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Sample records for pore complexes harbor

  1. Nuclear pore complex ion channels (review).

    PubMed

    Bustamante, J O; Liepins, A; Hanover, J A

    1994-01-01

    It is currently thought that nuclear pore complexes (NPCs) primarily govern nucleocytoplasmic interactions via selective recognition and active transport of macromolecules. However, in various nuclear preparations, patch-clamp and fluorescence, luminiscence and ion microscopy support classical microelectrode measurements indicating that monoatomic ion flow across the nuclear envelope (NE) is strictly regulated. Gating of large conductance nuclear envelope ion channels (NICs) somewhat resembles that of gap junctional channels. In other respects, NICs are distinct in that they require cytosolic factors, are blocked by wheat germ agglutinin and are blocked and/or modified by antibodies to epitopes of NPC glycoproteins. Therefore, NIC activity, recorded as electrical current/conductance is likely to be intrinsic to NPCs. This observation suggests a potential use for the patch-clamp technique in establishing the mechanisms underlying nuclear pore gating in response to cytosolic and nucleosolic factors such as transcription and growth factors, oncogene and proto-oncogene products and receptors for retinoids, steroids and thyroid hormone. NIC activity may also be useful in evaluating the mechanisms of nuclear import of foreign nucleic acid material such as that contained in virons and viroids. Finally, in consideration to the electrophysiological data accumulated so far, the study of nuclear pore ion channel activity may help our understanding of other important issues such as cell suicide, programmed cell death or apoptosis.

  2. Mutant Huntingtin Disrupts the Nuclear Pore Complex.

    PubMed

    Grima, Jonathan C; Daigle, J Gavin; Arbez, Nicolas; Cunningham, Kathleen C; Zhang, Ke; Ochaba, Joseph; Geater, Charlene; Morozko, Eva; Stocksdale, Jennifer; Glatzer, Jenna C; Pham, Jacqueline T; Ahmed, Ishrat; Peng, Qi; Wadhwa, Harsh; Pletnikova, Olga; Troncoso, Juan C; Duan, Wenzhen; Snyder, Solomon H; Ranum, Laura P W; Thompson, Leslie M; Lloyd, Thomas E; Ross, Christopher A; Rothstein, Jeffrey D

    2017-04-05

    Huntington's disease (HD) is caused by an expanded CAG repeat in the Huntingtin (HTT) gene. The mechanism(s) by which mutant HTT (mHTT) causes disease is unclear. Nucleocytoplasmic transport, the trafficking of macromolecules between the nucleus and cytoplasm, is tightly regulated by nuclear pore complexes (NPCs) made up of nucleoporins (NUPs). Previous studies offered clues that mHTT may disrupt nucleocytoplasmic transport and a mutation of an NUP can cause HD-like pathology. Therefore, we evaluated the NPC and nucleocytoplasmic transport in multiple models of HD, including mouse and fly models, neurons transfected with mHTT, HD iPSC-derived neurons, and human HD brain regions. These studies revealed severe mislocalization and aggregation of NUPs and defective nucleocytoplasmic transport. HD repeat-associated non-ATG (RAN) translation proteins also disrupted nucleocytoplasmic transport. Additionally, overexpression of NUPs and treatment with drugs that prevent aberrant NUP biology also mitigated this transport defect and neurotoxicity, providing future novel therapy targets.

  3. Structure, dynamics and function of nuclear pore complexes

    PubMed Central

    D’Angelo, M. A.; Hetzer, M. W.

    2009-01-01

    Nuclear pore complexes are large aqueous channels that penetrate the nuclear envelope, connecting the nuclear interior with the cytoplasm. Until recently, these macromolecular complexes were viewed as static structures whose only function was to control the molecular trafficking between the two compartments. It has now become evident that this simplistic scenario is inaccurate and that nuclear pore complexes are highly dynamic multiprotein assemblies involved in diverse cellular processes ranging from the organization of the cytoskeleton to gene expression. In this review, we will discuss the most recent developments in the nuclear pore complex field, focusing in the assembly, disassembly, maintenance and function of this macromolecular structure. PMID:18786826

  4. 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.

  5. Toward understanding the structure of the vertebrate nuclear pore complex.

    PubMed

    Beck, Martin; Glavy, Joseph S

    2014-01-01

    Nuclear pore complexes are large macromolecular assemblies that facilitate the nucleocytoplasmic exchange of macromolecules. Because of their intricate composition, membrane association, and sheer size, the integration of various, complementary structure determination approaches is a prerequisite for elucidating their structure. We have recently employed such an integrated strategy to analyze the scaffold structure of the cytoplasmic and nuclear rings of the human nuclear pore complex. In this extra view, we highlight two specific aspects of this work: the power of electron microscopy for bridging different resolution regimes and the importance of post-translational modifications for regulating nucleoporin interactions. We review recent technological developments and give a perspective toward future structure determination approaches.

  6. Crystal structure of human nuclear pore complex component NUP43.

    PubMed

    Xu, Chao; Li, Zhihong; He, Hao; Wernimont, Amy; Li, Yanjun; Loppnau, Peter; Min, Jinrong

    2015-10-24

    Nuclear pore complexes (NPC) form nuclear pores that cross the nuclear envelope and allow molecules to transport between the nucleus and the cytoplasm. We solved the crystal structure of human Nup43 (hNUP43), an important component in the Nup107 subcomplex of NPC. hNup43 adopts a seven-bladed β-propeller fold. We confirmed by ITC that neither human Nup37 (hNup37) nor human Nup133 (hNup133) interacts with hNup43. We demonstrated by analytical gel filtration that the human Nup85-Seh1L binary complex recruits hNup43 to form a ternary complex. Based on amino acid sequence analysis, we predicted the hNup85-hSeh1L binding surface of hNup43.

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

    PubMed

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

    2015-10-01

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

  8. Atomic structure of the Y complex of the nuclear pore.

    PubMed

    Kelley, Kotaro; Knockenhauer, Kevin E; Kabachinski, Greg; Schwartz, Thomas U

    2015-05-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. Here we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved core of the Y complex has six rather than seven members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.

  9. Intron or no intron: a matter for nuclear pore complexes

    PubMed Central

    Bonnet, Amandine; Palancade, Benoit

    2015-01-01

    Nuclear pore complexes (NPCs) have been shown to regulate distinct steps of the gene expression process, from transcription to mRNA export. In particular, mRNAs expressed from intron-containing genes are surveyed by a specific NPC-dependent quality control pathway ensuring that unspliced mRNAs are retained within the nucleus. In this Extra View, we summarize the different approaches that have been developed to evaluate the contribution of various NPC components to the expression of intron-containing genes. We further present the mechanistic models that could account for pre-mRNA retention at the nuclear side of NPCs. Finally, we discuss the possibility that other stages of intron-containing gene expression could be regulated by nuclear pores, in particular through the regulation of mRNA biogenesis factors by the NPC-associated SUMO protease Ulp1. PMID:26709543

  10. Relocalization of DNA lesions to the nuclear pore complex

    PubMed Central

    Freudenreich, Catherine H.; Su, Xiaofeng A.

    2016-01-01

    Early screens in yeast for mutations exhibiting sensitivity to DNA damage identified nuclear pore components, but their role in DNA repair was not well understood. Over the last decade, studies have revealed that several types of persistent DNA lesions relocate to either the nuclear pore complex (NPC) or nuclear envelope (NE). Of these two sites, the nuclear pore appears to be crucial for DNA repair of persistent double-strand breaks, eroded telomeres and sites of fork collapse at expanded CAG repeats. Using a combination of cell biological imaging techniques and yeast genetic assays for DNA repair, researchers have begun to understand both the how and why of lesion relocation to the NPC. Here we review the types of lesions that relocate to the NPC, mediators of relocation and the functional consequences of relocation understood to date. The emerging theme is that relocation to the NPC regulates recombination to influence repair pathway choice and provide a rescue mechanism for lesions or DNA structures that are resistant to repair. PMID:27799300

  11. The Structure Inventory of the Nuclear Pore Complex.

    PubMed

    Schwartz, Thomas U

    2016-05-22

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

  12. Perforating the nuclear boundary - how nuclear pore complexes assemble.

    PubMed

    Weberruss, Marion; Antonin, Wolfram

    2016-12-15

    The nucleus is enclosed by the nuclear envelope, a double membrane which creates a selective barrier between the cytoplasm and the nuclear interior. Its barrier and transport characteristics are determined by nuclear pore complexes (NPCs) that are embedded within the nuclear envelope, and control molecular exchange between the cytoplasm and nucleoplasm. In this Commentary, we discuss the biogenesis of these huge protein assemblies from approximately one thousand individual proteins. We will summarize current knowledge about distinct assembly modes in animal cells that are characteristic for different cell cycle phases and their regulation.

  13. Nuclear pore complexes in the maintenance of genome integrity.

    PubMed

    Bukata, Lucas; Parker, Stephanie L; D'Angelo, Maximiliano A

    2013-06-01

    Maintaining genome integrity is crucial for successful organismal propagation and for cell and tissue homeostasis. Several processes contribute to safeguarding the genomic information of cells. These include accurate replication of genetic information, detection and repair of DNA damage, efficient segregation of chromosomes, protection of chromosome ends, and proper organization of genome architecture. Interestingly, recent evidence shows that nuclear pore complexes, the channels connecting the nucleus with the cytoplasm, play important roles in these processes suggesting that these multiprotein platforms are key regulators of genome integrity.

  14. Nuclear pore complexes and regulation of gene expression.

    PubMed

    Raices, Marcela; D'Angelo, Maximiliano A

    2017-01-11

    Nuclear pore complexes (NPCs), are large multiprotein channels that penetrate the nuclear envelope connecting the nucleus to the cytoplasm. Accumulating evidence shows that besides their main role in regulating the exchange of molecules between these two compartments, NPCs and their components also play important transport-independent roles, including gene expression regulation, chromatin organization, DNA repair, RNA processing and quality control, and cell cycle control. Here, we will describe the recent findings about the role of these structures in the regulation of gene expression.

  15. 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

    2015-10-02

    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.

  16. Integrated structural analysis of the human nuclear pore complex scaffold.

    PubMed

    Bui, Khanh Huy; von Appen, Alexander; DiGuilio, Amanda L; Ori, Alessandro; Sparks, Lenore; Mackmull, Marie-Therese; Bock, Thomas; Hagen, Wim; Andrés-Pons, Amparo; Glavy, Joseph S; Beck, Martin

    2013-12-05

    The nuclear pore complex (NPC) is a fundamental component of all eukaryotic cells that facilitates nucleocytoplasmic exchange of macromolecules. It is assembled from multiple copies of about 30 nucleoporins. Due to its size and complex composition, determining the structure of the NPC is an enormous challenge, and the overall architecture of the NPC scaffold remains elusive. In this study, we have used an integrated approach based on electron tomography, single-particle electron microscopy, and crosslinking mass spectrometry to determine the structure of a major scaffold motif of the human NPC, the Nup107 subcomplex, in both isolation and integrated into the NPC. We show that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the NPC. This arrangement may explain how changes of the diameter are realized that would accommodate transport of huge cargoes.

  17. The nuclear pore complex: understanding its function through structural insight.

    PubMed

    Beck, Martin; Hurt, Ed

    2017-02-01

    Nuclear pore complexes (NPCs) fuse the inner and outer nuclear membranes to form channels across the nuclear envelope. They are large macromolecular assemblies with a complex composition and diverse functions. Apart from facilitating nucleocytoplasmic transport, NPCs are involved in chromatin organization, the regulation of gene expression and DNA repair. Understanding the molecular mechanisms underlying these functions has been hampered by a lack of structural knowledge about the NPC. The recent convergence of crystallographic and biochemical in vitro analysis of nucleoporins (NUPs), the components of the NPC, with cryo-electron microscopic imaging of the entire NPC in situ has provided first pseudo-atomic view of its central core and revealed that an unexpected network of short linear motifs is an important spatial organization principle. These breakthroughs have transformed the way we understand NPC structure, and they provide an important base for functional investigations, including the elucidation of the molecular mechanisms underlying clinically manifested mutations of the nucleocytoplasmic transport system.

  18. 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

  19. Towards reconciling structure and function in the nuclear pore complex

    PubMed Central

    Aebi, Ueli; Fahrenkrog, Birthe

    2008-01-01

    The spatial separation between the cytoplasm and the cell nucleus necessitates the continuous exchange of macromolecular cargo across the double-membraned nuclear envelope. Being the only passageway in and out of the nucleus, the nuclear pore complex (NPC) has the principal function of regulating the high throughput of nucleocytoplasmic transport in a highly selective manner so as to maintain cellular order and function. Here, we present a retrospective review of the evidence that has led to the current understanding of both NPC structure and function. Looking towards the future, we contemplate on how various outstanding effects and nanoscopic characteristics ought to be addressed, with the goal of reconciling structure and function into a single unified picture of the NPC. PMID:18228033

  20. Structure and gating of the nuclear pore complex

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  1. Structure and gating of the nuclear pore complex.

    PubMed

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

    2015-06-26

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

  2. A Change In Nuclear Pore Complex Composition Regulates Cell Differentiation

    PubMed Central

    D’Angelo, Maximiliano A.; Gomez-Cavazos, J. Sebastian; Mei, Arianna; Lackner, Daniel H.; Hetzer, Martin W.

    2011-01-01

    SUMMARY Nuclear pore complexes (NPCs) are built from ~30 different proteins called nucleoporins. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem (ES) cells but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ES cells into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination. PMID:22264802

  3. 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.

  4. 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.

  5. 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

  6. The nuclear pore complexes: guardians of the nuclear genome

    PubMed Central

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

    2013-01-01

    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 role 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 play critical roles in chromatin organization and gene regulation. These findings have sparked new enthusiasm to study the roles of this multi-protein complex in nuclear organization and explore novel functions that in some cases appear to go beyond a role in transport. Here, we discuss our current view of NPC biogenesis, which is tightly linked to proper cell cycle progression and cell differentiation. In addition we will summarize new data suggesting that NPCs represent dynamic hubs for the integration of gene regulation and nuclear transport processes. PMID:21502404

  7. Simple rules for passive diffusion through the nuclear pore complex

    PubMed Central

    Mironska, Roxana; Kim, Seung Joong

    2016-01-01

    Passive macromolecular diffusion through nuclear pore complexes (NPCs) is thought to decrease dramatically beyond a 30–60-kD size threshold. Using thousands of independent time-resolved fluorescence microscopy measurements in vivo, we show that the NPC lacks such a firm size threshold; instead, it forms a soft barrier to passive diffusion that intensifies gradually with increasing molecular mass in both the wild-type and mutant strains with various subsets of phenylalanine-glycine (FG) domains and different levels of baseline passive permeability. Brownian dynamics simulations replicate these findings and indicate that the soft barrier results from the highly dynamic FG repeat domains and the diffusing macromolecules mutually constraining and competing for available volume in the interior of the NPC, setting up entropic repulsion forces. We found that FG domains with exceptionally high net charge and low hydropathy near the cytoplasmic end of the central channel contribute more strongly to obstruction of passive diffusion than to facilitated transport, revealing a compartmentalized functional arrangement within the NPC. PMID:27697925

  8. 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

  9. Exceptional structural and mechanical flexibility of the nuclear pore complex.

    PubMed

    Liashkovich, Ivan; Meyring, Anne; Kramer, Armin; Shahin, Victor

    2011-03-01

    Nuclear pore complexes (NPCs) mediate all transport between the cytosol and the nucleus and therefore take centre stage in physiology. While transport through NPCs has been extensively investigated little is known about their structural and barley anything about their mechanical flexibility. Structural and mechanical flexibility of NPCs, however, are presumably of key importance. Like the cell and the cell nucleus, NPCs themselves are regularly exposed to physiological mechanical forces. Besides, NPCs reveal striking transport properties which are likely to require fairly high structural flexibility. The NPC transports up to 1,000 molecules per second through a physically 9 nm wide channel which repeatedly opens to accommodate macromolecules significantly larger than its physical diameter. We hypothesised that NPCs possess remarkable structural and mechanical stability. Here, we tested this hypothesis at the single NPC level using the nano-imaging and probing approach atomic force microscopy (AFM). AFM presents the NPC as a highly flexible structure. The NPC channel dilates by striking 35% on exposure to trans-cyclohexane-1,2-diol (TCHD), which is known to transiently collapse the hydrophobic phase in the NPC channel like receptor-cargo complexes do in transit. It constricts again to its initial size after TCHD removal. AFM-based nano-indentation measurements show that the 50 nm long NPC basket can astonishingly be squeezed completely into the NPC channel on exposure to incremental mechanical loads but recovers its original vertical position within the nuclear envelope plane when relieved. We conclude that the NPC possesses exceptional structural and mechanical flexibility which is important to fulfilling its functions.

  10. 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.

  11. Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling.

    PubMed

    Bischofberger, Mirko; Iacovache, Ioan; Boss, Daniel; Naef, Felix; van der Goot, F Gisou; Molina, Nacho

    2016-04-12

    Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

  12. Characterization of a nuclear pore protein sheds light on the roles and composition of the Toxoplasma gondii nuclear pore complex.

    PubMed

    Courjol, Flavie; Mouveaux, Thomas; Lesage, Kevin; Saliou, Jean-Michel; Werkmeister, Elisabeth; Bonabaud, Maurine; Rohmer, Marine; Slomianny, Christian; Lafont, Franck; Gissot, Mathieu

    2017-01-30

    The nuclear pore is a key structure in eukaryotes regulating nuclear-cytoplasmic transport as well as a wide range of cellular processes. Here, we report the characterization of the first Toxoplasma gondii nuclear pore protein, named TgNup302, which appears to be the orthologue of the mammalian Nup98-96 protein. We produced a conditional knock-down mutant that expresses TgNup302 under the control of an inducible tetracycline-regulated promoter. Under ATc treatment, a substantial decrease of TgNup302 protein in inducible knock-down (iKD) parasites was observed, causing a delay in parasite proliferation. Moreover, the nuclear protein TgENO2 was trapped in the cytoplasm of ATc-treated mutants, suggesting that TgNup302 is involved in nuclear transport. Fluorescence in situ hybridization revealed that TgNup302 is essential for 18S RNA export from the nucleus to the cytoplasm, while global mRNA export remains unchanged. Using an affinity tag purification combined with mass spectrometry, we identified additional components of the nuclear pore complex, including proteins potentially interacting with chromatin. Furthermore, reverse immunoprecipitation confirmed their interaction with TgNup302, and structured illuminated microscopy confirmed the NPC localization of some of the TgNup302-interacting proteins. Intriguingly, facilitates chromatin transcription complex (FACT) components were identified, suggesting the existence of an NPC-chromatin interaction in T. gondii. Identification of TgNup302-interacting proteins also provides the first glimpse at the NPC structure in Apicomplexa, suggesting a structural conservation of the NPC components between distant eukaryotes.

  13. SNARE Complex Zipping as a Driving Force in the Dilation of Proteinaceous Fusion Pores

    PubMed Central

    Jackson, Meyer B.

    2010-01-01

    The assembly of SNARE proteins into a tight complex has been hypothesized to drive membrane fusion. A model of the initial fusion pore as a proteinaceous channel formed by SNARE proteins places their membrane anchors in separate membranes. This leaves the possibility of a final assembly step that brings the membrane anchors together and drives fusion pore expansion. The present study develops a model for expansion in which the final SNARE complex zipping step drives a transition from a proteinaceous fusion pore to a lipidic fusion pore. An estimate of the energy released upon merger of the helical segment of the SNARE motif with the helical membrane anchor indicates that completing the assembly of a few SNARE complexes can overcome the elastic energy that opposes lipid bilayer deformation into a narrow fusion pore. The angle between the long axes of membrane anchor and SNARE motif serves as a useful reaction coordinate for this transition. Energy was calculated as a function of this angle, incorporating contributions from membrane bending, SNARE complex assembly, membrane anchor flexing, and hydrophobic interactions. The rate of this transition was evaluated as a process of diffusion over the barrier imposed by these combined energies, and the rates estimated were consistent with experimental measurements. PMID:20512644

  14. Study of the Protein Complex, Pore Diameter, and Pore-forming Activity of the Borrelia burgdorferi P13 Porin*

    PubMed Central

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

    2014-01-01

    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. PMID:24825899

  15. Integrating complex functions: coordination of nuclear pore complex assembly and membrane expansion of the nuclear envelope requires a family of integral membrane proteins.

    PubMed

    Schneiter, Roger; Cole, Charles N

    2010-01-01

    The nuclear envelope harbors numerous large proteinaceous channels, the nuclear pore complexes (NPCs), through which macromolecular exchange between the cytosol and the nucleoplasm occurs. This double-membrane nuclear envelope is continuous with the endoplasmic reticulum and thus functionally connected to such diverse processes as vesicular transport, protein maturation and lipid synthesis. Recent results obtained from studies in Saccharomyces cerevisiae indicate that assembly of the nuclear pore complex is functionally dependent upon maintenance of lipid homeostasis of the ER membrane. Previous work from one of our laboratories has revealed that an integral membrane protein Apq12 is important for the assembly of functional nuclear pores. Cells lacking APQ12 are viable but cannot grow at low temperatures, have aberrant NPCs and a defect in mRNA export. Remarkably, these defects in NPC assembly can be overcome by supplementing cells with a membrane fluidizing agent, benzyl alcohol, suggesting that Apq12 impacts the flexibility of the nuclear membrane, possibly by adjusting its lipid composition when cells are shifted to a reduced temperature. Our new study now expands these findings and reveals that an essential membrane protein, Brr6, shares at least partially overlapping functions with Apq12 and is also required for assembly of functional NPCs. A third nuclear envelope membrane protein, Brl1, is related to Brr6, and is also required for NPC assembly. Because maintenance of membrane homeostasis is essential for cellular survival, the fact that these three proteins are conserved in fungi that undergo closed mitoses, but are not found in metazoans or plants, may indicate that their functions are performed by proteins unrelated at the primary sequence level to Brr6, Brl1 and Apq12 in cells that disassemble their nuclear envelopes during mitosis.

  16. Modeling of the mechano-chemical behaviour of the nuclear pore complex: current research and perspectives

    PubMed Central

    Rodriguez Matas, Jose F.; Raimondi, Manuela T.

    2016-01-01

    Recent evidence suggests that mechanical deformation of the cell nucleus regulates the nuclear import of the transcriptional activators of genes involved in primary physiological cell responses such as stem cell differentiation. In addition, this nuclear mechanosensing response is de-regulated in pathological states, such as cancer and neurodegeneration. One hypothesis that could greatly advance the field is that the deformation of the nuclear envelope activates nuclear pore complexes through a direct mechanical link. The understanding of this possible mechanism for nuclear pore complex stretch-activation entails studying the mechanical connection of this complex to the nuclear envelope at the nanoscale. The nanomechanics of the nuclear pore complex is thus emerging as a novel research field, bridging nanoscience with nanotechnology. This review examines the frontier of research methodologies that are potentially useful for building a computational model of this interaction. This includes, for example, electron tomography to assess the geometrical features of the nuclear pore complex and nanoindentation to estimate its mechanical properties and that of the nuclear envelope. In order to summarize the state-of-the-art and perspectives in the field of NPC nanomechanics, this review covers highly interdisciplinary experimental and theoretical research methodologies pertaining to the fields of physics, chemistry, biology, materials and mechanics. PMID:27713975

  17. Modeling of the mechano-chemical behaviour of the nuclear pore complex: current research and perspectives.

    PubMed

    Garcia, Alberto; Rodriguez Matas, Jose F; Raimondi, Manuela T

    2016-10-10

    Recent evidence suggests that mechanical deformation of the cell nucleus regulates the nuclear import of the transcriptional activators of genes involved in primary physiological cell responses such as stem cell differentiation. In addition, this nuclear mechanosensing response is de-regulated in pathological states, such as cancer and neurodegeneration. One hypothesis that could greatly advance the field is that the deformation of the nuclear envelope activates nuclear pore complexes through a direct mechanical link. The understanding of this possible mechanism for nuclear pore complex stretch-activation entails studying the mechanical connection of this complex to the nuclear envelope at the nanoscale. The nanomechanics of the nuclear pore complex is thus emerging as a novel research field, bridging nanoscience with nanotechnology. This review examines the frontier of research methodologies that are potentially useful for building a computational model of this interaction. This includes, for example, electron tomography to assess the geometrical features of the nuclear pore complex and nanoindentation to estimate its mechanical properties and that of the nuclear envelope. In order to summarize the state-of-the-art and perspectives in the field of NPC nanomechanics, this review covers highly interdisciplinary experimental and theoretical research methodologies pertaining to the fields of physics, chemistry, biology, materials and mechanics.

  18. Towards understanding nuclear pore complex architecture and dynamics in the age of integrative structural analysis.

    PubMed

    Hurt, Ed; Beck, Martin

    2015-06-01

    Determining the functional architecture of the nuclear pore complex, that remains only partially understood, requires bridging across different length scales. Recent technological advances in quantitative and cross-linking mass spectrometry, super-resolution fluorescence microscopy and electron microscopy have enormously accelerated the integration of different types of data into coherent structural models. Moreover, high-resolution structural analysis of nucleoporins and their in vitro reconstitution into complexes is now facilitated by the use of thermostable orthologs. In this review we highlight how the application of such technologies has led to novel insights into nuclear pore architecture and to a paradigm shift. Today nuclear pores are not anymore seen as static facilitators of nucleocytoplasmic transport but ensembles of multiple overlaying functional states that are involved in various cellular processes.

  19. 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

  20. The diverse roles of the Nup93/Nic96 complex proteins - structural scaffolds of the nuclear pore complex with additional cellular functions.

    PubMed

    Vollmer, Benjamin; Antonin, Wolfram

    2014-05-01

    Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.

  1. Investigation of nuclear pore complex protein interactions and the implications for nuclear transport

    NASA Astrophysics Data System (ADS)

    Isgro, Timothy A.

    The nucleus of the cell is of central importance to an organism, serving to store and organize genetic material, while separating and protecting this very important information from the host of other cellular components. While the nucleus requires this protective isolation, it also needs to communicate with the rest of the cell, exchanging proteins and RNA, for a variety of nuclear and cytoplasmic processes which act in concert. The nuclear pore complex is responsible for controlling the transport of large molecules into and out of the cell nucleus. It is perhaps the largest protein structure in eukaryotic cells, and because of its size, pointed experimental study has been difficult. As a result, the mechanism by which the nuclear pore complex selectively allows "good" material across the nuclear envelope, while preventing the transit of "bad", remains unknown. Here, the computer has been used to study interactions between the transport receptors that shuttle material across the nuclear pore complex and FG-nucleoporins, proteins which compose the complex itself and are of great importance in allowing protected nuclear transport. Molecular dynamics simulations have been performed on transport complexes formed by the transport receptors importin-beta, NTF2, and Cse1p. The simulations confirm nearly all interactions previously known about from experimental data, while serving, in some cases, to provide greater detail about these interactions. Furthermore, the simulations uncover a host of previously unknown interactions between each transport receptor and FG-nups. When the interactions are compared across all three transport receptors, a novel binding pattern is revealed that indicates how the nuclear pore complex may recognize the difference between the macromolecules destined to cross the nuclear envelope and the host of other proteins for which it must protect against transport.

  2. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform.

    PubMed

    Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; Upla, Paula; Pellarin, Riccardo; Gagnon, Michael; Chemmama, Ilan E; Wang, Junjie; Nudelman, Ilona; Zhang, Wenzhu; Williams, Rosemary; Rice, William J; Stokes, David L; Zenklusen, Daniel; Chait, Brian T; Sali, Andrej; Rout, Michael P

    2016-11-17

    The last steps in mRNA export and remodeling are performed by the Nup82 complex, a large conserved assembly at the cytoplasmic face of the nuclear pore complex (NPC). By integrating diverse structural data, we have determined the molecular architecture of the native Nup82 complex at subnanometer precision. The complex consists of two compositionally identical multiprotein subunits that adopt different configurations. The Nup82 complex fits into the NPC through the outer ring Nup84 complex. Our map shows that this entire 14-MDa Nup82-Nup84 complex assembly positions the cytoplasmic mRNA export factor docking sites and messenger ribonucleoprotein (mRNP) remodeling machinery right over the NPC's central channel rather than on distal cytoplasmic filaments, as previously supposed. We suggest that this configuration efficiently captures and remodels exporting mRNP particles immediately upon reaching the cytoplasmic side of the NPC.

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

    PubMed

    Kabachinski, Greg; Schwartz, Thomas U

    2015-02-01

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

  4. Atomic Structure of the Y-Complex of the Nuclear Pore

    PubMed Central

    Kabachinski, Greg; Schwartz, Thomas U.

