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Sample records for pore expansion mediated

  1. Syndapin 3 modulates fusion pore expansion in mouse neuroendocrine chromaffin cells

    PubMed Central

    Samasilp, Prattana; Lopin, Kyle; Chan, Shyue-An; Ramachandran, Rajesh

    2014-01-01

    Adrenal neuroendocrine chromaffin cells receive excitatory synaptic input from the sympathetic nervous system and secrete hormones into the peripheral circulation. Under basal sympathetic tone, modest amounts of freely soluble catecholamine are selectively released through a restricted fusion pore formed between the secretory granule and the plasma membrane. Upon activation of the sympathoadrenal stress reflex, elevated stimulation drives fusion pore expansion, resulting in increased catecholamine secretion and facilitating release of copackaged peptide hormones. Thus regulated expansion of the secretory fusion pore is a control point for differential hormone release of the sympathoadrenal stress response. Previous work has shown that syndapin 1 deletion alters transmitter release and that the dynamin 1-syndapin 1 interaction is necessary for coupled endocytosis in neurons. Dynamin has also been shown to be involved in regulation of fusion pore expansion in neuroendocrine chromaffin cells through an activity-dependent association with syndapin. However, it is not known which syndapin isoform(s) contributes to pore dynamics in neuroendocrine cells. Nor is it known at what stage of the secretion process dynamin and syndapin associate to modulate pore expansion. Here we investigate the expression and localization of syndapin isoforms and determine which are involved in mediating fusion pore expansion. We show that all syndapin isoforms are expressed in the adrenal medulla. Mutation of the SH3 dynamin-binding domain of all syndapin isoforms shows that fusion pore expansion and catecholamine release are limited specifically by mutation of syndapin 3. The mutation also disrupts targeting of syndapin 3 to the cell periphery. Syndapin 3 exists in a persistent colocalized state with dynamin 1. PMID:24500282

  2. Free Energy Landscape of Rim-Pore Expansion in Membrane Fusion

    PubMed Central

    Risselada, Herre Jelger; Smirnova, Yuliya; Grubmüller, Helmut

    2014-01-01

    The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that changes with size. To determine this shape as well as the free energy along the pathway of rim-pore expansion, we derived a simple analytical free energy model. We argue that dilation of HD material via expansion of a rim-pore is favored over a regular, circular pore. Further, the expanding rim-pore faces a free energy barrier that linearly increases with HD size. In contrast, the tension required to expand the rim-pore decreases with HD size. Pore flickering, followed by sudden opening, occurs when the tension in the HD competes with the line energy of the rim-pore, and the rim-pore reaches its equilibrium size before reaching the critical pore size. The experimental observation of flickering and closing fusion pores (kiss-and-run) is very well explained by the observed behavior of rim-pores. Finally, the free energy landscape of rim-pore expansion/HD dilation may very well explain why some cellular fusion reactions, in their attempt to minimize energetic costs, progress via alternative formation and dilation of microscopic hemifusion intermediates. PMID:25418297

  3. Anisotropic thermal expansion of a 3D metal–organic framework with hydrophilic and hydrophobic pores

    SciTech Connect

    Kondo, Atsushi Maeda, Kazuyuki

    2015-01-15

    A 3D flexible metal–organic framework (MOF) with 1D hydrophilic and hydrophobic pores shows anisotropic thermal expansion with relatively large thermal expansion coefficient (α{sub a}=−21×10{sup −6} K{sup −1} and α{sub c}=79×10{sup −6} K{sup −1}) between 133 K and 383 K. Temperature change gives deformation of both pores, which expand in diameter and elongate in length on cooling and vice versa. The thermally induced structural change should be derived from a unique framework topology like “lattice fence”. Silica accommodation changes not only the nature of the MOF but also thermal responsiveness of the MOF. Since the hydrophobic pores in the material are selectively blocked by the silica, the MOF with the silica is considered as a hydrophilic microporous material. Furthermore, inclusion of silica resulted in a drastic pore contraction in diameter and anisotropically changed the thermal responsiveness of the MOF. - Graphical abstract: A 3D metal–organic framework with hydrophilic and hydrophobic pores shows anisotropic thermal expansion behavior. The influence of silica filler in the hydrophobic pore was investigated. - Highlights: • Thermally induced structural change of a 3D MOF with a lattice fence topology was investigated. • The structural change was analyzed by synchrotron X-ray diffraction patterns. • Temperature change induces anisotropic thermal expansion/contraction of the MOF. • Silica inclusion anisotropically changes the thermal responsiveness of the MOF.

  4. A new role for the dynamin GTPase in the regulation of fusion pore expansion

    PubMed Central

    Anantharam, Arun; Bittner, Mary A.; Aikman, Rachel L.; Stuenkel, Edward L.; Schmid, Sandra L.; Axelrod, Daniel; Holz, Ronald W.

    2011-01-01

    Dynamin is a master regulator of membrane fission in endocytosis. However, a function for dynamin immediately upon fusion has also been suspected from a variety of experiments that measured release of granule contents. The role of dynamin guanosine triphosphate hydrolase (GTPase) activity in controlling fusion pore expansion and postfusion granule membrane topology was investigated using polarization optics and total internal reflection fluorescence microscopy (pTIRFM) and amperometry. A dynamin-1 (Dyn1) mutant with increased GTPase activity resulted in transient deformations consistent with rapid fusion pore widening after exocytosis; a Dyn1 mutant with decreased activity slowed fusion pore widening by stabilizing postfusion granule membrane deformations. The experiments indicate that, in addition to its role in endocytosis, GTPase activity of dynamin regulates the rapidity of fusion pore expansion from tens of milliseconds to seconds after fusion. These findings expand the membrane-sculpting repertoire of dynamin to include the regulation of immediate postfusion events in exocytosis that control the rate of release of soluble granule contents. PMID:21460182

  5. Fusion pore expansion is a slow, discontinuous, and Ca2+-dependent process regulating secretion from alveolar type II cells.

