchable nanopores to mimic biological channels and pores, it remains a great challenge to realize long tubular pores with a dynamic open–closed motion. Here we report μm-long, dynamic tubular pores that undergo rapid switching between open and closed states in response to a thermal signal in water. The tubular walls consist of laterally associated primary fibrils stacked from disc-shaped molecules in which the discs readily tilt by means of thermally regulated dehydration of the oligoether chains placed on the wall surfaces. Notably, this pore switching mediates a controlled water-pumping catalytic action for the dehydrative cyclization of adenosine monophosphate to produce metabolically active cyclic adenosine monophosphate. We believe that our work may allow the creation of a variety of dynamic pore structures with complex functions arising from open–closed motion. PMID:26456695

  16. Pore Structure and the Low Frequency Permittivity of Sea Ice

    NASA Astrophysics Data System (ADS)

    O'Sadnick, M.; Ingham, M.; Eicken, H.

    2014-12-01

    Field and laboratory measurements of the dielectric permittivity of first-year sea ice both show that below a frequency of about 10 Hz the real part of the relative permittivity (ɛ') increases with decreasing frequency. Field measurements in Barrow, Alaska and McMurdo Sound suggest that this rise in low frequency ɛ' steepens as the ice warms, and is confined primarily to the upper 0.50m of the ice cover as it approaches maximum thickness. We propose that this behaviour may be related to membrane polarization occurring in the pore structure within the ice. With ice-liquid interfaces carrying a net charge, an electric double layer forms within the brine filled pores. Polarization occurs at grain boundaries, intragranular films and "necks" in the pore structure where the effective thickness of the double layer approaches the width of the pore resulting in differential transport of ions. This process is dependent on both the characteristic lengths and radii of pores relative to the length and radii of the "necks" or the geometry of inter/intragranular brine layers. By representing the measured dielectric permittivity in terms of a Cole-Cole model it is possible to show that the distribution of pore sizes evolves with temperature. Derived values of complex conductivity are also examined in relationship to the temporal evolution of pore geometry including smoothness of the pore-ice interface.

  17. Targeting Bcl-2 stability to sensitize cells harboring oncogenic ras.

    PubMed

    Peng, Bo; Ganapathy, Suthakar; Shen, Ling; Huang, Junchi; Yi, Bo; Zhou, Xiaodong; Dai, Wei; Chen, Changyan

    2015-09-01

    The pro-survival factor Bcl-2 and its family members are critical determinants of the threshold of the susceptibility of cells to apoptosis. Studies are shown that cells harboring an oncogenic ras were extremely sensitive to the inhibition of protein kinase C (PKC) and Bcl-2 could antagonize this apoptotic process. However, it remains unrevealed how Bcl-2 is being regulated in this apoptotic process. In this study, we investigate the role of Bcl-2 stability in sensitizing the cells harboring oncogenic K-ras to apoptosis triggered by PKC inhibitor GO6976. We demonstrated that Bcl-2 in Swiss3T3 cells ectopically expressing or murine lung cancer LKR cells harboring K-ras rapidly underwent ubiquitin-dependent proteasome pathway after the treatment of GO6976, accompanied with induction of apoptosis. In this process, Bcl-2 formed the complex with Keap-1 and Cul3. The mutation of serine-17 and deletion of BH-2 or 4 was required for Bcl-2 ubiquitination and degradation, which elevate the signal threshold for the induction of apoptosis in the cells following PKC inhibition. Thus, Bcl-2 appears an attractive target for the induction of apoptosis by PKC inhibition in cancer cells expressing oncogenic K-ras. PMID:26041886

  18. Designed membrane channels and pores.

    PubMed

    Bayley, H

    1999-02-01

    Advances in the synthesis and assembly of designed membrane channels and pores include addressable template-assisted synthetic protein (TASP) syntheses of helix bundles, the production of a new class of nanotubes and the ability to purify hetero-oligomeric pores. Channels and pores with altered functional properties and with built-in triggers and switches have been prepared. Progress in applications has been greatest in sensor technology, where sensor elements based on ligand activation, channel selectivity and channel block have been made. Structural information about natural membrane proteins is emerging to inspire new designs.

  19. Triggered pore-forming agents

    DOEpatents

    Bayley, Hagan; Walker, Barbara J.; Chang, Chung-yu; Niblack, Brett; Panchal, Rekha

    1998-01-01

    An inactive pore-forming agent which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell.

  20. Metal structures with parallel pores

    NASA Technical Reports Server (NTRS)

    Sherfey, J. M.

    1976-01-01

    Four methods of fabricating metal plates having uniformly sized parallel pores are studied: elongate bundle, wind and sinter, extrude and sinter, and corrugate stack. Such plates are suitable for electrodes for electrochemical and fuel cells.

  1. 33 CFR 80.1138 - Santa Cruz Harbor, CA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Santa Cruz Harbor, CA. 80.1138... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn from the seaward extremity of the Santa Cruz Harbor East Breakwater to Santa Cruz Harbor West...

  2. 33 CFR 80.1138 - Santa Cruz Harbor, CA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Santa Cruz Harbor, CA. 80.1138... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn from the seaward extremity of the Santa Cruz Harbor East Breakwater to Santa Cruz Harbor West...

  3. 33 CFR 80.1138 - Santa Cruz Harbor, CA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Santa Cruz Harbor, CA. 80.1138... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn from the seaward extremity of the Santa Cruz Harbor East Breakwater to Santa Cruz Harbor West...

  4. 33 CFR 80.1138 - Santa Cruz Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Santa Cruz Harbor, CA. 80.1138... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn from the seaward extremity of the Santa Cruz Harbor East Breakwater to Santa Cruz Harbor West...

  5. 33 CFR 80.1122 - Channel Islands Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Channel Islands Harbor, CA. 80... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor...

  6. 33 CFR 80.1122 - Channel Islands Harbor, CA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Channel Islands Harbor, CA. 80... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor...

  7. 33 CFR 80.1122 - Channel Islands Harbor, CA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Channel Islands Harbor, CA. 80... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor...

  8. 33 CFR 80.1122 - Channel Islands Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Channel Islands Harbor, CA. 80... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor...

  9. 33 CFR 80.1122 - Channel Islands Harbor, CA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Channel Islands Harbor, CA. 80... INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1122 Channel Islands Harbor, CA. (a) A line drawn from Channel Islands Harbor South Jetty Light 2 to Channel Islands Harbor...

  10. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... harbor will observe the following rule: The first steam vessel, or the first steam vessel with consort in tow, on entering the harbor for shelter, will proceed to the upper end of the breakwater. All steam vessels, and all steam vessels with consorts in tow, entering later, will place themselves in a...

  11. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... harbor will observe the following rule: The first steam vessel, or the first steam vessel with consort in tow, on entering the harbor for shelter, will proceed to the upper end of the breakwater. All steam vessels, and all steam vessels with consorts in tow, entering later, will place themselves in a...

  12. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... harbor will observe the following rule: The first steam vessel, or the first steam vessel with consort in tow, on entering the harbor for shelter, will proceed to the upper end of the breakwater. All steam vessels, and all steam vessels with consorts in tow, entering later, will place themselves in a...

  13. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... harbor will observe the following rule: The first steam vessel, or the first steam vessel with consort in tow, on entering the harbor for shelter, will proceed to the upper end of the breakwater. All steam vessels, and all steam vessels with consorts in tow, entering later, will place themselves in a...

  14. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... harbor will observe the following rule: The first steam vessel, or the first steam vessel with consort in tow, on entering the harbor for shelter, will proceed to the upper end of the breakwater. All steam vessels, and all steam vessels with consorts in tow, entering later, will place themselves in a...

  15. 33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... waters including Burnham Park Harbor and the southern part of Chicago Harbor, Lake Michigan, bounded...

  16. 33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone... waters including Burnham Park Harbor and the southern part of Chicago Harbor, Lake Michigan, bounded...

  17. Narrow harbors. Few joint ventures will find haven in the investment-interest safe harbor.

    PubMed

    Lepper, G J; Swoboda, J

    1991-12-01

    Investors and potential investors had hoped for meaningful guidance from the safe harbor regulations on appropriate structures for healthcare joint ventures. Unfortunately, the narrowly drawn final investment-interest safe harbor offers relatively little meaningful guidance or protection for the vast majority of such ventures. The Illegal Remuneration Statute (also known as the fraud and abuse statute) was first enacted in 1972 to prohibit members of the healthcare community from exchanging patient referrals for any kind of remuneration. In 1987 Congress instructed the secretary of Health and Human Services to create "safe harbors" for legitimate payment practices that, although they may violate the statute's strict prohibition, will be protected from prosecution. The investment-interest safe harbor has garnered the most attention. It provides two safe harbors, one for investments in large entities and one for investments in small entities. Both safe harbors contain onerous threshold requirements and other restrictions that diminish the usefulness of the safe harbor for all but a very few ventures. In addition, the Office of the Inspector General has created other obstacles to forming and preserving "safe" healthcare business ventures, including a refusal to "grandfather" or create a "safe harbor restructuring period" for existing business arrangements. Because most existing or planned joint ventures do not qualify for the investment-interest safe harbor, investors are forced to make their business decisions on the basis of the same factors used before publication of the safe harbor regulations. Such analysis will continue to focus on factors that demonstrate organizations' intent in making payments to investors as a return on investments.

  18. Bacterial secretins form constitutively open pores akin to general porins.

    PubMed

    Disconzi, Elena; Guilvout, Ingrid; Chami, Mohamed; Masi, Muriel; Huysmans, Gerard H M; Pugsley, Anthony P; Bayan, Nicolas

    2014-01-01

    Proteins called secretins form large multimeric complexes that are essential for macromolecular transit across the outer membrane of Gram-negative bacteria. Evidence suggests that the channels formed by some secretin complexes are not tightly closed, but their permeability properties have not been well characterized. Here, we used cell-free synthesis coupled with spontaneous insertion into liposomes to investigate the permeability of the secretin PulD. Leakage assays using preloaded liposomes indicated that PulD allows the efflux of small fluorescent molecules with a permeation cutoff similar to that of general porins. Other secretins were also found to form similar pores. To define the polypeptide region involved in determining the pore size, we analyzed a collection of PulD variants and studied the roles of gates 1 and 2, which were previously reported to affect the pore size of filamentous phage f1 secretin pIV, in assembly and pore formation. Liposome leakage and a novel in vivo assay showed that replacement of the conserved proline residue at position 443 in PulD by leucine increased the apparent size of the pore. The in vitro approach described here could be used to study the pore properties of membrane proteins whose production in vivo is toxic.

  19. Bacterial Secretins Form Constitutively Open Pores Akin to General Porins

    PubMed Central

    Disconzi, Elena; Guilvout, Ingrid; Chami, Mohamed; Masi, Muriel; Huysmans, Gerard H. M.; Pugsley, Anthony P.

    2014-01-01

    Proteins called secretins form large multimeric complexes that are essential for macromolecular transit across the outer membrane of Gram-negative bacteria. Evidence suggests that the channels formed by some secretin complexes are not tightly closed, but their permeability properties have not been well characterized. Here, we used cell-free synthesis coupled with spontaneous insertion into liposomes to investigate the permeability of the secretin PulD. Leakage assays using preloaded liposomes indicated that PulD allows the efflux of small fluorescent molecules with a permeation cutoff similar to that of general porins. Other secretins were also found to form similar pores. To define the polypeptide region involved in determining the pore size, we analyzed a collection of PulD variants and studied the roles of gates 1 and 2, which were previously reported to affect the pore size of filamentous phage f1 secretin pIV, in assembly and pore formation. Liposome leakage and a novel in vivo assay showed that replacement of the conserved proline residue at position 443 in PulD by leucine increased the apparent size of the pore. The in vitro approach described here could be used to study the pore properties of membrane proteins whose production in vivo is toxic. PMID:24142256

  20. The perforin pore facilitates the delivery of cationic cargos.

    PubMed

    Stewart, Sarah E; Kondos, Stephanie C; Matthews, Antony Y; D'Angelo, Michael E; Dunstone, Michelle A; Whisstock, James C; Trapani, Joseph A; Bird, Phillip I

    2014-03-28

    Cytotoxic lymphocytes eliminate virally infected or neoplastic cells through the action of cytotoxic proteases (granzymes). The pore-forming protein perforin is essential for delivery of granzymes into the cytoplasm of target cells; however the mechanism of this delivery is incompletely understood. Perforin contains a membrane attack complex/perforin (MACPF) domain and oligomerizes to form an aqueous pore in the plasma membrane; therefore the simplest (and best supported) model suggests that granzymes passively diffuse through the perforin pore into the cytoplasm of the target cell. Here we demonstrate that perforin preferentially delivers cationic molecules while anionic and neutral cargoes are delivered inefficiently. Furthermore, another distantly related pore-forming MACPF protein, pleurotolysin (from the oyster mushroom), also favors the delivery of cationic molecules, and efficiently delivers human granzyme B. We propose that this facilitated diffusion is due to conserved features of oligomerized MACPF proteins, which may include an anionic lumen. PMID:24558045

  1. 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

  2. Estuarine studies in upper Grays Harbor, Washington

    USGS Publications Warehouse

    Beverage, Joseph P.; Swecker, Milton N.

    1969-01-01

    Improved management of the water resources of Grays Harbor, Wash., requires more data on the water quality of the harbor and a better understanding of the influences of industrial and domestic wastes on the local fisheries resources. To provide a more comprehensive understanding of these influences, the U.S. Geological Survey joined other agencies in a cooperative study of Grays Harbor. This report summarizes the Survey's study of circulation patterns, description of water-quality conditions, and characterization of bottom material in the upper harbor. Salt water was found to intrude at least as far as Montesano, 28.4 nautical miles from the mouth of the harbor. Longitudinal salinity distributions were used to compute dispersion (diffusivity) coefficients ranging from 842 to 3,520 square feet per second. These values were corroborated by half-tidal-cycle dye studies. The waters of the harbor were found to be well mixed after extended periods of low fresh-water flow but stratified at high flows. Salinity data were used lo define the cumulative 'mean age' of the harbor water, which may be used to approximate a mean 'flushing time.' Velocity-time curves for the upper harbor are distorted from simple harmonic functions owing to channel geometry and frictional effects. Surface and bottom velocity data were used to estimate net tidal 'separation' distance, neglecting vertical mixing. Net separation distances between top and bottom water ranged from 1.65 nautical miles when fresh-water inflow was 610 cubic feet per second to 13.4 miles when inflow was 15,900 cubic feet per second. The cumulative mean age from integration of the fresh-water velocity equation was about twice that obtained from the salinity distribution. Excursion distances obtained with dye over half-tidal cycles exceeded those estimated from longitudinal salinity distributions and those obtained by earlier investigators who used floats. Net tidal excursions were as much as twice those obtained with floats

  3. Pore network model of electrokinetic transport through charged porous media

    NASA Astrophysics Data System (ADS)

    Obliger, Amaël; Jardat, Marie; Coelho, Daniel; Bekri, Samir; Rotenberg, Benjamin

    2014-04-01

    We introduce a method for the numerical determination of the steady-state response of complex charged porous media to pressure, salt concentration, and electric potential gradients. The macroscopic fluxes of solvent, salt, and charge are computed within the framework of the Pore Network Model (PNM), which describes the pore structure of the samples as networks of pores connected to each other by channels. The PNM approach is used to capture the couplings between solvent and ionic flows which arise from the charge of the solid surfaces. For the microscopic transport coefficients on the channel scale, we take a simple analytical form obtained previously by solving the Poisson-Nernst-Planck and Stokes equations in a cylindrical channel. These transport coefficients are upscaled for a given network by imposing conservation laws for each pores, in the presence of macroscopic gradients across the sample. The complex pore structure of the material is captured by the distribution of channel diameters. We investigate the combined effects of this complex geometry, the surface charge, and the salt concentration on the macroscopic transport coefficients. The upscaled numerical model preserves the Onsager relations between the latter, as expected. The calculated macroscopic coefficients behave qualitatively as their microscopic counterparts, except for the permeability and the electro-osmotic coupling coefficient when the electrokinetic effects are strong. Quantitatively, the electrokinetic couplings increase the difference between the macroscopic coefficients and the corresponding ones for a single channel of average diameter.

  4. Genetics Home Reference: Floating-Harbor syndrome

    MedlinePlus

    ... Arpin S, Afenjar A, Dubern B, Toutain A, Cabrol S, Héron D. Floating-Harbor Syndrome: report on a case ... G, Whiteford ML, Quaio CR, Gomy I, Bertola DR, Albrecht B, Platzer K, McGillivray G, Zou R, ...

  5. 16 CFR 312.10 - Safe harbors.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., issued by representatives of the marketing or online industries, or by other persons, that, after notice... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Safe harbors. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S...

  6. New Bedford Harbor Long Term Monitoring Program

    EPA Science Inventory

    New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a Superfund site in 1983 due to unacceptably high levels of sediment contamination by polychlorinated biphenyls (PCBs). Based on human health and environmental concerns, the decision was made to d...

  7. Sediment bioaccumulation testing: Manistique Harbor sediments

    EPA Science Inventory

    Manistique Harbor AOC public meeting and availability session on August 28th in Manistique, MI. This meeting/session is organized by GLNPO; they are EPA's lead on AOC restoration efforts. The goal of the meeting is to engage with the community with all the work that has been d...

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

    PubMed Central

    2015-01-01

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

  9. Sediment quality assessment studies in Boston Harbor, Massachusetts

    SciTech Connect

    Carr, R.S.; Chapman, D.C.; Biedenbach, J.M.; Long, E.R.; Thursby, G.; MacDonald, D.D.