    2015-01-01

    The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40 MDa ring-like structure. Here we present the 4.1 Å crystal structure of a heterotetrameric core element (‘hub’) of the Y-complex, the essential NPC building block, from Myceliophthora thermophila. Using the ‘hub’ structure together with known Y-complex fragments we built the entire ~0.5 MDa Y-complex. Our data reveal that the conserved core of the Y-complex has 6, rather than 7 members. Evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes. PMID:25822992

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

    PubMed

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

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Auger, Thomas; Auvray, Loic; Montel, Fabien

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

  7. 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.

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

    PubMed

    von Appen, Alexander; Beck, Martin

    2016-05-22

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

  9. Single hepatitis-B virus core capsid binding to individual nuclear pore complexes in Hela cells.

    PubMed

    Lill, Yoriko; Lill, Markus A; Fahrenkrog, Birthe; Schwarz-Herion, Kyrill; Paulillo, Sara; Aebi, Ueli; Hecht, Bert

    2006-10-15

    We investigate the interaction of hepatitis B virus capsids lacking a nuclear localization signal with nuclear pore complexes (NPCs) in permeabilized HeLa cells. Confocal and wide-field optical images of the nuclear envelope show well-spaced individual NPCs. Specific interactions of capsids with single NPCs are characterized by extended residence times of capsids in the focal volume which are characterized by fluorescence correlation spectroscopy. In addition, single-capsid-tracking experiments using fast wide-field fluorescence microscopy at 50 frames/s allow us to directly observe specific binding via a dual-color colocalization of capsids and NPCs. We find that binding occurs with high probability on the nuclear-pore ring moiety, at 44 +/- 9 nm radial distance from the central axis.

  10. MpWIP regulates air pore complex development in the liverwort Marchantia polymorpha.

    PubMed

    Jones, Victor A S; Dolan, Liam

    2017-04-15

    The colonisation of the land by plants was accompanied by the evolution of complex tissues and multicellular structures comprising different cell types as morphological adaptations to the terrestrial environment. Here, we show that the single WIP protein in the early-diverging land plant Marchantia polymorpha L. is required for the development of the multicellular gas exchange structure: the air pore complex. This 16-cell barrel-shaped structure surrounds an opening between epidermal cells that facilitates the exchange of gases between the chamber containing the photosynthetic cells inside the plant and the air outside. MpWIP is expressed in cells of the developing air pore complex and the morphogenesis of the complex is defective in plants with reduced MpWIP function. The role of WIP proteins in the control of different multicellular structures in M. polymorpha and the flowering plant Arabidopsis thaliana suggests that these proteins controlled the development of multicellular structures in the common ancestor of land plants. We hypothesise that WIP genes were subsequently co-opted in the control of morphogenesis of novel multicellular structures that evolved during the diversification of land plants.

  11. 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

    2013-04-02

    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.

  12. CKMT1 regulates the mitochondrial permeability transition pore in a process that provides evidence for alternative forms of the complex

    PubMed Central

    Datler, Christoph; Pazarentzos, Evangelos; Mahul-Mellier, Anne-Laure; Chaisaklert, Wanwisa; Hwang, Ming-Shih; Osborne, Foy; Grimm, Stefan

    2014-01-01

    ABSTRACT The permeability transition pore (PT-pore) mediates cell death through the dissipation of the mitochondrial membrane potential (ΔΨm). Because the exact composition of the PT-pore is controversial, it is crucial to investigate the actual molecular constituents and regulators of this complex. We found that mitochondrial creatine kinase-1 (CKMT1) is a universal and functionally necessary gatekeeper of the PT-pore, as its depletion induces mitochondrial depolarization and apoptotic cell death. This can be inhibited efficiently by bongkrekic acid, a compound that is widely used to inhibit the PT-pore. However, when the ‘classical’ PT-pore subunits cyclophilin D and VDAC1 are pharmacologically inhibited or their expression levels reduced, mitochondrial depolarization by CKMT1 depletion remains unaffected. At later stages of drug-induced apoptosis, CKMT1 levels are reduced, suggesting that CKMT1 downregulation acts to reinforce the commitment of cells to apoptosis. A novel high-molecular-mass CKMT1 complex that is distinct from the known CKMT1 octamer disintegrates upon treatment with cytotoxic drugs, concomitant with mitochondrial depolarization. Our study provides evidence that CKMT1 is a key regulator of the PT-pore through a complex that is distinct from the classical PT-pore. PMID:24522192

  13. Nuclear pore complex protein sequences determine overall copolymer brush structure and function.

    PubMed

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

    2014-05-06

    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.

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

    PubMed

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

    2015-01-01

    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 NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography 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 microscopy. 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.

  15. Choreography of importin-α/CAS complex assembly and disassembly at nuclear pores.

    PubMed

    Sun, Changxia; Fu, Guo; Ciziene, Danguole; Stewart, Murray; Musser, Siegfried M

    2013-04-23

    Nuclear pore complexes (NPCs) mediate the exchange of macromolecules between the cytoplasm and the nucleoplasm. Soluble nuclear transport receptors bind signal-dependent cargos to form transport complexes that diffuse through the NPC and are then disassembled. Although transport receptors enable the NPC's permeability barrier to be overcome, directionality is established by complex assembly and disassembly. Here, we delineate the choreography of importin-α/CAS complex assembly and disassembly in permeabilized cells, using single-molecule fluorescence resonance energy transfer and particle tracking. Monitoring interaction sequences in intact NPCs ensures spatiotemporal preservation of structures and interactions critical for activity in vivo. We show that key interactions between components are reversible, multiple outcomes are often possible, and the assembly and disassembly of complexes are precisely controlled to occur at the appropriate place and time. Importin-α mutants that impair interactions during nuclear import were used together with cytoplasmic Ran GTPase-activating factors to demonstrate that importin-α/CAS complexes form in the nuclear basket region, at the termination of protein import, and disassembly of importin-α/CAS complexes after export occurs in the cytoplasmic filament region of the NPC. Mathematical models derived from our data emphasize the intimate connection between transport and the coordinated assembly and disassembly of importin-α/CAS complexes for generating productive transport cycles.

  16. Functional insights from studies on the structure of the nuclear pore and coat protein complexes.

    PubMed

    Schwartz, Thomas

    2013-07-01

    The nuclear envelope (NE) is a specific extension of the endoplasmic reticulum (ER) that wraps around the nucleus and enables the spatial separation of gene transcription and protein translation, one of the signature features of eukaryotes. Rather than being completely closed, the double lipid bilayer of the NE is perforated at sites where the inner and outer nuclear membranes fuse, resulting in circular openings lined with sharply bent membranes. These openings are filled with nuclear pore complexes (NPCs), enormous protein assemblies that facilitate nuclear transport. The scaffold components of the NPC surprisingly share interesting similarities with elements of coat protein complexes, which have general implications for function and evolution of these membrane-coating complexes. Here I discuss, from a structural perspective, what these findings might teach us.

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

    SciTech Connect

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

    2009-11-06

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

  18. 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.

  19. Towards the atomic structure of the Nuclear Pore Complex: When top down meets bottom up

    PubMed Central

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

    2016-01-01

    Elucidating the structure of the nuclear pore complex (NPC) is a prerequisite for understanding the molecular mechanism of nucleocytoplasmic transport. However, due to 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, bridging the resolution gap from higher-order scaffold structure to near-atomic resolution and opening the door for structure-guided experimental interrogations of NPC function. PMID:27273515

  20. 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

  1. Architecture of the Xenopus nuclear pore complex revealed by three- dimensional cryo-electron microscopy

    PubMed Central

    1993-01-01

    The nuclear pore complex spans the nuclear envelope and functions as a macromolecular transporter in the ATP-dependent process of nucleocytoplasmic transport. In this report, we present three dimensional (3D) structures for both membrane-associated and detergent- extracted Xenopus NPCs, imaged in frozen buffers by cryo-electron microscopy. A comparison of the differing configurations present in the 3D maps suggests that the spokes may possess an intrinsic conformational flexibility. When combined with recent data from a 3D map of negatively stained NPCs (Hinshaw, J. E., B. O. Carragher, and R. A. Milligan. 1992. Cell. 69:1133-1141), these observations suggest a minimal domain model for the spoke-ring complex which may account for the observed plasticity of this assembly. Moreover, lumenal domains in adjacent spokes are interconnected by radial arm dimers, forming a lumenal ring that may be responsible for anchoring the NPC within the nuclear envelope pore. Importantly, the NPC transporter is visualized as a centrally tapered cylinder that spans the entire width of the NPC, in a direction normal to the nuclear envelope. The central positioning, tripartite structure, and hollow nature of the transporter suggests that it may form a macromolecular transport channel, with a globular gating domain at each end. Finally, the packing of the transporter within the spokes creates a set of eight internal channels that may be responsible, in part, for the diffusion of ions and small molecules across the nuclear envelope. PMID:8314837

  2. Structure-function mapping of a heptameric module in the nuclear pore complex.

    PubMed

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

    2012-02-20

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

  3. 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

  4. 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.

  5. Environmental Assessment for Building 88 Interior Demolition, Pearl Harbor Naval Complex, O’ahu, Hawaii

    DTIC Science & Technology

    2005-06-01

    Peninsula NAVMAG Pearl Harbor West Loch Branch Waipahu H-1 FreewayKamehameha Highway Fa rrin gto n H ighw ay F o rt W e a ve r R o a d H-1 Fr eew ay...Honolulu Not to Scale Kahuku Point Mokapu Point Makapu`u Point O`ahu Project Site Project Location Map Building 88 Interior Demolition Environmental

  6. Regulation of nuclear pore complex conformation by IP(3) receptor activation.

    PubMed Central

    Moore-Nichols, David; Arnott, Anne; Dunn, Robert C

    2002-01-01

    In recent years, both the molecular architecture and functional dynamics of nuclear pore complexes (NPCs) have been revealed with increasing detail. These large, supramolecular assemblages of proteins form channels that span the nuclear envelope of cells, acting as crucial regulators of nuclear import and export. From the cytoplasmic face of the nuclear envelope, nuclear pore complexes exhibit an eightfold symmetric ring structure encompassing a central lumen. The lumen often appears occupied by an additional structure alternatively referred to as the central granule, nuclear transport complex, or nuclear plug. Previous studies have suggested that the central granule may play a role in mediating calcium-dependent regulation of diffusion across the nuclear envelope for intermediate sized molecules (10-40 kDa). Using atomic force microscopy to measure the surface topography of chemically fixed Xenopus laevis oocyte nuclear envelopes, we present measurements of the relative position of the central granule within the NPC lumen under a variety of conditions known to modify nuclear Ca(2+) stores. These measurements reveal a large, approximately 9-nm displacement of the central granule toward the cytoplasmic face of the nuclear envelope under calcium depleting conditions. Additionally, activation of nuclear inositol triphosphate (IP(3)) receptors by the specific agonist, adenophostin A, results in a concentration-dependent displacement of central granule position with an EC(50) of ~1.2 nM. The displacement of the central granule within the NPC is observed on both the cytoplasmic and nucleoplasmic faces of the nuclear envelope. The displacement is blocked upon treatment with xestospongin C, a specific inhibitor of IP(3) receptor activation. These results extend previous models of NPC conformational dynamics linking central granule position to depletion of IP(3) sensitive nuclear envelope calcium stores. PMID:12202368

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  8. 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.

  9. Nucleoporin domain topology is linked to the transport status of the nuclear pore complex.

    PubMed

    Paulillo, Sara M; Phillips, Erica M; Köser, Joachim; Sauder, Ursula; Ullman, Katharine S; Powers, Maureen A; Fahrenkrog, Birthe

    2005-08-26

    Nuclear pore complexes (NPCs) facilitate macromolecular exchange between the nucleus and cytoplasm of eukaryotic cells. The vertebrate NPC is composed of approximately 30 different proteins (nucleoporins), of which around one third contain phenylalanine-glycine (FG)-repeat domains that are thought to mediate the main interaction between the NPC and soluble transport receptors. We have recently shown that the FG-repeat domain of Nup153 is flexible within the NPC, although this nucleoporin is anchored to the nuclear side of the NPC. By using domain-specific antibodies, we have now mapped the domain topology of Nup214 in Xenopus oocytes and in human somatic cells by immuno-EM. We have found that whereas Nup214 is anchored to the cytoplasmic side of the NPC via its N-terminal and central domain, its FG-repeat domain appears flexible, residing on both sides of the NPC. Moreover, the spatial distribution of the FG-repeat domains of both Nup153 and Nup214 shifts in a transport-dependent manner, suggesting that the location of FG-repeat domains within the NPC correlates with cargo/receptor interactions and that they concomitantly move with cargo through the central pore of the NPC.

  10. Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics

    PubMed Central

    Miao, Lingling; Schulten, Klaus

    2010-01-01

    Abstract The central pore of a nuclear pore complex (NPC) is filled with unstructured proteins that contain many FG-repeats separated by hydrophilic regions. An example of such protein is nsp1. By simulating an array of nsp1 segments, we identified, in an earlier study, a spontaneously formed brushlike structure that promises to explain selective transport in the NPC channel. Here we report four (350,000 atom, 200 ns) simulations probing this structure via its interaction with transport receptor NTF2 as well as with an inert protein. NTF2 dimers are observed to gradually enter the brush, but the inert protein is not. Both NTF2 and the inert protein are found to bind to FG-repeats, but binding periods lasted more briefly for the inert protein. A simulation also investigated the behavior of a brush made of mutant nsp1 that is known to be less effective in NPC-selective transport, finding that this brush does not attract NTF2. PMID:20409487

  11. How to operate a nuclear pore complex by Kap-centric control

    PubMed Central

    Lim, Roderick Y H; Huang, Binlu; Kapinos, Larisa E

    2015-01-01

    Nuclear pore complexes (NPCs) mediate molecular transport between the nucleus and cytoplasm in eukaryotic cells. Tethered within each NPC lie numerous intrinsically disordered proteins known as FG nucleoporins (FG Nups) that are central to this process. Over two decades of investigation has converged on a view that a barrier mechanism consisting of FG Nups rejects non-specific macromolecules while promoting the speed and selectivity of karyopherin (Kaps) receptors (and their cargoes). Yet, the number of NPCs in the cell is exceedingly small compared to the number of Kaps, so that in fact there is a high likelihood the pores are always populated by Kaps. Here, we contemplate a view where Kaps actively participate in regulating the selectivity and speed of transport through NPCs. This so-called “Kap-centric” control of the NPC accounts for Kaps as essential barrier reinforcements that play a prerequisite role in facilitating fast transport kinetics. Importantly, Kap-centric control reconciles both mechanistic and kinetic requirements of the NPC, and in so doing potentially resolves incoherent aspects of FG-centric models. On this basis, we surmise that Kaps prime the NPC for nucleocytoplasmic transport by fine-tuning the NPC microenvironment according to the functional needs of the cell. PMID:26338152

  12. The Nuclear Pore-Associated TREX-2 Complex Employs Mediator to Regulate Gene Expression

    PubMed Central

    Schneider, Maren; Hellerschmied, Doris; Schubert, Tobias; Amlacher, Stefan; Vinayachandran, Vinesh; Reja, Rohit; Pugh, B. Franklin; Clausen, Tim; Köhler, Alwin

    2015-01-01

    Summary Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription, and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with the Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent at specific genes. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing. Our data provide mechanistic insight into how an NPC-associated adaptor complex accesses the core transcription machinery. PMID:26317468

  13. 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

  14. Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.

    PubMed

    Upla, Paula; Kim, Seung Joong; Sampathkumar, Parthasarathy; Dutta, Kaushik; Cahill, Sean M; Chemmama, Ilan E; Williams, Rosemary; Bonanno, Jeffrey B; Rice, William J; Stokes, David L; Cowburn, David; Almo, Steven C; Sali, Andrej; Rout, Michael P; Fernandez-Martinez, Javier

    2017-03-07

    The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scattering methods to determine an integrative structure of the ∼120 kDa luminal domain of Pom152. Our structural analysis reveals that the luminal domain is formed by a flexible string-of-pearls arrangement of nine repetitive cadherin-like Ig-like domains, indicating an evolutionary connection between NPCs and the cell adhesion machinery. The 16 copies of Pom152 known to be present in the yeast NPC are long enough to form the observed membrane ring, suggesting how interactions between Pom152 molecules help establish and maintain the NPC architecture.

  15. Nuclear Pore Complexes and Nucleocytoplasmic Transport: From Structure to Function to Disease.

    PubMed

    Dickmanns, Achim; Kehlenbach, Ralph H; Fahrenkrog, Birthe

    2015-01-01

    Nucleocytoplasmic transport is an essential cellular activity and occurs via nuclear pore complexes (NPCs) that reside in the double membrane of the nuclear envelope. Significant progress has been made during the past few years in unravelling the ultrastructural organization of NPCs and their constituents, the nucleoporins, by cryo-electron tomography and X-ray crystallography. Mass spectrometry and genomic approaches have provided deeper insight into the specific regulation and fine tuning of individual nuclear transport pathways. Recent research has also focused on the roles nucleoporins play in health and disease, some of which go beyond nucleocytoplasmic transport. Here we review emerging results aimed at understanding NPC architecture and nucleocytoplasmic transport at the atomic level, elucidating the specific function individual nucleoporins play in nuclear trafficking, and finally lighting up the contribution of nucleoporins and nuclear transport receptors in human diseases, such as cancer and certain genetic disorders.

  16. Nuclear pore complex composition: a new regulator of tissue-specific and developmental functions.

    PubMed

    Raices, Marcela; D'Angelo, Maximiliano A

    2012-11-01

    Nuclear pore complexes (NPCs) are multiprotein aqueous channels that penetrate the nuclear envelope connecting the nucleus and the cytoplasm. NPCs consist of multiple copies of roughly 30 different proteins known as nucleoporins (NUPs). Due to their essential role in controlling nucleocytoplasmic transport, NPCs have traditionally been considered as structures of ubiquitous composition. The overall structure of the NPC is indeed conserved in all cells, but new evidence suggests that the protein composition of NPCs varies among cell types and tissues. Moreover, mutations in various nucleoporins result in tissue-specific diseases. These findings point towards a heterogeneity in NPC composition and function. This unexpected heterogeneity suggests that cells use a combination of different nucleoporins to assemble NPCs with distinct properties and specialized functions.

  17. 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.

  18. Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex.

    PubMed

    Ma, Jiong; Kelich, Joseph M; Junod, Samuel L; Yang, Weidong

    2017-02-15

    The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), 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. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside the sub-micrometer supramolecular complex. Here we combined super-resolution SPEED microscopy and nanobody specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveals both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provides evidence for their copy numbers of 8, 32, and 16 respectively per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes.

  19. 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

  20. 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.

  1. ELYS/MEL-28 chromatin association coordinates nuclear pore complex assembly and replication licensing.

    PubMed

    Gillespie, Peter J; Khoudoli, Guennadi A; Stewart, Graeme; Swedlow, Jason R; Blow, J Julian

    2007-10-09

    Xenopus egg extract supports all the major cell-cycle transitions in vitro. We have used a proteomics approach to identify proteins whose abundance on chromatin changes during the course of an in vitro cell cycle. One of the proteins we identified was ELYS/MEL-28, which has recently been described as the earliest-acting factor known to be required for nuclear pore complex (NPC) assembly [1-4]. ELYS interacts with the Nup107-160 complex and is required for its association with chromatin. ELYS contains an AT-hook domain, which we show binds to chromatin with a high affinity. This domain can compete with full-length ELYS for chromatin association, thereby blocking NPC assembly. This provides evidence that ELYS interacts directly with chromatin and that this interaction is essential for NPC assembly and compartmentalization of chromosomal DNA within the cell. Furthermore, we detected a physical association on chromatin between ELYS and the Mcm2-7 replication-licensing proteins. ELYS chromatin loading, NPC assembly, and nuclear growth were delayed when Mcm2-7 was prevented from loading onto chromatin. Because nuclear assembly is required to shut down licensing prior to entry into S phase, our results suggest a mechanism by which these two early cell-cycle events are coordinated with one another.

  2. Three-Dimensional Mapping of mRNA Export through the Nuclear Pore Complex

    PubMed Central

    Schnell, Steven J.; Ma, Jiong; Yang, Weidong

    2014-01-01

    The locations of transcription and translation of mRNA in eukaryotic cells are spatially separated by the nuclear envelope (NE). Plenty of nuclear pore complexes (NPCs) embedded in the NE function as the major gateway for the export of transcribed mRNAs from the nucleus to the cytoplasm. Whereas the NPC, perhaps one of the largest protein complexes, provides a relatively large channel for macromolecules to selectively pass through it in inherently three-dimensional (3D) movements, this channel is nonetheless below the diffraction limit of conventional light microscopy. A full understanding of the mRNA export mechanism urgently requires real-time mapping of the 3D dynamics of mRNA in the NPC of live cells with innovative imaging techniques breaking the diffraction limit of conventional light microscopy. Recently, super-resolution fluorescence microscopy and single-particle tracking (SPT) techniques have been applied to the study of nuclear export of mRNA in live cells. In this review, we emphasize the necessity of 3D mapping techniques in the study of mRNA export, briefly summarize the feasibility of current 3D imaging approaches, and highlight the new features of mRNA nuclear export elucidated with a newly developed 3D imaging approach combining SPT-based super-resolution imaging and 2D-to-3D deconvolution algorithms. PMID:25393401

  3. Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in ciliate Tetrahymena.

    PubMed

    Iwamoto, Masaaki; Osakada, Hiroko; Mori, Chie; Fukuda, Yasuhiro; Nagao, Koji; Obuse, Chikashi; Hiraoka, Yasushi; Haraguchi, Tokuko

    2017-04-06

    The nuclear pore complex (NPC), a gateway for nucleocytoplasmic trafficking, is composed of about 30 different proteins called nucleoporins. It remains unknown whether the NPCs within a species are homogeneous or vary depending on the cell type, or physiological condition. Here, we present evidence for compositionally distinct NPCs that form within a single cell in a binucleated ciliate. In Tetrahymena thermophila, each cell contains both a transcriptionally-active macronucleus (MAC) and a germline micronucleus (MIC). By combining in silico analysis, mass spectrometry analysis for immuno-isolated proteins, and subcellular localization analysis of GFP fused proteins, we identified numerous novel components of MAC and MIC NPCs. Core members of the Nup107-160 scaffold complex were enriched in MIC NPCs. Strikingly, two paralogs of Nup214 and of Nup153 localized exclusively to either MAC or MIC NPCs. Furthermore, the transmembrane components Pom121 and Pom82 localize exclusively to MAC and MIC NPCs, respectively. Our results argue that functional nuclear dimorphism in ciliates is likely to depend on compositional and structural specificity of NPCs.

  4. Biophysical Coarse-Grained Modeling Provides Insights into Transport through the Nuclear Pore Complex

    PubMed Central

    Moussavi-Baygi, R.; Jamali, Y.; Karimi, R.; Mofrad, M.R.K.

    2011-01-01

    The nuclear pore complex (NPC) is the gatekeeper of the nucleus, capable of actively discriminating between the active and inert cargo while accommodating a high rate of translocations. The biophysical mechanisms underlying transport, however, remain unclear due to the lack of information about biophysical factors playing role in transport. Based on published experimental data, we have established a coarse-grained model of an intact NPC structure to examine nucleocytoplasmic transport with refined spatial and temporal resolutions. Using our model, we estimate the transport time versus cargo sizes. Our findings suggest that the mean transport time of cargos smaller than 15 nm is independent of size, while beyond this size, there is a sharp increase in the mean transport time. The model confirms that kap-FG hydrophobicity is sufficient for active cargo transport. Moreover, our model predicts that during translocation, small and large cargo-complexes are hydrophobically attached to FG-repeat domains for 86 and 96% of their transport time, respectively. Inside the central channel FG-repeats form a thick layer on the wall leaving an open tube. The cargo-complex is almost always attached to this layer and diffuses back and forth, regardless of the cargo size. Finally, we propose a plausible model for transport in which the NPC can be viewed as a lubricated gate. This model incorporates basic assumptions underlying virtual-gate and reduction-of-dimensionality models with the addition of the FG-layer inside the central channel acting as a lubricant. PMID:21402022

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

    PubMed

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

    2014-01-01

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

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

    PubMed

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

    2016-05-10

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

  7. High content of a nuclear pore complex protein in cytoplasmic annulate lamellae of Xenopus oocytes.

    PubMed

    Cordes, V C; Reidenbach, S; Franke, W W

    1995-11-01

    The Xenopus laevis oocyte and egg represent an established model system to study nucleocytoplasmic transport and the assembly of the nuclear envelope (NE) and its pore complexes (PC). PCs, however, are not restricted to the NE but are also known to occur in cytoplasmic annulate lamellae (AL) in a variety of cells, including the Xenopus oocyte. However, the proportion of PCs found in such AL relative to those located in the NE, is unknown. In this study we have analyzed and quantified cytoplasmic AL in the full-grown (stage VI) Xenopus oocyte by immunolocalization at the light and electron microscopic level. Moreover, we have developed a method to enrich AL from enucleated oocytes, and have quantified a PC marker protein, nucleoporin p62, in both cytoplasmic AL and the NE. For this purpose we have used a specific monoclonal antibody (A225) which recognizes an epitope localized between amino acids 251 and 268 of Xenopus p62. We show that the number of PCs and p62 molecules present in AL far exceeds that of the NE. The possible implications of these findings to nucleocytoplasmic transport and nuclear PC (NPC) assembly are discussed.

  8. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

    PubMed Central

    Tan-Wong, Sue Mei; Wijayatilake, Hashanthi D.; Proudfoot, Nick J.

    2009-01-01

    Inducible genes in yeast retain a “memory” of recent transcriptional activity during periods of short-term repression, allowing them to be reactivated faster when reinduced. This confers a rapid and versatile gene expression response to the environment. We demonstrate that this memory mechanism is associated with gene loop interactions between the promoter and 3′ end of the responsive genes HXK1 and GAL1∷FMP27. The maintenance of these memory gene loops (MGLs) during intervening periods of transcriptional repression is required for faster RNA polymerase II (Pol II) recruitment to the genes upon reinduction, thereby facilitating faster mRNA accumulation. Notably, a sua7-1 mutant or the endogenous INO1 gene that lacks this MGL does not display such faster reinduction. Furthermore, these MGLs interact with the nuclear pore complex through association with myosin-like protein 1 (Mlp1). An mlp1Δ strain does not maintain MGLs, and concomitantly loses transcriptional memory. We predict that gene loop conformations enhance gene expression by facilitating rapid transcriptional response to changing environmental conditions. PMID:19933151

  9. 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

  10. 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

  11. 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

  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. Werner complex deficiency in cells disrupts the Nuclear Pore Complex and the distribution of lamin B1.

    PubMed

    Li, Zhi; Zhu, Yizhou; Zhai, Yujia; R Castroagudin, Michelle; Bao, Yifei; White, Tommy E; Glavy, Joseph S

    2013-12-01

    From the surrounding shell to the inner machinery, nuclear proteins provide the functional plasticity of the nucleus. This study highlights the nuclear association of Pore membrane (POM) protein NDC1 and Werner protein (WRN), a RecQ helicase responsible for the DNA instability progeria disorder, Werner Syndrome. In our previous publication, we connected the DNA damage sensor Werner's Helicase Interacting Protein (WHIP), a binding partner of WRN, to the NPC. Here, we confirm the association of the WRN/WHIP complex and NDC1. In established WRN/WHIP knockout cell lines, we further demonstrate the interdependence of WRN/WHIP and Nucleoporins (Nups). These changes do not completely abrogate the barrier of the Nuclear Envelope (NE) but do affect the distribution of FG Nups and the RAN gradient, which are necessary for nuclear transport. Evidence from WRN/WHIP knockout cell lines demonstrates changes in the processing and nucleolar localization of lamin B1. The appearance of "RAN holes" void of RAN corresponds to regions within the nucleolus filled with condensed pools of lamin B1. From WRN/WHIP knockout cell line extracts, we found three forms of lamin B1 that correspond to mature holoprotein and two potential post-translationally modified forms of the protein. Upon treatment with topoisomerase inhibitors lamin B1 cleavage occurs only in WRN/WHIP knockout cells. Our data suggest the link of the NDC1 and WRN as one facet of the network between the nuclear periphery and genome stability. Loss of WRN complex leads to multiple alterations at the NPC and the nucleolus.