    PubMed

    Haller, T; Dietl, P; Pfaller, K; Frick, M; Mair, N; Paulmichl, M; Hess, M W; Furst, J; Maly, K

    2001-10-15

    In alveolar type II cells, the release of surfactant is considerably delayed after the formation of exocytotic fusion pores, suggesting that content dispersal may be limited by fusion pore diameter and subject to regulation at a postfusion level. To address this issue, we used confocal FRAP and N-(3-triethylammoniumpropyl)-4-(4-[dibutylamino]styryl) pyridinium dibromide (FM 1-43), a dye yielding intense localized fluorescence of surfactant when entering the vesicle lumen through the fusion pore (Haller, T., J. Ortmayr, F. Friedrich, H. Volkl, and P. Dietl. 1998. Proc. Natl. Acad. Sci. USA. 95:1579-1584). Thus, we have been able to monitor the dynamics of individual fusion pores up to hours in intact cells, and to calculate pore diameters using a diffusion model derived from Fick's law. After formation, fusion pores were arrested in a state impeding the release of vesicle contents, and expanded at irregular times thereafter. The expansion rate of initial pores and the probability of late expansions were increased by elevation of the cytoplasmic Ca2+ concentration. Consistently, content release correlated with the occurrence of Ca2+ oscillations in ATP-treated cells, and expanded fusion pores were detectable by EM. This study supports a new concept in exocytosis, implicating fusion pores in the regulation of content release for extended periods after initial formation. PMID:11604423

  6. Increased Expression of the Diabetes Gene SOX4 Reduces Insulin Secretion by Impaired Fusion Pore Expansion.

    PubMed

    Collins, Stephan C; Do, Hyun Woong; Hastoy, Benoit; Hugill, Alison; Adam, Julie; Chibalina, Margarita V; Galvanovskis, Juris; Godazgar, Mahdieh; Lee, Sheena; Goldsworthy, Michelle; Salehi, Albert; Tarasov, Andrei I; Rosengren, Anders H; Cox, Roger; Rorsman, Patrik

    2016-07-01

    The transcription factor Sox4 has been proposed to underlie the increased type 2 diabetes risk linked to an intronic single nucleotide polymorphism in CDKAL1 In a mouse model expressing a mutant form of Sox4, glucose-induced insulin secretion is reduced by 40% despite normal intracellular Ca(2+) signaling and depolarization-evoked exocytosis. This paradox is explained by a fourfold increase in kiss-and-run exocytosis (as determined by single-granule exocytosis measurements) in which the fusion pore connecting the granule lumen to the exterior expands to a diameter of only 2 nm, which does not allow the exit of insulin. Microarray analysis indicated that this correlated with an increased expression of the exocytosis-regulating protein Stxbp6. In a large collection of human islet preparations (n = 63), STXBP6 expression and glucose-induced insulin secretion correlated positively and negatively with SOX4 expression, respectively. Overexpression of SOX4 in the human insulin-secreting cell EndoC-βH2 interfered with granule emptying and inhibited hormone release, the latter effect reversed by silencing STXBP6 These data suggest that increased SOX4 expression inhibits insulin secretion and increased diabetes risk by the upregulation of STXBP6 and an increase in kiss-and-run exocytosis at the expense of full fusion. We propose that pharmacological interventions promoting fusion pore expansion may be effective in diabetes therapy. PMID:26993066

  7. Increased expression of the diabetes gene SOX4 reduces insulin secretion by impaired fusion pore expansion

    PubMed Central

    Collins, Stephan C.; Do, Hyun Woong; Hastoy, Benoit; Hugill, Alison; Adam, Julie; Chibalina, Margarita V.; Galvanovskis, Juris; Godazgar, Mahdieh; Lee, Sheena; Goldsworthy, Michelle; Salehi, Albert; Tarasov, Andrei I.; Rosengren, Anders H.; Cox, Roger; Rorsman, Patrik

    2016-01-01

    The transcription factor Sox4 has been proposed to underlie the increased type-2 diabetes risk linked to an intronic SNP in CDKAL1. In a mouse model expressing a mutant form of Sox4, glucose-induced insulin secretion is reduced by 40% despite normal intracellular Ca2+ signalling and depolarization-evoked exocytosis. This paradox is explained by a 4-fold increase in kiss-and-run exocytosis (as determined by single-granule exocytosis measurements), in which the fusion pore connecting the granule lumen to the exterior only expands to a diameter of 2 nm that does not allow the exit of insulin. Microarray analysis indicated that this correlated with an increased expression of the exocytosis-regulating protein Stxbp6. In a large collection of human islet preparations (n=63), STXBP6 expression and GIIS correlated positively and negatively with SOX4 expression, respectively. Overexpression of SOX4 in the human insulin-secreting cell EndoC-βH2 interfered with granule emptying and inhibited hormone release, the latter effect was reversed by silencing of STXBP6. These data suggest that increased SOX4 expression inhibits insulin secretion and increased diabetes risk by upregulation of STXBP6 and an increase in kiss-and-run exocytosis at the expense of full fusion. We propose that pharmacological interventions promoting fusion pore expansion may be effective in diabetes therapy. PMID:26993066