    1995-12-31

    As part of NOAA`s National Status and Trends program, a bioeffects assessment study was conducted in the vicinity of Boston Harbor, Massachusetts. Surficial sediment samples were collected at 55 sites and subsamples were tested for toxicity using (1) the 10-day whole sediment test with Ampelisca abdita, (2) the sea urchin (Arbacia punctulata) fertilization and embryological development assays with sediment pore water, and (3) Microtox{trademark} assay with organic sediment extracts. Eleven percent of the samples were significantly toxic in the amphipod test, only 4% were toxic in the sea urchin fertilization test whereas all of the samples were highly toxic in the sea urchin embryological development assay; the Microtox assay determined 56% of the organic sediment extracts to be significantly toxic. Sediment chemical analyses for metals, AVS/SEM, PAHs, PCBs, and pesticides were performed on 30 of the 55 samples. Twenty-seven of the 30 samples exceeded at least one probable effects level (PEL) value. For the 20 samples that exceeded 5 or more PELS, the concordance between the predicted and observed toxicity was 20% for the amphipod test, 60% for the Microtox test, and 100% for the sea urchin embryological development assay. There were no significant correlations among the different toxicity tests or between the tests and the contaminant concentrations in the bulk sediment. Possible explanations for the apparent lack of correlation between the sediment chemistry and the toxicity tests will be discussed.

  10. Triggered pore-forming agents

    DOEpatents

    Bayley, H.; Walker, B.J.; Chang, C.Y.; Niblack, B.; Panchal, R.

    1998-07-07

    An inactive pore-forming agent is revealed which is activated to lytic function by a condition such as pH, light, heat, reducing potential, or metal ion concentration, or substance such as a protease, at the surface of a cell. 30 figs.

  11. Membrane pores induced by magainin

    SciTech Connect

    Ludtke, S.J.; He, Ke; Heller, W.T.

    1996-10-29

    Magainin, found in the skin of Xenopus laevis, belongs to a broad class of antimicrobial peptides which kill bacteria by permeabilizing the cytoplasmic membrane but do not lyse eukaryotic cells. The 23-residue peptide has been shown to form an amphiphilic helix when associated with membranes. However, its molecular mechanism of action has been controversial. Oriented circular dichroism has detected helical magainin oriented perpendicular to the plane of the membrane at high peptide concentrations, but Raman, fluorescence, differential scanning calorimetry, and NMR all indicate that the peptide is associated with the head groups of the lipid bilayer. Here we show that neutron in-plane scattering detects pores formed by magainin 2 in membranes only when a substantial fraction of the peptide is oriented perpendicular to the membrane. The pores are almost twice as large as the alamethicin pores. On the basis of the in-plane scattering data, we propose a toroidal (or wormhole) model, which differs from the barrel-stave model of alamethicin in that the lipid bends back on itself like the inside of a torus. The bending requires a lateral expansion in the head group region of the bilayer. Magainin monomers play the role of fillers in the expansion region thereby stabilizing the pore. This molecular configuration is consistent with all published magainin data. 33 refs., 5 figs.

  12. 76 FR 21862 - Takes of Marine Mammals Incidental to Specified Activities; Harbor Activities Related to the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-19

    ... not limited to, migration, breathing, nursing, breeding, feeding, or sheltering . Summary of Request... support Delta IV/EELV launch activities from the Space Launch Complex at VAFB Harbor and would occur in... the same activities from 2002 to 2010, with the last IHA expiring on September 3, 2010 (74 FR...

  13. PANORAMA, SHOWING COMMAND POST RELATION TO DUTCH HARBOR AND UNALASKA ...

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

    PANORAMA, SHOWING COMMAND POST RELATION TO DUTCH HARBOR AND UNALASKA FROM THE TOP OF LITTLE SOUTH AMERICA - Naval Operating Base Dutch Harbor & Fort Mears, Hill 400 Fixed Defense Battery Command Post, Unalaska, Aleutian Islands, AK

  14. 1. PANORAMA, SHOWING COMMAND POST RELATION TO DUTCH HARBOR AND ...

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

    1. PANORAMA, SHOWING COMMAND POST RELATION TO DUTCH HARBOR AND UNALASKA FROM THE TOP OF LITTLE SOUTH AMERICA - Naval Operating Base Dutch Harbor & Fort Mears, Hill 400 Fixed Defense Battery Command Post, Unalaska, Aleutian Islands, AK

  15. 33 CFR 80.1134 - Monterey Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from Monterey Harbor Light 6 to the...

  16. Decadal Changes In Benthic Community Measures In New York Harbor

    EPA Science Inventory

    Monitoring in New York Harbor, NY, as part of the Regional Environmental Monitoring and Assessment Program has spanned a decade, and includes habitat and water quality measures and sediment contaminant levels from four sub-basins (Upper NY Harbor, Lower NY Harbor, Newark Bay, and...

  17. 33 CFR 80.730 - Miami Harbor, FL.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Miami Harbor, FL. 80.730 Section... NAVIGATION RULES COLREGS DEMARCATION LINES Seventh District § 80.730 Miami Harbor, FL. A line drawn across the seaward extremity of the Miami Harbor Government Cut Jetties....

  18. 33 CFR 110.95 - Newport Bay Harbor, Calif.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Beach Harbor Ordinance No. 543 for recreational and small craft of such size and alignment as permitted.... Fore and aft moorings will be allowed in this area conforming to the City of Newport Beach Harbor... moorings will be allowed in this area conforming to the City of Newport Beach Harbor Ordinance No. 543...

  19. 33 CFR 110.95 - Newport Bay Harbor, Calif.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Beach Harbor Ordinance No. 543 for recreational and small craft of such size and alignment as permitted.... Fore and aft moorings will be allowed in this area conforming to the City of Newport Beach Harbor... moorings will be allowed in this area conforming to the City of Newport Beach Harbor Ordinance No. 543...

  20. Teaching about Pearl Harbor. Curriculum Enhancement Series #1.

    ERIC Educational Resources Information Center

    Shields, Anna Marshall

    These materials consist of sample lesson plans for teaching about the Japanese attack on Pearl Harbor on December 7, 1941, in both U.S. and world history classes. The lesson plans challenge students to examine how current attitudes toward the Japanese may be rooted in World War II and Pearl Harbor. Selected bibliographies on Pearl Harbor, World…

  1. 18 CFR 1304.404 - Commercial marina harbor limits.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true Commercial marina harbor... Miscellaneous § 1304.404 Commercial marina harbor limits. The landward limits of commercial marina harbor areas... at commercial marinas will be designated by TVA on the basis of the size and extent of facilities...

  2. 33 CFR 80.1136 - Moss Landing Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to...

  3. 33 CFR 80.1136 - Moss Landing Harbor, CA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to...

  4. 33 CFR 80.1136 - Moss Landing Harbor, CA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to...

  5. 33 CFR 80.1136 - Moss Landing Harbor, CA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to...

  6. 33 CFR 80.1136 - Moss Landing Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Moss Landing Harbor, CA. 80.1136... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1136 Moss Landing Harbor, CA. A line drawn from the seaward extremity of the pier located 0.3 mile south of Moss Landing Harbor Entrance to...

  7. 33 CFR 80.1134 - Monterey Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Monterey Harbor, CA. 80.1134 Section 80.1134 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1134 Monterey Harbor, CA. A line drawn from Monterey Harbor Light 6 to the...

  8. 33 CFR 80.1126 - Santa Barbara Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Santa Barbara Harbor, CA. 80.1126 Section 80.1126 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1126 Santa Barbara Harbor, CA. A line drawn from Santa Barbara Harbor Light 4...

  9. 33 CFR 80.1140 - Pillar Point Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Pillar Point Harbor, CA. 80.1140 Section 80.1140 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1140 Pillar Point Harbor, CA. A line drawn from Pillar Point Harbor Light 6...

  10. The historical significance of anaesthesia events at Pearl Harbor.

    PubMed

    Crowhurst, Ja

    2014-07-01

    Up to the end of World War II, less than 10% of the general anaesthetics administered was with intravenous barbiturates. The remaining 90% of anaesthetics given in the USA were with diethyl ether. In the United Kingdom and elsewhere, chloroform was also popular. Diethyl ether administration was a relatively safe and simple procedure, often delegated to nurses or junior doctors with little or no specific training in anaesthesia. During the Japanese attack on the US bases at Pearl Harbor, with reduced stocks of diethyl ether available, intravenous Sodium Pentothal(®), a most 'sophisticated and complex' drug, was used with devastating effects in many of those hypovolaemic, anaemic and septic patients. The hazards of spinal anaesthesia too were realised very quickly. These effects were compounded by the dearth of trained anaesthetists. This paper presents the significance of the anaesthesia tragedies at Pearl Harbor, and the discovery in the next few years of many other superior drugs that caused medical and other health professionals to realise that anaesthesia needed to be a specialist medical discipline in its own right. Specialist recognition, aided by the foundation of the National Health Service in the UK, the establishment of Faculties of Anaesthesia and appropriate training in pharmacology, physiology and other sciences soon followed. Modern anaesthesiology, as we understand it today, was born and a century or more of ether anaesthesia finally ceased.

  11. Beryllium in sediments of Nagoya harbor estuaries

    SciTech Connect

    Itoh, K.

    1986-06-01

    Beryllium occurs naturally in minerals and oils. Other than the natural sources, considerable quantity of beryllium has been discharged from its smelting industry. Soil pollutants caused by beryllium in the circumference of its smelting industry on the banks of Nagoya harbor estuaries have been reported. Several methods for the spectroscopic determination of beryllium can not eliminate the interference caused by fluoride ion which remains in the digestion solution when hydrofluoric acid is used to degradate the silicate lattice. Accordingly, the authors attempted to improve the pretreatment in order to eliminate the effect of fluoride ion, and to make the procedure simpler and faster with high precision. A simple and sensitive method is presented for the determination of beryllium in sediments by atomic absorption spectroscopy using methylisobutylketone extraction with acetylacetone. They have carried out an extensive investigation on the pollution of sea water and sediments of Nagoya harbor estuaries, which is located in one of the most active industrial areas in Japan.

  12. 33 CFR 117.603 - Manchester Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Manchester Harbor. 117.603... draw shall open on signal— (1) From Memorial Day through September 30 from 7 a.m. to 11 p.m.; (2) From April 1 to Memorial Day and from October 1 to November 1 from 9 a.m. to 1 p.m. and 2 p.m. to 6 p.m....

  13. Boson shells harboring charged black holes

    SciTech Connect

    Kleihaus, Burkhard; Kunz, Jutta; Laemmerzahl, Claus; List, Meike

    2010-11-15

    We consider boson shells in scalar electrodynamics coupled to Einstein gravity. The interior of the shells can be empty space, or harbor a black hole or a naked singularity. We analyze the properties of these types of solutions and determine their domains of existence. We investigate the energy conditions and present mass formulae for the composite black hole-boson shell systems. We demonstrate that these types of solutions violate black hole uniqueness.

  14. Light, Compact Pumper for Harbor Fires

    NASA Technical Reports Server (NTRS)

    Burns, R. A.

    1983-01-01

    Report describes development of new transportable water-pumping unit for fire-fighting. Compact, self-contained unit provides fire protection at coastal and inland ports and is lighter than standard firetruck pumper of same capacity. Used to fight fires in harbors, cities, forests, refineries, chemical plants, and offshore drilling platforms. Other possible applications include cleaning up oilspills, pumping out ships, and flood control pumping.

  15. Oil pollution in Shijiu Harbor studied

    SciTech Connect

    Miao Lutian

    1983-11-09

    This article describes an experimental model designed to forecast oil pollution in the newly constructed Shijiu Harbor, using a mixture of 30% used machine oil and 70% light diesel, in amounts of 200 kg per test. Plastic bags filled with the mixture are slit open and cast into the water generally along the axis of the major ocean current. Small boats are used to collect water specimens to trace the experimental pollutant. The density distribution and the horizontal diffusion coefficient are calculated to produce equations to study effects of the surface wind speed, the depth of the water, and the tidal waves on the oil drift. Each test is completed in about 2 hours. On the basis of statistical data of large Chinese harbors published by the ministry and related reports of foreign countries, the mean annual oil pollution load of Shijiu Harbor is computed in terms of the total estimated tonnage of cargo ships, tugboats, oil tankers, and fishing boats. The forecast model, the equations, and the computation processes are described in some detail.

  16. Old Harbor Scammon Bay Hydro Feasibility

    SciTech Connect

    Brent Petrie

    2007-06-27

    The grantee, Alaska Village Electric Cooperative (AVEC), is a non-profit member owned rural electric generation and distribution cooperative. The proposed Project is located near the community of Old Harbor, Alaska. Old Harbor is on the southeastern coast of Kodiak Island, approximately 70 miles southwest of the City of Kodiak and 320 miles southwest of Anchorage. In 1998 sufficient information had been developed to apply for a license to construct the project and the cost was estimated to be $2,445,000 for a 500 KW project on Lagoon Creek. Major features of the project included an eight-foot high diversion dam on Mountain Creek, a desander box, a 9,800-foot long penstock to the powerhouse on Lagoon Creek, and a 5,500-foot long access road. It was also anticipated that the project could provide an additional source of water to Old Harbor. The report details the history and lessons learned in designing and permiting the proposed hydroelectric facility.

  17. 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

  18. 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

  19. How Could SNARE Proteins Open a Fusion Pore?

    PubMed Central

    Fang, Qinghua

    2014-01-01

    The SNARE (Soluble NSF Attachment protein REceptor) complex, which in mammalian neurosecretory cells is composed of the proteins synaptobrevin 2 (also called VAMP2), syntaxin, and SNAP-25, plays a key role in vesicle fusion. In this review, we discuss the hypothesis that, in neurosecretory cells, fusion pore formation is directly accomplished by a conformational change in the SNARE complex via movement of the transmembrane domains. PMID:24985331

  20. 33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone. (a) Location. All waters of Lake Michigan within Burnham Park Harbor shoreward of a line across...

  1. 33 CFR 165.904 - Lake Michigan at Chicago Harbor & Burnham Park Harbor-Safety and Security Zone.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... & Burnham Park Harbor-Safety and Security Zone. 165.904 Section 165.904 Navigation and Navigable Waters... Guard District § 165.904 Lake Michigan at Chicago Harbor & Burnham Park Harbor—Safety and Security Zone. (a) Location. All waters of Lake Michigan within Burnham Park Harbor shoreward of a line across...

  2. Assembly of the nuclear pore: biochemically distinct steps revealed with NEM, GTP gamma S, and BAPTA

    PubMed Central

    1996-01-01

    A key event in nuclear formation is the assembly of functional nuclear pores. We have used a nuclear reconstitution system derived from Xenopus eggs to examine the process of nuclear pore assembly in vitro. With this system, we have identified three reagents which interfere with nuclear pore assembly, NEM, GTP gamma S, and the Ca++ chelator, BAPTA. These reagents have allowed us to determine that the assembly of a nuclear pore requires the prior assembly of a double nuclear membrane. Inhibition of nuclear vesicle fusion by pretreatment of the membrane vesicle fraction with NEM blocks pore complex assembly. In contrast, NEM treatment of already fused double nuclear membranes does not block pore assembly. This indicates that NEM inhibits a single step in pore assembly--the initial fusion of vesicles required to form a double nuclear membrane. The presence of GTP gamma S blocks pore assembly at two distinct steps, first by preventing fusion between nuclear vesicles, and second by blocking a step in pore assembly that occurs on already fused double nuclear membranes. Interestingly, when the Ca2+ chelator BAPTA is added to a nuclear assembly reaction, it only transiently blocks nuclear vesicle fusion, but completely blocks nuclear pore assembly. This results in the formation of a nucleus surrounded by a double nuclear membrane, but devoid of nuclear pores. To order the positions at which GTP gamma S and BAPTA interfere with pore assembly, a novel anchored nuclear assembly assay was developed. This assay revealed that the BAPTA-sensitive step in pore assembly occurs after the second GTP gamma S-sensitive step. Thus, through use of an in vitro nuclear reconstitution system, it has been possible to biochemically define and order multiple steps in nuclear pore assembly. PMID:8567730

  3. DESIGN INFORMATION ON FINE PORE AERATION SYSTEMS

    EPA Science Inventory

    Field studies were conducted over several years at municipal wastewater treatment plants employing line pore diffused aeration systems. These studies were designed to produce reliable information on the performance and operational requirements of fine pore devices under process ...