  14. Cholesterol stimulates and ceramide inhibits Sticholysin II-induced pore formation in complex bilayer membranes.

    PubMed

    Alm, Ida; García-Linares, Sara; Gavilanes, José G; Martínez-Del-Pozo, Álvaro; Slotte, J Peter

    2015-04-01

    The pore forming capacity of Sticholysin II (StnII; isolated from Stichodactyla helianthus) in bilayer membranes containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), palmitoylsphingomyelin (PSM) and either cholesterol or palmitoyl ceramide (PCer) has been examined. The aim of the study was to elucidate how the presence of differently ordered PSM domains affected StnII oligomerization and pore formation. Cholesterol is known to enhance pore formation by StnII, and our results confirmed this and provide kinetic information for the process. The effect of cholesterol on bilayer permeabilization kinetics was concentration-dependent. In the concentration regime used (2.5-10nmol cholesterol in POPC:PSM 80:20 by nmol), cholesterol also increased the acyl chain order in the fluid PSM domain and thus decreased bilayer fluidity, suggesting that fluidity per se was not responsible for cholesterol's effect. Addition of PCer (2.5-10nmol) to the POPC:PSM (80:20 by nmol) bilayers attenuated StnII-induced pore formation, again in a concentration-dependent fashion. This addition also led to the formation of a PCer-rich gel phase. Addition of cholesterol to PCer-containing membranes could partially reduce the inhibitory effect of PCer on StnII pore formation. We conclude that the physical state of PSM (as influenced by either cholesterol or PCer) affected StnII binding and pore formation under the conditions examined.

  15. A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations.

    PubMed

    Xie, Wei; Chojnowski, Alexandre; Boudier, Thomas; Lim, John S Y; Ahmed, Sohail; Ser, Zheng; Stewart, Colin; Burke, Brian

    2016-10-10

    The nuclear lamina is a universal feature of metazoan nuclear envelopes (NEs) [1]. In mammalian cells, it appears as a 10-30 nm filamentous layer at the nuclear face of the inner nuclear membrane (INM) and is composed primarily of A- and B-type lamins, members of the intermediate filament family [2]. While providing structural integrity to the NE, the lamina also represents an important signaling and regulatory platform [3]. Two A-type lamin isoforms, lamins A and C (LaA and LaC), are expressed in most adult human cells. Encoded by a single gene, these proteins are largely identical, diverging only in their C-terminal tail domains. By contrast with that of LaC, the unique LaA tail undergoes extensive processing, including farnesylation and endo-proteolysis [4, 5]. However, functional differences between LaA and LaC are still unclear. Compounding this uncertainty, the structure of the lamina remains ill defined. In this study, we used BioID, an in vivo proximity-labeling method to identify differential interactors of A-type lamins [6]. One of these, Tpr, a nuclear pore complex (NPC) protein, is highlighted by its selective association with LaC. By employing superresolution microscopy, we demonstrate that this Tpr association is mirrored in enhanced interaction of LaC with NPCs. Further superresolution studies visualizing both endogenous A- and B-type lamins have allowed us to construct a nanometer-scale model of the mammalian nuclear lamina. Our data indicate that different A- and B-type lamin species assemble into separate filament networks that together form an extended composite structure at the nuclear periphery providing attachment sites for NPCs, thereby regulating their distribution.

  16. 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.

  17. Heart Failure Induces Significant Changes in Nuclear Pore Complex of Human Cardiomyocytes

    PubMed Central

    Tarazón, Estefanía; Rivera, Miguel; Roselló-Lletí, Esther; Molina-Navarro, Maria Micaela; Sánchez-Lázaro, Ignacio José; España, Francisco; Montero, José Anastasio; Lago, Francisca; González-Juanatey, José Ramón; Portolés, Manuel

    2012-01-01

    Aims The objectives of this study were to analyse the effect of heart failure (HF) on several proteins of nuclear pore complex (NPC) and their relationship with the human ventricular function. Methods and Results A total of 88 human heart samples from ischemic (ICM, n = 52) and dilated (DCM, n = 36) patients undergoing heart transplant and control donors (CNT, n = 9) were analyzed by Western blot. Subcellular distribution of nucleoporins was analysed by fluorescence and immunocytochemistry. When we compared protein levels according to etiology, ICM showed significant higher levels of NDC1 (65%, p<0.0001), Nup160 (88%, p<0.0001) and Nup153 (137%, p = 0.004) than those of the CNT levels. Furthermore, DCM group showed significant differences for NDC1 (41%, p<0.0001), Nup160 (65%, p<0.0001), Nup153 (155%, p = 0.006) and Nup93 (88%, p<0.0001) compared with CNT. However, Nup155 and translocated promoter region (TPR) did not show significant differences in their levels in any etiology. Regarding the distribution of these proteins in cell nucleus, only NDC1 showed differences in HF. In addition, in the pathological group we obtained good relationship between the ventricular function parameters (LVEDD and LVESD) and Nup160 (r = −0382, p = 0.004; r = −0.290, p = 0.033; respectively). Conclusions This study shows alterations in specific proteins (NDC1, Nup160, Nup153 and Nup93) that compose NPC in ischaemic and dilated human heart. These changes, related to ventricular function, could be accompanied by alterations in the nucleocytoplasmic transport. Therefore, our findings may be the basis for a new approach to HF management. PMID:23152829

  18. Aberrant distributions of nuclear pore complex proteins in ALS mice and ALS patients.

    PubMed

    Shang, Jingwei; Yamashita, Toru; Nakano, Yumiko; Morihara, Ryuta; Li, Xianghong; Feng, Tian; Liu, Xia; Huang, Yong; Fukui, Yusuke; Hishikawa, Nozomi; Ohta, Yasuyuki; Abe, Koji

    2017-03-24

    Nuclear pore complexes (NPCs) play important roles in traffic of molecules between the nucleus and cytoplasm, aberrant distributions of components of NPCs were demonstrated in C9orf72 amyotrophic lateral sclerosis (C9-ALS) patients, but it is elusive whether such abnormities are also the case with other cause of ALS disease. In the present study, we investigated the spatiotemporal distributions of RanGAP1 and 4 representative nucleoporins (GP210, NUP205, NUP107 and NUP50) of NPCs in human Cu/Zn superoxide dismutase-1 mutation transgenic (SOD1-Tg) mice and sporadic ALS patients. Compared with wild type (WT), these proteins displayed age-dependent and progressive nuclear precipitations, and cytoplasmic aberrant expressions in motor neurons of lumbar cord in SOD1-Tg mice from 10 to 18weeks (W). Double immunofluorescent analysis showed abnormal nuclear retention and apparent co-localizations of RanGAPl with NUP205 and NUP205 with NUPl07, meanwhile, GP210 with NUP205 mainly co-localized in the nuclear envelope (NE) of motor neurons. Furthermore, RanGAP1, GP210 and NUP50 showed similarly abnormal nuclear precipitations and cytoplasmic upregulations in SOD1-Tg mice and ALS patients, moreover, aberrant co-localizations of RanGAP1 with TDP-43 and NUP205 with TDP-43 were also observed in motor neurons. The present study indicated that the mislocalization of these proteins of NPCs may underlie the pathogenesis of ALS both in SOD1-Tg mice and human sporadic ALS patients, and these dysfunctions may be a fundamental pathway for ALS that is not specific only in C9-ALS but also in SOD1-ALS, which may be amenable to pharmacotherapeutic intervention.

  19. Nuclear pore complex contains a family of glycoproteins that includes p62: glycosylation through a previously unidentified cellular pathway

    SciTech Connect

    Davis, L.I.; Blobel, G.

    1987-11-01

    Using a monoclonal antibody (mAb 414), the authors previously identified a protein of 62 kDa (p62) that was localized to the nuclear pore complex by immunoelectron microscopy. They also showed that p62 binds specifically to wheat germ agglutinin. Therefore, they proposed that this nuclear pore complex protein might be a member of a recently characterized family of glycoproteins that are labeled by in vitro galactosylation of rat liver nuclei and contain O-linked monosaccharidic GlcNAc residues. In support of this, they now show that incubation with N-acetylglucosaminidase reduces the molecular mass of p62 by approx. = 3 kDa because of the removal of terminal GlcNAc residues. Moreover, p62 can be galactosylated in vitro by using UDP-(/sup 3/H)galactose and galactosyltransferase. They also show that most of the GlcNAc residues are added within 5 min of synthesis, when p62 is soluble and cytosolic. Thus, the addition of GlcNAc is carried out in the cytoplasm and is clearly distinct from the N- and O-linked glycosylation pathways of the endoplasmic reticulum and Golgi complex. Using another mAb with a broad specificity for nuclear GlcNAc-containing proteins, they show by immunofluorescence and protein blotting of subnuclear fractions that some of these proteins are in the interior of the nucleus, and others are most likely located in the pore complex.

  20. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in postmitotic cells.

    PubMed

    D'Angelo, Maximiliano A; Raices, Marcela; Panowski, Siler H; Hetzer, Martin W

    2009-01-23

    In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of nuclear pores in postmitotic cells is unknown. Here, we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of NPC components, like Nup153 and Nup50, are continuously exchanged, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire cellular life span. Besides the lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs, leading to an increase in nuclear permeability and the leaking of cytoplasmic proteins into the nucleus. Our finding that nuclear "leakiness" is dramatically accelerated during aging and that a subset of nucleoporins is oxidatively damaged in old cells suggests that the accumulation of damage at the NPC might be a crucial aging event.

  1. Nuclear pore complex remodeling by p75(NTR) cleavage controls TGF-β signaling and astrocyte functions.

    PubMed

    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

    2015-08-01

    Astrocytes modulate neuronal activity and inhibit regeneration. We show that cleaved p75 neurotrophin receptor (p75(NTR)) is a component of the nuclear pore complex (NPC) required for glial scar formation and reduced gamma oscillations in mice via regulation of transforming growth factor (TGF)-β signaling. Cleaved p75(NTR) interacts with nucleoporins to promote Smad2 nucleocytoplasmic shuttling. Thus, NPC remodeling by regulated intramembrane cleavage of p75(NTR) controls astrocyte-neuronal communication in response to profibrotic factors.

  2. 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

  3. The Integral Membrane Protein Snl1p Is Genetically Linked to Yeast Nuclear Pore Complex Function

    PubMed Central

    Ho, Albert K.; Raczniak, Gregory A.; Ives, Eric B.; Wente, Susan R.

    1998-01-01

    Integral membrane proteins are predicted to play key roles in the biogenesis and function of nuclear pore complexes (NPCs). Revealing how the transport apparatus is assembled will be critical for understanding the mechanism of nucleocytoplasmic transport. We observed that expression of the carboxyl-terminal 200 amino acids of the nucleoporin Nup116p had no effect on wild-type yeast cells, but it rendered the nup116 null strain inviable at all temperatures and coincidentally resulted in the formation of nuclear membrane herniations at 23°C. To identify factors related to NPC function, a genetic screen for high-copy suppressors of this lethal nup116-C phenotype was conducted. One gene (designated SNL1 for suppressor of nup116-C lethal) was identified whose expression was necessary and sufficient for rescuing growth. Snl1p has a predicted molecular mass of 18.3 kDa, a putative transmembrane domain, and limited sequence similarity to Pom152p, the only previously identified yeast NPC-associated integral membrane protein. By both indirect immunofluorescence microscopy and subcellular fractionation studies, Snl1p was localized to both the nuclear envelope and the endoplasmic reticulum. Membrane extraction and topology assays suggested that Snl1p was an integral membrane protein, with its carboxyl-terminal region exposed to the cytosol. With regard to genetic specificity, the nup116-C lethality was also suppressed by high-copy GLE2 and NIC96. Moreover, high-copy SNL1 suppressed the temperature sensitivity of gle2–1 and nic96-G3 mutant cells. The nic96-G3 allele was identified in a synthetic lethal genetic screen with a null allele of the closely related nucleoporin nup100. Gle2p physically associated with Nup116p in vitro, and the interaction required the N-terminal region of Nup116p. Therefore, genetic links between the role of Snl1p and at least three NPC-associated proteins were established. We suggest that Snl1p plays a stabilizing role in NPC structure and function

  4. Sediment toxicity in Savannah Harbor

    USGS Publications Warehouse

    Winger, P.V.; Lasier, P.J.

    1995-01-01

    Savannah Harbor, located near the mouth of the Savannah River, Georgia and South Carolina, is impacted by industrial and municipal effluents. Potential release of contaminants stored in harbor sediments through dredging and shipping operations requires that contaminated areas be identified for proper management of the system and protection of wildlife resources. During 1991, Hyalella azteca were exposed in 10-d static-renewal toxicity tests to pore-water and solid-phase sediment samples collected from 26 sites within Savannah Harbor. Pore-water toxicity was more pronounced than that for solidphase sediment. Toxicity and reduced leaf consumption demonstrated impaired sediment quality at specific sites within Savannah Harbor and Back River. Factors responsible for the decreased sediment quality were ammonia, alkalinity, and metal concentrations (cadmium, chromium, lead, molybdenum, and nickel). Elevated concentrations of metals and toxicities in Back River sediments indicated impacts from adjacent dredge-spoil areas.

  5. Age-dependent deterioration of nuclear pore complexes causes a loss of nuclear integrity in post-mitotic cells

    PubMed Central

    D’Angelo, Maximiliano A.; Raices, Marcela; Panowski, Siler H.; Hetzer, Martin W.

    2009-01-01

    SUMMARY In dividing cells, nuclear pore complexes (NPCs) disassemble during mitosis and reassemble into the newly forming nuclei. However, the fate of these multi-protein transport channels in post-mitotic cells, where the mitotic renewal of pores is absent, is unknown. Here we show that NPCs, unlike other nuclear structures, do not turn over in differentiated cells. While a subset of nuclear pore components, like Nup153 and Nup50, are continuously exchanged at the NPC, scaffold nucleoporins, like the Nup107/160 complex, are extremely long-lived and remain incorporated in the nuclear membrane during the entire lifespan of a cell. In addition to a lack of nucleoporin expression and NPC turnover, we discovered an age-related deterioration of NPCs leading to a loss of the nuclear permeability barrier and the leaking of cytoplasmic proteins into the nuclear compartment. Our finding that nuclear ‘leakiness’ is dramatically accelerated during aging and that a subset of nucleoporins are found to be oxidatively damaged in old cells, suggest that the accumulation of damage at the NPC structure might be a crucial event in age-related loss of nuclear integrity. PMID:19167330

  6. Single Hepatitis-B Virus Core Capsid Binding to Individual Nuclear Pore Complexes in HeLa Cells

    PubMed Central

    Lill, Yoriko; Lill, Markus A.; Fahrenkrog, Birthe; Schwarz-Herion, Kyrill; Paulillo, Sara; Aebi, Ueli; Hecht, Bert

    2006-01-01

    We investigate the interaction of hepatitis B virus capsids lacking a nuclear localization signal with nuclear pore complexes (NPCs) in permeabilized HeLa cells. Confocal and wide-field optical images of the nuclear envelope show well-spaced individual NPCs. Specific interactions of capsids with single NPCs are characterized by extended residence times of capsids in the focal volume which are characterized by fluorescence correlation spectroscopy. In addition, single-capsid-tracking experiments using fast wide-field fluorescence microscopy at 50 frames/s allow us to directly observe specific binding via a dual-color colocalization of capsids and NPCs. We find that binding occurs with high probability on the nuclear-pore ring moiety, at 44 ± 9 nm radial distance from the central axis. PMID:16877503

  7. Enterobacter cloacae complex isolates harboring blaNMC-A or blaIMI-type class A carbapenemase genes on novel chromosomal integrative elements and plasmids.

    PubMed

    Boyd, David A; Mataseje, Laura F; Davidson, Ross; Delport, Johannes A; Fuller, Jeff; Hoang, Linda; Lefebvre, Brigitte; Levett, Paul; Roscoe, Diane L; Willey, Barbara M; Mulvey, Michael R

    2017-02-21

    Carbapenem-resistant Enterobacter cloacae complex isolates submitted to a reference laboratory from 2010 to 2015 were screened by PCR for seven common carbapenemase gene groups, namely, KPC, NDM, OXA-48, VIM, IMP, GES, and NMC-A/IMI. Nineteen of the submitted isolates (1.7%) were found to harbor Ambler class A blaNMC-A or blaIMI-type carbapenemases. All 19 isolates were resistant to at least one carbapenem but susceptible to aminoglycosides, trimethoprim-sulfamethoxazole, tigecycline, and ciprofloxacin. Most isolates (17/19) gave positive results with the Carba-NP test for phenotypic carbapenemase detection. Isolates were genetically diverse by pulsed-field gel electrophoresis macrorestriction analysis, multilocus sequence typing, and hsp60 gene analysis. The genes were found in various Enterobacter cloacae complex species, however blaNMC-A was highly associated with Enterobacter ludwiggii Whole genome sequencing and bioinformatics analysis revealed that all NMC-A (n=10), IMI-1 (n=5), and IMI-9 (n=2) producers harbored the carbapenemase gene on EludIMEX-1-like integrative mobile elements, EcloIMEXs, located in the identical chromosomal locus. Two novel genes, blaIMI-5 and blaIMI-6, were harbored on different IncFII-type plasmids. Enterobacter cloacae complex isolates harboring blaNMC-A/IMI-type carbapenemases are relatively rare in Canada. Though mostly found integrated into the chromosome, some variants are located on plasmids that may enhance their mobility potential.

  8. Immunocytochemical localization of the major polypeptides of the nuclear pore complex-lamina fraction. Interphase and mitotic distribution

    PubMed Central

    1978-01-01

    This laboratory has previously isolated a fraction from rat liver nuclei consisting of nuclear pore complexes associated with the proteinaceous lamina which underlies the inner nuclear membrane. Using protein eluted from sodium dodecyl sulfate (SDS) gels, we have prepared antibodies in chickens to each of the three predominant pore complex- lamina bands. Ouchterlony double diffusion analysis shows that each of these individual bands cross-reacts strongly with all three antisera. In immunofluorescence localization performed on tissue culture cells with these antibodies, we obtain a pattern of intense staining at the periphery of the interphase nucleus, with little or no cytoplasmic reaction. Electron microscope immunoperoxidase staining of rat liver nuclei with these antibodies labels exclusively the nuclear periphery. Furthermore, reaction occurs in areas which contain the lamina, but not at the pore complexes. While our isolation procedure extracts the internal contents of nuclei completely, semiquantitative Ouchterlony analysis shows that it releases negligible amounts of these lamina antigens. Considered together, our results indicate that these three bands represent major components of a peripheral nuclear lamina, and are not structural elements of an internal "nuclear protein matrix." Fluorescence microscopy shows that the perinuclear interphase localization of these lamina proteins undergoes dramatic changes during mitosis. Concomitant with nuclear envelope disassembly in prophase, these antigens assume a diffuse localization throughout the cell. This distribution persists until telophase, when the antigens become progressively and completely localized at the surface of the daughter chromosome masses. We propose that the lamina is a biological polymer which can undergo reversible disassembly during mitosis. PMID:102651

  9. 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.

  10. Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions.

    PubMed

    Batrakou, Dzmitry G; Kerr, Alastair R W; Schirmer, Eric C

    2009-02-15

    Since the discovery of several inherited diseases linked to the nuclear envelope the number of functions ascribed to this subcellular organelle has skyrocketed. However the molecular pathways underlying these functions are not clear in most cases, perhaps because of missing components. Several recent proteomic analyses of the nuclear envelope and nuclear pore complex proteomes have yielded not only enough missing components to potentially elucidate these pathways, but suggest an exponentially greater number of functions at the nuclear periphery than ever imagined. Many of these functions appear to derive from recapitulation of pathways utilized at the plasma membrane and from other membrane systems. Additionally, many proteins identified in the comparative nuclear envelope studies have sequence characteristics suggesting that they might also contribute to nuclear pore complex functions. In particular, the striking enrichment for proteins in the nuclear envelope fractions that carry phenylalanine-glycine (FG) repeats may be significant for the mechanism of nuclear transport. In retrospect, these findings are only surprising in context of the notion held for many years that the nuclear envelope was only a barrier protecting the genome. In fact, it is arguably the most complex membrane organelle in the cell.

  11. 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

  12. Structure of a Yeast Dyn2-Nup159 Complex and Molecular Basis for Dynein Light Chain-Nuclear Pore Interaction*

    PubMed Central

    Romes, Erin M.; Tripathy, Ashutosh; Slep, Kevin C.

    2012-01-01

    The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μm), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture. PMID:22411995

  13. Structure of a yeast Dyn2-Nup159 complex and molecular basis for dynein light chain-nuclear pore interaction.

    PubMed

    Romes, Erin M; Tripathy, Ashutosh; Slep, Kevin C

    2012-05-04

    The nuclear pore complex gates nucleocytoplasmic transport through a massive, eight-fold symmetric channel capped by a nucleoplasmic basket and structurally unique, cytoplasmic fibrils whose tentacles bind and regulate asymmetric traffic. The conserved Nup82 complex, composed of Nsp1, Nup82, and Nup159, forms the unique cytoplasmic fibrils that regulate mRNA nuclear export. Although the nuclear pore complex plays a fundamental, conserved role in nuclear trafficking, structural information about the cytoplasmic fibrils is limited. Here, we investigate the structural and biochemical interactions between Saccharomyces cerevisiae Nup159 and the nucleoporin, Dyn2. We find that Dyn2 is predominantly a homodimer and binds arrayed sites on Nup159, promoting the Nup159 parallel homodimerization. We present the first structure of Dyn2, determined at 1.85 Å resolution, complexed with a Nup159 target peptide. Dyn2 resembles homologous metazoan dynein light chains, forming homodimeric composite substrate binding sites that engage two independent 10-residue target motifs, imparting a β-strand structure to each peptide via antiparallel extension of the Dyn2 core β-sandwich. Dyn2 recognizes a highly conserved QT motif while allowing sequence plasticity in the flanking residues of the peptide. Isothermal titration calorimetric analysis of the comparative binding of Dyn2 to two Nup159 target sites shows similar affinities (18 and 13 μM), but divergent thermal binding modes. Dyn2 homodimers are arrayed in the crystal lattice, likely mimicking the arrayed architecture of Dyn2 on the Nup159 multivalent binding sites. Crystallographic interdimer interactions potentially reflect a cooperative basis for Dyn2-Nup159 complex formation. Our data highlight the determinants that mediate oligomerization of the Nup82 complex and promote a directed, elongated cytoplasmic fibril architecture.

  14. The crystal structure of the Ran-Nup153ZnF2 complex: a general Ran docking site at the nuclear pore complex.

    PubMed

    Schrader, Nils; Koerner, Carolin; Koessmeier, Katja; Bangert, Jan-Amadé; Wittinghofer, Alfred; Stoll, Raphael; Vetter, Ingrid R

    2008-07-01

    Nucleoporin (Nup) 153 is a highly mobile, multifunctional, and essential nuclear pore protein. It contains four zinc finger motifs that are thought to be crucial for the regulation of transport-receptor/cargo interactions via their binding to the small guanine nucleotide binding protein, Ran. We found this interaction to be independent of the phoshorylation state of the nucleotide. Ran binds with the highest affinity to the second zinc finger motif of Nup153 (Nup153ZnF2). Here we present the crystal structure of this complex, revealing a new type of Ran-Ran interaction partner interface together with the solution structure of Nup153ZnF2. According to our complex structure, Nup153ZnF2 binding to Ran excludes the formation of a Ran-importin-beta complex. This finding suggests a local Nup153-mediated Ran reservoir at the nucleoplasmic distal ring of the nuclear pore, where nucleotide exchange may take place in a ternary Nup153-Ran-RCC1 complex, so that import complexes are efficiently terminated.

  15. Cdk1 and okadaic acid-sensitive phosphatases control assembly of nuclear pore complexes in Drosophila embryos.

    PubMed

    Onischenko, Evgeny A; Gubanova, Natalia V; Kiseleva, Elena V; Hallberg, Einar

    2005-11-01

    Disassembly and reassembly of the nuclear pore complexes (NPCs) is one of the major events during open mitosis in higher eukaryotes. However, how this process is controlled by the mitotic machinery is not clear. To investigate this we developed a novel in vivo model system based on syncytial Drosophila embryos. We microinjected different mitotic effectors into the embryonic cytoplasm and monitored the dynamics of disassembly/reassembly of NPCs in live embryos using fluorescently labeled wheat germ agglutinin (WGA) or in fixed embryos using electron microscopy and immunostaining techniques. We found that in live embryos Cdk1 activity was necessary and sufficient to induce disassembly of NPCs as well as their cytoplasmic mimics: annulate lamellae pore complexes (ALPCs). Cdk1 activity was also required for keeping NPCs and ALPCs disassembled during mitosis. In agreement recombinant Cdk1/cyclin B was able to induce phosphorylation and dissociation of nucleoporins from the NPCs in vitro. Conversely, reassembly of NPCs and ALPCs was dependent on the activity of protein phosphatases, sensitive to okadaic acid (OA). Our findings suggest a model where mitotic disassembly/reassembly of the NPCs is regulated by a dynamic equilibrium of Cdk1 and OA-sensitive phosphatase activities and provide evidence that mitotic phosphorylation mediates disassembly of the NPC.

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

    PubMed Central

    Pan, Yong; Garg, Abhimanyu; Agarwal, Anil K.

    2007-01-01

    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 (HEK293) 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. PMID:17291448

  17. 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.

  18. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    SciTech Connect

    Cunningham, J; Gatenby, R

    2014-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  3. Suilysin-induced Platelet-Neutrophil Complexes Formation is Triggered by Pore Formation-dependent Calcium Influx

    PubMed Central

    Zhang, Shengwei; Zheng, Yuling; Chen, Shaolong; Huang, Shujing; Liu, Keke; Lv, Qingyu; Jiang, Yongqiang; Yuan, Yuan

    2016-01-01

    Platelet activation and platelet–neutrophil interactions have been found to be involved in inflammation, organ failure and soft-tissue necrosis in bacterial infections. Streptococcus suis, an emerging human pathogen, can cause streptococcal toxic-shock syndrome (STSS) similarly to Streptococcus pyogenes. Currently, S. suis–platelet interactions are poorly understood. Here, we found that suilysin (SLY), the S. suis cholesterol-dependent cytolysin (CDC), was the sole stimulus of S. suis that induced platelet-neutrophil complexes (PNC) formation. Furthermore, P-selectin released in α-granules mediated PNC formation. This process was triggered by the SLY-induced pore forming-dependent Ca2+ influx. Moreover, we demonstrated that the Ca2+ influx triggered an MLCK-dependent pathway playing critical roles in P-selectin activation and PNC formation, however, PLC-β-IP3/DAG-MLCK and Rho-ROCK-MLCK signalling were not involved. Additionally, the “outside-in” signalling had a smaller effect on the SLY-induced P-selectin release and PNC formation. Interestingly, other CDCs including pneumolysin and streptolysin O have also been found to induce PNC formation in a pore forming-dependent Ca2+ influx manner. It is possible that the bacterial CDC-mediated PNC formation is a similar response mechanism used by a wide range of bacteria. These findings may provide useful insight for discovering potential therapeutic targets for S. suis-associated STSS. PMID:27830834

  4. Model inspired by nuclear pore complex suggests possible roles for nuclear transport receptors in determining its structure.

    PubMed

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

    2013-12-17

    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.

  5. [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,…

  6. 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.

  7. 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.

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

    PubMed Central

    Muñoz-Santiburcio, Daniel; Marx, Dominik

    2016-01-01

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

  9. Host-derived, pore-forming toxin-like protein and trefoil factor complex protects the host against microbial infection.

    PubMed

    Xiang, Yang; Yan, Chao; Guo, Xiaolong; Zhou, Kaifeng; Li, Sheng'an; Gao, Qian; Wang, Xuan; Zhao, Feng; Liu, Jie; Lee, Wen-Hui; Zhang, Yun

    2014-05-06

    Aerolysins are virulence factors belonging to the bacterial β-pore-forming toxin superfamily. Surprisingly, numerous aerolysin-like proteins exist in vertebrates, but their biological functions are unknown. βγ-CAT, a complex of an aerolysin-like protein subunit (two βγ-crystallin domains followed by an aerolysin pore-forming domain) and two trefoil factor subunits, has been identified in frogs (Bombina maxima) skin secretions. Here, we report the rich expression of this protein, in the frog blood and immune-related tissues, and the induction of its presence in peritoneal lavage by bacterial challenge. This phenomena raises the possibility of its involvement in antimicrobial infection. When βγ-CAT was administrated in a peritoneal infection model, it greatly accelerated bacterial clearance and increased the survival rate of both frogs and mice. Meanwhile, accelerated Interleukin-1β release and enhanced local leukocyte recruitments were determined, which may partially explain the robust and effective antimicrobial responses observed. The release of interleukin-1β was potently triggered by βγ-CAT from the frog peritoneal cells and murine macrophages in vitro. βγ-CAT was rapidly endocytosed and translocated to lysosomes, where it formed high molecular mass SDS-stable oligomers (>170 kDa). Lysosomal destabilization and cathepsin B release were detected, which may explain the activation of caspase-1 inflammasome and subsequent interleukin-1β maturation and release. To our knowledge, these results provide the first functional evidence of the ability of a host-derived aerolysin-like protein to counter microbial infection by eliciting rapid and effective host innate immune responses. The findings will also largely help to elucidate the possible involvement and action mechanisms of aerolysin-like proteins and/or trefoil factors widely existing in vertebrates in the host defense against pathogens.