  8. Cholesterol Increases the Openness of SNARE-Mediated Flickering Fusion Pores.

    PubMed

    Stratton, Benjamin S; Warner, Jason M; Wu, Zhenyong; Nikolaus, Joerg; Wei, George; Wagnon, Emma; Baddeley, David; Karatekin, Erdem; O'Shaughnessy, Ben

    2016-04-12

    Flickering of fusion pores during exocytotic release of hormones and neurotransmitters is well documented, but without assays that use biochemically defined components and measure single-pore dynamics, the mechanisms remain poorly understood. We used total internal reflection fluorescence microscopy to quantify fusion-pore dynamics in vitro and to separate the roles of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and lipid bilayer properties. When small unilamellar vesicles bearing neuronal v-SNAREs fused with planar bilayers reconstituted with cognate t-SNARES, lipid and soluble cargo transfer rates were severely reduced, suggesting that pores flickered. From the lipid release times we computed pore openness, the fraction of time the pore is open, which increased dramatically with cholesterol. For most lipid compositions tested, SNARE-mediated and nonspecifically nucleated pores had similar openness, suggesting that pore flickering was controlled by lipid bilayer properties. However, with physiological cholesterol levels, SNAREs substantially increased the fraction of fully open pores and fusion was so accelerated that there was insufficient time to recruit t-SNAREs to the fusion site, consistent with t-SNAREs being preclustered by cholesterol into functional docking and fusion platforms. Our results suggest that cholesterol opens pores directly by reducing the fusion-pore bending energy, and indirectly by concentrating several SNAREs into individual fusion events. PMID:27074679

  9. Conformational modulation mediated by polyglutamine expansion in CAG repeat expansion disease-associated proteins.

    PubMed

    Verani, Margherita; Bustamante, Maria; Martufi, Paola; Daldin, Manuel; Cariulo, Cristina; Azzollini, Lucia; Fodale, Valentina; Puglisi, Francesca; Weiss, Andreas; Macdonald, Douglas; Petricca, Lara; Caricasole, Andrea

    2016-09-16

    We have previously reported TR-FRET based immunoassays to detect a conformational change imparted on huntingtin protein by the polyglutamine expansion, which we confirmed using biophysical methodologies. Using these immunoassays, we now report that polyglutamine expansion influences the conformational properties of other polyglutamine disease proteins, exemplified by the androgen receptor (associated with spinal bulbar muscular atrophy) and TATA binding protein (associated with spinocerebellar ataxia 17). Using artificial constructs bearing short or long polyglutamine expansions or a multimerized, unrelated epitope (mimicking the increase in anti-polyglutamine antibody epitopes present in polyglutamine repeats of increasing length) we confirmed that the conformational TR-FRET based immunoassay detects an intrinsic conformational property of polyglutamine repeats. The TR-FRET based conformational immunoassay may represent a rapid, scalable tool to identify modulators of polyglutamine-mediated conformational change in different proteins associated with CAG triplet repeat disorders. PMID:27520369

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

    PubMed

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

    2009-03-15

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

  11. INITIAL SIZE AND DYNAMICS OF VIRAL FUSION PORES ARE A FUNCTION OF THE FUSION PROTEIN MEDIATING MEMBRANE FUSION

    PubMed Central

    Plonsky, I.; Kingsley, D. H.; Rashtian, A.; Blank, P.S.; Zimmerberg, J.

    2013-01-01

    To investigate the role of the fusogenic protein in the initial size and dynamics of the pore that widens to finalize membrane fusion, two different fusion proteins expressed in the same cell line were investigated: the major glycoprotein of baculovirus Autographa californica (GP64) and the hemaggluttinin of influenza X31 (HA). The host Sf9 cells expressing these viral proteins, irrespective of protein species, fused to human red blood cells (RBC) upon acidification of the medium. High time resolution electrophysiological study of fusion pore conductance revealed fundamental differences in a) the initial pore conductance (pores created by HA were smaller than those created by GP64), b) the ability of pores to flicker (only HA-mediated pores flickered), and c) the time required for pore formation (HA-mediated pores took much longer to form following acidification). Thus 1) HA and GP64 have divergent electrophysiological phenotypes even when they fuse identical membranes, and 2) fusion proteins play a crucial role in determining initial fusion pore characteristics. The structure of the initial fusion pore detected by electrical conductance measurements is sensitive to the nature of the fusion protein. PMID:18208404

  12. The actin cytoskeleton inhibits pore expansion during PIV5 fusion protein-promoted cell-cell fusion

    SciTech Connect

    Wurth, Mark A.; Schowalter, Rachel M.; Smith, Everett Clinton; Moncman, Carole L.; Ellis Dutch, Rebecca; McCann, Richard O.

    2010-08-15

    Paramyxovirus fusion (F) proteins promote both virus-cell fusion, required for viral entry, and cell-cell fusion, resulting in syncytia formation. We used the F-actin stabilizing drug, jasplakinolide, and the G-actin sequestrant, latrunculin A, to examine the role of actin dynamics in cell-cell fusion mediated by the parainfluenza virus 5 (PIV5) F protein. Jasplakinolide treatment caused a dose-dependent increase in cell-cell fusion as measured by both syncytia and reporter gene assays, and latrunculin A treatment also resulted in fusion stimulation. Treatment with jasplakinolide or latrunculin A partially rescued a fusion pore opening defect caused by deletion of the PIV5 F protein cytoplasmic tail, but these drugs had no effect on fusion inhibited at earlier stages by either temperature arrest or by a PIV5 heptad repeat peptide. These data suggest that the cortical actin cytoskeleton is an important regulator of fusion pore enlargement, an energetically costly stage of viral fusion protein-mediated membrane merger.