  4. Primary structure analysis of an integral membrane glycoprotein of the nuclear pore

    PubMed Central

    1989-01-01

    The complete primary structure of an integral membrane glycoprotein of the nuclear pore was deduced from the cDNA sequence. The cDNA encodes a polypeptide of 204,205 D containing a 25-residue-long signal sequence, two hydrophobic segments that could function as transmembrane segments, and 13 potential N-linked oligosaccharide addition sites. Endoglycosidase H reduces the molecular mass by approximately 9 kD suggesting that not all of these 13 sites are used. We discuss possible models for the topology of this protein in the pore membrane as well as a possible role in the formation of pores and pore complexes. PMID:2738089

  5. NMDA receptor structures reveal subunit arrangement and pore architecture

    PubMed Central

    Lee, Chia-Hsueh; Lü, Wei; Michel, Jennifer Carlisle; Goehring, April; Du, Juan; Song, Xianqiang; Gouaux, Eric

    2014-01-01

    Summary N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present x-ray crystal structures of the GluN1/GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino terminal and ligand binding domains. The transmembrane domains harbor a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ~2-fold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors. PMID:25008524

  6. Viruses Challenge Selectivity Barrier of Nuclear Pores

    PubMed Central

    Labokha, Aksana A.; Fassati, Ariberto

    2013-01-01

    Exchange between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs) embedded in the double membrane of the nuclear envelope. NPC permeability barrier restricts the entry of inert molecules larger than 5 nm in diameter but allows facilitated entry of selected cargos, whose size can reach up to 39 nm. The translocation of large molecules is facilitated by nuclear transport receptors (NTRs) that have affinity to proteins of NPC permeability barrier. Viruses that enter the nucleus replicate evolved strategies to overcome this barrier. In this review, we will discuss the functional principles of NPC barrier and nuclear transport machinery, as well as the various strategies viruses use to cross the selective barrier of NPCs. PMID:24084236

  7. Antimicrobial Peptides in Toroidal and Cylindrical Pores

    PubMed Central

    Mihajlovic, Maja

    2010-01-01

    Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize biological membranes. Their mechanism of action is still not well understood. Here we investigate the preference of alamethicin and melittin for pores of different shapes, using molecular dynamics (MD) simulations of the peptides in pre-formed toroidal and cylindrical pores. When an alamethicin hexamer is initially embedded in a cylindrical pore, at the end of the simulation the pore remains cylindrical or closes if glutamines in the N-termini are not located within the pore. On the other hand, when a melittin tetramer is embedded in toroidal pore or in a cylindrical pore, at the end of the simulation the pore is lined both with peptides and lipid headgroups, and, thus, can be classified as a toroidal pore. These observations agree with the prevailing views that alamethicin forms barrel-stave pores whereas melittin forms toroidal pores. Both alamethicin and melittin form amphiphilic helices in the presence of membranes, but their net charge differs; at pH ~7, the net charge of alamethicin is −1 whereas that of melittin is +5. This gives rise to stronger electrostatic interactions of melittin with membranes than those of alamethicin. The melittin tetramer interacts more strongly with lipids in the toroidal pore than in the cylindrical one, due to more favorable electrostatic interactions. PMID:20403332

  8. Impacts of simulated drought on pore water chemistry of peatlands.

    PubMed

    Juckers, Myra; Watmough, Shaun A

    2014-01-01

    Northern peatlands are increasingly threatened by climate change and industrial activities. This study examined the impact of simulated droughts on pore water chemistry at six peatlands in Sudbury, Ontario, that differ in copper (Cu), nickel (Ni) and cobalt (Co) contamination, including a site that had been previously limed. All sites responded similarly to simulated drought: pore water pH declined significantly following the 30 day drought and the decline was greater following the 60 day drought treatment. The decline in pore water pH was due to increasing sulphate concentrations, whereas nitrate increased more in the 60 day drought treatment. Decreases in pH were accompanied by large increases in Ni and Co that greatly exceeded provincial water quality guidelines. In contrast, dissolved organic carbon (DOC) concentrations decreased significantly following drought, along with concentrations of Cu and Al, which are strongly complexed by organic acids.

  9. Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

    PubMed Central

    Paaby, Annalise B; White, Amelia G; Riccardi, David D; Gunsalus, Kristin C; Piano, Fabio; Rockman, Matthew V

    2015-01-01

    Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture. DOI: http://dx.doi.org/10.7554/eLife.09178.001 PMID:26297805

  10. Assembling the puzzle: Oligomerization of α-pore forming proteins in membranes☆

    PubMed Central

    García-Sáez, Ana J.

    2016-01-01

    Pore forming proteins (PFPs) share the ability of creating pores that allow the passage of ions, proteins or other constituents through a wide variety of target membranes, ranging from bacteria to humans. They often cause cell death, as pore formation disrupts the membrane permeability barrier required for maintaining cell homeostasis. The organization into supramolecular complexes or oligomers that pierce the membrane is a common feature of PFPs. However, the molecular pathway of self-assembly and pore opening remains unclear. Here, we review the most recent discoveries in the mechanism of membrane oligomerization and pore formation of a subset of PFPs, the α-PFPs, whose pore-forming domains are formed by helical segments. Only now we are starting to grasp the molecular details of their function, mainly thanks to the introduction of single molecule microscopy and nanoscopy techniques. PMID:26375417

  11. Pore formation by Cry toxins.

    PubMed

    Soberón, Mario; Pardo, Liliana; Muñóz-Garay, Carlos; Sánchez, Jorge; Gómez, Isabel; Porta, Helena; Bravo, Alejandra

    2010-01-01

    Bacillus thuringiensis (Bt) bacteria produce insecticidal Cry and Cyt proteins used in the biological control of different insect pests. In this review, we will focus on the 3d-Cry toxins that represent the biggest group of Cry proteins and also on Cyt toxins. The 3d-Cry toxins are pore-forming toxins that induce cell death by forming ionic pores into the membrane of the midgut epithelial cells in their target insect. The initial steps in the mode of action include ingestion of the protoxin, activation by midgut proteases to produce the toxin fragment and the interaction with the primary cadherin receptor. The interaction of the monomeric CrylA toxin with the cadherin receptor promotes an extra proteolytic cleavage, where helix alpha-1 of domain I is eliminated and the toxin oligomerization is induced, forming a structure of 250 kDa. The oligomeric structure binds to a secondary receptor, aminopeptidase N or alkaline phosphatase. The secondary receptor drives the toxin into detergent resistant membrane microdomains formingpores that cause osmotic shock, burst of the midgut cells and insect death. Regarding to Cyt toxins, these proteins have a synergistic effect on the toxicity of some Cry toxins. Cyt proteins are also proteolytic activated in the midgut lumen of their target, they bind to some phospholipids present in the mosquito midgut cells. The proposed mechanism of synergism between Cry and Cyt toxins is that Cyt1Aa function as a receptor for Cry toxins. The Cyt1A inserts into midgut epithelium membrane and exposes protein regions that are recognized by Cry11Aa. It was demonstrated that this interaction facilitates the oligomerization of Cry11Aa and also its pore formation activity.

  12. The mitochondrial permeability transition pore and its role in cell death.

    PubMed Central

    Crompton, M

    1999-01-01

    This article reviews the involvement of the mitochondrial permeability transition pore in necrotic and apoptotic cell death. The pore is formed from a complex of the voltage-dependent anion channel (VDAC), the adenine nucleotide translocase and cyclophilin-D (CyP-D) at contact sites between the mitochondrial outer and inner membranes. In vitro, under pseudopathological conditions of oxidative stress, relatively high Ca2+ and low ATP, the complex flickers into an open-pore state allowing free diffusion of low-Mr solutes across the inner membrane. These conditions correspond to those that unfold during tissue ischaemia and reperfusion, suggesting that pore opening may be an important factor in the pathogenesis of necrotic cell death following ischaemia/reperfusion. Evidence that the pore does open during ischaemia/reperfusion is discussed. There are also strong indications that the VDAC-adenine nucleotide translocase-CyP-D complex can recruit a number of other proteins, including Bax, and that the complex is utilized in some capacity during apoptosis. The apoptotic pathway is amplified by the release of apoptogenic proteins from the mitochondrial intermembrane space, including cytochrome c, apoptosis-inducing factor and some procaspases. Current evidence that the pore complex is involved in outer-membrane rupture and release of these proteins during programmed cell death is reviewed, along with indications that transient pore opening may provoke 'accidental' apoptosis. PMID:10393078

  13. Noise Exposure Criteria for Harbor Porpoises.

    PubMed

    Tougaard, Jakob; Wright, Andrew J; Madsen, Peter Teglberg

    2016-01-01

    Despite a major research effort, no generally accepted exposure limits are available for harbor porpoises. Recent studies of the temporary threshold shift (TTS) in porpoises indicate that the sound exposure levels (SELs) required to induce low levels of TTS depend on stimulus frequency and roughly parallel the shape of the audiogram. A number of studies on behavioral avoidance reactions (negative phonotaxis) to pingers, seal scarers, and pile driving show a similar dependence on stimulus frequency. Both TTS and behavioral data suggest that weighting sound pressure levels with a filter function resembling the inverted audiogram would be appropriate.

  14. Novel biometrics based on nose pore recognition

    NASA Astrophysics Data System (ADS)

    Song, Shangling; Ohnuma, Kazuhiko; Liu, Zhi; Mei, Liangmo; Kawada, Akira; Monma, Tomoyuki

    2009-05-01

    We present a new member of the biometrics family-i.e., nose pores-which uses particularly interesting properties of nose pores as a basis for noninvasive biometric assessment. The pore distribution on the nose is stable and easily inspected. More important, nose pore distribution features are distinguishable between different persons. Thus, these features can be used for personal identification. However, little work has been done on nose pores as a biometric identifier. We have developed an end-to-end recognition system based on nose pore features. We also made use of a database of nose pore images obtained over a long period to examine the performance of nose pores as a biometric identifier. This research showed that the nose pore is a promising candidate for biometric identification and deserves further research. The experimental results based on the unique nose pores database demonstrated that nose pores can give an 88.07% correct recognition rate for biometric identification, which showed this biometric identifier's feasibility and effectiveness.

  15. Diffusive resistance of avian eggshell pores.

    PubMed

    Tøien, O; Paganelli, C V; Rahn, H; Johnson, R R

    1988-12-01

    Resistance to gas diffusion through the avian eggshell resides in the microscopic pores which penetrate the shell. We calculated the resistance to water vapor diffusion of individual pores in the shells of 23 species of avian eggs, based on measurements of pore dimensions taken from drawings of 321 pore casts published by Tyler (1962, 1964, 1965) and Tyler and Simkiss (1959). Diffusive resistances were calculated from Fick's first law, using a 100-segment model of each pore. In addition, we added 2 series resistances, calculated from Stefan's law, to account for boundary layer resistances at the inner and outer pore apertures. Convective resistances for the same 100-segment model were computed from Poiseuille's law. A special, symmetrically branching model is presented for the diffusive resistance of the branched pores of ostrich eggshells, based on the drawings of Tyler and Simkiss (1959). The total aperture resistance was less than 6.2% of total pore resistance, while the outside aperture effect was on average only 1.5%. The calculated average pore conductance for all species was 5.4 micrograms (day Torr)-1, about three times higher than the average value of 1.6 micrograms (day Torr)-1 obtained by dividing measured shell conductance by the number of pores (Ar and Rahn, 1985). A possible explanation for this discrepancy is advanced. However, it is to be noted that in spite of the discrepancy, both calculated and functional values of pore conductance appear to be independent of egg mass.

  16. Glycosylation of the nuclear pore

    PubMed Central

    Li, Bin; Kohler, Jennifer J.

    2014-01-01

    The O-linked β-N-acetylglucosamine (O-GlcNAc) post-translational modification was first discovered thirty years ago and is highly concentrated in the nuclear pore. In the years since the discovery of this single sugar modification, substantial progress has been made in understanding the biochemistry of O-GlcNAc and its regulation. Nonetheless, O-GlcNAc modification of proteins continues to be overlooked, due in large part to the lack of reliable methods available for its detection. Recently, a new crop of immunological and chemical detection reagents has changed the research landscape. Using these tools, approximately 1000 O-GlcNAc-modified proteins have been identified. While other forms of glycosylation are typically associated with extracellular proteins, O-GlcNAc is abundant on nuclear and cytoplasmic proteins. In particular, phenylalanine-glycine (FG) nucleoporins (NUPs) are heavily O-GlcNAc-modified. Recent experiments are beginning to provide insight into the functional implications of O-GlcNAc modification on certain proteins, but its role in the nuclear pore has remained enigmatic. However, tantalizing new results suggest that O-GlcNAc may play roles in regulating nucleocytoplasmic transport. PMID:24423194

  17. 77 FR 50916 - Safety Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-23

    ... INFORMATION: Table of Acronyms DHS Department of Homeland Security FR Federal Register NPRM Notice of Proposed...) Zone for the drilling, blasting, and dredging operation on the navigable waters of Boston Inner Harbor... navigable waters during the drilling, blasting and dredging operations in support of the U.S. Army Corps...

  18. 77 FR 39411 - Safety Zone; Village of Sackets Harbor, Lake Ontario, Sackets Harbor, NY

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-03

    ... Sector Buffalo; telephone 716- 843-9343, email SectorBuffaloMarineSafety@uscg.mil . If you have questions... be held on Lake Ontario in Sackets Harbor, NY. The Captain of the Port Buffalo has determined that... Buffalo has determined that this temporary safety zone is necessary to ensure the safety of spectators...

  19. Ecological simulation model of Los Angeles Harbor

    NASA Astrophysics Data System (ADS)

    Kremer, James N.; Kremer, Patricia

    1983-05-01

    A quasi-steady state numerical ecosystem model was designed to help evaluate the potential impact of various scenarios of effluent treatment and of a landfill on the distribution of phytoplankton and inorganic nutrients in Los Angeles and Long Beach harbors Formulations included (a) tidal circulation, (b) phytoplankton growth and oxygen production as a function of temperature, light, and nutrients, (c) grazing by zooplankton, (d) respiration and nutrient regeneration by the benthos, (e) biochemical oxidation of organics, and (f) nitrification Phytoplankton nitrogen, ammonium, nitrate, and oxygen were the state variables, which were simulated with diel and spatial variability for a range of seasonal conditions. Physical circulation was indicated to be a primary factor governing the distribution of state variables, and the landfill resulted in significant alterations. Simulated phytoplankton stocks approximated the upper range of reported concentrations, indicating a satisfactory prediction of bloom conditions. The model indicated that while light may usually regulate maximum phytoplankton levels, under bloom conditions nutrient limitation may also be important Most of the outer Los Angeles Harbor was affected by the effluent, as shown by comparison to the case with zero input Simulations for secondary versus primary treatment converged a short distance from the outfall in response to high BOD oxidation rates. In general, total phytoplankton crop was not greatly affected by the change from primary to secondary treatment, and predation on phytoplankton was small

  20. A thermodynamic approach to Alamethicin pore formation

    PubMed Central

    Rahaman, Asif; Lazaridis, Themis

    2013-01-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11 Å radius are investigated using molecular dynamics simulations in an implicit membrane model that includes the free energy cost of acyl chain hydrophobic area exposure. Stable, low energy pores are obtained for certain combinations of radius and oligomeric number. The trimer and the tetramer formed 6 Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8 Å pore and the octamer in an 11 Å pore give the lowest effective energy per monomer. However, all oligomers beyond the pentamer have comparable energies, consistent with the observation of multiple conductance levels. The results are consistent with the widely accepted “barrel-stave” model. The N terminal portion of the molecule exhibits smaller tilt with respect to the membrane normal than the C terminal portion, resulting in a pore shape that is a hybrid between a funnel and an hourglass. Transmembrane voltage has little effect on the structure of the oligomers but enhances or decreases their stability depending on its orientation. Antiparallel bundles are lower in energy than the commonly accepted parallel ones and could be present under certain experimental conditions. Dry aggregates (without an aqueous pore) have lower average effective energy than the corresponding aggregates in a pore, suggesting that alamethicin pores may be excited states that are stabilized in part by voltage and in part by the ion flow itself. PMID:24071593

  1. Passive permeability and effective pore size of HeLa cell nuclear membranes.

    PubMed

    Samudram, Arunkarthick; Mangalassery, Bijeesh M; Kowshik, Meenal; Patincharath, Nandakumar; Varier, Geetha K

    2016-09-01

    Nuclear pore complexes in the nuclear membrane act as the sole gateway of transport of molecules from the cytoplasm to the nucleus and vice versa. Studies on biomolecular transport through nuclear membranes provide vital data on the nuclear pore complexes. In this work, we use fluorescein isothiocyanate-labeled dextran molecules as a model system and study the passive nuclear import of biomolecules through nuclear pore complexes in digitonin-permeabilized HeLa cells. Experiments are carried out under transient conditions in the time lapse imaging scheme using an in-house constructed confocal laser scanning microscope. Transport rates of dextran molecules having molecular weights of 4-70 kDa corresponding to Stokes radius of 1.4-6 nm are determined. Analyzing the permeability of the nuclear membrane for different sizes the effective pore radius of HeLa cell nuclear membrane is determined to be 5.3 nm, much larger than the value reported earlier using proteins as probe molecules. The range of values reported for the nuclear pore radius suggest that they may not be rigid structures and it is quite probable that the effective pore size of nuclear pore complexes is critically dependent on the probe molecules and on the environmental factors.

  2. Permeability characteristics of cell-membrane pores induced by ostreolysin A/pleurotolysin B, binary pore-forming proteins from the oyster mushroom.

    PubMed

    Schlumberger, Sébastien; Kristan, Katarina Črnigoj; Ota, Katja; Frangež, Robert; Molgό, Jordi; Sepčić, Kristina; Benoit, Evelyne; Maček, Peter

    2014-01-01

    Proteins from the oyster mushroom, 15 kDa ostreolysin A (OlyA), and 59 kDa pleurotolysin B (PlyB) with a membrane attack complex/perforin (MACPF) domain, damage cell membranes as a binary cytolytic pore-forming complex. Measurements of single-channel conductance and transmembrane macroscopic current reveal that OlyA/PlyB form non-selective ion-conducting pores with broad, skewed conductance distributions in N18 neuroblastoma and CHO-K1 cell membranes. Polyethylene-glycol 8000 (hydrodynamic radius of 3.78 nm) provides almost complete osmotic protection against haemolysis, which strongly suggests a colloid-osmotic type of erythrocyte lysis. Our data indicate that OlyA/PlyB form transmembrane pores of varied sizes, as other pore-forming proteins with a MACPF domain. PMID:24211835

  3. Permeability characteristics of cell-membrane pores induced by ostreolysin A/pleurotolysin B, binary pore-forming proteins from the oyster mushroom.