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

    PubMed

    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

    2014-05-01

    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.

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

    PubMed Central

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

    2015-01-01

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

  12. Environmental Assessment for Polaris Missile Training Facility Gantry Crane Tower Demolition, Ford Island, Pearl Harbor Naval Complex, O’ahu, Hawaii

    DTIC Science & Technology

    2005-07-01

    ve r R o a d H-1 Fr eew ay Mamala Bay...Moanalua F reew ay H -2 F re e w a y PEARL HARBOR NAVAL COMPLEX Admiral Clarey Bridge Ka`ena Point Barbers Point Honolulu Not to Scale Kahuku Point Mokapu...t A ve n u e Block Island St. S t. L o u is A ve . Le xin gt on B lvd . E s s e x S tr e e t Liscome Bay St. Enterprise St. Existing Ball

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

    PubMed Central

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

    2015-01-01

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

  14. Chm7 and Heh1 collaborate to link nuclear pore complex quality control with nuclear envelope sealing.

    PubMed

    Webster, Brant M; Thaller, David J; Jäger, Jens; Ochmann, Sarah E; Borah, Sapan; Lusk, C Patrick

    2016-11-15

    The integrity of the nuclear envelope barrier relies on membrane remodeling by the ESCRTs, which seal nuclear envelope holes and contribute to the quality control of nuclear pore complexes (NPCs); whether these processes are mechanistically related remains poorly defined. Here, we show that the ESCRT-II/III chimera, Chm7, is recruited to a nuclear envelope subdomain that expands upon inhibition of NPC assembly and is required for the formation of the storage of improperly assembled NPCs (SINC) compartment. Recruitment to sites of NPC assembly is mediated by its ESCRT-II domain and the LAP2-emerin-MAN1 (LEM) family of integral inner nuclear membrane proteins, Heh1 and Heh2. We establish direct binding between Heh2 and the "open" forms of both Chm7 and the ESCRT-III, Snf7, and between Chm7 and Snf7. Interestingly, Chm7 is required for the viability of yeast strains where double membrane seals have been observed over defective NPCs; deletion of CHM7 in these strains leads to a loss of nuclear compartmentalization suggesting that the sealing of defective NPCs and nuclear envelope ruptures could proceed through similar mechanisms.

  15. 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.

  16. 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.

  17. O-fucosylated glycoproteins form assemblies in close proximity to the nuclear pore complexes of Toxoplasma gondii

    PubMed Central

    Bandini, Giulia; Haserick, John R.; Motari, Edwin; Ouologuem, Dinkorma T.; Roos, David S.; Costello, Catherine E.; Robbins, Phillips W.; Samuelson, John

    2016-01-01

    Toxoplasma gondii is an intracellular parasite that causes disseminated infections in fetuses and immunocompromised individuals. Although gene regulation is important for parasite differentiation and pathogenesis, little is known about protein organization in the nucleus. Here we show that the fucose-binding Aleuria aurantia lectin (AAL) binds to numerous punctate structures in the nuclei of tachyzoites, bradyzoites, and sporozoites but not oocysts. AAL also binds to Hammondia and Neospora nuclei but not to more distantly related apicomplexans. Analyses of the AAL-enriched fraction indicate that AAL binds O-linked fucose added to Ser/Thr residues present in or adjacent to Ser-rich domains (SRDs). Sixty-nine Ser-rich proteins were reproducibly enriched with AAL, including nucleoporins, mRNA-processing enzymes, and cell-signaling proteins. Two endogenous SRDs-containing proteins and an SRD-YFP fusion localize with AAL to the nuclear membrane. Superresolution microscopy showed that the majority of the AAL signal localizes in proximity to nuclear pore complexes. Host cells modify secreted proteins with O-fucose; here we describe the O-fucosylation pathway in the nucleocytosol of a eukaryote. Furthermore, these results suggest O-fucosylation is a mechanism by which proteins involved in gene expression accumulate near the NPC. PMID:27663739

  18. 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.

  19. 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.

  20. Host-derived, pore-forming toxin–like protein and trefoil factor complex protects the host against microbial infection

    PubMed Central

    Xiang, Yang; Yan, Chao; Guo, Xiaolong; Zhou, Kaifeng; Li, Sheng’an; Gao, Qian; Wang, Xuan; Zhao, Feng; Liu, Jie; Lee, Wen-Hui; Zhang, Yun

    2014-01-01

    Aerolysins are virulence factors belonging to the bacterial β-pore–forming toxin superfamily. Surprisingly, numerous aerolysin-like proteins exist in vertebrates, but their biological functions are unknown. βγ-CAT, a complex of an aerolysin-like protein subunit (two βγ-crystallin domains followed by an aerolysin pore-forming domain) and two trefoil factor subunits, has been identified in frogs (Bombina maxima) skin secretions. Here, we report the rich expression of this protein, in the frog blood and immune-related tissues, and the induction of its presence in peritoneal lavage by bacterial challenge. This phenomena raises the possibility of its involvement in antimicrobial infection. When βγ-CAT was administrated in a peritoneal infection model, it greatly accelerated bacterial clearance and increased the survival rate of both frogs and mice. Meanwhile, accelerated Interleukin-1β release and enhanced local leukocyte recruitments were determined, which may partially explain the robust and effective antimicrobial responses observed. The release of interleukin-1β was potently triggered by βγ-CAT from the frog peritoneal cells and murine macrophages in vitro. βγ-CAT was rapidly endocytosed and translocated to lysosomes, where it formed high molecular mass SDS-stable oligomers (>170 kDa). Lysosomal destabilization and cathepsin B release were detected, which may explain the activation of caspase-1 inflammasome and subsequent interleukin-1β maturation and release. To our knowledge, these results provide the first functional evidence of the ability of a host-derived aerolysin-like protein to counter microbial infection by eliciting rapid and effective host innate immune responses. The findings will also largely help to elucidate the possible involvement and action mechanisms of aerolysin-like proteins and/or trefoil factors widely existing in vertebrates in the host defense against pathogens. PMID:24733922

  1. 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.

  2. Construction of "Toxin Complex" in a Mutant Serotype C Strain of Clostridium botulinum Harboring a Defective Neurotoxin Gene.

    PubMed

    Suzuki, Tomonori; Nagano, Thomas; Niwa, Koichi; Uchino, Masataka; Tomizawa, Motohiro; Sagane, Yoshimasa; Watanabe, Toshihiro

    2017-01-01

    A non-toxigenic mutant of the toxigenic serotype C Clostridium botulinum strain Stockholm (C-St), C-N71, does not produce the botulinum neurotoxin (BoNT). However, the original strain C-St produces botulinum toxin complex, in which BoNT is associated with non-toxic non-hemagglutinin (NTNHA) and three hemagglutinin proteins (HA-70, HA-33, and HA-17). Therefore, in this study, we aimed to elucidate the effects of bont gene knockout on the formation of the "toxin complex." Nucleotide sequence analysis revealed that a premature stop codon was introduced in the bont gene, whereas other genes were not affected by this mutation. Moreover, we successfully purified the "toxin complex" produced by C-N71. The "toxin complex" was identified as a mixture of NTNHA/HA-70/HA-17/HA-33 complexes with intact NTNHA or C-terminally truncated NTNHA, without BoNT. These results indicated that knockout of the bont gene does not affect the formation of the "toxin complex." Since the botulinum toxin complex has been shown to play an important role in oral toxin transport in the human and animal body, a non-neurotoxic "toxin complex" of C-N71 may be valuable for the development of an oral drug delivery system.

  3. AFM visualization of sub-50nm polyplex disposition to the nuclear pore complex without compromising the integrity of the nuclear envelope.

    PubMed

    Andersen, Helene; Parhamifar, Ladan; Hunter, A Christy; Shahin, Victor; Moghimi, S Moein

    2016-12-28

    It has been questioned as to whether polyplexes in the cytoplasm can reach the nuclear compartment and if so in what form. By applying atomic force microscopy (AFM) to the nuclear envelope and the nuclear pore complexes, we demonstrate that disposition of polyethylenimine (PEI)/DNA polyplexes that were microinjected into the oocytes of Xenopus laevis, as an example of a non-dividing cell, is exclusive to the nuclear pore complex (NPC). AFM images show NPCs clogged only with sub-50nm polyplexes. This mode of disposition neither altered the morphology/integrity of the nuclear membrane nor the NPC. AFM images further show polyplexes on the nucleoplasmic side of the envelope, presumably indicating species in transit. Transmission electron microscopy studies of ruptured nuclei from transfected human cell lines demonstrate the presence of sub-50nm particles resembling polyplexes in morphology compared with control preparations.

  4. Complexes of Peptide Blockers with Kv1.6 Pore Domain: Molecular Modeling and Studies with KcsA-Kv1.6 Channel.

    PubMed

    Nekrasova, O V; Volyntseva, A D; Kudryashova, K S; Novoseletsky, V N; Lyapina, E A; Illarionova, A V; Yakimov, S A; Korolkova, Yu V; Shaitan, K V; Kirpichnikov, M P; Feofanov, A V

    2016-09-17

    Potassium voltage-gated Kv1.6 channel, which is distributed primarily in neurons of central and peripheral nervous systems, is of significant physiological importance. To date, several high-affinity Kv1.6-channel blockers are known, but the lack of selective ones among them hampers the studies of tissue localization and functioning of Kv1.6 channels. Here we present an approach to advanced understanding of interactions of peptide toxin blockers with a Kv1.6 pore. It combines molecular modeling studies and an application of a new bioengineering system based on a KcsA-Kv1.6 hybrid channel for the quantitative fluorescent analysis of blocker-channel interactions. Using this system we demonstrate that peptide toxins agitoxin 2, kaliotoxin1 and OSK1 have similar high affinity to the extracellular vestibule of the K(+)-conducting pore of Kv1.6, hetlaxin is a low-affinity ligand, whereas margatoxin and scyllatoxin do not bind to Kv1.6 pore. Binding of toxins to Kv1.6 pore has considerable inverse dependence on the ionic strength. Model structures of KcsA-Kv1.6 and Kv1.6 complexes with agitoxin 2, kaliotoxin 1 and OSK1 were obtained using homology modeling and molecular dynamics simulation. Interaction interfaces, which are formed by 15-19 toxin residues and 10 channel residues, are described and compared. Specific sites of Kv1.6 pore recognition are identified for targeting of peptide blockers. Analysis of interactions between agitoxin 2 derivatives with point mutations (S7K, S11G, L19S, R31G) and KcsA-Kv1.6 confirms reliability of the calculated complex structure.

  5. Mechanisms of eukaryotic transcription: surfaces, complexes, and contexts. (Cold Spring Harbor Cancer Cells Meeting, August 30-September 3, 1995).

    PubMed

    Hansen, U

    1996-05-16

    As with other biological processes, evolution has resulted in numerous, alternative pathways to achieve regulation of gene expression. In the elaborate series of steps required to transcribe a gene, necessitating assembly and subsequent disassembly of multiple complexes, subtle alterations in specific protein-protein interactions can lead to dramatically different transcriptional consequences.

  6. Mitochondrial permeability transition pore induction is linked to formation of the complex of ATPase C-subunit, polyhydroxybutyrate and inorganic polyphosphate

    PubMed Central

    Elustondo, P A; Nichols, M; Negoda, A; Thirumaran, A; Zakharian, E; Robertson, G S; Pavlov, E V

    2016-01-01

    Mitochondrial permeability transition pore (mPTP) opening allows free movement of ions and small molecules leading to mitochondrial membrane depolarization and ATP depletion that triggers cell death. A multi-protein complex of the mitochondrial ATP synthase has an essential role in mPTP. However, the molecular identity of the central 'pore' part of mPTP complex is not known. A highly purified fraction of mammalian mitochondria containing C-subunit of ATPase (C-subunit), calcium, inorganic polyphosphate (polyP) and polyhydroxybutyrate (PHB) forms ion channels with properties that resemble the native mPTP. We demonstrate here that amount of this channel-forming complex dramatically increases in intact mitochondria during mPTP activation. This increase is inhibited by both Cyclosporine A, an inhibitor of mPTP and Ruthenium Red, an inhibitor of the Mitochondrial Calcium Uniporter. Similar increases in the amount of complex formation occurs in areas of mouse brain damaged by ischemia-reperfusion injury. These findings suggest that calcium-induced mPTP is associated with de novo assembly of a channel comprising C-subunit, polyP and PHB. PMID:27924223

  7. 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

  8. Cooperative Interactions between Different Classes of Disordered Proteins Play a Functional Role in the Nuclear Pore Complex of Baker’s Yeast

    PubMed Central

    Ando, David; Gopinathan, Ajay

    2017-01-01

    Nucleocytoplasmic transport is highly selective, efficient, and is regulated by a poorly understood mechanism involving hundreds of disordered FG nucleoporin proteins (FG nups) lining the inside wall of the nuclear pore complex (NPC). Previous research has concluded that FG nups in Baker’s yeast (S. cerevisiae) are present in a bimodal distribution, with the “Forest Model” classifying FG nups as either di-block polymer like “trees” or single-block polymer like “shrubs”. Using a combination of coarse-grained modeling and polymer brush modeling, the function of the di-block FG nups has previously been hypothesized in the Di-block Copolymer Brush Gate (DCBG) model to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. In this manuscript we work to extend the original DCBG model by first performing coarse grained simulations of the single-block FG nups which confirm that they have a single block polymer structure rather than the di-block structure of tree nups. Our molecular simulations also demonstrate that these single-block FG nups are likely cohesive, compact, collapsed coil polymers, implying that these FG nups are generally localized to their grafting location within the NPC. We find that adding a layer of single-block FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving single-block and di-block FG nups. This effect can explain the puzzling connection between single-block FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single-block and di-block FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability. PMID:28068389

  9. Nicotine-induced dystonic arousal complex in a mouse line harboring a human autosomal-dominant nocturnal frontal lobe epilepsy mutation.

    PubMed

    Teper, Yaroslav; Whyte, Douglas; Cahir, Elizabeth; Lester, Henry A; Grady, Sharon R; Marks, Michael J; Cohen, Bruce N; Fonck, Carlos; McClure-Begley, Tristan; McIntosh, J Michael; Labarca, Cesar; Lawrence, Andrew; Chen, Feng; Gantois, Ilse; Davies, Philip J; Petrou, Steven; Murphy, Mark; Waddington, John; Horne, Malcolm K; Berkovic, Samuel F; Drago, John

    2007-09-19

    We generated a mouse line harboring an autosomal-dominant nocturnal frontal lobe epilepsy (ADNFLE) mutation: the alpha4 nicotinic receptor S248F knock-in strain. In this mouse, modest nicotine doses (1-2 mg/kg) elicit a novel behavior termed the dystonic arousal complex (DAC). The DAC includes stereotypical head movements, body jerking, and forelimb dystonia; these behaviors resemble some core features of ADNFLE. A marked Straub tail is an additional component of the DAC. Similar to attacks in ADNFLE, the DAC can be partially suppressed by the sodium channel blocker carbamazepine or by pre-exposure to a very low dose of nicotine (0.1 mg/kg). The DAC is centrally mediated, genetically highly penetrant, and, surprisingly, not associated with overt ictal electrical activity as assessed by (1) epidural or frontal lobe depth-electrode electroencephalography or (2) hippocampal c-fos-regulated gene expression. Heterozygous knock-in mice are partially protected from nicotine-induced seizures. The noncompetitive antagonist mecamylamine does not suppress the DAC, although it suppresses high-dose nicotine-induced wild-type-like seizures. Experiments on agonist-induced 86Rb+ and neurotransmitter efflux from synaptosomes and on alpha4S248Fbeta2 receptors expressed in oocytes confirm that the S248F mutation confers resistance to mecamylamine blockade. Genetic background, gender, and mutant gene expression levels modulate expression of the DAC phenotype in mice. The S248F mouse thus appears to provide a model for the paroxysmal dystonic element of ADNFLE semiology. Our model complements what is seen in other ADNFLE animal models. Together, these mice cover the spectrum of behavioral and electrographic events seen in the human condition.

  10. Escherichia coli harboring a natural IncF conjugative F plasmid develops complex mature biofilms by stimulating synthesis of colanic acid and Curli.

    PubMed

    May, Thithiwat; Okabe, Satoshi

    2008-11-01

    It has been shown that Escherichia coli harboring the derepressed IncFI and IncFII conjugative F plasmids form complex mature biofilms by using their F-pilus connections, whereas a plasmid-free strain forms only patchy biofilms. Therefore, in this study we investigated the contribution of a natural IncF conjugative F plasmid to the formation of E. coli biofilms. Unlike the presence of a derepressed F plasmid, the presence of a natural IncF F plasmid promoted biofilm formation by generating the cell-to-cell mating F pili between pairs of F(+) cells (approximately two to four pili per cell) and by stimulating the formation of colanic acid and curli meshwork. Formation of colanic acid and curli was required after the initial deposition of F-pilus connections to generate a three-dimensional mushroom-type biofilm. In addition, we demonstrated that the conjugative factor of F plasmid, rather than a pilus synthesis function, was involved in curli production during biofilm formation, which promoted cell-surface interactions. Curli played an important role in the maturation process. Microarray experiments were performed to identify the genes involved in curli biosynthesis and regulation. The results suggested that a natural F plasmid was more likely an external activator that indirectly promoted curli production via bacterial regulatory systems (the EnvZ/OmpR two-component regulators and the RpoS and HN-S global regulators). These data provided new insights into the role of a natural F plasmid during the development of E. coli biofilms.

  11. Formation of Tap/NXT1 Heterodimers Activates Tap-Dependent Nuclear mRNA Export by Enhancing Recruitment to Nuclear Pore Complexes

    PubMed Central

    Wiegand, Heather L.; Coburn, Glen A.; Zeng, Yan; Kang, Yibin; Bogerd, Hal P.; Cullen, Bryan R.

    2002-01-01

    The Tap protein has been shown to activate the nuclear export of mRNA species bearing retroviral constitutive transport elements and is also believed to play an essential role in the sequence nonspecific export of cellular mRNAs. However, it has remained unclear how Tap activity is regulated in vivo. Here, we report that the small NXT1/p15-1 protein functions as a critical cofactor for Tap-mediated mRNA export in both human and invertebrate cells. In the absence of NXT1 binding, the Tap protein is unable to effectively interact with components of the nuclear pore complex and both Tap nucleocytoplasmic shuttling and the nuclear export of mRNA molecules tethered to Tap are therefore severely attenuated. Formation of a Tap/NXT1 heterodimer enhances nucleoporin binding both in vitro and in vivo and induces the formation of a Tap/NXT1/nucleoporin ternary complex that is likely to be a key intermediate in the process of nuclear mRNA export. The critical importance of NXT1 for the nuclear export of poly(A)+ RNA is emphasized by the finding that specific inhibition of the expression of the Drosophila homolog of human NXT1, by using RNA interference, results in the nuclear accumulation of poly(A)+ RNA in cultured insect cells. These data suggest that NXT1 may act as a molecular switch that regulates the ability of Tap to mediate nuclear mRNA export by controlling the interaction of Tap with components of the nuclear pore. PMID:11739738

  12. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-11-01

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

  15. 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

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

    PubMed

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

    2016-03-28

    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.

  17. 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

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

    PubMed Central

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

    2010-01-01

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

  19. Ion permeability of the nuclear pore complex and ion-induced macromolecular permeation as studied by scanning electrochemical and fluorescence microscopy.

    PubMed

    Kim, Jiyeon; Izadyar, Anahita; Shen, Mei; Ishimatsu, Ryoichi; Amemiya, Shigeru

    2014-02-18

    Efficient delivery of therapeutic macromolecules and nanomaterials into the nucleus is imperative for gene therapy and nanomedicine. Nucleocytoplasmic molecular transport, however, is tightly regulated by the nuclear pore complex (NPC) with the hydrophobic transport barriers based on phenylalanine and glycine repeats. Herein, we apply scanning electrochemical microscopy (SECM) to quantitatively study the permeability of the NPCs to small probe ions with a wide range of hydrophobicity as a measure of their hydrophobic interactions with the transport barriers. Amperometric detection of the redox-inactive probe ions is enabled by using the ion-selective SECM tips based on the micropipet- or nanopipet-supported interfaces between two immiscible electrolyte solutions. The remarkably high ion permeability of the NPCs is successfully measured by SECM and theoretically analyzed. This analysis demonstrates that the ion permeability of the NPCs is determined by the dimensions and density of the nanopores without a significant effect of the transport barriers on the transported ions. Importantly, the weak ion-barrier interactions become significant at sufficiently high concentrations of extremely hydrophobic ions, i.e., tetraphenylarsonium and perfluorobutylsulfonate, to permeabilize the NPCs to naturally impermeable macromolecules. Dependence of ion-induced permeabilization of the NPC on the pathway and mode of macromolecular transport is studied by using fluorescence microscopy to obtain deeper insights into the gating mechanism of the NPC as the basis of a new transport model.

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

    PubMed Central

    Paul, Biplab; Montpetit, Ben

    2016-01-01

    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. PMID:27385342

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  3. 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.

  4. 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

  5. A New Path through the Nuclear Pore.

    PubMed

    Gozalo, Alejandro; Capelson, Maya

    2016-11-17

    Knowing the configuration of the nuclear pore is essential for appreciating the underlying mechanisms of nucleo-cytoplasmic communication. Now, Fernandez-Martinez et al. present a high-resolution structure of the cytoplasmic nuclear pore-mRNA export holo-complex, challenging our textbook depiction of this massive membrane-embedded complex.

  6. 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.

  7. 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.

  8. Assembly and Preferential Localization of Nup116p on the Cytoplasmic Face of the Nuclear Pore Complex by Interaction with Nup82p

    PubMed Central

    Ho, Albert K.; Shen, Tian Xiang; Ryan, Kathryn J.; Kiseleva, Elena; Levy, Marilyn Aach; Allen, Terence D.; Wente, Susan R.

    2000-01-01

    The yeast Saccharomyces cerevisiae nucleoporin Nup116p serves as a docking site for both nuclear import and export factors. However, the mechanism for assembling Nup116p into the nuclear pore complex (NPC) has not been resolved. By conducting a two-hybrid screen with the carboxy (C)-terminal Nup116p region as bait, we identified Nup82p. The predicted coiled-coil region of Nup82p was not required for Nup116p interaction, making the binding requirements distinct from those for the Nsp1p-Nup82p-Nup159p subcomplex (N. Belgareh, C. Snay-Hodge, F. Pasteau, S. Dagher, C. N. Cole, and V. Doye, Mol. Biol. Cell 9:3475–3492, 1998). Immunoprecipitation experiments using yeast cell lysates resulted in the coisolation of a Nup116p-Nup82p subcomplex. Although the absence of Nup116p had no effect on the NPC localization of Nup82p, overexpression of C-terminal Nup116p in a nup116 null mutant resulted in Nup82p mislocalization. Moreover, NPC localization of Nup116p was specifically diminished in a nup82-Δ108 mutant after growth at 37°C. Immunoelectron microscopy analysis showed Nup116p was localized on both the cytoplasmic and nuclear NPC faces. Its distribution was asymmetric with the majority at the cytoplasmic face. Taken together, these results suggest that Nup82p and Nup116p interact at the cytoplasmic NPC face, with nucleoplasmic Nup116p localization utilizing novel binding partners. PMID:10891509

  9. Great Lakes Harbors Study

    DTIC Science & Technology

    1966-11-01

    Locally.assigned Library of Congress number: HE396 S25 U55 Nj 19. KEY WORDS (Continue on reverse side if necessary and identify by block number) 1. HARBORS 2... WATER TRANSPORTATION 3. ECONOMIC ANALYSIS 4. GREAT LJAKES - 20. ABSTRACT (Continue on ie.er.se side It necesaty nd identify by blocA number) Harbor...Scope 2 DESCRIPTION AND ECONOMIC DEVELOPMENT 3 Great Lakes-St. Lawrence Navigation System 2 4 Navigation Season 3 5 Water Levels 4 6 Tributary Area 6

  10. Moving Magnetic Features around a Pore

    NASA Astrophysics Data System (ADS)

    Kaithakkal, A. J.; Riethmüller, T. L.; Solanki, S. K.; Lagg, A.; Barthol, P.; Gandorfer, A.; Gizon, L.; Hirzberger, J.; vanNoort, M.; Blanco Rodríguez, J.; Del Toro Iniesta, J. C.; Orozco Suárez, D.; Schmidt, W.; Martínez Pillet, V.; Knölker, M.

    2017-03-01

    Spectropolarimetric observations from Sunrise/IMaX, obtained in 2013 June, are used for a statistical analysis to determine the physical properties of moving magnetic features (MMFs) observed near a pore. MMFs of the same and opposite polarity, with respect to the pore, are found to stream from its border at an average speed of 1.3 km s‑1 and 1.2 km s‑1, respectively, with mainly same-polarity MMFs found further away from the pore. MMFs of both polarities are found to harbor rather weak, inclined magnetic fields. Opposite-polarity MMFs are blueshifted, whereas same-polarity MMFs do not show any preference for up- or downflows. Most of the MMFs are found to be of sub-arcsecond size and carry a mean flux of ∼1.2 × 1017 Mx.

  11. 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.

  12. 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

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

    DOE PAGES

    Khairallah, Saad A.; Anderson, Andrew T.; Rubenchik, Alexander; ...

    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

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

    SciTech Connect

    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. 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.

  15. 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.

  16. Pearl Harbor Biological Survey

    DTIC Science & Technology

    1974-08-30

    Scalloped Hammerhead Shark , Sphyma leuini. In Hawaii", Pacific Science, 25(2):133-144. 2.1-11 "Surveillance, Sewage and Surprises", Navy Action 󈨌...Some fish tagged in the harbor were caught off Sand Island; others were returned from the Honolulu fish markets. The hammerhead shark {Sphyma...MYLIOBATIDAE Scalloped hammerhead shark ; Mano kihlkihi Sphyma lewini after K, S 4 W (16130101) ELOPIDAE fit. Spotted eagle ray; Hihimanu AetobatuB

  17. Building, roof, with machinery penthouses on left and harbor control ...

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

    Building, roof, with machinery penthouses on left and harbor control tower on right. Camera facing south - Naval Supply Center, Broadway Complex, Warehouse, 911 West Broadway, San Diego, San Diego County, CA

  18. 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

  19. 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.