  13. Temperature-mediated phase transformation, pore geometry and pore hysteresis transformation of borohydride derived in-born porous zirconium hydroxide nanopowders

    PubMed Central

    Nayak, Nadiya B.; Nayak, Bibhuti B.

    2016-01-01

    Development of in-born porous nature of zirconium hydroxide nanopowders through a facile hydrogen (H2) gas-bubbles assisted borohydride synthesis route using sodium borohydride (NaBH4) and novel information on the temperature-mediated phase transformation, pore geometry as well as pore hysteresis transformation of in-born porous zirconium hydroxide nanopowders with the help of X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) isotherm and Transmission Electron Microscopy (TEM) images are the main theme of this research work. Without any surfactants or pore forming agents, the borohydride derived amorphous nature of porous powders was stable up to 500 °C and then the seed crystals start to develop within the loose amorphous matrix and trapping the inter-particulate voids, which led to develop the porous nature of tetragonal zirconium oxide at 600 °C and further sustain this porous nature as well as tetragonal phase of zirconium oxide up to 800 °C. The novel hydrogen (H2) gas-bubbles assisted borohydride synthesis route led to develop thermally stable porous zirconium hydroxide/oxide nanopowders with an adequate pore size, pore volume, and surface area and thus these porous materials are further suggested for promising use in different areas of applications. PMID:27198738

  14. Temperature-mediated phase transformation, pore geometry and pore hysteresis transformation of borohydride derived in-born porous zirconium hydroxide nanopowders

    NASA Astrophysics Data System (ADS)

    Nayak, Nadiya B.; Nayak, Bibhuti B.

    2016-05-01

    Development of in-born porous nature of zirconium hydroxide nanopowders through a facile hydrogen (H2) gas-bubbles assisted borohydride synthesis route using sodium borohydride (NaBH4) and novel information on the temperature-mediated phase transformation, pore geometry as well as pore hysteresis transformation of in-born porous zirconium hydroxide nanopowders with the help of X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) isotherm and Transmission Electron Microscopy (TEM) images are the main theme of this research work. Without any surfactants or pore forming agents, the borohydride derived amorphous nature of porous powders was stable up to 500 °C and then the seed crystals start to develop within the loose amorphous matrix and trapping the inter-particulate voids, which led to develop the porous nature of tetragonal zirconium oxide at 600 °C and further sustain this porous nature as well as tetragonal phase of zirconium oxide up to 800 °C. The novel hydrogen (H2) gas-bubbles assisted borohydride synthesis route led to develop thermally stable porous zirconium hydroxide/oxide nanopowders with an adequate pore size, pore volume, and surface area and thus these porous materials are further suggested for promising use in different areas of applications.

  15. Temperature-mediated phase transformation, pore geometry and pore hysteresis transformation of borohydride derived in-born porous zirconium hydroxide nanopowders.

    PubMed

    Nayak, Nadiya B; Nayak, Bibhuti B

    2016-01-01

    Development of in-born porous nature of zirconium hydroxide nanopowders through a facile hydrogen (H2) gas-bubbles assisted borohydride synthesis route using sodium borohydride (NaBH4) and novel information on the temperature-mediated phase transformation, pore geometry as well as pore hysteresis transformation of in-born porous zirconium hydroxide nanopowders with the help of X-ray diffraction (XRD), Brunauer-Emmett-Teller (BET) isotherm and Transmission Electron Microscopy (TEM) images are the main theme of this research work. Without any surfactants or pore forming agents, the borohydride derived amorphous nature of porous powders was stable up to 500 °C and then the seed crystals start to develop within the loose amorphous matrix and trapping the inter-particulate voids, which led to develop the porous nature of tetragonal zirconium oxide at 600 °C and further sustain this porous nature as well as tetragonal phase of zirconium oxide up to 800 °C. The novel hydrogen (H2) gas-bubbles assisted borohydride synthesis route led to develop thermally stable porous zirconium hydroxide/oxide nanopowders with an adequate pore size, pore volume, and surface area and thus these porous materials are further suggested for promising use in different areas of applications. PMID:27198738

  16. Lantibiotic Immunity: Inhibition of Nisin Mediated Pore Formation by NisI

    PubMed Central

    AlKhatib, Zainab; Lagedroste, Marcel; Fey, Iris; Kleinschrodt, Diana; Abts, André; Smits, Sander H. J.