    PubMed

    Schlumberger, Sébastien; Kristan, Katarina Črnigoj; Ota, Katja; Frangež, Robert; Molgό, Jordi; Sepčić, Kristina; Benoit, Evelyne; Maček, Peter

    2014-01-01

    Proteins from the oyster mushroom, 15 kDa ostreolysin A (OlyA), and 59 kDa pleurotolysin B (PlyB) with a membrane attack complex/perforin (MACPF) domain, damage cell membranes as a binary cytolytic pore-forming complex. Measurements of single-channel conductance and transmembrane macroscopic current reveal that OlyA/PlyB form non-selective ion-conducting pores with broad, skewed conductance distributions in N18 neuroblastoma and CHO-K1 cell membranes. Polyethylene-glycol 8000 (hydrodynamic radius of 3.78 nm) provides almost complete osmotic protection against haemolysis, which strongly suggests a colloid-osmotic type of erythrocyte lysis. Our data indicate that OlyA/PlyB form transmembrane pores of varied sizes, as other pore-forming proteins with a MACPF domain.

  4. Pore-water chemistry explains zinc phytotoxicity in soil.

    PubMed

    Kader, Mohammed; Lamb, Dane T; Correll, Ray; Megharaj, Mallavarapu; Naidu, Ravi

    2015-12-01

    Zinc (Zn) is a widespread soil contaminant arising from a numerous anthropogenic sources. However, adequately predicting toxicity of Zn to ecological receptors remains difficult due to the complexity of soil characteristics. In this study, we examined solid-solution partitioning using pore-water data and toxicity of Zn to cucumber (Cucumis sativus L.) in spiked soils. Pore-water effective concentration (ECx, x=10%, 20% and 50% reduction) values were negatively related to pH, indicating lower Zn pore water concentration were needed to cause phytotoxicity at high pH soils. Total dissolved zinc (Znpw) and free zinc (Zn(2+)) in soil-pore water successfully described 78% and 80.3% of the variation in relative growth (%) in the full dataset. When the complete data set was used (10 soils), the estimated EC50pw was 450 and 79.2 µM for Znpw and Zn(2+), respectively. Total added Zn, soil pore water pH (pHpw) and dissolve organic carbon (DOC) were the best predictors of Znpw and Zn(2+) in pore-water. The EC10 (total loading) values ranged from 179 to 5214 mg/kg, depending on soil type. Only pH measurements in soil were related to ECx total Zn data. The strongest relationship to ECx overall was pHca, although pHw and pHpw were in general related to Zn ECx. Similarly, when a solution-only model was used to predict Zn in shoot, DOC was negatively related to Zn in shoot, indicating a reduction in uptake/ translocation of Zn from solution with increasing DOC.

  5. Pearl Harbor: strategy and principles of war. Student report

    SciTech Connect

    Isaman, R.J.

    1986-04-01

    Analysis of the Japanese attack on Pearl Harbor is presented to be used in developing programs of instruction for the Air Command and Staff College at the Air University. Chapter One provides a brief biographical sketch of Japanese Fleet Admiral Isoroku Yamamoto. Chapter Two consists of the prelude to battle, a battle description, and aftermath of the attack on Pearl Harbor. Chapter Three describes the Japanese strategy process which lead to the attack on Pearl Harbor while Chapter Four presents an analysis of the Japanese application of the principles of war at Pearl Harbor. The paper concludes with a guided discussion format for instructional use.

  6. Open-pore polyurethane product

    DOEpatents

    Jefferson, R.T.; Salyer, I.O.

    1974-02-17

    The method is described of producing an open-pore polyurethane foam having a porosity of at least 50% and a density of 0.1 to 0.5 g per cu cm, and which consists of coherent spherical particles of less than 10 mu diam separated by interconnected interstices. It is useful as a filter and oil absorbent. The product is admirably adapted to scavenging of crude oil from the surface of seawater by preferential wicking. The oil-soaked product may then be compressed to recover the oil or burned for disposal. The crosslinked polyurethane structures are remarkably solvent and heat-resistance as compared with known thermoplastic structures. Because of their relative inertness, they are useful filters for gasoline and other hydrocarbon compounds. (7 claims)

  7. Fine structures at pore boundary

    NASA Astrophysics Data System (ADS)

    Bharti, L.; Quintero Noda, C.; Joshi, C.; Rakesh, S.; Pandya, A.

    2016-10-01

    We present high resolution observations of fine structures at pore boundaries. The inner part of granules towards umbra show dark striations which evolve into a filamentary structure with dark core and `Y' shape at the head of the filaments. These filaments migrate into the umbra similar to penumbral filaments. These filaments show higher temperature, lower magnetic field strength and more inclined field compared to the background umbra. The optical depth stratification of physical quantities suggests their similarity with penumbral filaments. However, line-of-sight velocity pattern is different from penumbral filaments where they show downflows in the deeper layers of the atmosphere while the higher layers show upflows. These observations show filamentation in a simple magnetic configuration.

  8. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

    Robertson, Alex W; Lee, Gun-Do; He, Kuang; Gong, Chuncheng; Chen, Qu; Yoon, Euijoon; Kirkland, Angus I; Warner, Jamie H

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert.

  9. Analysis of solute diffusion across the C5b-9 membrane lesion of complement: evidence that individual C5b-9 complexes do not function as discrete, uniform pores.

    PubMed

    Sims, P J; Lauf, P K

    1980-12-01

    We have investigated the diffusion of radiolabeled nonelectrolytes across the membranes of resealed erythrocyte ghosts that had been treated with the terminal complement components C5b-9 and incubated under nonlytic steady state conditions. For all solutes tested, we note that diffusion across the C5b-9 lesion is retarded to rates more than 2 orders of magnitude slower than can be anticipated for a transmembrane diffusional channel of the dimensions suggested by the ultrastructure of the C5b-9 membrane lesion. Furthermore, direct measurement of the relative selectivity of the C5b-9 membrane lesions to permeation by solutes of differing molecular radii suggests that individual membrane lesions are not of uniform functional size. Data are presented that suggest that the functional heterogeneity of the membrane lesion is due to the aggregation of individual membrane bound C5b-9 complexes into larger functional units and not due to variable stoichiometry of C9 within the individual C5b-9 complex.

  10. The mechanism of a nuclear pore assembly: a molecular biophysics view.

    PubMed

    Kuvichkin, Vasily V

    2011-06-01

    The basic problem of nuclear pore assembly is the big perinuclear space that must be overcome for nuclear membrane fusion and pore creation. Our investigations of ternary complexes: DNA-PC liposomes-Mg²⁺, and modern conceptions of nuclear pore structure allowed us to introduce a new mechanism of nuclear pore assembly. DNA-induced fusion of liposomes (membrane vesicles) with a single-lipid bilayer or two closely located nuclear membranes is considered. After such fusion on the lipid bilayer surface, traces of a complex of ssDNA with lipids were revealed. At fusion of two identical small liposomes (membrane vesicles) < 100 nm in diameter, a "big" liposome (vesicle) with ssDNA on the vesicle equator is formed. ssDNA occurrence on liposome surface gives a biphasic character to the fusion kinetics. The "big" membrane vesicle surrounded by ssDNA is the base of nuclear pore assembly. Its contact with the nuclear envelope leads to fast fusion of half of the vesicles with one nuclear membrane; then ensues a fusion delay when ssDNA reaches the membrane. The next step is to turn inside out the second vesicle half and its fusion to other nuclear membrane. A hole is formed between the two membranes, and nucleoporins begin pore complex assembly around the ssDNA. The surface tension of vesicles and nuclear membranes along with the kinetic energy of a liquid inside a vesicle play the main roles in this process. Special cases of nuclear pore formation are considered: pore formation on both nuclear envelope sides, the difference of pores formed in various cell-cycle phases and linear nuclear pore clusters.

  11. Modeling the interaction of ultrasound with pores

    NASA Technical Reports Server (NTRS)

    Lu, Yichi; Wadley, Haydn N. G.; Parthasarathi, Sanjai

    1991-01-01

    Factors that affect ultrasonic velocity sensing of density during consolidation of metal powders are examined. A comparison is made between experimental results obtained during the final stage of densification and the predictions of models that assume either a spherical or a spheroidal pore shape. It is found that for measurements made at low frequencies during the final stage of densification, relative density (pore fraction) and pore shape are the two most important factors determining the ultrasonic velocity, the effect of pore size is negligible.

  12. 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

  13. Effects of pore-size and shape distributions on diffusion pore imaging by nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Kuder, Tristan Anselm; Laun, Frederik Bernd

    2015-08-01

    In medical imaging and porous media research, NMR diffusion measurements are extensively used to investigate the structure of diffusion restrictions such as cell membranes. Recently, several methods have been proposed to unambiguously determine the shape of arbitrary closed pores or cells filled with an NMR-visible medium by diffusion experiments. The first approach uses a combination of a long and a short diffusion-weighting gradient pulse, while the other techniques employ short gradient pulses only. While the eventual aim of these methods is to determine pore-size and shape distributions, the focus has been so far on identical pores. Thus, the aim of this work is to investigate the ability of these different methods to resolve pore-size and orientation distributions. Simulations were performed comparing the various pore imaging techniques employing different distributions of pore size and orientation and varying timing parameters. The long-narrow gradient profile is most advantageous to investigate pore distributions, because average pore images can be directly obtained. The short-gradient methods suppress larger pores or induce a considerable blurring. Moreover, pore-shape-specific artifacts occur; for example, the central part of a distribution of cylinders may be largely underestimated. Depending on the actual pore distribution, short-gradient methods may nonetheless yield good approximations of the average pore shape. Furthermore, the application of short-gradient methods can be advantageous to differentiate whether pore-size distributions or intensity distributions, e.g., due to surface relaxation, are predominant.

  14. Pore Characteristics of Chitosan Scaffolds Studied by Electrochemical Impedance Spectroscopy

    PubMed Central

    Tully-Dartez, Stephanie; Cardenas, Henry E.

    2010-01-01

    In this study, a novel approach, electrochemical impedance spectroscopy (EIS), was used to examine the pore characteristics of chitosan scaffolds under aqueous conditions. The EIS was run with a constant current of 0.1 mA with the frequency sweep of 106 to 10−4 Hz. The resulting complex impedance measurement was then used to calculate porosity, which was determined to be 71%. Scanning electron microscopy (SEM) and mercury intrusion porosimetry (MIP), two commonly used methods for scaffold characterization, were used to independently evaluate the pore characteristics and compare with that of EIS. The SEM and MIP were performed and analyzed under standard conditions. The pore diameter values found by SEM and MIP are 107 μm and 82 μm, respectively, indicating that both the image-based (SEM) and pressure-based (MIP) analyses provide similar results. The porosity of 73% calculated by MIP is comparable to that of EIS. From these results, it can be suggested that EIS, a relatively nondestructive test, is able to obtain comparable data on pore characteristics, as compared to SEM and MIP. The advantage of the EIS as an nondestructive test is that it can be performed under physiologically relevant conditions, whereas SEM and MIP require dry samples and vacuum conditions for measurement. These benefits make EIS a viable option for the characterization and long-term observation of tissue-engineered scaffolds. PMID:19580421

  15. Sediment toxicity in Boston Harbor: Magnitude, extent, and relationships with chemical toxicants. Technical memo

    SciTech Connect

    Long, E.R.; Sloane, G.M.; Carr, R.S.; Scott, K.J.; Thursby, G.B.

    1996-06-01

    A survey of the toxicity of sediments throughout Boston Harbor and vicinity was conducted by NOAA`s National Status and Trends (NS&T) Program. The objectives of the survey were to determine the magnitude and spatial extent of toxicity and the relationship between measures of toxicity and the concentrations of chemical toxicants in the sediments. Multiple toxicity tests were performed including: an amphipod survival test performed with whole sediments, a microbial bioluminescence test performed with organic solvent extracts of the sediments, and sea urchin fertilization and embryological development tests performed with the pore waters extracted from the sediments. Chemical analyses were performed on selected samples for trace metals, polynuclear aromatic hydrcarbons, chlorinated pesticides, PCBs, and butyltins.

  16. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...

  17. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...

  18. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...

  19. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...

  20. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...

  1. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...

  2. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...

  3. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...

  4. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...

  5. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...

  6. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...

  7. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...

  8. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...

  9. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...

  10. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...

  11. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...

  12. 46 CFR 7.30 - New York Harbor, NY.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false New York Harbor, NY. 7.30 Section 7.30 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.30 New York Harbor, NY. A line drawn from East Rockaway Inlet Breakwater Light to Ambrose...

  13. 33 CFR 80.165 - New York Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false New York Harbor. 80.165 Section 80.165 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Atlantic Coast § 80.165 New York Harbor. A line drawn from...

  14. 33 CFR 117.802 - New Rochelle Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false New Rochelle Harbor. 117.802... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New York § 117.802 New Rochelle Harbor. (a) The draw of the Glen Island Bridge, mile 0.8, at New Rochelle, New York, shall open on signal, except...

  15. 33 CFR 110.147 - New London Harbor, Conn.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false New London Harbor, Conn. 110.147... ANCHORAGE REGULATIONS Anchorage Grounds § 110.147 New London Harbor, Conn. (a) The anchorage grounds—(1... Thames River southward of New London, bounded by lines connecting points which are the following...

  16. 46 CFR 7.30 - New York Harbor, NY.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false New York Harbor, NY. 7.30 Section 7.30 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.30 New York Harbor, NY. A line drawn from East Rockaway Inlet Breakwater Light to Ambrose...

  17. 33 CFR 80.1480 - Hilo Harbor, Hawaii, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Hilo Harbor, Hawaii, HI. 80.1480 Section 80.1480 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1480 Hilo Harbor, Hawaii, HI. A line...

  18. 33 CFR 80.1470 - Kawaihae Harbor, Hawaii, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kawaihae Harbor, Hawaii, HI. 80.1470 Section 80.1470 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1470 Kawaihae Harbor, Hawaii,...

  19. 33 CFR 80.1460 - Kahului Harbor, Maui, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Kahului Harbor, Maui, HI. 80.1460 Section 80.1460 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1460 Kahului Harbor, Maui, HI. A line...

  20. 33 CFR 80.1450 - Nawiliwili Harbor, Kauai, HI.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nawiliwili Harbor, Kauai, HI. 80.1450 Section 80.1450 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Islands § 80.1450 Nawiliwili Harbor, Kauai,...

  1. 18 CFR 1304.404 - Commercial marina harbor limits.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Commercial marina... ALTERATIONS Miscellaneous § 1304.404 Commercial marina harbor limits. The landward limits of commercial marina... of harbors at commercial marinas will be designated by TVA on the basis of the size and extent...

  2. 18 CFR 1304.404 - Commercial marina harbor limits.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Commercial marina... ALTERATIONS Miscellaneous § 1304.404 Commercial marina harbor limits. The landward limits of commercial marina... of harbors at commercial marinas will be designated by TVA on the basis of the size and extent...

  3. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., 1940, along the West side of the harbor, said harbor line runs parallel to the overall alignment of... the Grant Park bulkhead's overall alignment between its North and South ends, said bulkhead runs... to the overall alignment of the Grant Park bulkhead between its North and South ends,...

  4. 33 CFR 117.722 - Great Egg Harbor Bay.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Great Egg Harbor Bay. 117.722 Section 117.722 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.722 Great Egg Harbor Bay. The draw...

  5. 76 FR 26311 - Agency Information Collection Activities: Harbor Maintenance Fee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-06

    ... SECURITY U.S. Customs and Border Protection Agency Information Collection Activities: Harbor Maintenance... concerning the Harbor Maintenance Fee (CBP Forms 349 and 350). This request for comment is being made... keepers from the collection of information (a total capital/startup costs and operations and...

  6. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Buffalo Harbor, N.Y. 110.208 Section 110.208 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.208 Buffalo Harbor, N.Y. (a) The anchorage...

  7. 33 CFR 110.87 - Henderson Harbor, N.Y.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Henderson Harbor, N.Y. 110.87 Section 110.87 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.87 Henderson Harbor, N.Y. (a) Area A. The area in...

  8. 77 FR 27625 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-11

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY..., Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI at (414) 747-7188, email Jon.K.Grob....935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, at the following time for the following events:...

  9. 75 FR 49848 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-16

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY..., WI at 414-747-7154, e-mail Adam.D.Kraft@uscg.mil . SUPPLEMENTARY INFORMATION: The Coast Guard will enforce the safety zone listed in 33 CFR 165.935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, for...

  10. 77 FR 27625 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-11

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY..., call or email CWO Jon Grob, Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI at... safety zone listed in 33 CFR 165.935, Safety Zone, Milwaukee Harbor, Milwaukee, WI, for the...

  11. 75 FR 22234 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-28

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY... BM1 Adam Kraft, Prevention Department, Coast Guard Sector Lake Michigan, Milwaukee, WI at 414-747-7154... zone listed in 33 CFR 165.935, Safety Zones, Milwaukee Harbor, Milwaukee, WI, for the following...

  12. 78 FR 37456 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-21

    ... SECURITY Coast Guard 33 CFR Part 165 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY: Coast Guard, DHS... Sector Lake Michigan, Milwaukee, WI at (414) 747-7148, email joseph.p.mccollum@uscg.mil . SUPPLEMENTARY... Harbor, Milwaukee, WI, at the following times for the following events: (1) Polish Fest fireworks...