  20. The Fission Yeast Nup107-120 Complex Functionally Interacts with the Small GTPase Ran/Spi1 and Is Required for mRNA Export, Nuclear Pore Distribution, and Proper Cell Division

    PubMed Central

    Baï, Siau Wei; Rouquette, Jacques; Umeda, Makoto; Faigle, Wolfgang; Loew, Damarys; Sazer, Shelley; Doye, Valérie

    2004-01-01

    We have characterized Schizosaccharomyces pombe open reading frames encoding potential orthologues of constituents of the evolutionarily conserved Saccharomyces cerevisiae Nup84 vertebrate Nup107-160 nuclear pore subcomplex, namely Nup133a, Nup133b, Nup120, Nup107, Nup85, and Seh1. In spite of rather weak sequence conservation, in vivo analyses demonstrated that these S. pombe proteins are localized at the nuclear envelope. Biochemical data confirmed the organization of these nucleoporins within conserved complexes. Although examination of the S. cerevisiae and S. pombe deletion mutants revealed different viability phenotypes, functional studies indicated that the involvement of this complex in nuclear pore distribution and mRNA export has been conserved between these highly divergent yeasts. Unexpectedly, microscopic analyses of some of the S. pombe mutants revealed cell division defects at the restrictive temperature (abnormal septa and mitotic spindles and chromosome missegregation) that were reminiscent of defects occurring in several S. pombe GTPase Ran (RanSp)/Spi1 cycle mutants. Furthermore, deletion of nup120 moderately altered the nuclear location of RanSp/Spi1, whereas overexpression of a nonfunctional RanSp/Spi1-GFP allele was specifically toxic in the Δnup120 and Δnup133b mutant strains, indicating a functional and genetic link between constituents of the S. pombe Nup107-120 complex and of the RanSp/Spi1 pathway. PMID:15226438

  1. Isolated pores dissected from human two-pore channel 2 are functional

    PubMed Central

    Penny, Christopher J.; Rahman, Taufiq; Sula, Altin; Miles, Andrew J.; Wallace, B. A.; Patel, Sandip

    2016-01-01

    Multi-domain voltage-gated ion channels appear to have evolved through sequential rounds of intragenic duplication from a primordial one-domain precursor. Whereas modularity within one-domain symmetrical channels is established, little is known about the roles of individual regions within more complex asymmetrical channels where the domains have undergone substantial divergence. Here we isolated and characterised both of the divergent pore regions from human TPC2, a two-domain channel that holds a key intermediate position in the evolution of voltage-gated ion channels. In HeLa cells, each pore localised to the ER and caused Ca2+ depletion, whereas an ER-targeted pore mutated at a residue that inactivates full-length TPC2 did not. Additionally, one of the pores expressed at high levels in E. coli. When purified, it formed a stable, folded tetramer. Liposomes reconstituted with the pore supported Ca2+ and Na+ uptake that was inhibited by known blockers of full-length channels. Computational modelling of the pore corroborated cationic permeability and drug interaction. Therefore, despite divergence, both pores are constitutively active in the absence of their partners and retain several properties of the wild-type pore. Such symmetrical ‘pore-only’ proteins derived from divergent channel domains may therefore provide tractable tools for probing the functional architecture of complex ion channels. PMID:27941820

  2. Norovirus Infection in Harbor Porpoises

    PubMed Central

    Bodewes, Rogier; van Elk, Cornelis E.; van de Bildt, Marco; Getu, Sarah; Aron, Georgina I.; Verjans, Georges M.G.M.; Osterhaus, Albert D.M.E.; van den Brand, Judith M.A.; Kuiken, Thijs; Koopmans, Marion P.G.

    2017-01-01

    A norovirus was detected in harbor porpoises, a previously unknown host for norovirus. This norovirus had low similarity to any known norovirus. Viral RNA was detected primarily in intestinal tissue, and specific serum antibodies were detected in 8 (24%) of 34 harbor porpoises from the North Sea. PMID:27983498

  3. Genetics Home Reference: Floating-Harbor syndrome

    MedlinePlus

    ... Understand Genetics Home Health Conditions Floating-Harbor syndrome Floating-Harbor syndrome Enable Javascript to view the expand/ ... boxes. Download PDF Open All Close All Description Floating-Harbor syndrome is a disorder involving short stature, ...

  4. 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.

  5. 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.

  6. Differences in soluble organic carbon chemistry in pore waters sampled from different pore size domains

    DOE PAGES

    Bailey, Vanessa L.; Smith, A. P.; Tfaily, Malak; ...

    2017-01-11

    Spatial isolation of soil organic carbon (SOC) in different sized pores may be a mechanism by which otherwise labile carbon (C) could be protected in soils. When soil water content increases, the hydrologic connectivity of soil pores also increases, allowing greater transport of SOC and other resources from protected locations, to microbially colonized locations more favorable to decomposition. The heterogeneous distribution of specialized decomposers, C, and other resources throughout the soil indicates that the metabolism or persistence of soil C compounds is highly dependent on short-distance transport processes. The objective of this research was to characterize the complexity of Cmore » in pore waters held at weak and strong water tensions (effectively soil solution held behind coarse- and fine-pore throats, respectively) and evaluate the microbial decomposability of these pore waters. We saturated intact soil cores and extracted pore waters with increasing suction pressures to sequentially sample pore waters from increasingly fine pore domains. Ultrahigh resolution mass spectrometry of the SOC was used to profile the major biochemical classes (i.e., lipids, proteins, lignin, carbohydrates, and condensed aromatics) of compounds present in the pore waters; some of these samples were then used as substrates for growth of Cellvibrio japonicus (DSMZ 16018), Streptomyces cellulosae (ATCC® 25439™), and Trichoderma reseei (QM6a) in 7 day incubations. The soluble C in finer pores was more complex than the soluble C in coarser pores, and the incubations revealed that the more complex C in these fine pores is not recalcitrant. The decomposition of this complex C led to greater losses of C through respiration than the simpler C from coarser pore waters. Our research suggests that soils that experience repeated cycles of drying and wetting may be accompanied by repeated cycles of increased CO2 fluxes that are driven by i) the transport of C from protected pools into

  7. Identification of acute toxicants in New Bedford Harbor sediments

    SciTech Connect

    Ho, K.T.; McKinney, R.A.; Kuhn, A.; Pelletier, M.C.; Burgess, R.M.

    1997-03-01

    New Bedford Harbor (NBH) is a marine Superfund site contaminated with high concentrations of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and metals. Experiments were conducted to determine the causal toxic agent(s) in pore waters from New Bedford Harbor sediments to amphipods and mysid shrimp. Chemical manipulations to characterize toxicity revealed that pore-water toxicity was organic in nature. Fractionation and subsequent mass spectral identification of peaks in the toxic fraction indicated that PCBs. PAHs, and unknown compounds were present. Comparisons of PAH LC50s and PAH concentrations in this fraction indicated that the toxicity was not due to PAHs because the PAH concentrations were much lower than the reported PAH LC50s. One unknown peak was positively identified as bis(2-ethylhexyl) phthalate, and the other tentatively identified as pyrazole. Toxicity tests and comparison of toxicity in the blank and toxic fractions eliminated the two unknowns as toxic causal agents. The authors determined the range of PCB LC50s to fall between 10 and 110 ppb for Mysidopsis bahia and Ampelisca abdita. Concentrations of PCBs for the toxic fractions ranged from 12 to 27 ppb. This range falls within the observed PCB LC50s for M. bahia and A. abdita. Based upon these PCB concentrations, they concluded that PCBs were the acute toxic agents in NBH pore waters. Other compounds in the toxic fractions, or compounds that coeluted and were undistinguished from PCBs had minor contributions to the measured toxicity.

  8. 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.

  9. Flux theory for Poisson distributed pores with Gaussian permeability.

    PubMed

    Salinas, Dino G

    2016-01-01

    The mean of the solute flux through membrane pores depends on the random distribution and permeability of the pores. Mathematical models including such randomness factors make it possible to obtain statistical parameters for pore characterization. Here, assuming that pores follow a Poisson distribution in the lipid phase and that their permeabilities follow a Gaussian distribution, a mathematical model for solute dynamics is obtained by applying a general result from a previous work regarding any number of different kinds of randomly distributed pores. The new proposed theory is studied using experimental parameters obtained elsewhere, and a method for finding the mean single pore flux rate from liposome flux assays is suggested. This method is useful for pores without requiring studies by patch-clamp in single cells or single-channel recordings. However, it does not apply in the case of ion-selective channels, in which a more complex flux law combining the concentration and electrical gradient is required.

  10. A TB-RBP and Ter ATPase complex accompanies specific mRNAs from nuclei through the nuclear pores and into intercellular bridges in mouse male germ cells.

    PubMed

    Morales, Carlos R; Lefrancois, Stephane; Chennathukuzhi, Vargheese; El-Alfy, Mohamed; Wu, XinQi; Yang, Juxiang; Gerton, George L; Hecht, Norman B

    2002-06-15

    The testis brain RNA-binding protein (TB-RBP) functions as an RNA-binding protein in brain and testis, binding to conserved sequence elements present in specific mRNAs, such as protamine 1 and 2. We show here by RNA gel shift assays, immunoprecipitation, and by a novel in situ hybridization immunohistochemical technique that TB-RBP binds to AKAP4 mRNA in male mouse germ cells. AKAP4 is a component of the fibrous sheath and functions as a scaffolding protein in the sperm flagellum. AKAP4 is encoded by an X-linked gene, is expressed solely in postmeiotic (haploid) male germ cells, and is an essential protein in all spermatozoa, requiring its transport between spermatids as a protein or mRNA. AKAP4 mRNA forms a complex with TB-RBP and the Ter ATPase in nuclei and remains associated with these proteins as it exits nuclei into the cytoplasm and as it passes through intercellular bridges between spermatids. A similar mRNA-TB-RBP-Ter ATPase association is seen for protamine 2 mRNA, which is stored in the cytoplasm of postmeiotic germ cells about 7 days before translation. In contrast, no association is seen with PGK-2 mRNA which is initially transcribed early in meiosis with increased transcription in postmeiotic male germ cells. Although PGK-2 mRNA is subject to translational control, it lacks TB-RBP-binding sequences in its mRNA. The AKAP4 or protamine 2 mRNA-protein complexes dissociate in late-stage male germ cells when the mRNAs are translated. We propose that TB-RBP and the Ter ATPase are part of a complex that accompanies specific mRNAs in haploid mouse male germ cells in intracellular and intercellular movement. The temporal relationship of TB-RBP binding and mRNA inactivation in conjunction with the subsequent dissociation of the mRNA-protein complex at the time of mRNA translation suggests a role in translational suppression and/or mRNA stabilization.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. Modeling branching pore structures in membrane filters

    NASA Astrophysics Data System (ADS)

    Sanaei, Pejman; Cummings, Linda J.

    2016-11-01

    Membrane filters are in widespread industrial use, and mathematical models to predict their efficacy are potentially very useful, as such models can suggest design modifications to improve filter performance and lifetime. Many models have been proposed to describe particle capture by membrane filters and the associated fluid dynamics, but most such models are based on a very simple structure in which the pores of the membrane are assumed to be simple circularly-cylindrical tubes spanning the depth of the membrane. Real membranes used in applications usually have much more complex geometry, with interconnected pores which may branch and bifurcate. Pores are also typically larger on the upstream side of the membrane than on the downstream side. We present an idealized mathematical model, in which a membrane consists of a series of bifurcating pores, which decrease in size as the membrane is traversed. Feed solution is forced through the membrane by applied pressure, and particles are removed from the feed either by sieving, or by particle adsorption within pores (which shrinks them). Thus the membrane's permeability decreases as the filtration progresses, ultimately falling to zero. We discuss how filtration efficiency depends on the characteristics of the branching structure. Partial support from NSF DMS 1261596 is gratefully acknowledged.

  16. Accelerated Implementation of Harbor Processes Research

    DTIC Science & Technology

    2006-05-31

    WATERSHEDS, *BIODEGRADATION, *SEDIMENTS, INDUSTRIES, STRATEGY, WATER, NAVY, SITES, SEASONAL VARIATIONS, SAMPLING, CONTAMINANTS, HARBORS, OCEAN BOTTOM, ANALYTICAL CHEMISTRY , TOXICOLOGY, OCEANOGRAPHY, ESTUARIES.

  17. 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

  18. Model Pores of Molecular Dimension

    PubMed Central

    Quinn, J. A.; Anderson, J. L.; Ho, W. S.; Petzny, W. J.

    1972-01-01

    Extremely uniform pores of near molecular dimension can be formed by the irradiation-etching technique first demonstrated by Price and Walker. The technique has now been developed to the stage where it can be used to fabricate model membranes for examining the various steric, hydrodynamic, and electrodynamic phenomena encountered in transport through molecular-size pores. Methods for preparing and characterizing membranes with pores as small as 25 A (radius) are described in this paper. Results on pore size determination via Knudsen gas flow and electrolyte conduction are compared. Pore wall modification by monolayer deposition is also discussed. PMID:4339801

  19. Selective NO trapping in the pores of chain-type complex assemblies based on electronically activated paddlewheel-type [Ru2(II,II)]/[Rh2(II,II)] dimers.

    PubMed

    Kosaka, Wataru; Yamagishi, Kayo; Hori, Akihiro; Sato, Hiroshi; Matsuda, Ryotaro; Kitagawa, Susumu; Takata, Masaki; Miyasaka, Hitoshi

    2013-12-11

    The design of porous materials that undergo selective adsorption of a specific molecule is a critical issue in research on porous coordination polymers or metal-organic frameworks. For the purpose of the selective capture of molecules possessing an electron-acceptor character such as nitric oxide (NO), one-dimensional chain compounds possessing a high donor character have been synthesized using 4-chloroanisate-bridged paddlewheel-type dimetal(II, II) complexes with M = Ru and Rh and phenazine (phz) as the chain linker: [M2(4-Cl-2-OMePhCO2)4(phz)]·n(CH2Cl2) (M = Ru, 1; Rh, 2). These compounds are isostructural and are composed of chains with a [-{M2}-phz-] repeating unit and CH2Cl2 occupying the void space between the chains. Compounds 1 and 2 change to a new phase (1-dry and 2-dry) upon evacuating the crystallization solvent (CH2Cl2) and almost lose their pores in the drying process: no void space in 1-dry and 31.8 Å(3), corresponding to 2.9% of the cell volume, in 2-dry. Nevertheless, the compounds show a unique gas accommodation ability. Accompanied by a structural transformation (i.e., the first gate-opening) at low pressures of <10 kPa, both compounds show a typical physisorption isotherm for O2 (90 K) and CO2 (195 K), with the adsorption amount of ca. 2-4 gas molecules per [M2] unit. In addition, the adsorption isotherm for NO (121 K) involves the first gate-opening followed by a second gate-opening anomaly at NO pressures of ≈52 kPa for 1-dry and ≈21 kPa for 2-dry. At the first gate-opening, the absorbed amount of NO is ca. 4 molecules per [M2] unit, and then it reaches 8.4 and 6.3 for 1-dry and 2-dry, respectively, at 95 kPa. Only the isotherm for NO exhibits hysteresis in the desorption process, and some of the NO molecules are trapped in pores even after evacuating at 121 K, although it recovers to the original dried sample on heating to room temperature. The adsorbed NO molecules accrue a significant electron donation from the host framework even in

  20. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 3 2012-07-01 2012-07-01 false Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. 207.480 Section 207.480 Navigation and Navigable Waters CORPS... Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. (a) All boats, barges, and...

  1. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 3 2014-07-01 2014-07-01 false Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. 207.480 Section 207.480 Navigation and Navigable Waters CORPS... Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. (a) All boats, barges, and...

  2. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 3 2013-07-01 2013-07-01 false Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. 207.480 Section 207.480 Navigation and Navigable Waters CORPS... Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. (a) All boats, barges, and...

  3. 33 CFR 207.480 - Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 3 2011-07-01 2011-07-01 false Lake Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. 207.480 Section 207.480 Navigation and Navigable Waters CORPS... Huron, Mich.; Harbor of refuge, Harbor Beach; use and navigation. (a) All boats, barges, and...

  4. 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.

  5. Army Engineers at Pearl Harbor

    DTIC Science & Technology

    2011-01-01

    the Honolulu Engi- neer District, then part of the South Pacific Division. Colonel Albert K.B. Lyman , a native Hawaiian who later attained the rank...aircraft dis- persal at Wheeler Field. On the civil side, Lieutenant Colonel Theodore Wyman, the Honolulu District Engineer, had offices employing 10...Army Engineers at Pearl Harbor Past in Review Native Hawaiian Colonel Albert K.B. Lyman , the Army’s Ha- waiian Department engineer during the attack

  6. 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.

  7. Open-closed switching of synthetic tubular pores

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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.

  8. 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

  9. Submarine harbor navigation using image data

    NASA Astrophysics Data System (ADS)

    Stubberud, Stephen C.; Kramer, Kathleen A.

    2017-01-01

    The process of ingress and egress of a United States Navy submarine is a human-intensive process that takes numerous individuals to monitor locations and for hazards. Sailors pass vocal information to bridge where it is processed manually. There is interest in using video imaging of the periscope view to more automatically provide navigation within harbors and other points of ingress and egress. In this paper, video-based navigation is examined as a target-tracking problem. While some image-processing methods claim to provide range information, the moving platform problem and weather concerns, such as fog, reduce the effectiveness of these range estimates. The video-navigation problem then becomes an angle-only tracking problem. Angle-only tracking is known to be fraught with difficulties, due to the fact that the unobservable space is not the null space. When using a Kalman filter estimator to perform the tracking, significant errors arise which could endanger the submarine. This work analyzes the performance of the Kalman filter when angle-only measurements are used to provide the target tracks. This paper addresses estimation unobservability and the minimal set of requirements that are needed to address it in this complex but real-world problem. Three major issues are addressed: the knowledge of navigation beacons/landmarks' locations, the minimal number of these beacons needed to maintain the course, and update rates of the angles of the landmarks as the periscope rotates and landmarks become obscured due to blockage and weather. The goal is to address the problem of navigation to and from the docks, while maintaining the traversing of the harbor channel based on maritime rules relying solely on the image-based data. The minimal number of beacons will be considered. For this effort, the image correlation from frame to frame is assumed to be achieved perfectly. Variation in the update rates and the dropping of data due to rotation and obscuration is considered

  10. Nuclear Pore-Like Structures in a Compartmentalized Bacterium

    PubMed Central

    Sagulenko, Evgeny; Green, Kathryn; Yee, Benjamin; Morgan, Garry; Leis, Andrew; Lee, Kuo-Chang; Butler, Margaret K.; Chia, Nicholas; Pham, Uyen Thi Phuong; Lindgreen, Stinus; Catchpole, Ryan; Poole, Anthony M.; Fuerst, John A.

    2017-01-01

    Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence. PMID:28146565

  11. Mechanics of membrane fusion/pore formation.

    PubMed

    Fuhrmans, Marc; Marelli, Giovanni; Smirnova, Yuliya G; Müller, Marcus

    2015-01-01

    Lipid bilayers play a fundamental role in many biological processes, and a considerable effort has been invested in understanding their behavior and the mechanism of topological changes like fusion and pore formation. Due to the time- and length-scale on which these processes occur, computational methods have proven to be an especially useful tool in their study. With their help, a number of interesting findings about the shape of fusion intermediates could be obtained, and novel hypotheses about the mechanism of topological changes and the involvement of peptides therein were suggested. In this work, we try to present a summary of these developments together with some hitherto unpublished results, featuring, among others, the shape of stalks and fusion pores, possible modes of action of the influenza HA fusion peptide and the SNARE protein complex, the mechanism of supported lipid bilayer formation by vesicle spreading, and the free energy and transition pathway of the fusion process.

  12. 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...

  13. 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

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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.

  20. 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.

  1. Hydrate formation and growth in pores

    NASA Astrophysics Data System (ADS)

    Jung, Jong-Won; Santamarina, J. Carlos

    2012-04-01

    Gas hydrates consist of guest gas molecules encaged in water cages. Methane hydrate forms in marine and permafrost sediments. In this study, we use optical, mechanical and electrical measurements to monitor hydrate formation and growth in small pores to better understand the hydrate pore habit in hydrate-bearing sediments. Hydrate formation in capillary tubes exposes the complex and dynamic interactions between nucleation, gas diffusion and gas solubility. The observation of hydrate growth in a droplet between transparent plates shows that the hydrate shell does not grow homogeneously but advances in the form of lobes that invade the water phase; in fact, the hydrate shell must be discontinuous and possibly cracked to justify the relatively fast growth rates observed in these experiments. Volume expansion during hydrate formation causes water to flow out of menisci; expelled water either spreads on the surface of water-wet substrates and forms a thin hydrate sheet, or remains next to menisci when substrates are oil-wet. Hydrate formation is accompanied by ion exclusion, yet, there is an overall increase in electrical resistance during hydrate formation. Hydrate growth may become salt-limited in trapped water conditions; in this case, aqueous brine and gas CH4 may be separated by hydrate and the three-phase system remains stable within the pore space of sediments.

  2. Role of the synaptobrevin C terminus in fusion pore formation

    PubMed Central

    Ngatchou, Annita N.; Kisler, Kassandra; Fang, Qinghua; Walter, Alexander M.; Zhao, Ying; Bruns, Dieter; Sørensen, Jakob B.; Lindau, Manfred

    2010-01-01

    Neurotransmitter release is mediated by the SNARE proteins synaptobrevin II (sybII, also known as VAMP2), syntaxin, and SNAP-25, generating a force transfer to the membranes and inducing fusion pore formation. However, the molecular mechanism by which this force leads to opening of a fusion pore remains elusive. Here we show that the ability of sybII to support exocytosis is inhibited by addition of one or two residues to the sybII C terminus depending on their energy of transfer from water to the membrane interface, following a Boltzmann distribution. These results suggest that following stimulation, the SNARE complex pulls the C terminus of sybII deeper into the vesicle membrane. We propose that this movement disrupts the vesicular membrane continuity leading to fusion pore formation. In contrast to current models, the experiments suggest that fusion pore formation begins with molecular rearrangements at the intravesicular membrane leaflet and not between the apposed cytoplasmic leaflets. PMID:20937897

  3. The role of the C terminus of the SNARE protein SNAP-25 in fusion pore opening and a model for fusion pore mechanics

    PubMed Central

    Fang, Qinghua; Berberian, Khajak; Gong, Liang-Wei; Hafez, Ismail; Sørensen, Jakob B.; Lindau, Manfred

    2008-01-01

    Formation of a fusion pore between a vesicle and its target membrane is thought to involve the so-called SNARE protein complex. However, there is no mechanistic model explaining how the fusion pore is opened by conformational changes in the SNARE complex. It has been suggested that C-terminal zipping triggers fusion pore opening. A SNAP-25 mutant named SNAP-25Δ9 (lacking the last nine C-terminal residues) should lead to a less-tight C-terminal zipping. Single exocytotic events in chromaffin cells expressing this mutant were characterized by carbon fiber amperometry and cell-attached patch capacitance measurements. Cells expressing SNAP-25Δ9 displayed smaller amperometric “foot-current” currents, reduced fusion pore conductances, and lower fusion pore expansion rates. We propose that SNARE/lipid complexes form proteolipid fusion pores. Fusion pores involving the SNAP-25Δ9 mutant will be less tightly zipped and may lead to a longer fusion pore structure, consistent with the observed decrease of fusion pore conductance. PMID:18829435

  4. 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

  5. Geostatistical Modeling of Pore Velocity

    SciTech Connect

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

    1981-06-01

    A significant part of evaluating a geologic formation as a nuclear waste repository involves the modeling of contaminant transport in the surrounding media in the event the repository is breached. The commonly used contaminant transport models are deterministic. However, the spatial variability of hydrologic field parameters introduces uncertainties into contaminant transport predictions. This paper discusses the application of geostatistical techniques to the modeling of spatially varying hydrologic field parameters required as input to contaminant transport analyses. Kriging estimation techniques were applied to Hanford Reservation field data to calculate hydraulic conductivity and the ground-water potential gradients. These quantities were statistically combined to estimate the groundwater pore velocity and to characterize the pore velocity estimation error. Combining geostatistical modeling techniques with product error propagation techniques results in an effective stochastic characterization of groundwater pore velocity, a hydrologic parameter required for contaminant transport analyses.

  6. Hospital Room Floors May Harbor 'Superbugs'

    MedlinePlus

    ... fullstory_163886.html Hospital Room Floors May Harbor 'Superbugs' But that area often overlooked when it comes ... Hospital room floors may be more of a "superbug" threat than many hospital staffers realize, new research ...

  7. 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.

  8. West Harbor, Ohio Recreational Navigation Improvement. Revision.

    DTIC Science & Technology

    1979-03-01

    natural sand beach at Gem Beach, and a length of shoreline which is essentially stable but which periodically ex- periences slight fluctuations in...dually to form an essentially flat plateau of land in the shoreward -11- direction. However, a few hundred feet to the east the beach rises from the...Harbor, which has remained essentially in its natural state in spite of the recreational and residential development of East and West Harbors, has been

  9. Restricted Transport in Small Pores

    PubMed Central

    Anderson, John L.; Quinn, John A.

    1974-01-01

    The basic hydrodynamic equations governing transport in submicron pores are reexamined. Conditions necessary for a simplified, one-dimensional treatment of the diffusion/convection process are established. Steric restrictions and Brownian motion are incorporated directly into the resulting model. Currently available fluid mechanical results are used to evaluate an upper limit on hindered diffusion; this limit is valid for small particle-to-pore ratios. Extensions of the analysis are shown to depend on numerical solutions of the related hydrodynamic problem, that of asymmetrical particle motion in a bounded fluid. PMID:4813157

  10. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  11. GATED PORES IN THE FERRITIN PROTEIN NANOCAGE

    PubMed Central

    Theil, Elizabeth C.; Liu, Xiaofeng S.; Tosha, Takehiko

    2008-01-01

    Synopsis and pictogram: Gated pores in the ferritin family of protein nanocages, illustrated in the pictogram, control transfer of ferrous iron into and out of the cages by regulating contact between hydrated ferric oxide mineral inside the protein cage, and reductants such as FMNH2 on the outside. The structural and functional homology between the gated ion channel proteins in inaccessible membranes and gated ferritin pores in the stable, water soluble nanoprotein, make studies of ferritin pores models for gated pores in many ion channel proteins. Properties of ferritin gated pores, which control rates of FMNH2 reduction of ferric iron in hydrated oxide minerals inside the protein nanocage, are discussed in terms of the conserved pore gate residues (arginine 72-apspartate 122 and leucine 110-leucine 134), of pore sensitivity to heat at temperatures 30 °C below that of the nanocage itself, and of pore sensitivity to physiological changes in urea (1–10 mM). Conditions which alter ferritin pore structure/function in solution, coupled with the high evolutionary conservation of the pore gates, suggest the presence of molecular regulators in vivo that recognize the pore gates and hold them either closed or open, depending on biological iron need. The apparent homology between ferrous ion transport through gated pores in the ferritin nanocage and ion transport through gated pores in ion channel proteins embedded in cell membranes, make studies of water soluble ferritin and the pore gating folding/unfolding a useful model for other gated pores. PMID:19262678

  12. Smectic pores and defect cores

    PubMed Central

    Matsumoto, Elisabetta A.; Kamien, Randall D.; Santangelo, Christian D.

    2012-01-01

    Riemann's minimal surfaces, a one-parameter family of minimal surfaces, describe a bicontinuous lamellar system with pores connecting alternating layers. We demonstrate explicitly that Riemann's minimal surfaces are composed of a nonlinear sum of two oppositely handed helicoids. PMID:24098846

  13. 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.

  14. 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.

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1126 Santa Barbara Harbor, CA. A line drawn from Santa Barbara Harbor Light 4 to Santa Barbara Harbor Breakwater Light....

  1. 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... 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. Effect of Confinement on the Bubble Points of Hydrocarbons in Controlled-Pore Glasses

    NASA Astrophysics Data System (ADS)

    Luo, Sheng; Lutkenhaus, Jodie; Nasrabadi, Hadi; Hadi Nasrabadi Team

    2015-03-01

    Phase behavior in shale remains a challenging problem in the petroleum industry due to many complexities. One complexity is the strong surface-fluid interactions in shale nano-scale pores. These interactions can lead to a heterogeneous distribution of molecules, which conventional bulk-phase thermodynamics fails to describe. Herein, we report a study on the bubble points of various hydrocarbons confined in nanoporous controlled-pore glasses of 4.3 to 38.1 nm pore diameter. Differential scanning calorimetry is used to measure the temperature at which the gas phase begins to form (i.e. bubble point). Besides pore diameter, the relative hydrocarbon loading in the controlled-pore glass is evaluated. The findings suggest that the bubble point is dramatically affected by pore diameter.

  3. 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...

  4. Pore Water PAH Transport in Amended Sediment Caps

    NASA Astrophysics Data System (ADS)

    Gidley, P. T.; Kwon, S.; Ghosh, U.

    2009-05-01

    Capping is a common remediation strategy for contaminated sediments that creates a physical barrier between contaminated sediments and the water column. Diffusive flux of contaminants through a sediment cap is small. However, under certain hydrodynamic conditions such as groundwater potential and tidal pumping, groundwater advection can accelerate contaminant transport. Hydrophobic organic contaminants such as polycyclic aromatic hydrocarbons (PAHs) could be transported through the cap under advective conditions. To better understand PAH migration under these conditions, physical models of sediment caps were evaluated in the laboratory through direct measurement of pore water using solid phase micro-extraction with gas chromatography and mass spectrometry. Contaminated sediment and capping material was obtained from an existing Superfund site that was capped at Eagle Harbor, Washington. A PAH dissolution model linked to an advection-dispersion equation with retardation using published organic carbon-water partitioning coefficients (Koc) was compared to measured PAHs in the sediment and cap porewater of the physical model.

  5. Sediment resuspension characteristics in Baltimore Harbor, Maryland

    USGS Publications Warehouse

    Maa, J.P.-Y.; Sanford, L.; Halka, J.P.