    2014-01-01

    Nisin, a 3.4 kDa antimicrobial peptide produced by some Lactococcus lactis strains is the most prominent member of the lantibiotic family. Nisin can inhibit cell growth and penetrates the target Gram-positive bacterial membrane by binding to Lipid II, an essential cell wall synthesis precursor. The assembled nisin-Lipid II complex forms pores in the target membrane. To gain immunity against its own-produced nisin, Lactococcus lactis is expressing two immunity protein systems, NisI and NisFEG. Here, we show that the NisI expressing strain displays an IC50 of 73±10 nM, an 8–10-fold increase when compared to the non-expressing sensitive strain. When the nisin concentration is raised above 70 nM, the cells expressing full-length NisI stop growing rather than being killed. NisI is inhibiting nisin mediated pore formation, even at nisin concentrations up to 1 µM. This effect is induced by the C-terminus of NisI that protects Lipid II. Its deletion showed pore formation again. The expression of NisI in combination with externally added nisin mediates an elongation of the chain length of the Lactococcus lactis cocci. While the sensitive strain cell-chains consist mainly of two cells, the NisI expressing cells display a length of up to 20 cells. Both results shed light on the immunity of lantibiotic producer strains, and their survival in high levels of their own lantibiotic in the habitat. PMID:25014359

  17. Lantibiotic immunity: inhibition of nisin mediated pore formation by NisI.

    PubMed

    AlKhatib, Zainab; Lagedroste, Marcel; Fey, Iris; Kleinschrodt, Diana; Abts, André; Smits, Sander H J

    2014-01-01

    Nisin, a 3.4 kDa antimicrobial peptide produced by some Lactococcus lactis strains is the most prominent member of the lantibiotic family. Nisin can inhibit cell growth and penetrates the target Gram-positive bacterial membrane by binding to Lipid II, an essential cell wall synthesis precursor. The assembled nisin-Lipid II complex forms pores in the target membrane. To gain immunity against its own-produced nisin, Lactococcus lactis is expressing two immunity protein systems, NisI and NisFEG. Here, we show that the NisI expressing strain displays an IC50 of 73 ± 10 nM, an 8-10-fold increase when compared to the non-expressing sensitive strain. When the nisin concentration is raised above 70 nM, the cells expressing full-length NisI stop growing rather than being killed. NisI is inhibiting nisin mediated pore formation, even at nisin concentrations up to 1 µM. This effect is induced by the C-terminus of NisI that protects Lipid II. Its deletion showed pore formation again. The expression of NisI in combination with externally added nisin mediates an elongation of the chain length of the Lactococcus lactis cocci. While the sensitive strain cell-chains consist mainly of two cells, the NisI expressing cells display a length of up to 20 cells. Both results shed light on the immunity of lantibiotic producer strains, and their survival in high levels of their own lantibiotic in the habitat. PMID:25014359

  18. Caspase-2 is an initiator caspase responsible for pore-forming toxin-mediated apoptosis.

    PubMed

    Imre, Gergely; Heering, Jan; Takeda, Armelle-Natsuo; Husmann, Matthias; Thiede, Bernd; zu Heringdorf, Dagmar Meyer; Green, Douglas R; van der Goot, F Gisou; Sinha, Bhanu; Dötsch, Volker; Rajalingam, Krishnaraj

    2012-05-30

    Bacterial pathogens modulate host cell apoptosis to establish a successful infection. Pore-forming toxins (PFTs) secreted by pathogenic bacteria are major virulence factors and have been shown to induce various forms of cell death in infected cells. Here we demonstrate that the highly conserved caspase-2 is required for PFT-mediated apoptosis. Despite being the second mammalian caspase to be identified, the role of caspase-2 during apoptosis remains enigmatic. We show that caspase-2 functions as an initiator caspase during Staphylococcus aureus α-toxin- and Aeromonas aerolysin-mediated apoptosis in epithelial cells. Downregulation of caspase-2 leads to a strong inhibition of PFT-mediated apoptosis. Activation of caspase-2 is PIDDosome-independent, and endogenous caspase-2 is recruited to a high-molecular-weight complex in α-toxin-treated cells. Interestingly, prevention of PFT-induced potassium efflux inhibits the formation of caspase-2 complex, leading to its inactivation, thus resisting apoptosis. These results revealed a thus far unknown, obligatory role for caspase-2 as an initiator caspase during PFT-mediated apoptosis. PMID:22531785

  19. Mitochondrial Outer Membrane Proteins Assist Bid in Bax-mediated Lipidic Pore Formation

    PubMed Central

    Schafer, Blanca; Quispe, Joel; Choudhary, Vineet; Chipuk, Jerry E.; Ajero, Teddy G.; Du, Han; Schneiter, Roger

    2009-01-01

    Mitochondrial outer membrane permeabilization (MOMP) is a critical step in apoptosis and is regulated by Bcl-2 family proteins. In vitro systems using cardiolipin-containing liposomes have demonstrated the key features of MOMP induced by Bax and cleaved Bid; however, the nature of the “pores” and how they are formed remain obscure. We found that mitochondrial outer membranes contained very little cardiolipin, far less than that required for liposome permeabilization, despite their responsiveness to Bcl-2 family proteins. Strikingly, the incorporation of isolated mitochondrial outer membrane (MOM) proteins into liposomes lacking cardiolipin conferred responsiveness to cleaved Bid and Bax. Cardiolipin dependence was observed only when permeabilization was induced with cleaved Bid but not with Bid or Bim BH3 peptide or oligomerized Bax. Therefore, we conclude that MOM proteins specifically assist cleaved Bid in Bax-mediated permeabilization. Cryoelectron microscopy of cardiolipin-liposomes revealed that cleaved Bid and Bax produced large round holes with diameters of 25–100 nm, suggestive of lipidic pores. In sum, we propose that activated Bax induces lipidic pore formation and that MOM proteins assist cleaved Bid in this process in the absence of cardiolipin. PMID:19244344

  20. Permeability Transition Pore-Mediated Mitochondrial Superoxide Flashes Regulate Cortical Neural Progenitor Differentiation