  13. 75 FR 44141 - Safety Zone; Milwaukee Harbor, Milwaukee, WI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-28

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Milwaukee Harbor, Milwaukee, WI AGENCY... Sector Lake Michigan, Milwaukee, WI at 414-747-7154, e-mail Adam.D.Kraft@uscg.mil . SUPPLEMENTARY... Harbor, Milwaukee, WI, for the following events: (1) Arab World Festival fireworks display on August...

  14. 33 CFR 110.238 - Apra Harbor, Guam.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Apra Harbor, Guam. 110.238 Section 110.238 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.238 Apra Harbor, Guam. (a) The anchorage grounds (Datum: WGS 84). (1) General Anchorage. The...

  15. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., White Lake, Pentwater, Ludington, Manistee, Portage Lake (Manistee County), Frankfort, Charlevoix, and... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Harbors on Lake Michigan. 162.120...) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  16. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., White Lake, Pentwater, Ludington, Manistee, Portage Lake (Manistee County), Frankfort, Charlevois, and... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Harbors on Lake Michigan. 162.120...) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  17. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., White Lake, Pentwater, Ludington, Manistee, Portage Lake (Manistee County), Frankfort, Charlevoix, and... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Harbors on Lake Michigan. 162.120...) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  18. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., White Lake, Pentwater, Ludington, Manistee, Portage Lake (Manistee County), Frankfort, Charlevoix, and... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Harbors on Lake Michigan. 162.120...) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  19. 33 CFR 165.1309 - Eagle Harbor, Bainbridge Island, WA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 2 2013-07-01 2013-07-01 false Eagle Harbor, Bainbridge Island, WA. 165.1309 Section 165.1309 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Eagle Harbor, Bainbridge Island, WA. (a) Regulated area. A regulated navigation area is established...

  20. 33 CFR 165.1309 - Eagle Harbor, Bainbridge Island, WA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 2 2012-07-01 2012-07-01 false Eagle Harbor, Bainbridge Island, WA. 165.1309 Section 165.1309 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Eagle Harbor, Bainbridge Island, WA. (a) Regulated area. A regulated navigation area is established...

  1. 33 CFR 165.1309 - Eagle Harbor, Bainbridge Island, WA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Eagle Harbor, Bainbridge Island, WA. 165.1309 Section 165.1309 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Eagle Harbor, Bainbridge Island, WA. (a) Regulated area. A regulated navigation area is established...

  2. 33 CFR 165.1309 - Eagle Harbor, Bainbridge Island, WA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Eagle Harbor, Bainbridge Island, WA. 165.1309 Section 165.1309 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Eagle Harbor, Bainbridge Island, WA. (a) Regulated area. A regulated navigation area is established...

  3. 78 FR 52783 - Boston Harbor Islands Advisory Council Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-26

    ... National Park Service Boston Harbor Islands Advisory Council Meeting AGENCY: National Park Service... Islands Advisory Council. The agenda includes discussion of 2016 celebration planning for the 300th Anniversary of Boston Light, 20th Anniversary of Boston Harbor Islands National Recreation Area (NRA),...

  4. 33 CFR 165.1309 - Eagle Harbor, Bainbridge Island, WA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Eagle Harbor, Bainbridge Island, WA. 165.1309 Section 165.1309 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... Eagle Harbor, Bainbridge Island, WA. (a) Regulated area. A regulated navigation area is established...

  5. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) Floats for marking anchors in place will be allowed; stakes or mooring piles are prohibited. 33 CFR Ch. I... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Ponce Harbor, P.R. 110.255... ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  6. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) Floats for marking anchors in place will be allowed; stakes or mooring piles are prohibited. 33 CFR Ch. I... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Ponce Harbor, P.R. 110.255... ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  7. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) Floats for marking anchors in place will be allowed; stakes or mooring piles are prohibited. 33 CFR Ch. I... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Ponce Harbor, P.R. 110.255... ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  8. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) Floats for marking anchors in place will be allowed; stakes or mooring piles are prohibited. 33 CFR Ch. I... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Ponce Harbor, P.R. 110.255... ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  9. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) Floats for marking anchors in place will be allowed; stakes or mooring piles are prohibited. 33 CFR Ch. I... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Ponce Harbor, P.R. 110.255... ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  10. 33 CFR 80.165 - New York Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false New York Harbor. 80.165 Section 80.165 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Atlantic Coast § 80.165 New York Harbor. A line drawn from...

  11. 33 CFR 110.26 - Marblehead Harbor, Marblehead, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...

  12. 33 CFR 110.142 - Nantucket Harbor, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...

  13. 33 CFR 110.38 - Edgartown Harbor, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...

  14. 33 CFR 110.38 - Edgartown Harbor, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...

  15. 33 CFR 110.38 - Edgartown Harbor, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...

  16. 33 CFR 110.26 - Marblehead Harbor, Marblehead, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...

  17. 33 CFR 110.142 - Nantucket Harbor, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...

  18. 33 CFR 110.26 - Marblehead Harbor, Marblehead, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...

  19. 33 CFR 110.29 - Boston Inner Harbor, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...

  20. 33 CFR 110.142 - Nantucket Harbor, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...

  1. 33 CFR 110.37 - Sesuit Harbor, Dennis, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...

  2. 33 CFR 110.37 - Sesuit Harbor, Dennis, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...

  3. 33 CFR 110.29 - Boston Inner Harbor, Mass.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...

  4. 33 CFR 110.29 - Boston Inner Harbor, Mass.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...

  5. 33 CFR 110.37 - Sesuit Harbor, Dennis, Mass.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...

  6. 33 CFR 117.722 - Great Egg Harbor Bay.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Great Egg Harbor Bay. 117.722 Section 117.722 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.722 Great Egg Harbor Bay. The draw...

  7. 33 CFR 117.722 - Great Egg Harbor Bay.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Great Egg Harbor Bay. 117.722 Section 117.722 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.722 Great Egg Harbor Bay. The draw...

  8. 33 CFR 117.722 - Great Egg Harbor Bay.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Great Egg Harbor Bay. 117.722 Section 117.722 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.722 Great Egg Harbor Bay. The draw...

  9. 33 CFR 117.722 - Great Egg Harbor Bay.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Great Egg Harbor Bay. 117.722 Section 117.722 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements New Jersey § 117.722 Great Egg Harbor Bay. The draw...

  10. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., 1940, along the West side of the harbor, said harbor line runs parallel to the overall alignment of... the Grant Park bulkhead's overall alignment between its North and South ends, said bulkhead runs... to the overall alignment of the Grant Park bulkhead between its North and South ends,...

  11. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., 1940, along the West side of the harbor, said harbor line runs parallel to the overall alignment of... the Grant Park bulkhead's overall alignment between its North and South ends, said bulkhead runs... to the overall alignment of the Grant Park bulkhead between its North and South ends,...

  12. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., 1940, along the West side of the harbor, said harbor line runs parallel to the overall alignment of... the Grant Park bulkhead's overall alignment between its North and South ends, said bulkhead runs... to the overall alignment of the Grant Park bulkhead between its North and South ends,...

  13. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., 1940, along the West side of the harbor, said harbor line runs parallel to the overall alignment of... the Grant Park bulkhead's overall alignment between its North and South ends, said bulkhead runs... to the overall alignment of the Grant Park bulkhead between its North and South ends,...

  14. 78 FR 63381 - Safety Zones; Hawaiian Island Commercial Harbors, HI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-24

    ...: Table of Acronyms DHS Department of Homeland Security FR Federal Register A. Regulatory History and... harbors in the event a tsunami warning is issued for the main Hawaiian Islands. DATES: This rule is... order to evacuate any or all of Hawaii's nine commercial harbors in response to a tsunami warning....

  15. 78 FR 28619 - Boston Harbor Islands Advisory Council Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-15

    ...: Bruce Jacobson, DFO, Boston Harbor Islands National Recreation Area, 15 State Street, Suite 1100, Boston, MA 02109; telephone (617) 223-8669; email Bruce_Jacobson@nps.gov . SUPPLEMENTARY INFORMATION: This... Official (DFO) for the Boston Harbor Islands Advisory Council, Bruce Jacobson, by mail at State...

  16. 78 FR 9730 - Boston Harbor Islands Advisory Council Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-11

    ... Jacobson, DFO, Boston Harbor Islands National Recreation Area, 408 Atlantic Avenue, Suite 228, Boston, MA 02110; telephone (617) 223-8669; email Bruce_Jacobson@nps.gov . SUPPLEMENTARY INFORMATION: This meeting... Official for the Boston Harbor Islands Advisory Council, Bruce Jacobson, by mail at 408 Atlantic...

  17. 6. FOUNDATION PLAN OF HARBOR MASTER'S BUILDING ON PIER #4, ...

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

    6. FOUNDATION PLAN OF HARBOR MASTER'S BUILDING ON PIER #4, DWG. NO. 185, 3/8" = 1'0", MADE BY J.L.R. - Baltimore Inner Harbor, Pier 4, South side of Pratt Street between Frederick Street & Market Place, Baltimore, Independent City, MD

  18. 33 CFR 110.111 - Marina del Rey Harbor, Calif.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Marina del Rey Harbor, Calif. 110.111 Section 110.111 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.111 Marina del Rey Harbor, Calif. An area...

  19. 18 CFR 1304.404 - Commercial marina harbor limits.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 2 2014-04-01 2014-04-01 false Commercial marina... ALTERATIONS Miscellaneous § 1304.404 Commercial marina harbor limits. The landward limits of commercial marina... of harbors at commercial marinas will be designated by TVA on the basis of the size and extent...

  20. 18 CFR 1304.404 - Commercial marina harbor limits.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Commercial marina... ALTERATIONS Miscellaneous § 1304.404 Commercial marina harbor limits. The landward limits of commercial marina... of harbors at commercial marinas will be designated by TVA on the basis of the size and extent...

  1. 26 CFR 1.475(a)-4 - Valuation safe harbor.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...) Dealer business model. The safe harbor is based on the business model for a derivatives dealer. Under this model, the dealer seeks to capture and profit from bid-ask spreads in the marketplace by entering..., the safe harbor is available only if the taxpayer's operations make significant business use...

  2. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Buffalo Harbor, N.Y. 110.208 Section 110.208 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.208 Buffalo Harbor, N.Y. (a) The anchorage...

  3. 33 CFR 80.1108 - Oceanside Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oceanside Harbor, CA. 80.1108 Section 80.1108 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1108 Oceanside Harbor, CA. A line drawn from Oceanside South Jetty Light 4...

  4. 33 CFR 80.1116 - Redondo Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Redondo Harbor, CA. 80.1116 Section 80.1116 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1116 Redondo Harbor, CA. A line drawn from Redondo Beach East Jetty Light 2 to...

  5. 33 CFR 80.1152 - Crescent City Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Crescent City Harbor, CA. 80.1152 Section 80.1152 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1152 Crescent City Harbor, CA. A line drawn from Crescent City Entrance Light...

  6. 33 CFR 80.1110 - Dana Point Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Dana Point Harbor, CA. 80.1110 Section 80.1110 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1110 Dana Point Harbor, CA. A line drawn from Dana Point Jetty Light 6 to...

  7. 33 CFR 80.1138 - Santa Cruz Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Santa Cruz Harbor, CA. 80.1138 Section 80.1138 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1138 Santa Cruz Harbor, CA. A line drawn from the seaward extremity of the...

  8. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Harbors on Lake Michigan. 162.120...) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake Michigan... City, Indiana; St. Joseph, South Haven, Saugatuck, Holland (Lake Macatawa), Grand Haven,...

  9. 33 CFR 80.1142 - San Francisco Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false San Francisco Harbor, CA. 80.1142 Section 80.1142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1142 San Francisco Harbor, CA. A straight...

  10. 33 CFR 110.90 - San Diego Harbor, Calif.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false San Diego Harbor, Calif. 110.90... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.90 San Diego Harbor, Calif. (a) Area A-1. In North San...) Area A-1a. In North San Diego Bay, the Shelter Island Roadstead Anchorage east of Shelter Island,...

  11. 33 CFR 110.210 - San Diego Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false San Diego Harbor, CA. 110.210... ANCHORAGE REGULATIONS Anchorage Grounds § 110.210 San Diego Harbor, CA. (a) The anchorage grounds. (1... Commander, Naval Base, San Diego, CA. The administration of these anchorages is exercised by the...

  12. 33 CFR 80.1104 - San Diego Harbor, CA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false San Diego Harbor, CA. 80.1104 Section 80.1104 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1104 San Diego Harbor, CA. A line drawn...

  13. 33 CFR 80.1104 - San Diego Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Diego Harbor, CA. 80.1104 Section 80.1104 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1104 San Diego Harbor, CA. A line drawn...

  14. 33 CFR 110.210 - San Diego Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Diego Harbor, CA. 110.210... ANCHORAGE REGULATIONS Anchorage Grounds § 110.210 San Diego Harbor, CA. (a) The anchorage grounds. (1... Commander, Naval Base, San Diego, CA. The administration of these anchorages is exercised by the...

  15. 33 CFR 110.90 - San Diego Harbor, Calif.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Diego Harbor, Calif. 110.90... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.90 San Diego Harbor, Calif. (a) Area A-1. In North San...) Area A-1a. In North San Diego Bay, the Shelter Island Roadstead Anchorage east of Shelter Island,...

  16. 33 CFR 80.1142 - San Francisco Harbor, CA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false San Francisco Harbor, CA. 80.1142 Section 80.1142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1142 San Francisco Harbor, CA. A straight...

  17. 33 CFR 110.29 - Boston Inner Harbor, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...

  18. 33 CFR 110.142 - Nantucket Harbor, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...

  19. 33 CFR 110.26 - Marblehead Harbor, Marblehead, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...

  20. 33 CFR 110.37 - Sesuit Harbor, Dennis, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...

  1. 33 CFR 110.37 - Sesuit Harbor, Dennis, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Sesuit Harbor, Dennis, Mass. 110.37 Section 110.37 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.37 Sesuit Harbor, Dennis, Mass. All the...

  2. 33 CFR 110.26 - Marblehead Harbor, Marblehead, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Marblehead Harbor, Marblehead, Mass. 110.26 Section 110.26 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND..., Mass. The area comprises that portion of the harbor lying between the extreme low water line...

  3. 33 CFR 110.142 - Nantucket Harbor, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Nantucket Harbor, Mass. 110.142 Section 110.142 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.142 Nantucket Harbor, Mass. (a) The anchorage grounds. In...

  4. 33 CFR 110.29 - Boston Inner Harbor, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Boston Inner Harbor, Mass. 110.29 Section 110.29 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.29 Boston Inner Harbor, Mass. (a) Vicinity of...

  5. 33 CFR 110.38 - Edgartown Harbor, Mass.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...

  6. 33 CFR 110.38 - Edgartown Harbor, Mass.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Edgartown Harbor, Mass. 110.38 Section 110.38 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.38 Edgartown Harbor, Mass. An area in the inner...

  7. Stress fields around two pores in an elastic body: exact quadrature domain solutions

    PubMed Central

    Crowdy, Darren

    2015-01-01

    Analytical solutions are given for the stress fields, in both compression and far-field shear, in a two-dimensional elastic body containing two interacting non-circular pores. The two complex potentials governing the solutions are found by using a conformal mapping from a pre-image annulus with those potentials expressed in terms of the Schottky–Klein prime function for the annulus. Solutions for a three-parameter family of elastic bodies with two equal symmetric pores are presented and the compressibility of a special family of pore pairs is studied in detail. The methodology extends to two unequal pores. The importance for boundary value problems of plane elasticity of a special class of planar domains known as quadrature domains is also elucidated. This observation provides the route to generalization of the mathematical approach here to finding analytical solutions for the stress fields in bodies containing any finite number of pores. PMID:26339198

  8. Physical understanding of pore formation on supported lipid bilayer by bacterial toxins

    NASA Astrophysics Data System (ADS)

    Bhattacharya, R.; Agrawal, A.; Ayappa, K. G.; Visweswariah, S. S.; Basu, J. K.

    2013-02-01

    Pore forming toxins are being classified in the protein community based on their ability of forming pores in living cell membranes. Some initial study has apparently pointed out the crystallographic pathway rather can be viewed as a structural as well as morphological changes of proteins in terms of self assembly before and during the pore formation process in surfactant medium. Being a water soluble compound, it changes its conformation and originates some pre-pore complex, which later partially goes inside the cell membrane causing a pore. The physical mechanism for this whole process is still unknown. In this study we have tried to understand these types of biological processes from physical point of view by using supported lipid bilayer as a model system.

  9. Protein targeting to the nuclear pore. What can we learn from plants. [Nuclear pore complex

    SciTech Connect

    Smith, H.M.S.; Raikhel, N.V. . DOE Plant Research Lab.)

    1999-04-01

    Characteristic of eukaryotic cells are the numerous types of membrane-bound organelles or compartments found in the cytoplasm, with each type carrying out an essential function for the cell. The spatial separation of proteins and biochemical pathways typical of the various types of organelles requires selective targeting apparatuses. Because each type of organelle contains its own targeting apparatus, proteins destined for a particular organelle must contain the proper targeting signal(s) for entry. These signal-dependent targeting pathways ensure that proteins are targeted to the proper organelle. Understanding how proteins are targeted to the different types of organelles is an important goal in the field of cell biology. In plants recent studies have highlighted a number of unusual features, and as the understanding of import in plants increases, the authors have gained new insights, such as a model for the targeting of proteins from the cytoplasm to the NPC. These advances will contribute to further expansion of the knowledge of nuclear import in eukaryotes.