    1998-01-01

    Critical bed shear stress for sediment resuspension and sediment erosion rate were measured in-situ at sites from inner to outer Baltimore Harbor using the VIMS Sea Carousel. Clay mineral contents and biological conditions were almost the same at the four study sites. The experimental results indicated that the erosion rate increased from the outer harbor toward the inner harbor with a maximum difference of about 10 times at an excess bed shear stress of 0.1 Pa. The measured critical bed shear stress strongly depended on the existence of a fluff layer. It was approximately 0.05 Pa if a fluff layer existed, and increases to about 0.1 Pa in the absence of a fluff layer.

  6. Single nuclear pores visualized by confocal microscopy and image processing.

    PubMed Central

    Kubitscheck, U; Wedekind, P; Zeidler, O; Grote, M; Peters, R

    1996-01-01

    How nuclear pore complexes, mediating the transport of nucleic acids, proteins, and metabolites between cell nucleus and cytoplasm, are arranged in the nuclear envelope is essentially unknown. Here we describe a method combining high-resolution confocal imaging with image processing and pattern recognition to visualize single nuclear pore complexes (120 nm diameter), determine their relative positions with nanometer accuracy, and analyze their distribution in situ. The method was tested by means of a model system in which the very same sample areas could be imaged by confocal and electron microscopy. It was thus found that single fluorescent beads of 105 nm nominal diameter could be localized with a lateral accuracy of <20 nm and an axial accuracy of approximately 20 nm. The method was applied to digitonin-permeabilized 3T3 cells, whose nuclear pore complexes were fluorescently labeled with the anti-nucleoporin antibody mAb414. Stacks of optical sections were generated by confocal imaging at high resolution. Herein the nuclear pore complexes appeared as bright diffraction-limited spots whose centers were localized by fitting them by three-dimensional gaussians. The nearest-neighbor distribution function and the pair correlation function were calculated and found to agree well with those of randomly distributed hard cylinders of 138 +/- 17 nm diameter, but not with those of randomly distributed points or nonrandomly distributed cylinders. This was supported by a cluster analysis. Implications for the direct observation of the transport of single particles and molecules through individual nuclear pore complexes are discussed. Images FIGURE 1 FIGURE 2 FIGURE 4 PMID:9172731

  7. Precipitation in pores: A geochemical frontier

    DOE PAGES

    Stack, Andrew G.

    2015-07-29

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

  8. 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

  9. Emergence of carbapenem non-susceptible multidrug resistant Acinetobacter baumannii strains of clonal complexes 103(B) and 92(B) harboring OXA-type carbapenemases and metallo-β-lactamases in Southern India.

    PubMed

    Saranathan, Rajagopalan; Vasanth, Vaidyanathan; Vasanth, Thamodharan; Shabareesh, Pidathala Raghavendra Venkata; Shashikala, P; Devi, Chandrakesan Sheela; Kalaivani, Ramakrishnan; Asir, Johny; Sudhakar, Pagal; Prashanth, K

    2015-05-01

    The molecular epidemiology and carbapenem resistance mechanisms of clinical isolates of Acinetobacter baumannii obtained from a south Indian tertiary care hospital were investigated by repetitive extragenic palindromic sequence PCR (REP-PCR) and multi-locus sequence typing (MLST). Analysis of resistant determinants was achieved by PCR screening for the presence of genes encoding OXA-carbapenemases, metallo-β-lactamases (MBLs) and efflux pumps. REP-PCR generated around eight clusters of high heterogeneity; of these, two major clusters (I and V) appeared to be clonal in origin. Analysis of representative isolates from different clusters by MLST revealed that most of the isolates belonged to sequence type 103 of CC103(B) . Second most prevalent ST belonged to clonal complex (CC) 92(B) which is also referred to as international clone II. Most of the isolates were multi-drug resistant, being susceptible only to polymyxin-B and newer quinolones. Class D β-lactamases such as blaOXA-51-like (100%), blaOXA-23-like (56.8%) and blaOXA-24-like (14.8%) were found to be predominant, followed by a class B β-lactamase, namely blaIMP-1 (40.7%); none of the isolates had blaOXA-58 like, blaNDM-1 or blaSIM-1 . Genes of efflux-pump adeABC were predominant, most of isolates being biofilm producers that were PCR-positive for autoinducer synthase gene (>94%). Carbapenem non-susceptible isolates were highly diverse and present throughout the hospital irrespective of type of ward or intensive care unit. Although previous reports have documented diverse resistant mechanisms in A. baumannii, production of MBL and OXA-type of carbapenamases were found to be the predominant mechanism(s) of carbapenem resistance identified in strains isolated from Southern India.

  10. Protein crystal nucleation in pores

    PubMed Central

    Nanev, Christo N.; Saridakis, Emmanuel; Chayen, Naomi E.

    2017-01-01

    The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials. PMID:28091515

  11. 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 ...

  12. 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

  13. Long-pore Electrostatics in Inward-rectifier Potassium Channels

    PubMed Central

    Robertson, Janice L.; Palmer, Lawrence G.; Roux, Benoît

    2008-01-01

    Inward-rectifier potassium (Kir) channels differ from the canonical K+ channel structure in that they possess a long extended pore (∼85 Å) for ion conduction that reaches deeply into the cytoplasm. This unique structural feature is presumably involved in regulating functional properties specific to Kir channels, such as conductance, rectification block, and ligand-dependent gating. To elucidate the underpinnings of these functional roles, we examine the electrostatics of an ion along this extended pore. Homology models are constructed based on the open-state model of KirBac1.1 for four mammalian Kir channels: Kir1.1/ROMK, Kir2.1/IRK, Kir3.1/GIRK, and Kir6.2/KATP. By solving the Poisson-Boltzmann equation, the electrostatic free energy of a K+ ion is determined along each pore, revealing that mammalian Kir channels provide a favorable environment for cations and suggesting the existence of high-density regions in the cytoplasmic domain and cavity. The contribution from the reaction field (the self-energy arising from the dielectric polarization induced by the ion's charge in the complex geometry of the pore) is unfavorable inside the long pore. However, this is well compensated by the electrostatic interaction with the static field arising from the protein charges and shielded by the dielectric surrounding. Decomposition of the static field provides a list of residues that display remarkable correspondence with existing mutagenesis data identifying amino acids that affect conduction and rectification. Many of these residues demonstrate interactions with the ion over long distances, up to 40 Å, suggesting that mutations potentially affect ion or blocker energetics over the entire pore. These results provide a foundation for understanding ion interactions in Kir channels and extend to the study of ion permeation, block, and gating in long, cation-specific pores. PMID:19001143

  14. Sumoylation and transcription regulation at nuclear pores.

    PubMed

    Texari, Lorane; Stutz, Françoise

    2015-03-01

    Increasing evidence indicates that besides promoters, enhancers, and epigenetic modifications, nuclear organization is another parameter contributing to optimal control of gene expression. Although differences between species exist, the influence of gene positioning on expression seems to be a conserved feature from yeast to Drosophila and mammals. The nuclear periphery is one of the nuclear compartments implicated in gene regulation. It consists of the nuclear envelope (NE) and the nuclear pore complexes (NPC), which have distinct roles in the control of gene expression. The NPC has recently been shown to tether proteins involved in the sumoylation pathway. Here, we will focus on the importance of gene positioning and NPC-linked sumoylation/desumoylation in transcription regulation. We will mainly discuss observations made in the yeast Saccharomyces cerevisiae model system and highlight potential parallels in metazoan species.

  15. Pore Topology Effects in Positron Annihilation Spectroscopy of Zeolites.

    PubMed

    Zubiaga, Asier; Warringham, Robbie; Mitchell, Sharon; Gerchow, Lars; Cooke, David; Crivelli, Paolo; Pérez-Ramírez, Javier

    2016-12-14

    Positron annihilation spectroscopy (PAS) is a powerful method to study the size and connectivity of pores in zeolites. The lifetime of positronium within the host material is commonly described by the Tao-Eldrup model. However, one of its largest limitations arises from the simple geometries considered for the shape of the pores, which cannot describe accurately the complex topologies in zeolites. Here, an atomic model that combines the Tao potential with the crystallographic structure is introduced to calculate the distribution and lifetime of Ps intrinsic to a given framework. A parametrization of the model is undertaken for a set of widely applied zeolite framework types (*BEA, FAU, FER, MFI, MOR, UTL), before extending the model to all known structures. The results are compared to structural and topological descriptors, and to the Tao-Eldrup model adapted for zeolites, demonstrating the intricate dependence of the lifetime on the pore architecture.

  16. Impact of pore size variability and network coupling on electrokinetic transport in porous media

    NASA Astrophysics Data System (ADS)

    Alizadeh, Shima; Bazant, Martin Z.; Mani, Ali

    2016-11-01

    We have developed and validated an efficient and robust computational model to study the coupled fluid and ion transport through electrokinetic porous media, which are exposed to external gradients of pressure, electric potential, and concentration. In our approach a porous media is modeled as a network of many pores through which the transport is described by the coupled Poisson-Nernst-Planck-Stokes equations. When the pore sizes are random, the interactions between various modes of transport may provoke complexities such as concentration polarization shocks and internal flow circulations. These phenomena impact mixing and transport in various systems including deionization and filtration systems, supercapacitors, and lab-on-a-chip devices. In this work, we present simulations of massive networks of pores and we demonstrate the impact of pore size variation, and pore-pore coupling on the overall electrokinetic transport in porous media.

  17. 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

  18. A quantitative investigation of the effect of pore morphology on soil aggregate stability

    NASA Astrophysics Data System (ADS)

    Papadopoulos, A.

    2009-04-01

    Soil structure determines the operating environment for all physical, chemical and biological processes within the soil. Soil aggregate stability is an important measure for assessing soil structure quality. Non-destructive tomography techniques such as X-ray Computed Tomography (CT) offer great opportunities to quantitatively investigate the soil porous architecture which can provide important information for understanding soil processes and function in a multi-scale manner. For instance, the intra-aggregate pore space is of great importance for microbial activity, the sequestration of organic carbon and water flow. This paper investigates the effect of pore morphology on soil aggregate stability. Apparent porosity, pore size distribution, average pore size and fractal perimeter dimension (pore roughness) were measured from the images of the reconstructed 2-D image stacks. A new theoretical concept of soil aggregate stability is proposed. A strong relationship was observed between soil aggregate stability and pore morphological complexity.

  19. Effect of bioirrigation on sediment-water exchange of methylmercury in Boston Harbor, Massachusetts.

    PubMed

    Benoit, Janina M; Shull, David H; Harvey, Rebecca M; Beal, Samuel A

    2009-05-15

    Coastal marine sediments are important sites of methylmercury (MMHg) production, and dissolved efflux provides an important source of MMHg to near-shore, and possibly offshore, water columns and food webs. We measured the flux of MMHg across the sediment-water interface at four stations in Boston Harbor that span a range of infaunal population densities and bioirrigation intensities. At each station we carried out total MMHg flux measurements using core incubations and collected near-surface pore waters to establish MMHg gradients for diffusive flux calculations. The flux cores were also imaged by CT scanning to determine the distribution of infaunal burrows, and pore-water sulfide and 222Rn profiles were measured. Total MMHg fluxes, measured using core incubations, ranged from -4 to 191 pmol m(-2) d(-1), and total MMHg fluxes were strongly correlated with burrow densities at the stations. Estimated diffusive fluxes, calculated based on MMHg concentration gradients below the sediment-water interface, were much lower than total fluxes at three of the stations, ranging from 2-19 pmol m(-2) d(-1). These results indicate that MMHg exchange may be significantly enhanced over molecular diffusion in bioturbated sediments. Furthermore, burrow density provides a strong predictor of total MMHg flux. Pore-water exchange of both dissolved MMHg and 222Rn, a naturally occurring pore-watertracer, increased across the range of observed burrow densities, suggesting that the presence of burrows enhances both MMHg production and flux.

  20. 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.

  1. 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...

  2. 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...

  3. 16 CFR 312.10 - Safe harbors.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., issued by representatives of the marketing or online industries, or by other persons, that, after notice... 16 Commercial Practices 1 2013-01-01 2013-01-01 false Safe harbors. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S...

  4. 16 CFR 312.10 - Safe harbors.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., issued by representatives of the marketing or online industries, or by other persons, that, after notice... 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...

  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. 16 CFR 312.10 - Safe harbors.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ..., issued by representatives of the marketing or online industries, or by other persons, that, after notice... 16 Commercial Practices 1 2012-01-01 2012-01-01 false Safe harbors. 312.10 Section 312.10 Commercial Practices FEDERAL TRADE COMMISSION REGULATIONS UNDER SPECIFIC ACTS OF CONGRESS CHILDREN'S...

  7. 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.

  8. Capillary Properties of Model Pores.

    NASA Astrophysics Data System (ADS)

    Walsh, Tim J.

    Available from UMI in association with The British Library. Liquid menisci in small pores exhibit a curved surface across which there is a significant pressure difference. In the past it has been difficult to calculate the curvatures, of this class of menisci. Some recent studies have shown that a relatively straightforward, but hitherto neglected, method originated by Mayer & Stowe (1965) and Princen (1969a) can be applied to analyse wedging menisci. However, the method has lacked a comprehensive experimental verification. This investigation follows on from the previously limited studies. A standardised method for the application of the analysis is described, the results from which are compared to observations made using modified experimental procedures. The behaviour of the capillary surfaces formed in several model pores are analysed with the method. The model systems studied are rectangular ducts, the pores formed by a rod in an angled corner, by two contacting rods and a plate and the space between a rod and a plate. For the latter two shapes the analysis is extended to include systems of mixed wettability which have a particular bearing on enhanced oil recovery operations. Experiments in which curvatures are inferred from observations of capillary rise, are performed using two comparative techniques. An involved procedure confirms predictions of meniscus curvature to within 0.3%. Use of a more straightforward, through less accurate, technique enables variations of curvature with tube shape or contact angle(s) to be conveniently studied. Results obtained are excellent and confirm the theory within the determined experimental errors. (Abstract shortened by UMI.).

  9. A theoretical analysis and prediction of pore size and pore size distribution in electrospun multilayer nanofibrous materials.

    PubMed

    Bagherzadeh, Roohollah; Najar, Saeed Shaikhzadeh; Latifi, Masoud; Tehran, Mohammad Amani; Kong, Lingxue

    2013-07-01

    Electrospinning process can fabricate nanomaterials with unique nanostructures for potential biomedical and environmental applications. However, the prediction and, consequently, the control of the porous structure of these materials has been impractical due to the complexity of the electrospinning process. In this research, a theoretical model for characterizing the porous structure of the electrospun nanofibrous network has been developed by combining the stochastic and stereological probability approaches. From consideration of number of fiber-to-fiber contacts in an electrospun nanofibrous assembly, geometrical and statistical theory relating morphological and structural parameters of the network to the characteristic dimensions of interfibers pores is provided. It has been shown that these properties are strongly influenced by the fiber diameter, porosity, and thickness of assembly. It is also demonstrated that at a given network porosity, increasing fiber diameter and thickness of the network reduces the characteristic dimensions of pores. It is also discussed that the role of fiber diameter and number of the layer in the assembly is dominant in controlling the pore size distribution of the networks. The theory has been validated experimentally and results compared with the existing theory to predict the pore size distribution of nanofiber mats. It is believed that the presented theory for estimation of pore size distribution is more realistic and useful for further studies of multilayer random nanofibrous assemblies.

  10. 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

  11. 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

  12. Boussinesq Modeling for Inlets, Harbors, and Structures (Bouss-2D)

    DTIC Science & Technology

    2015-10-30

    approach to evaluate the performance of navigation and flooding projects to advance coastal and hydraulic engineering practice and guidance. This...decision support technology maybe used in design/repair of ports/harbors and costal infrastructures, flood levees, flooding and inundation of...Mississippi River Gulf Outlet, New Orleans Flood Control Gates, LA; Buffalo Harbor, NY; Tau Harbor, and Faleasao Harbor, American Samoa. BMT helps

  13. 33 CFR 110.205 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Chicago Harbor, Ill. 110.205... ANCHORAGE REGULATIONS Anchorage Grounds § 110.205 Chicago Harbor, Ill. (a) The anchorage grounds—(1...) Anchorage D, Chicago Harbor Lock South. Beginning at a point 35.5 feet South (16 feet South of the...

  14. 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... South of the South face of the former Naval Armory Dock, and 100 feet East of said bulkhead, that point... and bulkhead, 1,705 feet to a point that is 100 feet East of said harbor line and 150 feet East of...

  15. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 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, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules...

  16. 77 FR 73889 - National Pearl Harbor Remembrance Day, 2012

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-11

    ... Part V The President Proclamation 8914--National Pearl Harbor Remembrance Day, 2012 Executive Order... National Pearl Harbor Remembrance Day, 2012 By the President of the United States of America A Proclamation... American people. In less than 2 hours, the bombs that rained on Pearl Harbor robbed thousands of men,...

  17. 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…

  18. 78 FR 68735 - Reduction or Suspension of Safe Harbor Contributions

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-15

    ... Internal Revenue Service 26 CFR Part 1 RIN 1545-BI64 Reduction or Suspension of Safe Harbor Contributions... guidance on permitted mid-year reductions or suspensions of safe harbor nonelective contributions in... requirements for permitted mid-year reductions or suspensions of safe harbor matching contributions for...

  19. 7. Photocopy of c 1837 map of Cleveland Harbor with ...

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

    7. Photocopy of c 1837 map of Cleveland Harbor with two plans for additonal harbor. This is the first map to show the Cleveland Breakwater. Original in the Corps' files, Buffalo District. - Cleveland Breakwater at Cleveland Harbor, Cleveland, Cuyahoga County, OH

  20. 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...

  1. 33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Sandusky and Huron Harbors, Ohio. 162.155 Section 162.155 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles...

  2. 33 CFR 162.155 - Sandusky and Huron Harbors, Ohio.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Sandusky and Huron Harbors, Ohio. 162.155 Section 162.155 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY... Harbors, Ohio. (a) In Sandusky Harbor, no vessel greater than 40 feet in length may exceed 10 miles...

  3. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 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, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules...

  4. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules...

  5. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 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, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules...

  6. 32 CFR 765.6 - Regulations for Pearl Harbor, Hawaii.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 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, U.S. Naval Base, Pearl Harbor, Hawaii, is responsible for prescribing and enforcing such rules...

  7. 78 FR 21597 - Marine Mammals: Alaska Harbor Seal Habitats

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-11

    ... National Oceanic and Atmospheric Administration RIN 0648-BB71 Marine Mammals: Alaska Harbor Seal Habitats... measures to protect glacially-associated harbor seal habitats in Alaska (78 FR 15669; March 12, 2013). During the workshops NMFS will present information regarding harbor seal habitat usage and...

  8. 33 CFR 117.272 - Boot Key Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Boot Key Harbor. 117.272 Section... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.272 Boot Key Harbor. The draw of the Boot Key Harbor drawbridge, mile 0.13, between Marathon and Boot Key, will open as necessary on...

  9. 33 CFR 117.272 - Boot Key Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Boot Key Harbor. 117.272 Section... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Florida § 117.272 Boot Key Harbor. The draw of the Boot Key Harbor drawbridge, mile 0.13, between Marathon and Boot Key, will open as necessary on...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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

  16. A thermodynamic approach to alamethicin pore formation.

    PubMed

    Rahaman, Asif; Lazaridis, Themis

    2014-01-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å 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 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å 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.

  17. A thermodynamic approach to alamethicin pore formation.

    PubMed

    Rahaman, Asif; Lazaridis, Themis

    2014-05-01

    The structure and energetics of alamethicin Rf30 monomer to nonamer in cylindrical pores of 5 to 11Å 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 6Å pores that appear closed while the larger oligomers formed open pores at their optimal radius. The hexamer in an 8Å pore and the octamer in an 11Å 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.

  18. 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.

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

    PubMed

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

    2016-09-01

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

  20. How Lipid Membranes Affect Pore Forming Toxin Activity.

    PubMed

    Rojko, Nejc; Anderluh, Gregor

    2015-12-15

    Pore forming toxins (PFTs) evolved to permeate the plasma membrane of target cells. This is achieved in a multistep mechanism that usually involves binding of soluble protein monomer to the lipid membrane, oligomerization at the plane of the membrane, and insertion of part of the polypeptide chain across the lipid membrane to form a conductive channel. Introduced pores allow uncontrolled transport of solutes across the membrane, inflicting damage to the target cell. PFTs are usually studied from the perspective of structure-function relationships, often neglecting the important role of the bulk membrane properties on the PFT mechanism of action. In this Account, we discuss how membrane lateral heterogeneity, thickness, and fluidity influence the pore forming process of PFTs. In general, lipid molecules are more accessible for binding in fluid membranes due to steric reasons. When PFT specifically binds ordered domains, it usually recognizes a specific lipid distribution pattern, like sphingomyelin (SM) clusters or SM/cholesterol complexes, and not individual lipid species. Lipid domains were also suggested to act as an additional concentration platform facilitating PFT oligomerization, but this is yet to be shown. The last stage in PFT action is the insertion of the transmembrane segment across the membranes to build the transmembrane pore walls. Conformational changes are a spontaneous process, and sufficient free energy has to be available for efficient membrane penetration. Therefore, fluid bilayers are permeabilized more readily in comparison to highly ordered and thicker liquid ordered lipid phase (Lo). Energetically more costly insertion into the Lo phase can be driven by the hydrophobic mismatch between the thinner liquid disordered phase (Ld) and large protein complexes, which are unable to tilt like single transmembrane segments. In the case of proteolipid pores, membrane properties can directly modulate pore size, stability, and even selectivity. Finally

  1. Monitoring water transparency and diver visibility in ports and harbors using aircraft hyperspectral remote sensing

    NASA Astrophysics Data System (ADS)

    Trees, Charles C.; Bissett, Paul W.; Dierssen, Heidi; Kohler, David D. R.; Moline, Mark A.; Mueller, James L.; Pieper, Richard E.; Twardowski, Michael S.; Zaneveld, J. Ronald V.

    2005-05-01

    Diver visibility analyses and predictions, and water transparency in general, are of significant military and commercial interest. This is especially true in our current state, where ports and harbors are vulnerable to terrorist attacks from a variety of platforms both on and below the water (swimmers, divers, AUVs, ships, submarines, etc.). Aircraft hyperspectral imagery has been previously used successfully to classify coastal bottom types and map bathymetry and it is time to transition this observational tool to harbor and port security. Hyperspectral imagery is ideally suited for monitoring small-scale features and processes in these optically complex waters, because of its enhanced spectral (1-3 nm) and spatial (1-3 meters) resolutions. Under an existing NOAA project (CICORE), a field experiment was carried out (November 2004) in coordination with airborne hyperspectral ocean color overflights to develop methods and models for relating hyperspectral remote sensing reflectances to water transparency and diver visibility in San Pedro and San Diego Bays. These bays were focused areas because: (1) San Pedro harbor, with its ports of Los Angeles and Long Beach, is the busiest port in the U.S. and ranks 3rd in the world and (2) San Diego Harbor is one of the largest Naval ports, serving a diverse mix of commercial, recreational and military traffic, including more than 190 cruise ships annual. Maintaining harbor and port security has added complexity for these Southern California bays, because of the close proximity to the Mexican border. We will present in situ optical data and hyperspectral aircraft ocean color imagery from these two bays and compare and contrast the differences and similarities. This preliminary data will then be used to discuss how water transparency and diver visibility predictions improve harbor and port security.

  2. Remembering Pearl Harbor at 75 Years.

    PubMed

    Liehr, Patricia; Sopcheck, Janet; Milbrath, Gwyneth

    2016-12-01

    : On December 7, 1941, the Sunday-morning quiet of the U.S. naval base in Pearl Harbor, Hawaii, was shattered by dive-bombing Japanese fighter planes. The planes came in two waves-and when it was all over, more than 2,400 were killed and more than 1,100 were injured.Nurses were stationed at U.S. Naval Hospital Pearl Harbor, Tripler General Hospital (now Tripler Army Medical Center), Hickam Field Hospital, Schofield Barracks Station Hospital, and aboard the USS Solace, and witnessed the devastation. But they also did what nurses do in emergencies-they responded and provided care to those in need. Here are the stories of a few of those nurses.

  3. An elliptical-pore model for late-stage planar viscous sintering

    NASA Astrophysics Data System (ADS)

    Crowdy, Darren G.

    2004-02-01

    A simple ‘elliptical-pore model’ of the shrinkage of compressible pores in late-stage planar viscous sintering is proposed. The model is in the spirit of matched asymptotics and relies on splitting the flow into an ‘inner’ and ‘outer’ problem. The inner problem in the vicinity of any given pore involves solving for its free-surface evolution exactly using complex-variable methods. The outer flow due to all other pores is assumed to be given by an assembly of point sinks/sources. As a test of the model, the evolution of a singly infinite periodic row of compressible pores is considered in detail. The effectiveness of the simple model is tested by comparison with a full numerical simulation. A novel boundary integral method based on Cauchy potentials and conformal mapping is used. In the case of pores with constant pressure, it is found that pores shrink faster than if in isolation. Compressible pores obeying the ideal gas law are also studied and are found to tend to a quasi-steady non-circular state. A higher-order model is also presented and compared with numerical simulations of the viscous sintering of a doubly periodic array of pores in Stokes flow.

  4. 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.

  5. 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)

  6. Evaluation of Sediment Contamination in Pearl Harbor

    DTIC Science & Technology

    1992-06-01

    configuration) largely engaged in the taking of skipjack tuna (aku) after purse seining for baitfish (nehu) in estuar- ies such as Pearl Harbor. Algae. A group...purpurea), a species used as a baitfish in the offshore tuna , "aku," fishery. This species is the most important bait- fish resource in Hawaii, and Pearl...34Science, risk, and public policy ," Science, vol. 221, pp. 1026-1028. Russell, M., and M. Gruber, 1987. "Risk assessment in environmental policy

  7. Taxonomic Evaluation of Cleveland Harbor Lake Areas

    DTIC Science & Technology

    2014-01-01

    Immature. Comparison to previous collections Although benthic invertebrates were not previously collected for USACE- LRB from the current study areas...areas in the lake. There were considerable differences in invertebrate community taxa between Vermillion and Cleveland Harbor, including the presence...Griffiths. 1984. Benthic invertebrates of the nearshore zone of eastern Lake Huron, Georgian Bay, and North Channel. Journal of Great Lakes Research 10:407

  8. A Guide for Marina and Harbor Managers

    DTIC Science & Technology

    1991-03-01

    recommend changes in the context and format, - 1o determine possible future uses or futurp =* -s. Ten small boat harbor and marinas were selected...managers were asked if there were ways to improve the guide by adding information, deleting information, or changing the format. None of the managers...felt that any of 37 the information should be deleted, some recommendations were made for format changes , and all of the managers had recommendations

  9. 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.

  10. 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.

  11. Barbers Point Harbor, Hawaii, Jetty Modification Study

    DTIC Science & Technology

    2008-11-01

    meter studies of the circulation patterns and flows in the channel, and (d) input from the sponsor, EPA , and harbor pilots. DISCLAIMER: The...tests and review study results. Participating in this meeting were Stanley Boc, HED, Dr. Wendy I. Wiltse, U.S. Environmental Protection Agency ( EPA ...U.S. Environmental Protection Agency ( EPA ), Capt. Dave Lyman, Hawaii Pilots Association, Capt. Thomas L. Heberle, Hawaii Pilots Association, and Capt

  12. Gulfport Harbor, Mississippi. Final Environmental Impact Statement

    DTIC Science & Technology

    1989-06-01

    EIS-4 Littoral Zone Disposal Area EIS-75 EIS-5 Gulf of Mexico Ocean Dredge Material Disposal Sites EIS-76 EIS-6 Entrance Channel Alignment Alternatives...400-foot channel across Snip is’,rnd bar into the Gulf of Mexico . This --t ,recommendation al-eo included the modificatio.ri of the existing harbor...disposal in the Gulf of Mexico ; and 15.64 million cubic yards would be deposited by pipeline dredge in Mississippi Sound. Two economically and engineeringly

  13. 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

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Lake Michigan at Chicago Harbor & 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...

  14. 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.

  15. 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.

  16. 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.