    PubMed Central

    Hou, Yan; Mattson, Mark P.; Cheng, Aiwu

    2013-01-01

    In the process of neurogenesis, neural progenitor cells (NPCs) cease dividing and differentiate into postmitotic neurons that grow dendrites and an axon, become excitable, and establish synapses with other neurons. Mitochondrial biogenesis and aerobic metabolism provide energy substrates required to support the differentiation, growth and synaptic activity of neurons. Mitochondria may also serve signaling functions and, in this regard, it was recently reported that mitochondria can generate rapid bursts of superoxide (superoxide flashes), the frequency of which changes in response to environmental conditions and signals including oxygen levels and Ca2+ fluxes. Here we show that the frequency of mitochondrial superoxide flashes increases as embryonic cerebral cortical neurons differentiate from NPCs, and provide evidence that the superoxide flashes serve a signaling function that is critical for the differentiation process. The superoxide flashes are mediated by mitochondrial permeability transition pore (mPTP) opening, and pharmacological inhibition of the mPTP suppresses neuronal differentiation. Moreover, superoxide flashes and neuronal differentiation are inhibited by scavenging of mitochondrial superoxide. Conversely, manipulations that increase superoxide flash frequency accelerate neuronal differentiation. Our findings reveal a regulatory role for mitochondrial superoxide flashes, mediated by mPTP opening, in neuronal differentiation. PMID:24116142

  1. Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell

    PubMed Central

    Tattikota, Sudhir G.; Rathjen, Thomas; McAnulty, Sarah J.; Wessels, Hans-Hermann; Akerman, Ildem; van de Bunt, Martijn; Hausser, Jean; Esguerra, Jonathan L.S.; Musahl, Anne; Pandey, Amit K.; You, Xintian; Chen, Wei; Herrera, Pedro L.; Johnson, Paul R.; O’Carroll, Donal; Eliasson, Lena; Zavolan, Mihaela; Gloyn, Anna L.; Ferrer, Jorge; Shalom-Feuerstein, Ruby; Aberdam, Daniel; Poy, Matthew N.

    2014-01-01

    Summary Pancreatic β cells adapt to compensate for increased metabolic demand during insulin resistance. Although the microRNA pathway has an essential role in β cell proliferation, the extent of its contribution is unclear. Here, we report that miR-184 is silenced in the pancreatic islets of insulin-resistant mouse models and type 2 diabetic human subjects. Reduction of miR-184 promotes the expression of its target Argonaute2 (Ago2), a component of the microRNA-induced silencing complex. Moreover, restoration of miR-184 in leptin-deficient ob/ob mice decreased Ago2 and prevented compensatory β cell expansion. Loss of Ago2 during insulin resistance blocked β cell growth and relieved the regulation of miR-375-targeted genes, including the growth suppressor Cadm1. Lastly, administration of a ketogenic diet to ob/ob mice rescued insulin sensitivity and miR-184 expression and restored Ago2 and β cell mass. This study identifies the targeting of Ago2 by miR-184 as an essential component of the compensatory response to regulate proliferation according to insulin sensitivity. PMID:24361012

  2. Immune mediated Disorders in Women with a Fragile X Expansion and FXTAS

    PubMed Central

    Jalnapurkar, Isha; Rafika, Nuva; Tassone, Flora; Hagerman, Randi

    2014-01-01

    Premutation alleles in FMR1 can cause the late-onset neurodegenerative disorder, fragile X-associated tremor ataxia syndrome (FXTAS) and/or the fragile X-associated primary ovarian insufficiency in approximately 20% of heterozygotes. Heterozygotes of the FMR1 premutation have a higher incidence of immune mediated disorders such as autoimmune thyroid disorder, especially when accompanied by FXTAS motor signs. We describe the time course of symptoms of immune mediated disorders and the subsequent development of FXTAS in four women with an FMR1 CGG expansion, including three with the premutation and one with a gray zone expansion. These patients developed an immune mediated disorder followed by neurological symptoms that become consistent with FXTAS. In all patients we observed a pattern involving an initial appearance of disease symptoms – often after a period of heightened stress (depression, anxiety, divorce, general surgery) followed by the onset of tremor and/or ataxia. Immune mediated diseases are associated with the manifestations of FXTAS temporally, although further studies are needed to clarify this association. If a cause and effect relationship can be established, treatment of pre-existing immune mediated disorders may benefit patients with pathogenic FMR1 mutations. PMID:25399540

  3. Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion.

    PubMed

    Faber, Franziska; Tran, Lisa; Byndloss, Mariana X; Lopez, Christopher A; Velazquez, Eric M; Kerrinnes, Tobias; Nuccio, Sean-Paul; Wangdi, Tamding; Fiehn, Oliver; Tsolis, Renée M; Bäumler, Andreas J

    2016-06-30

    Changes in the gut microbiota may underpin many human diseases, but the mechanisms that are responsible for altering microbial communities remain poorly understood. Antibiotic usage elevates the risk of contracting gastroenteritis caused by Salmonella enterica serovars, increases the duration for which patients shed the pathogen in their faeces, and may on occasion produce a bacteriologic and symptomatic relapse. These antibiotic-induced changes in the gut microbiota can be studied in mice, in which the disruption of a balanced microbial community by treatment with the antibiotic streptomycin leads to an expansion of S. enterica serovars in the large bowel. However, the mechanisms by which streptomycin treatment drives an expansion of S. enterica serovars are not fully resolved. Here we show that host-mediated oxidation of galactose and glucose promotes post-antibiotic expansion of S. enterica serovar Typhimurium (S. Typhimurium). By elevating expression of the gene encoding inducible nitric oxide synthase (iNOS) in the caecal mucosa, streptomycin treatment increased post-antibiotic availability of the oxidation products galactarate and glucarate in the murine caecum. S. Typhimurium used galactarate and glucarate within the gut lumen of streptomycin pre-treated mice, and genetic ablation of the respective catabolic pathways reduced S. Typhimurium competitiveness. Our results identify host-mediated oxidation of carbohydrates in the gut as a mechanism for post-antibiotic pathogen expansion. PMID:27309805