  10. Pore-scale studies of multiphase flow and reaction involving CO2 sequestration in geologic formations

    NASA Astrophysics Data System (ADS)

    Kang, Q.; Wang, M.; Lichtner, P. C.

    2008-12-01

    In geologic CO2 sequestration, pore-scale interfacial phenomena ultimately govern the key processes of fluid mobility, chemical transport, adsorption, and reaction. However, spatial heterogeneity at the pore scale cannot be resolved at the continuum scale, where averaging occurs over length scales much larger than typical pore sizes. Natural porous media, such as sedimentary rocks and other geological media encountered in subsurface formations, are inherently heterogeneous. This pore-scale heterogeneity can produce variabilities in flow, transport, and reaction processes that take place within a porous medium, and can result in spatial variations in fluid velocity, aqueous concentrations, and reaction rates. Consequently, the unresolved spatial heterogeneity at the pore scale may be important for reactive transport modeling at the larger scale. In addition, current continuum models of surface complexation reactions ignore a fundamental property of physical systems, namely conservation of charge. Therefore, to better understand multiphase flow and reaction involving CO2 sequestration in geologic formations, it is necessary to quantitatively investigate the influence of the pore-scale heterogeneity on the emergent behavior at the field scale. We have applied the lattice Boltzmann method to simulating the injection of CO2 saturated brine or supercritical CO2 into geological formations at the pore scale. Multiple pore-scale processes, including advection, diffusion, homogeneous reactions among multiple aqueous species, heterogeneous reactions between the aqueous solution and minerals, ion exchange and surface complexation, as well as changes in solid and pore geometry are all taken into account. The rich pore scale information will provide a basis for upscaling to the continuum scale.

  11. 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

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  15. 77 FR 59551 - Safety Zone, Changes to Original Rule; Boston Harbor's Rock Removal Project, Boston Inner Harbor...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-28

    ... Department of Homeland Security FR Federal Register NPRM Notice of Proposed Rulemaking COTP Captain of the... Zone; Boston Harbor's Rock Removal Project, Boston Inner Harbor, Boston, MA'' (77 FR 50916). This new... Captain of the Port (COTP) Zone for the drilling, blasting, and dredging operation on the navigable...

  16. Low Pore Connectivity Increases Bacterial Diversity in Soil▿

    PubMed Central

    Carson, Jennifer K.; Gonzalez-Quiñones, Vanesa; Murphy, Daniel V.; Hinz, Christoph; Shaw, Jeremy A.; Gleeson, Deirdre B.

    2010-01-01

    One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P < 0.012), but they were not affected by texture (P > 0.553). Bacterial diversity increased at water potentials of ≤2.5 kPa in sand and ≤4.0 kPa in silt+clay, equivalent to ≤56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P < 0.001) and was correlated with WFPS (sum of squared correlations [δ2] = 0.88, P < 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil. PMID:20418420

  17. Three-dimensional structure of the anthrax toxin pore inserted into lipid nanodiscs and lipid vesicles

    PubMed Central

    Katayama, H.; Wang, J.; Tama, F.; Chollet, L.; Gogol, E. P.; Collier, R. J.; Fisher, M. T.

    2010-01-01

    A major goal in understanding the pathogenesis of the anthrax bacillus is to determine how the protective antigen (PA) pore mediates translocation of the enzymatic components of anthrax toxin across membranes. To obtain structural insights into this mechanism, we constructed PA-pore membrane complexes and visualized them by using negative-stain electron microscopy. Two populations of PA pores were visualized in membranes, vesicle-inserted and nanodisc-inserted, allowing us to reconstruct two virtually identical PA-pore structures at 22-Å resolution. Reconstruction of a domain 4-truncated PA pore inserted into nanodiscs showed that this domain does not significantly influence pore structure. Normal mode flexible fitting of the x-ray crystallographic coordinates of the PA prepore indicated that a prominent flange observed within the pore lumen is formed by the convergence of mobile loops carrying Phe427, a residue known to catalyze protein translocation. Our results have identified the location of a crucial functional element of the PA pore and documented the value of combining nanodisc technology with electron microscopy to examine the structures of membrane-interactive proteins. PMID:20142512

  18. Soluble Oligomers of the Pore-forming Toxin Cytolysin A from Escherichia coli Are Off-pathway Products of Pore Assembly.

    PubMed

    Roderer, Daniel; Benke, Stephan; Schuler, Benjamin; Glockshuber, Rudi

    2016-03-11

    The α-pore-forming toxin Cytolysin A (ClyA) is responsible for the hemolytic activity of various Escherichia coli and Salmonella enterica strains. Soluble ClyA monomers spontaneously assemble into annular dodecameric pore complexes upon contact with membranes or detergent. At ClyA monomer concentrations above ∼100 nm, the rate-limiting step in detergent- or membrane- induced pore assembly is the unimolecular reaction from the monomer to the assembly-competent protomer, which then oligomerizes rapidly to active pore complexes. In the absence of detergent, ClyA slowly forms soluble oligomers. Here we show that soluble ClyA oligomers cannot form dodecameric pore complexes after the addition of detergent and are hemolytically inactive. In addition, we demonstrate that the natural cysteine pair Cys-87/Cys-285 of ClyA forms a disulfide bond under oxidizing conditions and that both the oxidized and reduced ClyA monomers assemble to active pores via the same pathway in the presence of detergent, in which an unstructured, monomeric intermediate is transiently populated. The results show that the oxidized ClyA monomer assembles to pore complexes about one order of magnitude faster than the reduced monomer because the unstructured intermediate of oxidized ClyA is less stable and dissolves more rapidly than the reduced intermediate. Moreover, we show that oxidized ClyA forms soluble, inactive oligomers in the absence of detergent much faster than the reduced monomer, providing an explanation for several contradictory reports in which oxidized ClyA had been described as inactive. PMID:26757820

  19. Soluble Oligomers of the Pore-forming Toxin Cytolysin A from Escherichia coli Are Off-pathway Products of Pore Assembly.

    PubMed

    Roderer, Daniel; Benke, Stephan; Schuler, Benjamin; Glockshuber, Rudi

    2016-03-11

    The α-pore-forming toxin Cytolysin A (ClyA) is responsible for the hemolytic activity of various Escherichia coli and Salmonella enterica strains. Soluble ClyA monomers spontaneously assemble into annular dodecameric pore complexes upon contact with membranes or detergent. At ClyA monomer concentrations above ∼100 nm, the rate-limiting step in detergent- or membrane- induced pore assembly is the unimolecular reaction from the monomer to the assembly-competent protomer, which then oligomerizes rapidly to active pore complexes. In the absence of detergent, ClyA slowly forms soluble oligomers. Here we show that soluble ClyA oligomers cannot form dodecameric pore complexes after the addition of detergent and are hemolytically inactive. In addition, we demonstrate that the natural cysteine pair Cys-87/Cys-285 of ClyA forms a disulfide bond under oxidizing conditions and that both the oxidized and reduced ClyA monomers assemble to active pores via the same pathway in the presence of detergent, in which an unstructured, monomeric intermediate is transiently populated. The results show that the oxidized ClyA monomer assembles to pore complexes about one order of magnitude faster than the reduced monomer because the unstructured intermediate of oxidized ClyA is less stable and dissolves more rapidly than the reduced intermediate. Moreover, we show that oxidized ClyA forms soluble, inactive oligomers in the absence of detergent much faster than the reduced monomer, providing an explanation for several contradictory reports in which oxidized ClyA had been described as inactive.

  20. Silver speciation in wastewater effluent, surface waters, and pore waters

    SciTech Connect

    Adams, N.W.H.; Kramer, J.R.

    1999-12-01

    Silver, inorganic sulfide, and thiol compounds were measured in municipal wastewater effluent, receiving waters, and pore waters from an anoxic lake sediment in order to predict silver speciation in these systems. The authors found submicromolar concentrations of inorganic sulfide even in fully oxic surface water. This inorganic sulfide is likely to exist in the form of colloidal metal sulfides, which have been shown to be stable under oxidizing conditions for periods of several hours. Inorganic sulfide in both the wastewater effluent and receiving waters was found to be 200 to 300 times in excess of silver concentrations, whereas inorganic sulfide in pore waters was 1,000 to 15,000 times in excess of silver concentrations. With sulfide in excess of silver, the authors predict silver sulfide complexes to dominate silver speciation. Thiols were present at low nanomolar levels in pore waters but were not detectable in wastewater effluent or receiving waters. Thiols do not appear to be important to silver speciation in these freshwater systems. Partitioning of silver into particular, colloidal, and dissolved size fractions showed that a significant proportion of silver is in the colloidal and dissolved phases. Dissolved phase concentrations were relatively constant in the treatment plant effluent and receiving waters, suggesting that silver in the <10-kDa size fraction is strongly complexed by ligands that are not significantly affected by aggregation or sorption processes.

  1. Characteristics of pore migration controlled by diffusion through the pore-filling fluid

    NASA Astrophysics Data System (ADS)

    Petrishcheva, E.; Renner, J.

    2010-10-01

    We analyze drag and drop of pores filled with a fluid phase, e.g., water or melt, in which the constituting elements of the solid matrix are dissolved. Assuming that the diffusion through the fluid-phase dominates bulk transport kinetics, we address the problem of pore motion and calculate the pore mobility and the critical velocity of elongated and lenticular pores on a grain boundary for arbitrary dihedral angle. The found variations in critical velocity and mobility with dihedral angle are modest for given volume of pores with the two considered geometries. For given pore size, however, the dependence on dihedral angle accounts for several orders of magnitude in pore mobility and critical velocity.

  2. Modeling of the lithium-air battery cathodes with broad pore size distribution

    NASA Astrophysics Data System (ADS)

    Sergeev, Artem V.; Chertovich, Alexander V.; Itkis, Daniil M.

    2016-09-01

    Achieving theoretical promises of 1000 W h/kg specific energy for lithium-air batteries is quite challenging due to limited transport in the cathode along with electrode passivation. Transport can be enhanced in the electrodes with complex hierarchical pore architecture. Here, using computer simulations we analyze the effects of cathode pore size distribution (PSD) on capacity and discharge curve shape. Calculations considering a broad PSD revealed that even small discharge product resistivity prevents larger pores from accumulating the discharge product and thus turning them into non-clogging oxygen supply channels. Thus optimization of cathode architecture by adding of large-scale cavities enables cell capacity enhancement.

  3. Fusion pore regulation of transmitter release.

    PubMed

    Fernández-Peruchena, Carlos; Navas, Sergio; Montes, María A; Alvarez de Toledo, Guillermo

    2005-09-01

    During the last decade a wealth of new information about the properties of the exocytotic fusion pore is changing our current view of exocytosis. The exocytotic fusion pore, a necessary stage before the full merging of the vesicle membrane with the plasma membrane, is becoming a key cellular structure that might critically control the amount of neurotransmitter released into the synaptic cleft and that can be subjected to control by second messengers and phosphorylated proteins. Fusion pores form, expand to fully merge membranes, or can close leaving an intact and identical synaptic vesicle in place for a new round of exocytosis. Transient formation of fusion pores is the mechanistic representation of the "kiss-and-run" hypothesis of transmitter release and offers new alternatives for synaptic vesicle recycling besides to the classical mechanism mediated by clathrin coat endocytosis. For vesicle recycling transient fusion pores ensures a fast mechanism for maintaining an active pool of synaptic vesicles. The size reached by transient fusion pores and the time spent on the open state can determine the release of subquantal synaptic transmission, which could be a mechanism of synaptic potentiation. In this review we will described the electrophysiological and fluorescence methods that contribute to further explore the biophysical properties of the exocytotic fusion pore and the relevant experiments obtained by these methods.

  4. Potential for Polychlorinated Biphenyl Biodegradation in Sediments from Indiana Harbor and Ship Canal

    PubMed Central

    Liang, Yi; Martinez, Andres; Hornbuckle, Keri C.; Mattes, Timothy E.

    2014-01-01

    Polychlorinated biphenyls (PCBs) are carcinogenic, persistent, and bioaccumulative contaminants that pose risks to human and environmental health. In this study, we evaluated the PCB biodegradation of sediments from Indiana Harbor and Ship Canal (IHSC), a PCB-contaminated site (average PCB concentration = 12,570 ng/g d.w.). PCB congener profiles and bacterial community structure in a core sediment sample (4.57 m long) were characterized. Analysis of vertical PCB congener profile patterns in sediment and pore water strongly suggest that in situ dechlorination occurred in sediments. However, 16S rRNA genes from putative PCB-dechlorinating Chloroflexi were relatively more abundant in upper 2 m sediments, as were genes indicative of aerobic biodegradation potential (i.e. biphenyl dioxygenase (bphA)). Characterization of the bacterial community by terminal restriction fragment length polymorphism and comparison of these with sediment and pore water PCB congener profiles with the Mantel test revealed a statistical correlation (p<0.001). Sequences classified as Acinetobacter and Acidovorax were highly abundant in deep sediments. Overall, our results suggest that PCB dechlorination has already occurred, and that IHSC sediments have the potential for further aerobic and anaerobic PCB biodegradation. PMID:24764649

  5. High temperature ion channels and pores

    NASA Technical Reports Server (NTRS)

    Kang, Xiaofeng (Inventor); Gu, Li Qun (Inventor); Cheley, Stephen (Inventor); Bayley, Hagan (Inventor)

    2011-01-01

    The present invention includes an apparatus, system and method for stochastic sensing of an analyte to a protein pore. The protein pore may be an engineer protein pore, such as an ion channel at temperatures above 55.degree. C. and even as high as near 100.degree. C. The analyte may be any reactive analyte, including chemical weapons, environmental toxins and pharmaceuticals. The analyte covalently bonds to the sensor element to produce a detectable electrical current signal. Possible signals include change in electrical current. Detection of the signal allows identification of the analyte and determination of its concentration in a sample solution. Multiple analytes present in the same solution may also be detected.

  6. Control of pore size in epoxy systems.

    SciTech Connect

    Sawyer, Patricia Sue; Lenhart, Joseph Ludlow; Lee, Elizabeth; Kallam, Alekhya; Majumdar, Partha; Dirk, Shawn M.; Gubbins, Nathan; Chisholm, Bret J.; Celina, Mathias Christopher; Bahr, James; Klein, Robert J.

    2009-01-01

    Both conventional and combinatorial approaches were used to study the pore formation process in epoxy based polymer systems. Sandia National Laboratories conducted the initial work and collaborated with North Dakota State University (NDSU) using a combinatorial research approach to produce a library of novel monomers and crosslinkers capable of forming porous polymers. The library was screened to determine the physical factors that control porosity, such as porogen loading, polymer-porogen interactions, and polymer crosslink density. We have identified the physical and chemical factors that control the average porosity, pore size, and pore size distribution within epoxy based systems.

  7. Enlarged facial pores: an update on treatments.

    PubMed

    Dong, Joanna; Lanoue, Julien; Goldenberg, Gary

    2016-07-01

    Enlarged facial pores remain a common dermatologic and cosmetic concern from acne and rosacea, among other conditions, that is difficult to treat due to the multifactorial nature of their pathogenesis and negative impact on patients' quality of life. Enlarged facial pores are primarily treated through addressing associative factors, such as increased sebum production and cutaneous aging. We review the current treatment modalities for enlarged or dense facial pores, including topical retinoids, chemical peels, oral antiandrogens, and lasers and devices, with a focus on newer therapies. PMID:27529707

  8. Block copolymer structures in nano-pores

    NASA Astrophysics Data System (ADS)

    Pinna, Marco; Guo, Xiaohu; Zvelindovsky, Andrei

    2010-03-01

    We present results of coarse-grained computer modelling of block copolymer systems in cylindrical and spherical nanopores on Cell Dynamics Simulation. We study both cylindrical and spherical pores and systematically investigate structures formed by lamellar, cylinders and spherical block copolymer systems for various pore radii and affinity of block copolymer blocks to the pore walls. The obtained structures include: standing lamellae and cylinders, ``onions,'' cylinder ``knitting balls,'' ``golf-ball,'' layered spherical, ``virus''-like and mixed morphologies with T-junctions and U-type defects [1]. Kinetics of the structure formation and the differences with planar films are discussed. Our simulations suggest that novel porous nano-containers can be formed by confining block copolymers in pores of different geometries [1,2]. [4pt] [1] M. Pinna, X. Guo, A.V. Zvelindovsky, Polymer 49, 2797 (2008).[0pt] [2] M. Pinna, X. Guo, A.V. Zvelindovsky, J. Chem. Phys. 131, 214902 (2009).

  9. 1. VIEW TO NORTHEAST ACROSS RICHMOND INNER HARBOR FROM RICHMOND ...

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

    1. VIEW TO NORTHEAST ACROSS RICHMOND INNER HARBOR FROM RICHMOND SHIPYARD NO. 3. - Rosie the Riveter National Historical Park, Ford Assembly Plant, 1400 Harbour Way South, Richmond, Contra Costa County, CA

  10. 33 CFR 110.212 - Newport Bay Harbor, Calif.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... line 120 feet in length bearing 203° from the point of the pierhead line off the west end of Harbor Island; and southwest of the pierhead line off the northeast shore of Lido Isle extended. (2)...