  17. Nanoscale pore formation dynamics during aluminum anodization.

    PubMed

    Thamida, Sunil Kumar; Chang, Hsueh-Chia

    2002-03-01

    A theoretical analysis of nanoscale pore formation during anodization reveals its fundamental instability mechanism to be a field focusing phenomenon when perturbations on the minima of the two oxide interfaces are in phase. Lateral leakage of the layer potential at high wave number introduces a layer tension effect that balances the previous destabilizing effect to produce a long-wave instability and a selected pore separation that scales linearly with respect to voltage. At pH higher than 1.77, pores do not form due to a very thick barrier layer. A weakly nonlinear theory based on long-wave expansion of double free surface problem yields two coupled interface evolution equations that can be reduced to one without altering the dispersion relationship by assuming an equal and in-phase amplitude for the two interfaces. This interface evolution equation faithfully reproduces the initial pore ordering and their dynamics. A hodograph transformation technique is then used to determine the interior dimension of the well-developed pores in two dimensions. The ratio of pore diameter to pore separation is found to be a factor independent of voltage but varies with the pH of the electrolyte. Both the predicted pH range where pores are formed and the predicted pore dimensions are favorably compared to experimental data. (c) 2002 American Institute of Physics.

  18. Anaerobic, sulfate-dependent degradation of polycyclic aromatic hydrocarbons in petroleum-contaminated harbor sediment.

    PubMed

    Rothermich, Mary M; Hayes, Lory A; Lovley, Derek R

    2002-11-15

    It has previously been demonstrated that [14C]-labeled polycyclic aromatic hydrocarbons (PAHs) can be oxidized to 14CO2 in anoxic, PAH-contaminated, marine harbor sediments in which sulfate reduction is the terminal electron-accepting process. However, it has not previously been determined whether this degradation of [14C]-PAHs accurately reflects the degradation of the in situ pools of contaminant PAHs. In coal tar-contaminated sediments from Boston Harbor, [14C]-naphthalene was readily oxidized to 14CO2, but, after 95 d of incubation under anaerobic conditions, there was no significant decrease in the detectable pool of in situ naphthalene in these sediments. Therefore, to better evaluate the anaerobic biodegradation of the in situ PAH pools, the concentrations of these contaminants were monitored for ca. 1 year during which the sediments were incubated under conditions that mimicked those found in situ. There was loss of all of the PAHs that were monitored (2-5 ring congeners), including high molecular weight PAHs, such as benzo[a]pyrene, that have not previously been shown to be degraded under anaerobic conditions. There was no significant change in the PAH levels in the sediments amended with molybdate to inhibit sulfate-reducing bacteria or in sediments in which all microorganisms had been killed with glutaraldehyde. In some instances, over half of the detectable pools of in situ 2-3 ring PAHs were degraded. In general, the smaller PAHs were degraded more rapidly than the larger PAHs. A distinct exception in the Boston Harbor sediment was naphthalene which was degraded very slowly at a rate comparable to the larger PAHs. In a similar in situ-like study of fuel-contaminated sediments from Liepaja Harbor, Latvia, there was no decline in PAH levels in samples that were sulfate-depleted. However, when the Latvia sediments were supplemented with sufficient sodium sulfate or gypsum to elevate pore water levels of sulfate to approximately 14-25 mM there was a 90

  19. The Unique Molecular Choreography of Giant Pore Formation by the Cholesterol-Dependent Cytolysins of Gram-Positive Bacteria.

    PubMed

    Tweten, Rodney K; Hotze, Eileen M; Wade, Kristin R

    2015-01-01

    The mechanism by which the cholesterol-dependent cytolysins (CDCs) assemble their giant β-barrel pore in cholesterol-rich membranes has been the subject of intense study in the past two decades. A combination of structural, biophysical, and biochemical analyses has revealed deep insights into the series of complex and highly choreographed secondary and tertiary structural transitions that the CDCs undergo to assemble their β-barrel pore in eukaryotic membranes. Our knowledge of the molecular details of these dramatic structural changes in CDCs has transformed our understanding of how giant pore complexes are assembled and has been critical to our understanding of the mechanisms of other important classes of pore-forming toxins and proteins across the kingdoms of life. Finally, there are tantalizing hints that the CDC pore-forming mechanism is more sophisticated than previously imagined and that some CDCs are employed in pore-independent processes.

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

    PubMed

    Crowdy, Darren

    2015-08-08

    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.

  1. 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.

  2. Construction of Representative Pore Morphologies in Disordered Nanoporous Two-Phase Materials

    SciTech Connect

    Toney, Michael F

    2003-04-01

    Materials with nanometer size heterogeneities are commonplace in the physical and biological sciences and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties (e.g., transport and reaction processes), it is often difficult to accurately characterize. We describe a method, using a novel analysis of small angle x-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials (one class of heterogeneous materials) where the morphology is disordered. This is applied to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology. This methodology will be valuable for characterizing two-phase systems, such as polymer blends, microemulsions, porous geological materials, bones, cements and ceramics.

  3. 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

  4. Cavitation and pore blocking in nanoporous glasses.

    PubMed

    Reichenbach, C; Kalies, G; Enke, D; Klank, D

    2011-09-06

    In gas adsorption studies, porous glasses are frequently referred to as model materials for highly disordered mesopore systems. Numerous works suggest that an accurate interpretation of physisorption isotherms requires a complete understanding of network effects upon adsorption and desorption, respectively. The present article deals with nitrogen and argon adsorption at different temperatures (77 and 87 K) performed on a series of novel nanoporous glasses (NPG) with different mean pore widths. NPG samples contain smaller mesopores and significantly higher microporosity than porous Vycor glass or controlled pore glass. Since the mean pore width of NPG can be tuned sensitively, the evolution of adsorption characteristics with respect to a broadening pore network can be investigated starting from the narrowest nanopore width. With an increasing mean pore width, a H2-type hysteresis develops gradually which finally transforms into a H1-type. In this connection, a transition from a cavitation-induced desorption toward desorption controlled by pore blocking can be observed. Furthermore, we find concrete hints for a pore size dependence of the relative pressure of cavitation in highly disordered pore systems. By comparing nitrogen and argon adsorption, a comprehensive insight into adsorption mechanisms in novel disordered materials is provided.

  5. Fluctuation of surface charge in membrane pores.

    PubMed Central

    Bashford, C Lindsay; Alder, Glenn M; Pasternak, Charles A

    2002-01-01

    Surface charge in track-etched polyethylene terephthalate (PET) membranes with narrow pores has been probed with a fluorescent cationic dye (3,3'-diethyloxacarbocyanine iodide (diO-C2-(3))) using confocal microscopy. Staining of negatively charged PET membranes with diO-C2-(3) is a useful measure of surface charge for the following reasons: 1) the dye inhibits K(+) currents through the pores and reduces their selectivity for cations; 2) it inhibits [3H]-choline+ transport and promotes 36Cl- transport across the membrane in a pH- and ionic-strength-dependent fashion; and 3) staining of pores by diO-C2-(3) is reduced by low pH and by the presence of divalent cations such as Ca2+ and Zn2+. Measurement of the time dependence of cyanine staining of pores shows fluctuations of fluorescence intensity that occur on the same time scale as do fluctuations of ionic current in such pores. These data support our earlier proposal that fluctuations in ionic current across pores in synthetic and biological membranes reflect fluctuations in the surface charge of the pore walls in addition to molecular changes in pore proteins. PMID:11916860

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

    SciTech Connect

    Yang, Xiaofan; Mehmani, Yashar; Perkins, William A.; Pasquali, Andrea; Schonherr, 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.

    2015-09-28

    In this study, 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

  7. 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.

  8. 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

  9. Molecular simulation study of water--methanol mixtures in activated carbon pores

    SciTech Connect

    Shevade, Abhijit V.; Jiang, Shaoyi; Gubbins, Keith E.

    2000-10-22

    We report a theoretical study of the adsorption behavior of water--methanol mixtures in slit activated carbon micropores. The adsorption isotherms are obtained for a pore of width 2 nm at a temperature of 298 K from grand canonical ensemble Monte Carlo simulations. The water molecules are modeled using the four point transferable intermolecular potential functions (TIP4P) and methanol by the optimized potentials for liquid simulations (OPLS). Carboxyl (COOH) groups are used as active sites on a structured carbon surface. The effect of the relative contributions from dispersion and hydrogen bonding interactions of adsorbates, and of the chemical activation of adsorbents on adsorption behavior is investigated. The adsorption of the mixture components in activated carbon pores occurs by continuous filling, without the sharp capillary condensation observed in graphite pores. Water is preferentially adsorbed over methanol in activated carbon pores for a wide range of pressures, except at lower pressures. The hydrophilic nature of activated carbon pores results in the complexation of both water and methanol molecules with the active sites on the surfaces, leading to bulklike water behavior over the entire pore width. Solvation forces are also calculated as a function of pore size. The negative values found for the solvation force for all pore sizes reflect the hydrophilic interactions of the mixtures with the activated carbon surfaces. {copyright} 2000 American Institute of Physics [S0021-9606(00)51339-7

  10. 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.

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

    PubMed Central

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

    2016-01-01

    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

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... at the time. (c) The use of chains in making fast to the breakwater will not be permitted. Lines must... floating property making fast to the breakwater must at once place such fenders between themselves and the... piece of floating property made fast to the breakwater, or anchored in the harbor, must keep...

  13. Anomalous mobility of highly charged particles in pores

    DOE PAGES

    Qiu, Yinghua; Yang, Crystal; Hinkle, Preston; ...

    2015-07-16

    Single micropores in resistive-pulse technique were used to understand a complex dependence of particle mobility on its surface charge density. We show that the mobility of highly charged carboxylated particles decreases with the increase of the solution pH due to an interplay of three effects: (i) ion condensation, (ii) formation of an asymmetric electrical double layer around the particle, and (iii) electroosmotic flow induced by the charges on the pore walls and the particle surfaces. The results are important for applying resistive-pulse technique to determine surface charge density and zeta potential of the particles. As a result, the experiments alsomore » indicate the presence of condensed ions, which contribute to the measured current if a sufficiently high electric field is applied across the pore.« less

  14. Anomalous mobility of highly charged particles in pores

    SciTech Connect

    Qiu, Yinghua; Yang, Crystal; Hinkle, Preston; Vlassiouk, Ivan V.; Siwy, Zuzanna S.

    2015-07-16

    Single micropores in resistive-pulse technique were used to understand a complex dependence of particle mobility on its surface charge density. We show that the mobility of highly charged carboxylated particles decreases with the increase of the solution pH due to an interplay of three effects: (i) ion condensation, (ii) formation of an asymmetric electrical double layer around the particle, and (iii) electroosmotic flow induced by the charges on the pore walls and the particle surfaces. The results are important for applying resistive-pulse technique to determine surface charge density and zeta potential of the particles. As a result, the experiments also indicate the presence of condensed ions, which contribute to the measured current if a sufficiently high electric field is applied across the pore.

  15. 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.

  16. A STUDY OF MARINE FOULING IN MONTEREY HARBOR.

    DTIC Science & Technology

    PIERS, *FOULING, *HARBORS, *MARINE BIOLOGY, CALIFORNIA, PACIFIC OCEAN, NAVAL RESEARCH, CRUSTACEA, ANIMALS, PERIODIC VARIATIONS, ENVIRONMENTAL TESTS, TIME, DISTRIBUTION, SEA WATER, PLATYHELMINTHES , OCEANOGRAPHIC DATA.

  17. Analytical applications for pore-forming proteins.

    PubMed

    Kasianowicz, John J; Balijepalli, Arvind K; Ettedgui, Jessica; Forstater, Jacob H; Wang, Haiyan; Zhang, Huisheng; Robertson, Joseph W F

    2016-03-01

    Proteinaceous nanometer-scale pores are ubiquitous in biology. The canonical ionic channels (e.g., those that transport Na(+), K(+), Ca(2+), and Cl(-) across cell membranes) play key roles in many cellular processes, including nerve and muscle activity. Another class of channels includes bacterial pore-forming toxins, which disrupt cell function, and can lead to cell death. We describe here the recent development of these toxins for a wide range of biological sensing applications. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale.

  18. 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.

  19. 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.

  20. Effects of Tributyltin Antifouling Paint Leachates on Pearl Harbor Organisms. Site-Specific Flowthrough Bioassay Tests.

    DTIC Science & Technology

    1985-12-01

    Organotin paint leachate. antifoulitip coa~tings. marine n~ii r, isms.A.benthicFIEL GRUP SB GOUP organisms. harbor pollutani fributt Iti omplx cmmuitie...of organotins should be closely monitored for ossible shifts in dominance of specific organisms- ~ 20 DISTRIBUJTION, AVAILABIUITY OF ABSTRACT 21...d* J 77. EXECUTIVE SUMMARY Site-specific bioassay tests were performed to determine the effects of organotin paint leachate on complex communities of

  1. Grays Harbor and Chehalis River Improvements to Navigation Environmental Studies. Benthic Invertebrate Studies in Grays Harbor, Washington,

    DTIC Science & Technology

    1982-04-01

    invertebrates of the central California coast. Univ. of Calif. Press, Berkeley. 716 p. Tegelberg, H. C. 1969. A new Pacific razor clam species, Siliqua...favors: Drs. Ron Thom and John Armstrong, U.S. Army Corps of EnFineers; Dr. David Armstrong, University of ashinrton; Diane Carter, Grays Harbor College...Harbor, ashinfton, 1980-El...................... 102 49. Clam abundance for subtidal stations by season, Cr ’s Harbor, !ashinrtcn, 1980-l

  2. Armillaria luteobubalina mycelium develops air pores that conduct oxygen to rhizomorph clusters.

    PubMed

    Pareek, Mamta; Allaway, William G; Ashford, Anne E

    2006-01-01

    Armillaria luteobubalina produces air pores in culture. They consist of two parts: a basal region of tissue elevated to form a mound covered with a rind continuous with that of the colony, but perforated; and an apical region of long parallel hyphae, cemented together by scattered patches of extracellular material. This forms a hydrophobic structure that is elevated above the general level of the mycelial crust and does not easily become waterlogged. Air pores develop near the inoculum plug shortly after inoculation, arising directly from the mycelium, and rhizomorphs are initiated from them. The air pore contains a complex system of gas space connecting the atmosphere with the central canal of each rhizomorph. The tissue beneath the melanised colony crust also contains gas space, especially near air pores. This is also connected with the gas space of each rhizomorph and of each air pore. Measurements with oxygen electrodes show that air pores and their associated rhizomorphs conduct oxygen. The average oxygen conductance of a group of air pores with associated rhizomorphs, within agar blocks, but with rhizomorph apices cut off, was about 700 x 10(-12) m3s(-1), equivalent to about 200 x 10(-12) m3s(-1) for each air-pore. We conclude that the air pores conduct oxygen into the gas space below the pigmented mycelium of the colony, where the rhizomorphs - which also conduct oxygen - originate. A. luteobubalina thus has a complex aerating system which allows efficient diffusion of oxygen into rhizomorphs, and this is likely to facilitate extension of inoculum into low-oxygen environments.

  3. 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.

  4. 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).

  5. OBSERVATIONS OF SAUSAGE MODES IN MAGNETIC PORES

    SciTech Connect

    Morton, R. J.; Erdelyi, R.; Jess, D. B.; Mathioudakis, M. E-mail: Robertus@sheffield.ac.uk

    2011-03-10

    We present here evidence for the observation of the magnetohydrodynamic (MHD) sausage modes in magnetic pores in the solar photosphere. Further evidence for the omnipresent nature of acoustic global modes is also found. The empirical decomposition method of wave analysis is used to identify the oscillations detected through a 4170 A 'blue continuum' filter observed with the Rapid Oscillations in the Solar Atmosphere (ROSA) instrument. Out of phase, periodic behavior in pore size and intensity is used as an indicator of the presence of magnetoacoustic sausage oscillations. Multiple signatures of the magnetoacoustic sausage mode are found in a number of pores. The periods range from as short as 30 s up to 450 s. A number of the magnetoacoustic sausage mode oscillations found have periods of 3 and 5 minutes, similar to the acoustic global modes of the solar interior. It is proposed that these global oscillations could be the driver of the sausage-type magnetoacoustic MHD wave modes in pores.

  6. Mitochondrial genes at Cold Spring Harbor.

    PubMed

    Grivell, L A

    1981-12-01

    The flowering dogwood trees and green lawns of Cold Spring Harbor provided the setting for a meeting devoted to Mitochondrial Genes from May 13-17th, 1981. Dedicated to the memory of Boris Ephrussi, who pioneered mitochondrial genetics at a time when the only kinds of genetics were nuclear or unclear, the meeting showed that the study of mtDNA has had impact on many areas of molecular biology including the genetic code and decoding, tRNA function, mechanisms of splicing and molecular evolution. Curiously, as Herschel Roman pointed out in his opening address, Ephrussi took great pains to avoid any mention of mitochondrial DNA in connection with his observations on cytoplasmic inheritance, preferring instead to refer to 'cytoplasmic particles, endowed with genetic continuity' (Ephrussi 1953). This reticence was not shared by participants at the meeting, as the following, brief report will show.

  7. More Than a Pore: The Interplay of Pore-Forming Proteins and Lipid Membranes.

    PubMed

    Ros, Uris; García-Sáez, Ana J

    2015-06-01

    Pore-forming proteins (PFPs) punch holes in their target cell membrane to alter their permeability. Permeabilization of lipid membranes by PFPs has received special attention to study the basic molecular mechanisms of protein insertion into membranes and the development of biotechnological tools. PFPs act through a general multi-step mechanism that involves (i) membrane partitioning, (ii) insertion into the hydrophobic core of the bilayer, (iii) oligomerization, and (iv) pore formation. Interestingly, PFPs and membranes show a dynamic interplay. As PFPs are usually produced as soluble proteins, they require a large conformational change for membrane insertion. Moreover, membrane structure is modified upon PFPs insertion. In this context, the toroidal pore model has been proposed to describe a pore architecture in which not only protein molecules but also lipids are directly involved in the structure. Here, we discuss how PFPs and lipids cooperate and remodel each other to achieve pore formation, and explore new evidences of protein-lipid pore structures.

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

    SciTech Connect

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

    2013-04-01

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

  9. 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

  10. 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

  11. Charleston Harbor Deepening Project. Charleston Harbor and Shipyard River, South Carolina.

    DTIC Science & Technology

    1976-04-01

    the diamondback terrapin . Other turtles that occur in the harbor and offshore waters include the Atlantic loggerhead and the Atlantic green turtle...king snake, southern co )erhead, pigmy rattlesnake, canebrake rattlesnake, eastern diamondback rattlesnake, southern toad, spring peener, green tree...Unpolluted body Of Salt Or-c tr’.n~iiu~vAo crustaceans, mollusks, * nkw ln to, it coiii re~i ertilies, ti, terrapin will not i, it tcd !)% ii uc u

  12. Sediment Budget for the Indiana Shore from Michigan City Harbor to Burns Waterway Harbor

    DTIC Science & Technology

    2012-08-01

    Engineer District, Chicago 111 N Canal Suite 600 Chicago, IL 60606 ERDC/CHL TR-12-17 ii Abstract Net sediment transport in the littoral cell...being filled with sand. The shoreline shows some additional trapping east of the NIPSCO BGS outfall canal and minor loss between the cross-shore...at Waukegan, Great Lakes, Wilmette, and Chicago in Illinois and Indiana Harbor and Ship Canal in East Chicago, Indiana, almost totally interrupted

  13. 33 CFR 110.83 - Chicago Harbor, Ill.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Chicago Harbor, Ill. 110.83... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.83 Chicago Harbor, Ill. (a) Grant Park North-A. Beginning at a point 2,120 feet South of the intersection of the North line of the Chicago Yacht...

  14. 33 CFR 117.181 - Oakland Inner Harbor Tidal Canal.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Oakland Inner Harbor Tidal Canal. 117.181 Section 117.181 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY BRIDGES DRAWBRIDGE OPERATION REGULATIONS Specific Requirements California § 117.181 Oakland Inner Harbor Tidal Canal. The draws of the...

  15. 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... NAVIGATION RULES COLREGS DEMARCATION LINES Pacific Coast § 80.1152 Crescent City Harbor, CA. A line drawn from Crescent City Entrance Light to the southeasternmost extremity of Whaler Island....

  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 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  18. 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...

  19. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 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...

  20. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 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...

  1. 33 CFR 110.208 - Buffalo Harbor, N.Y.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 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...

  2. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  3. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  4. 33 CFR 110.255 - Ponce Harbor, P.R.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Ponce Harbor, P.R. 110.255 Section 110.255 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Anchorage Grounds § 110.255 Ponce Harbor, P.R. (a) Small-craft anchorage. On...

  6. 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...

  7. 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,...

  8. 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...

  9. 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,...

  10. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 5 2010-07-01 2010-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  20. 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...

  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 110.29 - 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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...

  15. 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...

  16. 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...

  17. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 5 2011-07-01 2011-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...

  18. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 5 2012-07-01 2012-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...

  19. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 5 2014-07-01 2014-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...

  20. 32 CFR 705.31 - USS Arizona Memorial, Pearl Harbor.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 5 2013-07-01 2013-07-01 false USS Arizona Memorial, Pearl Harbor. 705.31... NAVY REGULATIONS AND OFFICIAL RECORDS PUBLIC AFFAIRS REGULATIONS § 705.31 USS Arizona Memorial, Pearl Harbor. (a) Limited space and the desirability of keeping the Memorial simple and dignified require...

  1. 49 CFR 578.7 - Criminal safe harbor provision.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 7 2010-10-01 2010-10-01 false Criminal safe harbor provision. 578.7 Section 578... SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION (CONTINUED) CIVIL AND CRIMINAL PENALTIES § 578.7 Criminal safe harbor provision. (a) Scope. This section sets forth the requirements regarding...

  2. 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...

  3. 33 CFR 80.130 - Boston Harbor entrance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Boston Harbor entrance. 80.130 Section 80.130 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY INTERNATIONAL NAVIGATION RULES COLREGS DEMARCATION LINES Atlantic Coast § 80.130 Boston Harbor entrance. A line drawn...

  4. 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...

  5. 46 CFR 7.65 - Charleston Harbor, SC.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Charleston Harbor, SC. 7.65 Section 7.65 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC BOUNDARY LINES Atlantic Coast § 7.65 Charleston Harbor, SC. A line drawn from Charleston Light on Sullivans Island to latitude...

  6. 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...

  7. 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,...

  8. 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...

  9. 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...

  10. 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,...

  11. 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,...

  12. 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...

  13. 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,...

  14. 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...

  15. 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,...

  16. 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...

  17. 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...

  18. 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...

  19. 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,...

  20. 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,...

  1. 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,...

  2. 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 Section 162.120 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  3. 33 CFR 162.145 - Monroe Harbor, Mich.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Monroe Harbor, Mich. 162.145 Section 162.145 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.145 Monroe Harbor, Mich. (a)...

  4. 33 CFR 162.120 - Harbors on Lake Michigan.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 2 2011-07-01 2011-07-01 false Harbors on Lake Michigan. 162.120 Section 162.120 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.120 Harbors on Lake...

  5. 33 CFR 162.145 - Monroe Harbor, Mich.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Monroe Harbor, Mich. 162.145 Section 162.145 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) PORTS AND WATERWAYS SAFETY INLAND WATERWAYS NAVIGATION REGULATIONS § 162.145 Monroe Harbor, Mich. (a)...

  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, 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...

  8. 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...

  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 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...

  11. 78 FR 28619 - Boston Harbor Islands Advisory Council Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-15

    ... Boston Harbor Islands Advisory Council Meeting AGENCY: National Park Service, Interior. ACTION: Notice of Meeting. SUMMARY: This notice announces a meeting of the Boston Harbor Islands Advisory Council. The agenda includes a presentation by author John Galluzzo, ``Peddocks Island, As Seen from Pemberton...

  12. 78 FR 9730 - Boston Harbor Islands Advisory Council Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-11

    ... National Park Service Boston Harbor Islands Advisory Council Meeting AGENCY: National Park Service... Islands Advisory Council. The agenda includes a presentation by Sally Snowman, 70th keeper of Boston Light... Jacobson, DFO, Boston Harbor Islands National Recreation Area, 408 Atlantic Avenue, Suite 228, Boston,...

  13. 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...

  14. 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...

  15. 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...

  16. 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),...

  17. 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...

  18. 76 FR 50489 - Agency Information Collection Activities: Harbor Maintenance Fee

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-15

    ... Fee AGENCY: U.S. Customs and Border Protection, Department of Homeland Security. ACTION: 30-Day Notice... approval in accordance with the Paperwork Reduction Act: Harbor Maintenance Fee (CBP Forms 349 and 350... information collection: Title: Harbor Maintenance Fee. OMB Number: 1651-0055. Form Number: CBP Forms 349...

  19. 78 FR 63381 - Safety Zones; Hawaiian Island Commercial Harbors, HI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-24

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zones; Hawaiian Island Commercial Harbors, HI.... 14-1414 Safety Zones; Hawaiian Islands Commercial Harbors; HI. (a) Location. The following...

  20. 78 FR 29089 - Safety Zones; Hawaiian Island Commercial Harbors, HI

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-17

    ... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zones; Hawaiian Island Commercial Harbors, HI... Safety Zones; Hawaiian Islands Commercial Harbors; HI. (a) Location. The following areas are safety...

  1. 33 CFR 110.147 - New London Harbor, Conn.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... emergencies, vessels shall not anchor in New London Harbor or the approaches thereto outside the anchorages... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false New London Harbor, Conn. 110.147 Section 110.147 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY...

  2. 33 CFR 110.115 - Santa Barbara Harbor, Calif.

    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, Calif. 110... ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.115 Santa Barbara Harbor, Calif. North of the Santa Barbara breakwater; seaward of the line of mean high water; and southwest of a line bearing...

  3. 12 CFR 18.11 - Safe harbor provision.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Safe harbor provision. 18.11 Section 18.11 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT OF THE TREASURY DISCLOSURE OF FINANCIAL AND OTHER INFORMATION BY NATIONAL BANKS § 18.11 Safe harbor provision. The provisions of § 18.10(c)...

  4. 33 CFR 80.1142 - San Francisco Harbor, CA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 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...

  5. 33 CFR 80.1142 - San Francisco Harbor, CA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 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...

  6. 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...

  7. 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...

  8. 33 CFR 80.1142 - San Francisco Harbor, CA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. The MACPF/CDC family of pore-forming toxins

    PubMed Central

    Rosado, Carlos J; Kondos, Stephanie; Bull, Tara E; Kuiper, Michael J; Law, Ruby H P; Buckle, Ashley M; Voskoboinik, Ilia; Bird, Phillip I; Trapani, Joseph A; Whisstock, James C; Dunstone, Michelle A

    2008-01-01

    Pore-forming toxins (PFTs) are commonly associated with bacterial pathogenesis. In eukaryotes, however, PFTs operate in the immune system or are deployed for attacking prey (e.g. venoms). This review focuses upon two families of globular protein PFTs: the cholesterol-dependent cytolysins (CDCs) and the membrane attack complex/perforin superfamily (MACPF). CDCs are produced by Gram-positive bacteria and lyse or permeabilize host cells or intracellular organelles during infection. In eukaryotes, MACPF proteins have both lytic and non-lytic roles and function in immunity, invasion and development. The structure and molecular mechanism of several CDCs are relatively well characterized. Pore formation involves oligomerization and assembly of soluble monomers into a ring-shaped pre-pore which undergoes conformational change to insert into membranes, forming a large amphipathic transmembrane β-barrel. In contrast, the structure and mechanism of MACPF proteins has remained obscure. Recent crystallographic studies now reveal that although MACPF and CDCs are extremely divergent at the sequence level, they share a common fold. Together with biochemical studies, these structural data suggest that lytic MACPF proteins use a CDC-like mechanism of membrane disruption, and will help understand the roles these proteins play in immunity and development. PMID:18564372

  15. 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.

  16. Aqueous-, pore-water-, and sediment-phase cadmium: Toxicity relationships for a meiobenthic copepod

    SciTech Connect

    Green, A.S.; Chandler, G.T.; Blood, E.R. . Dept. of Environmental Health Sciences)

    1993-08-01

    Comparative effects of aqueous-, pore-water-, and sediment-phase cadmium on mortality of an infaunal laboratory-cultured copepod, Amphiascus tenuiremis, were determined using acute 96-h bioassays. Experimental design included five cadmium concentrations, three replicates per concentration, and 50 adult copepods per replicate for each of the exposure. Exposures included cadmium solubilized in seawater only, whole sediment, and pore water only. In addition, two whole-sediment bioassays were compared in which pore-water cadmium concentrations were altered experimentally but sediment concentrations remained the same. Results of these experiments showed that for Amphiascus tenuiremis, cadmium is most toxic in the aqueous phase, less toxic in the pore-water phase, and last toxic in the sediment-bound phase. The lowered toxicity of cadmium in the pore water was most likely due to complexation of cadmium with DOC, because concentrations of DOC were six times higher in the pore-water phase than in the aqueous phase. In whole sediments, pore-water-phase cadmium was the primary source of acute toxicity, as sediment-associated cadmium contributed negligible effects.