  4. Pore Velocity Estimation Uncertainties

    NASA Astrophysics Data System (ADS)

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

    1982-08-01

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

  5. BIM-Mediated Membrane Insertion of the BAK Pore Domain Is an Essential Requirement for Apoptosis

    PubMed Central

    Weber, Kathrin; Harper, Nicholas; Schwabe, John; Cohen, Gerald M.

    2013-01-01

    Summary BAK activation represents a key step during apoptosis, but how it converts into a mitochondria-permeabilizing pore remains unclear. By further delineating the structural rearrangements involved, we reveal that BAK activation progresses through a series of independent steps: BH3-domain exposure, N-terminal change, oligomerization, and membrane insertion. Employing a “BCL-XL-addiction” model, we show that neutralization of BCL-XL by the BH3 mimetic ABT-737 resulted in death only when cells were reconstituted with BCL-XL:BAK, but not BCL-2/ BCL-XL:BIM complexes. Although this resembles the indirect model, release of BAK from BCL-XL did not result in spontaneous adoption of the pore conformation. Commitment to apoptosis required association of the direct activator BIM with oligomeric BAK promoting its conversion to a membrane-inserted pore. The sequential nature of this cascade provides multiple opportunities for other BCL-2 proteins to interfere with or promote BAK activation and unites aspects of the indirect and direct activation models. PMID:24120870

  6. Three-dimensional structure of Bax-mediated pores in membrane bilayers

    PubMed Central

    Xu, X-P; Zhai, D; Kim, E; Swift, M; Reed, J C; Volkmann, N; Hanein, D

    2013-01-01

    B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ∼3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery. PMID:23788040

  7. Three-dimensional structure of Bax-mediated pores in membrane bilayers.

    PubMed

    Xu, X-P; Zhai, D; Kim, E; Swift, M; Reed, J C; Volkmann, N; Hanein, D

    2013-01-01

    B-cell lymphoma 2 (Bcl-2)-associated X protein (Bax) is a member of the Bcl-2 protein family having a pivotal role in triggering cell commitment to apoptosis. Bax is latent and monomeric in the cytosol but transforms into its lethal, mitochondria-embedded oligomeric form in response to cell stress, leading to the release of apoptogenic factors such as cytochrome C. Here, we dissected the structural correlates of Bax membrane insertion while oligomerization is halted. This strategy was enabled through the use of nanometer-scale phospholipid bilayer islands (nanodiscs) the size of which restricts the reconstituted system to single Bax-molecule activity. Using this minimal reconstituted system, we captured structural correlates that precede Bax homo-oligomerization elucidating previously inaccessible steps of the core molecular mechanism by which Bcl-2 family proteins regulate membrane permeabilization. We observe that, in the presence of BH3 interacting domain death agonist (Bid) BH3 peptide, Bax monomers induce the formation of ~3.5-nm diameter pores and significantly distort the phospholipid bilayer. These pores are compatible with promoting release of ions as well as proteinaceous components, suggesting that membrane-integrated Bax monomers in the presence of Bid BH3 peptides are key functional units for the activation of the cell demolition machinery. PMID:23788040

  8. Oxytocin mediates atrial natriuretic peptide release and natriuresis after volume expansion in the rat.

    PubMed

    Haanwinckel, M A; Elias, L K; Favaretto, A L; Gutkowska, J; McCann, S M; Antunes-Rodrigues, J

    1995-08-15

    Our previous studies have shown that stimulation of the anterior ventral third ventricular region increases atrial natriuretic peptide (ANP) release, whereas lesions of this structure, the median eminence, or removal of the neural lobe of the pituitary block ANP release induced by blood volume expansion (BVE). These results indicate that participation of the central nervous system is crucial in these responses, possibly through mediation by neurohypophysial hormones. In the present research we investigated the possible role of oxytocin, one of the two principal neurohypophysial hormones, in the mediation of ANP release. Oxytocin (1-10 nmol) injected i.p. caused significant, dose-dependent increases in urinary osmolality, natriuresis, and kaliuresis. A delayed antidiuretic effect was also observed. Plasma ANP concentrations increased nearly 4-fold (P < 0.01) 20 min after i.p. oxytocin (10 nmol), but there was no change in plasma ANP values in control rats. When oxytocin (1 or 10 nmol) was injected i.v., it also induced a dose-related increase in plasma ANP at 5 min (P < 0.001). BVE by intra-atrial injection of isotonic saline induced a rapid (5 min postinjection) increase in plasma oxytocin and ANP concentrations and a concomitant decrease in plasma arginine vasopressin concentration. Results were similar with hypertonic volume expansion, except that this induced a transient (5 min) increase in plasma arginine vasopressin. The findings are consistent with the hypothesis that baroreceptor activation of the central nervous system by BVE stimulates the release of oxytocin from the neurohypophysis. This oxytocin then circulates to the right atrium to induce release of ANP, which circulates to the kidney and induces natriuresis and diuresis, which restore body fluid volume to normal levels. PMID:7644511