  11. BLDG 47, FRONT ELEVATION DETAIL OF NE END OF HARBOR ...

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

    BLDG 47, FRONT ELEVATION DETAIL OF NE END OF HARBOR SIDE WITH POLE. - Naval Magazine Lualualei, West Loch Branch, Explosive & Small Train Depot, Main wharf area adjacent to Wharf No. 3, Pearl City, Honolulu County, HI

  12. BLDG 47, ELEVATION DETAIL AT NE END OF HARBOR SIDE. ...

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

    BLDG 47, ELEVATION DETAIL AT NE END OF HARBOR SIDE. - Naval Magazine Lualualei, West Loch Branch, Explosive & Small Train Depot, Main wharf area adjacent to Wharf No. 3, Pearl City, Honolulu County, HI

  13. 33 CFR 110.50d - Mystic Harbor, Noank, Conn.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.50d Mystic Harbor, Noank, Conn. (a) The area... or buoys for marking anchors will be allowed but fixed piles or stakes are prohibited. All...

  14. 33 CFR 100.107 - Windjammer Days, Boothbay Harbor, Maine.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... follows: a line drawn due east from the southwest (43-50-10 North; 069-38-20 West to the Spruce Point Shore; thence following the shore north along Spruce Point and around the Boothbay Harbor to...

  15. Ground-water status report, Pearl Harbor area, Hawaii, 1978

    USGS Publications Warehouse

    Soroos, Ronald L.; Ewart, Charles J.

    1979-01-01

    Increasing demand for freshwater in Hawaii has placed heavy stress on many of the State 's basal aquifer systems. The most heavily stressed of these systems is the Pearl Harbor on Oahu. The Pearl Harbor basal aquifer supplies as much as 277 million gallons per day. Since early in this century, spring discharge has been declining while pumpage has been increasing. Total ground-water discharge has remained steady despite short-term fluctuations. Some wells show general increases in chloride concentration while others remain steady. Chloride concentrations throughout the area show no apparent increase since 1970. Basal water head maps of the Pearl Harbor area clearly reflect the natural discharge points, which are the springs located along the shore near the center of Pearl Harbor. Basal-water hydrographs show a general decline of about 0.09 foot per year. This implies depletion of storage at a rate of about 25 million gallons per day. (USGS).

  16. 33 CFR 110.212 - Newport Bay Harbor, Calif.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... the harbor master. (ii) Vessels anchoring in Temporary Anchorages C-1 and C-2 shall comply with all... master. (2) Vessels anchoring in these areas shall comply with all applicable Pilot Rules, including...

  17. ADSORPTION OF POLYCYCLIC AROMATIC HYDROCARBONS IN AGED HARBOR SEDIMENTS

    EPA Science Inventory

    Polycyclic aromatic hydrocarbons (PAHs) are a group of hydrophobic organic contaminants which have low aqueous solubilities and are common pollutants in harbor sediments. Adsorption and desorption isotherms for PAHs are conducted to study the abiotic sorption of PAHs in uncontami...

  18. 33 CFR 117.541 - Baltimore Harbor-Patapsco River.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.541 Baltimore Harbor... Western Maryland railroad bridge, mile 12.5 across the Middle Branch of the Patapsco River at...

  19. 33 CFR 117.541 - Baltimore Harbor-Patapsco River.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.541 Baltimore Harbor... Western Maryland railroad bridge, mile 12.5 across the Middle Branch of the Patapsco River at...

  20. To the pore and through the pore: a story of mRNA export kinetics.

    PubMed

    Oeffinger, Marlene; Zenklusen, Daniel

    2012-06-01

    The evolutionary 'decision' to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transport mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing. PMID:22387213

  1. To the Pore and Through the Pore: A Story of mRNA Export Kinetics

    PubMed Central

    Oeffinger, Marlene; Zenklusen, Daniel

    2012-01-01

    Summary The evolutionary ‘decision’ to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transports mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. PMID:22387213

  2. Colloid dispersion on the pore scale.

    PubMed

    Baumann, Thomas; Toops, Laura; Niessner, Reinhard

    2010-02-01

    Dispersion describes the spreading of a tracer or contaminant in an aquifer. Detailed knowledge of dispersion is the key to successful risk assessment in case of groundwater pollution or groundwater protection. The dispersion of colloids on the pore scale is controlled by flow velocity, ionic strength, colloid size, colloid concentration, and colloid-matrix interactions. The objective of this study was to provide quantitative data and to assess the scale dependency of colloid dispersion on the pore scale. The positions of carboxylated polystyrene microspheres (1 microm, 0.5 microm) were recorded during transport experiments in silicon micromodels with three pore topologies. The positions were combined into particle trajectories revealing the flow path of individual colloids. More than thousand trajectories were evaluated for each experiment to obtain the dispersivity of the colloids for flow distances between 10 and 1000 microm. All experiments were run at high Peclet numbers. The pore scale dispersivity was on the order of 8-30% of the flow distance with pure water, dependent on the heterogeneity of the pore topology. The dispersivity was positively correlated with the ionic strength and inversely correlated with the colloid size and the flow velocity. A coating of the micromodel surface with humic acid also increased dispersivity. The quantitative data set presented here supports the theoretical framework for colloid transport and allows to parametrize colloid transport on the pore scale.

  3. Colloid dispersion on the pore scale.

    PubMed

    Baumann, Thomas; Toops, Laura; Niessner, Reinhard

    2010-02-01

    Dispersion describes the spreading of a tracer or contaminant in an aquifer. Detailed knowledge of dispersion is the key to successful risk assessment in case of groundwater pollution or groundwater protection. The dispersion of colloids on the pore scale is controlled by flow velocity, ionic strength, colloid size, colloid concentration, and colloid-matrix interactions. The objective of this study was to provide quantitative data and to assess the scale dependency of colloid dispersion on the pore scale. The positions of carboxylated polystyrene microspheres (1 microm, 0.5 microm) were recorded during transport experiments in silicon micromodels with three pore topologies. The positions were combined into particle trajectories revealing the flow path of individual colloids. More than thousand trajectories were evaluated for each experiment to obtain the dispersivity of the colloids for flow distances between 10 and 1000 microm. All experiments were run at high Peclet numbers. The pore scale dispersivity was on the order of 8-30% of the flow distance with pure water, dependent on the heterogeneity of the pore topology. The dispersivity was positively correlated with the ionic strength and inversely correlated with the colloid size and the flow velocity. A coating of the micromodel surface with humic acid also increased dispersivity. The quantitative data set presented here supports the theoretical framework for colloid transport and allows to parametrize colloid transport on the pore scale. PMID:20042215

  4. 33 CFR 110.147 - New London Harbor, Conn.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... and distances from New London Harbor Light (latitude 41°18′59″ N., longitude 72°05′25″ W.): 002°, 2... New London Harbor Light, a point bearing 270°, 575 yards from New London Ledge Light (latitude 41°18′21″ N., longitude 72°04′41″ W.), and a point bearing 270°, 1,450 yards from New London Ledge...

  5. 33 CFR 110.147 - New London Harbor, Conn.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... and distances from New London Harbor Light (latitude 41°18′59″ N., longitude 72°05′25″ W.): 002°, 2... New London Harbor Light, a point bearing 270°, 575 yards from New London Ledge Light (latitude 41°18′21″ N., longitude 72°04′41″ W.), and a point bearing 270°, 1,450 yards from New London Ledge...

  6. Radiological survey results at Beverly Harbor, Beverly, Massachusetts (VB025)

    SciTech Connect

    Foley, R.D.; Johnson, C.A.

    1992-08-01

    At the request of the US Department of Energy (DOE), a team from Oak Ridge National Laboratory conducted a radiological survey at Beverly Harbor, Beverly, Massachusetts. The survey was performed in may 1991. The purpose of the survey was to determine if uranium from work performed under government contract at the former Ventron facility had migrated off-site to the harbor and neighboring areas. The survey included a surface gamma scan and the collection of soil and biological samples for radionuclide analyses.

  7. HHS Inspector General publishes final safe harbor regulations.

    PubMed

    Valiant, C

    1991-01-01

    The Department of Health and Human Services Office of Inspector General has finally published the long-awaited Medicare/Medicaid final safe harbor regulations. The regulations, implementing the Medicare and Medicaid Patient and Program Protection Act of 1987, protect from criminal and civil sanctions certain payment practices that could otherwise be proscribed under the Medicare/Medicaid antikickback statute. Unfortunately, the final safe harbors appear not to reach many common business arrangements among health care providers currently in place.

  8. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .... 341, 62 Stat. 799; 18 U.S.C. 2152, 33 U.S.C. 475; E.O. 8143, 4 FR 2179, 3 CFR 1943 Cum. Supp. 504) ... 32 National Defense 5 2011-07-01 2011-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander,...

  9. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .... 341, 62 Stat. 799; 18 U.S.C. 2152, 33 U.S.C. 475; E.O. 8143, 4 FR 2179, 3 CFR 1943 Cum. Supp. 504) ... 32 National Defense 5 2012-07-01 2012-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander,...

  10. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .... 341, 62 Stat. 799; 18 U.S.C. 2152, 33 U.S.C. 475; E.O. 8143, 4 FR 2179, 3 CFR 1943 Cum. Supp. 504) ... 32 National Defense 5 2013-07-01 2013-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander,...

  11. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    .... 341, 62 Stat. 799; 18 U.S.C. 2152, 33 U.S.C. 475; E.O. 8143, 4 FR 2179, 3 CFR 1943 Cum. Supp. 504) ... 32 National Defense 5 2010-07-01 2010-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander,...

  12. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    .... 341, 62 Stat. 799; 18 U.S.C. 2152, 33 U.S.C. 475; E.O. 8143, 4 FR 2179, 3 CFR 1943 Cum. Supp. 504) ... 32 National Defense 5 2014-07-01 2014-07-01 false Regulations for Pearl Harbor, Hawaii. 765.6... RULES RULES APPLICABLE TO THE PUBLIC § 765.6 Regulations for Pearl Harbor, Hawaii. The Commander,...

  13. HHS Inspector General publishes final safe harbor regulations.

    PubMed

    Valiant, C

    1991-01-01

    The Department of Health and Human Services Office of Inspector General has finally published the long-awaited Medicare/Medicaid final safe harbor regulations. The regulations, implementing the Medicare and Medicaid Patient and Program Protection Act of 1987, protect from criminal and civil sanctions certain payment practices that could otherwise be proscribed under the Medicare/Medicaid antikickback statute. Unfortunately, the final safe harbors appear not to reach many common business arrangements among health care providers currently in place. PMID:10114719

  14. Pore Scale Dynamics of Microemulsion Formation.

    PubMed

    Unsal, Evren; Broens, Marc; Armstrong, Ryan T

    2016-07-19

    Experiments in various porous media have shown that multiple parameters come into play when an oleic phase is displaced by an aqueous solution of surfactant. In general, the displacement efficiency is improved when the fluids become quasi-miscible. Understanding the phase behavior oil/water/surfactant systems is important because microemulsion has the ability to generate ultralow interfacial tension (<10(-2) mN m(-1)) that is required for miscibility to occur. Many studies focus on microemulsion formation and the resulting properties under equilibrium conditions. However, the majority of applications where microemulsion is present also involve flow, which has received relatively less attention. It is commonly assumed that the characteristics of an oil/water/surfactant system under flowing conditions are identical to the one under equilibrium conditions. Here, we show that this is not necessarily the case. We studied the equilibrium phase behavior of a model system consisting of n-decane and an aqueous solution of olefin sulfonate surfactant, which has practical applications for enhanced oil recovery. The salt content of the aqueous solution was varied to provide a range of different microemulsion compositions and oil-water interfacial tensions. We then performed microfluidic flow experiments to study the dynamic in situ formation of microemulsion by coinjecting bulk fluids of n-decane and surfactant solution into a T-junction capillary geometry. A solvatochromatic fluorescent dye was used to obtain spatially resolved compositional information. In this way, we visualized the microemulsion formation and the flow of it along with the excess phases. A complex interaction between the flow patterns and the microemulsion properties was observed. The formation of microemulsion influenced the flow regimes, and the flow regimes affected the characteristics of the microemulsion formation. In particular, at low flow rates, slug flow was observed, which had profound

  15. 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.

  16. Unstable Pore-Water Flow in Intertidal Wetlands

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  17. Hydrogeology and hydrodynamics of coral reef pore waters

    SciTech Connect

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

    1988-06-29

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

  18. MCU encodes the pore conducting mitochondrial calcium currents.

    PubMed

    Chaudhuri, Dipayan; Sancak, Yasemin; Mootha, Vamsi K; Clapham, David E

    2013-06-04

    Mitochondrial calcium (Ca(2+)) import is a well-described phenomenon regulating cell survival and ATP production. Of multiple pathways allowing such entry, the mitochondrial Ca(2+) uniporter is a highly Ca(2+)-selective channel complex encoded by several recently-discovered genes. However, the identity of the pore-forming subunit remains to be established, since knockdown of all the candidate uniporter genes inhibit Ca(2+) uptake in imaging assays, and reconstitution experiments have been equivocal. To definitively identify the channel, we use whole-mitoplast voltage-clamping, the technique that originally established the uniporter as a Ca(2+) channel. We show that RNAi-mediated knockdown of the mitochondrial calcium uniporter (MCU) gene reduces mitochondrial Ca(2+) current (I MiCa ), whereas overexpression increases it. Additionally, a classic feature of I MiCa , its sensitivity to ruthenium red inhibition, can be abolished by a point mutation in the putative pore domain without altering current magnitude. These analyses establish that MCU encodes the pore-forming subunit of the uniporter channel. DOI:http://dx.doi.org/10.7554/eLife.00704.001.

  19. Direct correlation of internal gradients and pore size distributions with low field NMR.

    PubMed

    Zhang, Yan; Xiao, Lizhi; Liao, Guangzhi; Blümich, Bernhard

    2016-06-01

    Internal magnetic field gradients Gint, which arise from the magnetic susceptibility difference Δχ between solid matrix and fluid in porous media relate to the pore geometry. However, this relationship is complex and not well understood. Here we correlate internal-gradient distributions to pore-size distributions directly to examine internal gradients in detail at low field NMR. The pore-size distributions were obtained by the method of Decay due to Diffusion in the Internal Field (DDIF), and the internal-gradient distributions were measured with the Carr-Purcell-Meiboom-Gill (CPMG) method. The internal-gradient-pore-size distributions correlation maps were obtained for water in packs of glass beads with different diameter and in a sandstone sample. The relationship between internal gradients and pore structure is analyzed in detail by considering the restricted diffusion of fluids in porous samples. For each case diffusion regimes are assigned by plotting normalized CPMG data and comparing the diffusion lengths, the dephasing lengths and pore diameters. In the free-diffusion limit, the correlation maps reveal the true relationship between pore structure and internal gradients so that Δχ can be approximated from the correlation maps. This limit is met most easily at low field. It provides information about porous media, which is expected to benefit the oil industry, in particular NMR well logging.

  20. Direct correlation of internal gradients and pore size distributions with low field NMR

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Xiao, Lizhi; Liao, Guangzhi; Blümich, Bernhard

    2016-06-01

    Internal magnetic field gradients Gint, which arise from the magnetic susceptibility difference Δχ between solid matrix and fluid in porous media relate to the pore geometry. However, this relationship is complex and not well understood. Here we correlate internal-gradient distributions to pore-size distributions directly to examine internal gradients in detail at low field NMR. The pore-size distributions were obtained by the method of Decay due to Diffusion in the Internal Field (DDIF), and the internal-gradient distributions were measured with the Carr-Purcell-Meiboom-Gill (CPMG) method. The internal-gradient-pore-size distributions correlation maps were obtained for water in packs of glass beads with different diameter and in a sandstone sample. The relationship between internal gradients and pore structure is analyzed in detail by considering the restricted diffusion of fluids in porous samples. For each case diffusion regimes are assigned by plotting normalized CPMG data and comparing the diffusion lengths, the dephasing lengths and pore diameters. In the free-diffusion limit, the correlation maps reveal the true relationship between pore structure and internal gradients so that Δχ can be approximated from the correlation maps. This limit is met most easily at low field. It provides information about porous media, which is expected to benefit the oil industry, in particular NMR well logging.

  1. Direct correlation of internal gradients and pore size distributions with low field NMR.

    PubMed

    Zhang, Yan; Xiao, Lizhi; Liao, Guangzhi; Blümich, Bernhard

    2016-06-01

    Internal magnetic field gradients Gint, which arise from the magnetic susceptibility difference Δχ between solid matrix and fluid in porous media relate to the pore geometry. However, this relationship is complex and not well understood. Here we correlate internal-gradient distributions to pore-size distributions directly to examine internal gradients in detail at low field NMR. The pore-size distributions were obtained by the method of Decay due to Diffusion in the Internal Field (DDIF), and the internal-gradient distributions were measured with the Carr-Purcell-Meiboom-Gill (CPMG) method. The internal-gradient-pore-size distributions correlation maps were obtained for water in packs of glass beads with different diameter and in a sandstone sample. The relationship between internal gradients and pore structure is analyzed in detail by considering the restricted diffusion of fluids in porous samples. For each case diffusion regimes are assigned by plotting normalized CPMG data and comparing the diffusion lengths, the dephasing lengths and pore diameters. In the free-diffusion limit, the correlation maps reveal the true relationship between pore structure and internal gradients so that Δχ can be approximated from the correlation maps. This limit is met most easily at low field. It provides information about porous media, which is expected to benefit the oil industry, in particular NMR well logging. PMID:27111138

  2. Effective pore-scale dispersion upscaling with a correlated continuous time random walk approach

    NASA Astrophysics Data System (ADS)

    Le Borgne, T.; Bolster, D.; Dentz, M.; de Anna, P.; Tartakovsky, A.