  17. 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.

  18. 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.

  19. Effect of contact angle on capillary displacement curvatures in pore throats formed by spheres

    SciTech Connect

    Mason, G. . Dept. of Chemical Engineering); Morrow, N.R. )

    1994-11-01

    The curvature of an interface in a pore depends upon the shape of the pore and the operative contact angle that the interface makes with the solid surface. Even relatively simple pores formed by the surfaces of equal spheres have a complex shape including nonaxisymmetric cross-section and converging-diverging geometry. For such pores, a theory for meniscus behavior has been devised that uses a combination of a theory for meniscus curvature in rods together with the toroidal approximation of Purcell. The results of the theory show that converging-diverging geometry tends to compensate for the effect of contact angle. This is because the position at which the nonzero contact angle meniscus has maximum curvature in a converging-diverging pore is not the narrowest part of the pore throat. Due to this compensation, the effect of contact angle on maximum meniscus curvatures for drainage is approximately proportional to cos 2/3 [theta] (rather than the cos [theta] appropriate for cylindrical tubes). Experiments on pores formed by PTFE spheres using partially wetting liquids confirmed the theoretical prediction. Contact angle measurements on the PTFE spheres also demonstrated that, because of microscopic surface roughness, receding contact angles (these being operative with respect to drainage) on ground surfaces are significantly lower than values for smooth surfaces.

  20. Charlotte Harbor initiative: assessing the ecological health of southwest Florida's Charlotte Harbor estuary.

    PubMed

    Pierce, Richard H; Wetzel, Dana L; Estevez, Ernest D

    2004-04-01

    Charlotte Harbor is the largest and one of the least impacted estuaries on the southwest Florida coast, encompassing about 270 square miles (700 km2) with a watershed of 4400 square miles (11,400 km2). The Harbor is distinguished by extensive phosphate mining in its watershed and declining freshwater inflows, more protected submerged and intertidal areas than most Gulf ecosystems, and is part of the National Estuary Program. A hypoxic event occurs annually in the Harbor for possibly natural rather than anthropogenic reasons providing an opportunity for the study of hypoxic effects on the ecology of a large subtropical ecosystem. A 5-year, multimillion dollar study was begun in 2001 to enable scientists of Mote Marine Laboratory (MML, Sarasota, Florida) to collaborate on ecological characterization of the estuary and provide data necessary for resource managers to predict consequences of future population growth in the region. Initial studies were organized around themes of preservation, conservation and restoration while subsequent years of work are organized around a core program of physical, chemical and biological studies that track the ecological consequences of freshwater inflow, hypoxia and anthropogenic-derived contaminants. Along with MML, scientists in federal and state agencies along with a number of colleges and universities are cooperating in the project.

  1. 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

  2. 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.

  3. Single particle imaging of mRNAs crossing the nuclear pore: Surfing on the edge.

    PubMed

    Palazzo, Alexander F; Truong, Mathew

    2016-08-01

    Six years ago, the Singer lab published a landmark paper which described how individual mRNA particles cross the nuclear pore complex in mammalian tissue culture cells. This involved the simultaneous imaging of mRNAs, each labeled by a large number of tethered fluorescent proteins and fluorescently tagged nuclear pore components. Now two groups have applied this technique to the budding yeast Saccharomyces cerevisiae. Their results indicate that in the course of nuclear export, mRNAs likely engage complexes that are present on either side of the pore and that these interactions are modulated by proteins present in the messenger ribonucleoprotein (mRNP) complex. These findings lend support to the notion that just before and/or after the completion of nuclear export, mRNPs undergo one or more maturation steps that prepare the packaged mRNAs for translation. These results represent new and exciting insights into the mechanism of mRNA nuclear export.

  4. 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.

  5. Low Pore Connectivity in Natural Rock

    SciTech Connect

    Hu, Qinhong; Ewing, Robert P.; Dultz, Stefan

    2012-05-15

    As repositories for CO₂ 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.

  6. 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

    2008-04-02

    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.

  7. Stepwise visualization of membrane pore formation by suilysin, a bacterial cholesterol-dependent cytolysin.

    PubMed

    Leung, Carl; Dudkina, Natalya V; Lukoyanova, Natalya; Hodel, Adrian W; Farabella, Irene; Pandurangan, Arun P; Jahan, Nasrin; Pires Damaso, Mafalda; Osmanović, Dino; Reboul, Cyril F; Dunstone, Michelle A; Andrew, Peter W; Lonnen, Rana; Topf, Maya; Saibil, Helen R; Hoogenboom, Bart W

    2014-12-02

    Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming proteins that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from the soluble monomeric form to oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron microscopy (EM), and atomic structure fitting, we have mapped the structure and assembly pathways of a bacterial CDC in unprecedented detail and accuracy, focussing on suilysin from Streptococcus suis. We show that suilysin assembly is a noncooperative process that is terminated before the protein inserts into the membrane. The resulting ring-shaped pores and kinetically trapped arc-shaped assemblies are all seen to perforate the membrane, as also visible by the ejection of its lipids. Membrane insertion requires a concerted conformational change of the monomeric subunits, with a marked expansion in pore diameter due to large changes in subunit structure and packing.

  8. Some specifics of influence of pore pressure on physical properties of deformable rocks

    NASA Astrophysics Data System (ADS)

    Sobolev, G. A.; Stakhovskaya, Z. I.; Mikayelyan, A. O.

    1984-07-01

    A study was made of a range of problems related to the physical and mechanical properties of limestones from the region of the Ingura hydroelectric powerplant under hydrostatic pore pressure with additional axial pressure. The purpose was to estimate the significance and effect of pore pressure on physical properties in rocks as a function of the stressed state under conditions of hydrostatic pressure and hydrostatic pressure with additional axial loading. The P wave velocity, resistivity and longitudinal deformation were measured under pressure with specimens which had been carefully dried and saturated under vacuum conditions with a 2 n solution of NaCl. Cyclical variations of pore pressure were found to cause compaction of the rock. Cyclical variations of pore pressure under complex stress conditions facilitate fracture and strength loss of the rock.

  9. Hydrochromic Approaches to Mapping Human Sweat Pores.

    PubMed

    Park, Dong-Hoon; Park, Bum Jun; Kim, Jong-Man

    2016-06-21

    Hydrochromic materials, which undergo changes in their light absorption and/or emission properties in response to water, have been extensively investigated as humidity sensors. Recent advances in the design of these materials have led to novel applications, including monitoring the water content of organic solvents, water-jet-based rewritable printing on paper, and hydrochromic mapping of human sweat pores. Our interest in this area has focused on the design of hydrochromic materials for human sweat pore mapping. We recognized that materials appropriate for this purpose must have balanced sensitivities to water. Specifically, while they should not undergo light absorption and/or emission transitions under ambient moisture conditions, the materials must have sufficiently high hydrochromic sensitivities that they display responses to water secreted from human sweat pores. In this Account, we describe investigations that we have carried out to develop hydrochromic substances that are suitable for human sweat pore mapping. Polydiacetylenes (PDAs) have been extensively investigated as sensor matrices because of their stimulus-responsive color change property. We found that incorporation of headgroups composed of hygroscopic ions such as cesium or rubidium and carboxylate counterions enables PDAs to undergo a blue-to-red colorimetric transition as well as a fluorescence turn-on response to water. Very intriguingly, the small quantities of water secreted from human sweat pores were found to be sufficient to trigger fluorescence turn-on responses of the hydrochromic PDAs, allowing precise mapping of human sweat pores. Since the hygroscopic ion-containing PDAs developed in the initial stage display a colorimetric transition under ambient conditions that exist during humid summer periods, a new system was designed. A PDA containing an imidazolium ion was found to be stable under all ambient conditions and showed temperature-dependent hydrochromism corresponding to a

  10. Unlocking the Physiochemical Controls on Organic Carbon Dynamics from the Soil Pore- to Core-Scale

    NASA Astrophysics Data System (ADS)

    Smith, A. P.; Tfaily, M. M.; Bond-Lamberty, B. P.; Todd-Brown, K. E.; Bailey, V. L.

    2015-12-01

    The physical organization of soil includes pore networks of varying size and connectivity. These networks control microbial access to soil organic carbon (C) by spatially separating microorganisms and C by both distance and size exclusion. The extent to which this spatially isolated C is vulnerable to microbial transformation under hydrologically dynamic conditions is unknown, and limits our ability to predict the source and sink capacity of soils. We investigated the effects of shifting hydrologic connectivity and soil structure on greenhouse gas C emissions from surface soils collected from the Disney Wilderness Preserve (Florida, USA). We subjected intact soil cores and re-packed homogenized soil cores to simulated groundwater rise or precipitation, monitoring their CO2 and CH4 emissions over 24 hours. Soil pore water was then extracted from each core using different suctions to sample water retained by pore throats of different sizes and then characterized by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. Greater respiration rates were observed from homogenized cores compared to intact cores, and from soils wet from below, in which the wetting front is driven by capillary forces, filling fine pores first. This suggests that C located in fine pores may turn over via diffusion processes that lead to the colocation of this C with other resources and microorganisms. Both the complexity and concentration of soluble-C increased with decreasing pore size domains. Pore water extracted from homogenized cores had greater C concentrations than from intact cores, with the greatest concentrations in pore waters sampled from very fine pores, highlighting the importance of soil structure in physically protecting C. These results suggest that the spatial separation of decomposers from C is a key mechanism stabilizing C in these soils. Further research is ongoing to accurately represent this protection mechanism, and the conditions under which it breaks

  11. On the hysteresis of argon adsorption in a uniform closed end slit pore.

    PubMed

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

    2013-09-01

    We present a molecular simulation study of adsorption and desorption in slit mesopores of uniform width with one end closed and explore the effects of pore dimensions (width and length), temperature and surface affinity on the hysteresis loop: its position, lower and upper closure points, area and shape. Our results show that the metastability, brought about by structural change in the adsorbate, is the reason for the existence of hysteresis, and contrast with reports suggesting that reversibility invariably prevails for adsorption in closed end pores. The shape, area and position of the hysteresis loop are complex functions of pore width, length and temperature. We establish a parametric map of the boundary separating reversible and hysteretic regions. Our simulation results also show a number of interesting observations that have not been previously reported or generally recognised: (1) the fluid within the core of the pore behaves like a bulk liquid as the pore is progressively filled, via the movement of the meniscus from the closed end to the pore mouth, but as the pore fills, the fluid in the core becomes structured, (2) the shape of the meniscus changes as adsorption progresses but is constant during desorption because of the constant thickness of the adsorbed layer in the two-phase region, (3) the hysteresis loop is larger for a longer pore, (4) the area of the hysteresis loop increases with pore width up to a certain width, beyond which it decreases and finally disappears, (5) as temperature approaches the critical hysteresis temperature, the hysteresis loop area decreases, but it retains its Type H1 character.

  12. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  13. Modeling tissue growth within nonwoven scaffolds pores.

    PubMed

    Edwards, Sharon L; Church, Jeffrey S; Alexander, David L J; Russell, Stephen J; Ingham, Eileen; Ramshaw, John A M; Werkmeister, Jerome A

    2011-02-01

    In this study we present a novel approach for predicting tissue growth within the pores of fibrous tissue engineering scaffolds. Thin nonwoven polyethylene terephthalate scaffolds were prepared to characterize tissue growth within scaffold pores, by mouse NR6 fibroblast cells. On the basis of measurements of tissue lengths at fiber crossovers and along fiber segments, mathematical models were determined during the proliferative phase of cell growth. Tissue growth at fiber crossovers decreased with increasing interfiber angle, with exponential relationships determined on day 6 and 10 of culture. Analysis of tissue growth along fiber segments determined two growth profiles, one with enhanced growth as a result of increased tissue lengths near the fiber crossover, achieved in the latter stage of culture. Derived mathematical models were used in the development of a software program to visualize predicted tissue growth within a pore. This study identifies key pore parameters that contribute toward tissue growth, and suggests models for predicting this growth, based on fibroblast cells. Such models may be used in aiding scaffold design, for optimum pore infiltration during the tissue engineering process.

  14. Performance of Small Pore Microchannel Plates

    NASA Technical Reports Server (NTRS)

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

    1995-01-01

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

  15. 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

  16. 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.

  17. Modeling of N2 adsorption in MCM-41 materials: hexagonal pores versus cylindrical pores.

    PubMed

    Ustinov, Eugene A

    2009-07-07

    Low-temperature nitrogen adsorption in hexagonal pores and equivalent cylindrical pores is analyzed using nonlocal density functional theory extended to amorphous solids (NLDFT-AS). It is found that, despite significant difference of the density distribution over the cross-section of the pore, the capillary condensation/evaporation pressure is not considerably affected by the pore shape being slightly lower in the case of hexagonal geometry. However, the condensation/evaporation step in the hexagonal pore is slightly larger than that in the equivalent cylindrical pore because in the latter case the pore wall surface area and, hence, the amount adsorbed at pressures below the evaporation pressure are underestimated by 5%. We show that a dimensionless parameter defined as the ratio of the condensation/evaporation step and the upper value of the amount adsorbed at the condensation/evaporation pressure can be used as an additional criterion of the correct choice of the gas-solid molecular parameters along with the dependence of condensation/evaporation pressure on the pore diameter. Application of the criteria to experimental data on nitrogen adsorption on a series of MCM-41 silica at 77 K corroborates some evidence that the capillary condensation occurs at equilibrium conditions.

  18. Chromatographic performance of large-pore versus small-pore columns in micellar liquid chromatography.

    PubMed

    McCormick, Timothy J; Foley, Joe P; Lloyd, David K

    2003-02-25

    Micellar liquid chromatography (MLC) is useful in bioanalysis because proteinaceous biofluids can be directly injected onto the column. The technique has been limited in part because of the apparently weak eluting power of micellar mobile phases. It has recently been shown [Anal. Chem. 72 (2000) 294] that this may be overcome by the use of large pore size stationary phases. In this work, large-pore (1000 A) C(18) stationary phases were evaluated relative to conventional small-pore (100 A) C(18) stationary phases for the direct sample injection of drugs in plasma. Furthermore, the difference between the large and small pore phases in gradient elution separations of mixtures of widely varying hydrophobicities was investigated. Large-pore stationary phases were found to be very effective for eluting moderately to highly hydrophobic compounds such as ibuprofen, crotamiton, propranolol, and dodecanophenone, which were highly retained on the small-pore stationary phases typically used in MLC. The advantages of direct introduction of biological samples (drugs in plasma) and rapid column re-equilibration after gradient elution in MLC were maintained with large-pore phases. Finally, recoveries, precision, linearity, and detection limits for the determination of quinidine and DPC 961 in spiked bovine plasma were somewhat better using MLC with wide pore phases.

  19. A combo-pore approach for the programmable extraction of peptides/proteins

    NASA Astrophysics Data System (ADS)

    Qian, Kun; Zhou, Liang; Zhang, Jun; Lei, Chang; Yu, Chengzhong

    2014-04-01

    A novel combo-pore approach has been designed for the programmable purification, minimisation of sample complexity, enrichment and sensitive detection of peptides in biosamples. This approach has a superior performance to conventional protocols and commercial products.A novel combo-pore approach has been designed for the programmable purification, minimisation of sample complexity, enrichment and sensitive detection of peptides in biosamples. This approach has a superior performance to conventional protocols and commercial products. Electronic supplementary information (ESI) available: Experimental and supporting data. See DOI: 10.1039/c4nr00633j

  20. Ruminant feces harbor diverse uncultured symbiotic actinobacteria.

    PubMed

    Tan, Hongming; Deng, Qingli; Cao, Lixiang

    2014-03-01

    To isolate actinobacteria from ruminant feces and elucidate their correlations with ruminants, the actinobacterial community in sheep (Ovis aries) and cattle (Bos taurus) feces was determined by cultivation and clone library methods. Most of actinobacteria isolated belonged to Streptomyces, Amycolatopsis, Micromonospora, and Cellulosimicrobium genera. The strains showed above 99 % similarity with the type strains, respectively. All the strains isolated could grow on media containing pectin, cellulose, or xylan as the sole carbon sources. However, most antibacterial and antifungal activities were found in Streptomyces species. Clone library analysis revealed that the genera Mycobacterium, Aeromicrobium, Rhodococcus, Cellulomonas were present in cattle and sheep feces. In contrast, the 16S rRNA genes showed less than 98 % similarity with the type strains. The analysis of actinobacterial community in ruminant feces by clone library and cultivation yielded a total of 10 actinobacterial genera and three uncultured actinobacterial taxa. The ruminant feces harbored diverse actinobacterial community. Ruminants may represent an underexplored reservoir of novel actinomycetes of potential interest for probiotics and drug discovery.

  1. Recycling of harbor sediment as lightweight aggregate.

    PubMed

    Wei, Yu-Ling; Yang, Jing-Chiang; Lin, Yong-Yang; Chuang, Shih-Yu; Wang, H Paul

    2008-01-01

    Sediment sampled from Taichung Harbor was mixed with local reservoir sediment at different weight ratios to prepare lightweight aggregate at 1050, 1100, and 1150 degrees C. A pressure of 3000 or 5000 psi was used to shape the powder mixtures into pellets before the heating processes. The results indicate that the leaching levels of trace metals from the lightweight aggregate samples are considerably reduced to levels less than Taiwan Environmental Protection Administration regulatory limits. Increasing final process temperature tends to reduce the bulk density and crushing intensity of lightweight aggregate with a concomitant increase in water sorption capability. Lightweight aggregate with the lowest bulk density, 0.49 g cm(-3) for the 5000 psi sample, was obtained with the heating process to 1150 degrees C. Based on the X-ray absorption near edge structure results, FeSO(4) decomposition with a concomitant release of SO(x) (x = 2,3) is suggested to play an important role for the bloating process in present study.

  2. Foam invasion through a single pore.

    PubMed

    Delbos, Aline; Pitois, Olivier

    2011-07-01

    We investigate experimentally the behavior of liquid foams pumped at a given flow rate through a single pore, in the situation where the pore diameter is smaller than the bubble diameter. Results reveal that foam invasion can be observed only within a restricted range of values for the dimensionless flow rate and the foam liquid fraction. Within this foam invasion regime, the liquid content of invading foams is measured to be three times higher than the initial liquid content. Outside this regime, both gas alone and liquid alone invasion regimes can be observed. The gas invasion regime results from the rupture of foam films during local T1, during bubble rearrangements events induced by foam flow, whereas the liquid invasion regime is allowed by the formation of a stable cluster of jammed bubbles at the pore's opening.

  3. Unplugging the callose plug from sieve pores.

    PubMed

    Xie, Bo; Hong, Zonglie

    2011-04-01

    The presence of callose in sieve plates has been known for a long time, but how this polysaccharide plug is synthesized has remained unsolved. Two independent laboratories have recently reported the identification of callose synthase 7 (CalS7), also known as glucan synthase-like 7 (GSL7), as the enzyme responsible for callose deposition in sieve plates. Mutant plants defective in this enzyme failed to synthesize callose in developing sieve plates during phloem formation and were unable to accumulate callose in sieve pores in response to stress treatments. The mutant plants developed less open pores per sieve plate and the pores were smaller in diameter. As a result, phloem conductivity was reduced significantly and the mutant plants were shorter and set fewer seeds.

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

    NASA Astrophysics Data System (ADS)

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

    2006-12-01

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

  5. Scaffold pore space modulation through intelligent design of dissolvable microparticles.

    PubMed

    Liebschner, Michael A K; Wettergreen, Matthew

    2012-01-01

    The goal of this area of research is to manipulate the pore space of scaffolds through the application of an intelligent design concept on dissolvable microparticles. To accomplish this goal, we developed an efficient and repeatable process for fabrication of microparticles from multiple materials using a combination of rapid prototyping (RP) and soft lithography. Phase changed 3D printing was used to create masters for PDMS molds. A photocrosslinkable polymer was then delivered into these molds to make geometrically complex 3D microparticles. This repeatable process has demonstrated to generate the objects with greater than 95% repeatability with complete pattern transfer. This process was illustrated for three different shapes of various complexities. The shapes were based on the extrusion of 2D shapes. This may allow simplification of the fabrication process in the future combined with a direct transfer of the findings. Altering the shapes of particles used for porous scaffold fabrication will allow for tailoring of the pore shapes, and therefore their biological function within a porous tissue engineering scaffold. Through permeation experiments, we have shown that the pore geometry may alter the permeability coefficient of scaffolds while influencing mechanical properties to a lesser extent. By selecting different porogen shapes, the nutrition transport and scaffold degradation can be significantly influenced with minimal effect on the mechanical integrity of the construct. In addition, the different shapes may allow a control of drug release by modifying their surface-to-volume ratio, which could modulate drug delivery over time. While soft lithography is currently used with photolithography, its high precision is offset by high cost of production. The employment of RP to a specific resolution offers a much less expensive alternative with increased throughput due to the speed of current RP systems.

  6. Assessing Coating Reliability Through Pore Architecture Evaluation

    NASA Astrophysics Data System (ADS)

    Paul, S.

    2010-06-01

    Plasma-sprayed thermal barrier coatings (TBCs) exhibit many interlamellar pores, voids, and microcracks. These microstructural features are primarily responsible for the low global stiffness and the low thermal conductivity commonly exhibited by such coatings. The pore architecture thus has an important influence on such thermophysical properties. In the present work, the effect of heat treatment (at temperatures up to 1400 °C, for times of up to 20 h) on the pore architecture of detached YSZ top coats with different impurity levels have been characterized by mercury intrusion porosimetry and gas-sorption techniques. Stiffness and thermal conductivity were also monitored to assess the effect of change in pore architecture on properties. While the overall porosity level remained relatively unaffected (at around 10-12%) after the heat treatments concerned, there were substantial changes in the pore size distribution and the (surface-connected) specific surface area. Fine pores (<~50 nm) rapidly disappeared, while the specific surface area dropped dramatically, particularly at high-treatment temperatures (~1400 °C). These changes are thought to be associated with intrasplat microcrack healing, improved intersplat bonding and increased contact area, leading to disappearance of much of the fine porosity. These microstructural changes are reflected in sharply increased stiffness and thermal conductivity. Increase in thermal conductivity and stiffness were found to be more pronounced for coatings with higher impurity content (particularly alumina and silica). Reliability issues surrounding such increase in thermal conductivity and stiffness are discussed along with a brief note on the effect of impurities on TBC life.

  7. Inner/Outer nuclear membrane fusion in nuclear pore assembly: biochemical demonstration and molecular analysis.

    PubMed

    Fichtman, Boris; Ramos, Corinne; Rasala, Beth; Harel, Amnon; Forbes, Douglass J

    2010-12-01

    Nuclear pore complexes (NPCs) are large proteinaceous channels embedded in double nuclear membranes, which carry out nucleocytoplasmic exchange. The mechanism of nuclear pore assembly involves a unique challenge, as it requires creation of a long-lived membrane-lined channel connecting the inner and outer nuclear membranes. This stabilized membrane channel has little evolutionary precedent. Here we mapped inner/outer nuclear membrane fusion in NPC assembly biochemically by using novel assembly intermediates and membrane fusion inhibitors. Incubation of a Xenopus in vitro nuclear assembly system at 14°C revealed an early pore intermediate where nucleoporin subunits POM121 and the Nup107-160 complex were organized in a punctate pattern on the inner nuclear membrane. With time, this intermediate progressed to diffusion channel formation and finally to complete nuclear pore assembly. Correct channel formation was blocked by the hemifusion inhibitor lysophosphatidylcholine (LPC), but not if a complementary-shaped lipid, oleic acid (OA), was simultaneously added, as determined with a novel fluorescent dextran-quenching assay. Importantly, recruitment of the bulk of FG nucleoporins, characteristic of mature nuclear pores, was not observed before diffusion channel formation and was prevented by LPC or OA, but not by LPC+OA. These results map the crucial inner/outer nuclear membrane fusion event of NPC assembly downstream of POM121/Nup107-160 complex interaction and upstream or at the time of FG nucleoporin recruitment.

  8. Active Polymer Translocation through Flickering Pores

    NASA Astrophysics Data System (ADS)

    Cohen, Jack A.; Chaudhuri, Abhishek; Golestanian, Ramin

    2011-12-01

    Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  10. Molecular Sensing with an Artificial Pore

    NASA Astrophysics Data System (ADS)

    Saleh, Omar A.

    2002-03-01

    While microfluidic systems are routinely integrated with optical schemes to measure biological macromolecules, there are relatively few examples of experiments in which electronic techniques are used. There are, however, good reasons to perform electronic measurements- macromolecules do not need to be fluorescently tagged, and different parameters of the analyte can be investigated. To begin to take advantage of these differences, we have developed a chip-based device that uses resistive sensing of a micro-fabricated pore to characterize solutions of particles. The device can perform size-based differentiation of polydisperse solutions of colloids with a precision of 10 nm in diameter^*. This level of precision could be utilized to perform simple binding or immuno-assays whereby the attachment of the appropriate ligand to a receptor immobilized on the colloid surface causes a detectable increase in the colloid’s diameter. Furthermore, the relatively simple design can easily be scaled up to create arrays of pores on a single chip, thus adding the capability to perform multiple assays in parallel. Finally, reductions in pore size have allowed us to detect successfully single molecules of lambda-phage DNA passing through the pore. This particular achievement represents a first step towards a host of bio-molecular sensing applications. ^*O. A. Saleh and L. L. Sohn, Rev. Sci. Instrum. 72, 4449 (2001)

  11. Drainage Studies Using Pore-Scale Approaches

    NASA Astrophysics Data System (ADS)

    Liu, E. B.; Reed, A. H.; Hilpert, M.

    2007-12-01

    The process of drainage has wide spread applications in soil hydrology, irrigation, and the remediation of contaminants in the subsurface. In this paper, we present the comparison of experimental and pore-scale modeling results for drainage. Using a HD-500 microCT system, X-ray tomographic images (21 micron voxels) of saturation during a drainage experiment were obtained in a porous medium consisting of 20/30 mesh (590- 840 microns) Accusand. Utilizing the segmented microtomographic images of the pore space, we modeled drainage using two pore-scale approaches: (1) the pore-morphology-based simulator (PMBS) developed by Hilpert and Miller (2001), and (2) a Lattice Boltzmann (LB) model. Invasion pathways and pressure-saturation relations obtained from both the PMBS and the LB model were compared with those obtained from experiments. The results of PMBS modeling displayed good agreement with experimental observations, except at high suction and low water saturation values, where both CT resolution and model assumptions become an issue. The LB model is currently being refined, and the results of these simulations will also be presented.

  12. Channel gating pore: a new therapeutic target.

    PubMed

    Kornilov, Polina; Peretz, Asher; Attali, Bernard

    2013-09-01

    Each subunit of voltage-gated cation channels comprises a voltage-sensing domain and a pore region. In a paper recently published in Cell Research, Li et al. showed that the gating charge pathway of the voltage sensor of the KCNQ2 K+ channel can accommodate small opener molecules and offer a new target to treat hyperexcitability disorders.

  13. Pore-Forming Toxins Trigger the Purge.

    PubMed

    Bonfini, Alessandro; Buchon, Nicolas

    2016-12-14

    The intestinal epithelium responds to pathogens by coordinating microbial elimination with tissue repair, both required to survive an infection. In this issue of Cell Host & Microbe, Lee et al. (2016) discover a rapid and evolutionarily conserved response to pore-forming toxins in the gut, involving cytoplasm ejection and enterocyte regrowth.

  14. 160. VIEW FROM NEW YORK HARBOR SHOWING THE JERSEY WATER ...

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

    160. VIEW FROM NEW YORK HARBOR SHOWING THE JERSEY WATER FRONT. PLEASE NOTE THAT ARROWS WERE ON ORIGINAL PHOTOGRAPH AND WHAT THEY POINT OUT IS NOT CERTAIN. - Morris Canal, Phillipsburg, Warren County, NJ

  15. 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

  16. 77 FR 22489 - Special Anchorage Regulations, Newport Bay Harbor, CA

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-16

    ... special anchorage areas in Newport Bay Harbor, California, to encompass and replace temporary anchorage... safety that might disproportionately affect children. Indian Tribal Governments This rule does not have tribal implications under Executive Order 13175, Consultation and Coordination with Indian...

  17. 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

  18. 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

  19. 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).

  20. 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...