    2011-12-01

    We investigate the upscaling of dispersion from a pore-scale analysis of Lagrangian velocities. A key challenge in the upscaling procedure is to relate the temporal evolution of spreading to the pore-scale velocity field properties. We test the hypothesis that one can represent Lagrangian velocities at the pore scale as a Markov process in space. The resulting effective transport model is a continuous time random walk (CTRW) characterized by a correlated random time increment, here denoted as correlated CTRW. We consider a simplified sinusoidal wavy channel model as well as a more complex heterogeneous pore space. For both systems, the predictions of the correlated CTRW model, with parameters defined from the velocity field properties (both distribution and correlation), are found to be in good agreement with results from direct pore-scale simulations over preasymptotic and asymptotic times. In this framework, the nontrivial dependence of dispersion on the pore boundary fluctuations is shown to be related to the competition between distribution and correlation effects. In particular, explicit inclusion of spatial velocity correlation in the effective CTRW model is found to be important to represent incomplete mixing in the pore throats.

  3. Pore pressure embrittlement in a volcanic edifice

    NASA Astrophysics Data System (ADS)

    Farquharson, Jamie; Heap, Michael J.; Baud, Patrick; Reuschlé, Thierry; Varley, Nick R.

    2016-01-01

    The failure mode of porous rock in compression—dilatant or compactant—is largely governed by the overlying lithostatic pressure and the pressure of pore fluids within the rock (Wong, Solid Earth 102:3009-3025, 1997), both of which are subject to change in space and time within a volcanic edifice. While lithostatic pressure will tend to increase monotonously with depth due to the progressive accumulation of erupted products, pore pressures are prone to fluctuations (during periods of volcanic unrest, for example). An increase in pore fluid pressure can result in rock fracture, even at depths where the lithostatic pressure would otherwise preclude such dilatant behaviour—a process termed pore fluid-induced embrittlement. We explore this phenomenon through a series of targeted triaxial experiments on typical edifice-forming andesites (from Volcán de Colima, Mexico). We first show that increasing pore pressure over a range of timescales (on the order of 1 min to 1 day) can culminate in brittle failure of otherwise intact rock. Irrespective of the pore pressure increase rate, we record comparable accelerations in acoustic emission and strain prior to macroscopic failure. We further show that oscillating pore fluid pressures can cause iterative and cumulative damage, ultimately resulting in brittle failure under relatively low effective mean stress conditions. We find that macroscopic failure occurs once a critical threshold of damage is surpassed, suggesting that only small increases in pore pressure may be necessary to trigger failure in previously damaged rocks. Finally, we observe that inelastic compaction of volcanic rock (as we may expect in much of the deep edifice) can be overprinted by shear fractures due to this mechanism of embrittlement. Pore fluid-induced embrittlement of edifice rock during volcanic unrest is anticipated to be highest closer to the conduit and, as a result, may assist in the development of a fractured halo zone surrounding the

  4. Mechanical properties, pore size distribution, and pore solution of fly ash-belite cement mortars

    SciTech Connect

    Guerrero, A.; Goni, S.; Macias, A.; Luxan, M.P.

    1999-11-01

    The mechanical properties, pore size distribution, and extracted pore solution of fly ash-belite cement (FABC) mortars were studied for a period of 200 days. The influence of the calcination temperature, which ranged from 700 to 900 C, of the fly ash-belite cement was discussed. The evolution with hydration time of the pore size distribution was followed by mercury intrusion porosimetry, and the results correlated with those of flexural and compressive strength. The pore solution was expressed and analyzed at different times of hydration.

  5. Quantitative classification of harbor seal breeding calls in Georgia Strait, Canada.

    PubMed

    Nikolich, Katrina; Frouin-Mouy, Héloïse; Acevedo-Gutiérrez, Alejandro

    2016-08-01

    During breeding season, male harbor seals (Phoca vitulina) produce underwater calls used in sexual competition and advertisement. Call characteristics vary among populations, and within-population differences are thought to represent individual variation. However, vocalizations have not been described for several populations of this widely-distributed and genetically diverse species. This study describes the vocal repertoire of harbor seals from British Columbia, Canada. Underwater recordings were made near Hornby Island during the summer of 2014 using a single hydrophone. A wide variability was detected in breeding vocalizations within this single breeding site. Four candidate call types were identified, containing six subtypes. Linear discriminant analysis showed 88% agreement with subjective classification of call types, and 74% agreement for call subtypes. Classification tree analysis gave a 92% agreement with candidate call types, with all splits made on the basis of call duration. Differences in duration may have reflected individual differences among seals. This study suggests that the vocal repertoire of harbor seals in this area comprises a vocal continuum rather than discrete call types. Further work with the ability to localize calls may help to determine whether this complexity represents variability due to propagation conditions, animal orientation, or differences among individual seals.

  6. Quantitative classification of harbor seal breeding calls in Georgia Strait, Canada.

    PubMed

    Nikolich, Katrina; Frouin-Mouy, Héloïse; Acevedo-Gutiérrez, Alejandro

    2016-08-01

    During breeding season, male harbor seals (Phoca vitulina) produce underwater calls used in sexual competition and advertisement. Call characteristics vary among populations, and within-population differences are thought to represent individual variation. However, vocalizations have not been described for several populations of this widely-distributed and genetically diverse species. This study describes the vocal repertoire of harbor seals from British Columbia, Canada. Underwater recordings were made near Hornby Island during the summer of 2014 using a single hydrophone. A wide variability was detected in breeding vocalizations within this single breeding site. Four candidate call types were identified, containing six subtypes. Linear discriminant analysis showed 88% agreement with subjective classification of call types, and 74% agreement for call subtypes. Classification tree analysis gave a 92% agreement with candidate call types, with all splits made on the basis of call duration. Differences in duration may have reflected individual differences among seals. This study suggests that the vocal repertoire of harbor seals in this area comprises a vocal continuum rather than discrete call types. Further work with the ability to localize calls may help to determine whether this complexity represents variability due to propagation conditions, animal orientation, or differences among individual seals. PMID:27586756

  7. Architecture of the symmetric core of the nuclear pore.

    PubMed

    Lin, Daniel H; Stuwe, Tobias; Schilbach, Sandra; Rundlet, Emily J; Perriches, Thibaud; Mobbs, George; Fan, Yanbin; Thierbach, Karsten; Huber, Ferdinand M; Collins, Leslie N; Davenport, Andrew M; Jeon, Young E; Hoelz, André

    2016-04-15

    The nuclear pore complex (NPC) controls the transport of macromolecules between the nucleus and cytoplasm, but its molecular architecture has thus far remained poorly defined. We biochemically reconstituted NPC core protomers and elucidated the underlying protein-protein interaction network. Flexible linker sequences, rather than interactions between the structured core scaffold nucleoporins, mediate the assembly of the inner ring complex and its attachment to the NPC coat. X-ray crystallographic analysis of these scaffold nucleoporins revealed the molecular details of their interactions with the flexible linker sequences and enabled construction of full-length atomic structures. By docking these structures into the cryoelectron tomographic reconstruction of the intact human NPC and validating their placement with our nucleoporin interactome, we built a composite structure of the NPC symmetric core that contains ~320,000 residues and accounts for ~56 megadaltons of the NPC's structured mass. Our approach provides a paradigm for the structure determination of similarly complex macromolecular assemblies.

  8. Nuclear pore proteins and the control of genome functions

    PubMed Central

    Ibarra, Arkaitz

    2015-01-01

    Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation. PMID:25691464

  9. Facial skin pores: a multiethnic study.

    PubMed

    Flament, Frederic; Francois, Ghislain; Qiu, Huixia; Ye, Chengda; Hanaya, Tomoo; Batisse, Dominique; Cointereau-Chardon, Suzy; Seixas, Mirela Donato Gianeti; Dal Belo, Susi Elaine; Bazin, Roland

    2015-01-01

    Skin pores (SP), as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc) that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage) on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 μm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm(2)) and determination of their respective sizes in mm(2). Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage) that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1) were recorded in all studied subjects; 2) varied greatly with ethnicity; 3) plateaued with age in most cases; and 4) globally refected self-assessment by subjects, in particular those who self-declare having "enlarged pores" like Brazilian women. Inversely, Chinese women were clearly distinct from other ethnicities in having very low density and sizes. Analyzing the present results suggests that facial skin pore's morphology as perceived by human eye less result from functional criteria of associated appendages such as sebaceous glands. To what extent skin pores may be viewed as additional criteria of a photo-altered skin is an issue to be further addressed. PMID:25733918

  10. Low pore connectivity in natural rock.

    PubMed

    Hu, Qinhong; Ewing, Robert P; Dultz, Stefan

    2012-05-15

    As repositories for CO(2) and radioactive waste, as oil and gas reservoirs, and as contaminated sites needing remediation, rock formations play a central role in energy and environmental management. The connectivity of the rock's porespace strongly affects fluid flow and solute transport. This work examines pore connectivity and its implications for fluid flow and chemical transport. Three experimental approaches (imbibition, tracer concentration profiles, and imaging) were used in combination with network modeling. In the imbibition results, three types of imbibition slope [log (cumulative imbibition) vs. log (imbibition time)] were found: the classical 0.5, plus 0.26, and 0.26 transitioning to 0.5. The imbibition slope of 0.26 seen in Indiana sandstone, metagraywacke, and Barnett shale indicates low pore connectivity, in contrast to the slope of 0.5 seen in the well-connected Berea sandstone. In the tracer profile work, rocks exhibited different distances to the plateau porosity, consistent with the pore connectivity from the imbibition tests. Injection of a molten metal into connected pore spaces, followed by 2-D imaging of the solidified alloy in polished thin sections, allowed direct assessment of pore structure and lateral connection in the rock samples. Pore-scale network modeling gave results consistent with measurements, confirming pore connectivity as the underlying cause of both anomalous behaviors: imbibition slope not having the classical value of 0.5, and accessible porosity being a function of distance from the edge. A poorly connected porespace will exhibit anomalous behavior in fluid flow and chemical transport, such as a lower imbibition slope (in air-water system) and diffusion rate than expected from classical behavior.

  11. Evaluation of upland disposal of Oakland Harbor, California, sediment. Volume 2: Inner and outer harbor sediments. Final report

    SciTech Connect

    Lee, C.R.; Brandon, D.L.; Tatem, H.E.; Simmers, J.W.; Skogerboe, J.G.

    1993-08-01

    This report describes testing and evaluation performed by the Environmental Laboratory of the U.S. Army Engineer Waterways Experiment Station on sediment from Oakland Inner and Outer Harbor, California. Test protocols from the U.S. Environmental Protection Agency (EPA)/U.S. Army Corps of Engineers' Technical Framework for the Management of Dredged Material were used in the present evaluation to determine the potential for migration of contaminants into effluent, surface runoff, leachate, plants, and animals at an undetermined upland disposal site. One composite sediment each from Oakland Inner Harbor and Oakland Outer Harbor was tested. The composite sample consisted of sediment cores taken from the mud line to 44-ft depth. Both Oakland Harbor sediments had clayey sand textures. Total organic carbon concentrations in sediment from Oakland Inner and Outer Harbors were 3,364 and 6,042 mg/kg, respectively. Based on test results, Oakland Harbor sediments will require management of suspended solids in effluent and surface runoff and a mixing zone of at least 20 to 1 to meet the strictest assumed water quality criteria or standards. Management controls should be considered at the upland site, since plants grew poorly and contained elevated cadmium, lead, and selenium and earthworms accumulated arsenic, cadmium, and nickel. Contaminant migration, Sediment testing, Contaminated sediments, Upland disposal, Dredged material.

  12. Screening of pi-basic naphthalene and anthracene amplifiers for pi-acidic synthetic pore sensors.

    PubMed

    Hagihara, Shinya; Gremaud, Ludovic; Bollot, Guillaume; Mareda, Jiri; Matile, Stefan

    2008-04-01

    Synthetic ion channels and pores attract current attention as multicomponent sensors in complex matrixes. This application requires the availability of reactive signal amplifiers that covalently capture analytes and drag them into the pore. pi-Basic 1,5-dialkoxynaphthalenes (1,5-DAN) are attractive amplifiers because aromatic electron donor-acceptor (AEDA) interactions account for their recognition within pi-acidic naphthalenediimide (NDI) rich synthetic pores. Focusing on amplifier design, we report here the synthesis of a complete collection of DAN and dialkoxyanthracene amplifiers, determine their oxidation potentials by cyclic voltammetry, and calculate their quadrupole moments. Blockage experiments reveal that subtle structural changes in regioisomeric DAN amplifiers can be registered within NDI pores. Frontier orbital overlap in AEDA complexes, oxidation potentials, and, to a lesser extent, quadrupole moments are shown to contribute to isomer recognition by synthetic pores. Particularly important with regard to practical applications of synthetic pores as multianalyte sensors, we further demonstrate that application of the lessons learned with DAN regioisomers to the expansion to dialkoxyanthracenes provides access to privileged amplifiers with submicromolar activity.

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

    PubMed

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

    2011-04-01

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

  14. Estimating methane production rates in bogs and landfills by deuterium enrichment of pore water

    USGS Publications Warehouse

    Siegel, D.I.; Chanton, J.P.; Glaser, P.H.; Chasar, L.S.; Rosenberry, D.O.

    2001-01-01

    Raised bogs and municipal waste landfills harbor large populations of methanogens within their domed deposits of anoxic organic matter. Although the methane emissions from these sites have been estimated by various methods, limited data exist on the activity of the methanogens at depth. We therefore analyzed the stable isotopic signature of the pore waters in two raised bogs from northern Minnesota to identify depth intervals in the peat profile where methanogenic metabolism occurs. Methanogenesis enriched the deuterium (2H) content of the deep peat pore waters by as much as +11% (Vienna Standard Mean Sea Water), which compares to a much greater enrichment factor of +70% in leachate from New York City's Fresh Kills landfill. The bog pore waters were isotopically dated by tritium (3H) to be about 35 years old at 1.5 m depth, whereas the landfill leachate was estimated as ~ 17 years old from Darcy flow calculations. According to an isotopic mass balance the observed deuterium enrichment indicates that about 1.2 g of CH4m-3 d-1 were produced within the deeper peat, compared to about 2.8 g CH4 m-3 d-1 in the landfill. The values for methane production in the bog peat are substantially higher than the flux rates measured at the surface of the bogs or at the landfill, indicating that deeper methane production may be much higher than was previously assumed.

  15. Estimating methane production rates in bogs and landfills by deuterium enrichment of pore water

    NASA Astrophysics Data System (ADS)

    Siegel, D. I.; Chanton, J. R.; Glaser, P. H.; Chasar, L. S.; Rosenberry, D. O.

    2001-12-01

    Raised bogs and municipal waste landfills harbor large populations of methanogens within their domed deposits of anoxic organic matter. Although the methane emissions from these sites have been estimated by various methods, limited data exist on the activity of the methanogens at depth. We therefore analyzed the stable isotopic signature of the pore waters in two raised bogs from northern Minnesota to identify depth intervals in the peat profile where methanogenic metabolism occurs. Methanogenesis enriched the deuterium (2H) content of the deep peat pore waters by as much as +11‰ (Vienna Standard Mean Sea Water), which compares to a much greater enrichment factor of +70‰ in leachate from New York City's Fresh Kills landfill. The bog pore waters were isotopically dated by tritium (3H) to be about 35 years old at 1.5 m depth, whereas the landfill leachate was estimated as ˜17 years old from Darcy flow calculations. According to an isotopic mass balance the observed deuterium enrichment indicates that about 1.2 g of CH4 m-3 d-1 were produced within the deeper peat, compared to about 2.8 g CH4 m-3 d-1 in the landfill. The values for methane production in the bog peat are substantially higher than the flux rates measured at the surface of the bogs or at the landfill, indicating that deeper methane production may be much higher than was previously assumed.

  16. 33 CFR 165.512 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., Northwest and Inner Harbors, Baltimore, MD. 165.512 Section 165.512 Navigation and Navigable Waters COAST... Guard District § 165.512 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD. (a... CONSTELLATION, while operating in the Inner Harbor, the Northwest Harbor and the Patapsco River. (c)...

  17. 33 CFR 165.512 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., Northwest and Inner Harbors, Baltimore, MD. 165.512 Section 165.512 Navigation and Navigable Waters COAST... Guard District § 165.512 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD. (a... CONSTELLATION, while operating in the Inner Harbor, the Northwest Harbor and the Patapsco River. (c)...

  18. 33 CFR 165.512 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., Northwest and Inner Harbors, Baltimore, MD. 165.512 Section 165.512 Navigation and Navigable Waters COAST... Guard District § 165.512 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD. (a... CONSTELLATION, while operating in the Inner Harbor, the Northwest Harbor and the Patapsco River. (c)...

  19. 33 CFR 165.512 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ..., Northwest and Inner Harbors, Baltimore, MD. 165.512 Section 165.512 Navigation and Navigable Waters COAST... Guard District § 165.512 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD. (a... CONSTELLATION, while operating in the Inner Harbor, the Northwest Harbor and the Patapsco River. (c)...

  20. 33 CFR 165.512 - Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ..., Northwest and Inner Harbors, Baltimore, MD. 165.512 Section 165.512 Navigation and Navigable Waters COAST... Guard District § 165.512 Safety Zone; Patapsco River, Northwest and Inner Harbors, Baltimore, MD. (a... CONSTELLATION, while operating in the Inner Harbor, the Northwest Harbor and the Patapsco River. (c)...