  9. Anion translocation through an Slc26 transporter mediates lumen expansion during tubulogenesis

    PubMed Central

    Deng, Wei; Nies, Florian; Feuer, Anja; Bočina, Ivana; Oliver, Dominik; Jiang, Di

    2013-01-01

    Lumen formation is a critical event in biological tube formation, yet its molecular mechanisms remain poorly understood. Specifically, how lumen expansion is coordinated with other processes of tubulogenesis is not well known, and the role of membrane transporters in tubulogenesis during development has not been adequately addressed. Here we identify a solute carrier 26 (Slc26) family protein as an essential regulator of tubulogenesis using the notochord of the invertebrate chordate Ciona intestinalis as a model. Ci-Slc26aα is indispensable for lumen formation and expansion, but not for apical/luminal membrane formation and lumen connection. Ci-Slc26aα acts as an anion transporter, mediating the electrogenic exchange of sulfate or oxalate for chloride or bicarbonate and electroneutral chloride:bicarbonate exchange. Mutant rescue assays show that this transport activity is essential for Ci-Slc26aα’s in vivo function. Our work reveals the consequences and relationships of several key processes in lumen formation, and establishes an in vivo assay for studying the molecular basis of the transport properties of SLC26 family transporters and their related diseases. PMID:23980138

  10. KCNK10, a Tandem Pore Domain Potassium Channel, Is a Regulator of Mitotic Clonal Expansion during the Early Stage of Adipocyte Differentiation

    PubMed Central

    Nishizuka, Makoto; Hayashi, Takahiro; Asano, Mami; Osada, Shigehiro; Imagawa, Masayoshi

    2014-01-01

    KCNK10, a member of tandem pore domain potassium channel family, gives rise to leak K+ currents. It plays important roles in stabilizing the negative resting membrane potential and in counterbalancing depolarization. We previously demonstrated that kcnk10 expression is quickly elevated during the early stage of adipogenesis of 3T3-L1 cells and that reduction of kcnk10 expression inhibits adipocyte differentiation. However, the molecular mechanism of KCNK10 in adipocyte differentiation remains unclear. Here we revealed that kcnk10 is induced by 3-isobutyl-1-methylxanthine, a cyclic nucleotide phosphodiesterase inhibitor and a potent inducer of adipogenesis, during the early stage of adipocyte differentiation. We also demonstrated that KCNK10 functions as a positive regulator of mitotic clonal expansion (MCE), a necessary process for terminal differentiation. The reduction of kcnk10 expression repressed the expression levels of CCAAT/enhancer-binding protein β (C/EBPβ) and C/EBPδ as well as the phosphorylation level of Akt during the early phase of adipogenesis. In addition, knockdown of kcnk10 expression suppressed insulin-induced Akt phosphorylation. These results indicate that KCNK10 contributes to the regulation of MCE through the control of C/EBPβ and C/EBPδ expression and insulin signaling. PMID:25501330

  11. C/EBPβ promotes BCR-ABL-mediated myeloid expansion and leukemic stem cell exhaustion.

    PubMed

    Hayashi, Y; Hirai, H; Kamio, N; Yao, H; Yoshioka, S; Miura, Y; Ashihara, E; Fujiyama, Y; Tenen, D G; Maekawa, T

    2013-03-01

    The BCR-ABL fusion oncoprotein accelerates differentiation and proliferation of myeloid cells during the chronic phase of chronic myeloid leukemia (CP-CML). Here, the role of CCAAT/enhancer binding protein β (C/EBPβ), a regulator for 'emergency granulopoiesis,' in the pathogenesis of CP-CML was examined. C/EBPβ expression was upregulated in Lineage(-) CD34(+) CD38(-) hematopoietic stem cells (HSCs) and myeloid progenitors isolated from bone marrow of patients with CP-CML. In EML cells, a mouse HSC line, BCR-ABL upregulated C/EBPβ, at least in part, through the activation of STAT5. Myeloid differentiation and proliferation induced by BCR-ABL was significantly impaired in C/EBPβ-deficient bone marrow cells in vitro. Mice that were transplanted with BCR-ABL-transduced C/EBPβ knockout bone marrow cells survived longer than mice that received BCR-ABL-transduced wild-type (WT) bone marrow cells. Significantly higher levels of leukemic stem cells were maintained in BCR-ABL-transduced C/EBPβ-deficient cells than in BCR-ABL-transduced WT cells. These results suggest that C/EBPβ is involved in BCR-ABL-mediated myeloid expansion. Further elucidation of the molecular mechanisms underlying the C/EBPβ-mediated stem cell loss might reveal a novel therapeutic strategy for eradication of CML stem cells. PMID:22948537

  12. Permeability Transition Pore-Mediated Mitochondrial Superoxide Flashes Mediate an Early Inhibitory Effect of Aβ1–42 on Neural Progenitor Cell Proliferation

    PubMed Central

    Hou, Yan; Ghosh, Paritosh; Wan, Ruiqian; Ouyang, Xin; Cheng, Heping; Mattson, Mark P.; Cheng, Aiwu

    2013-01-01

    Cellular damage by reactive oxygen species (ROS) and altered neurogenesis are implicated in the etiology of AD and the pathogenic actions of amyloid β-peptide (Aβ); the underlying mechanisms and the early oxidative intracellular events triggered by Aβ are not established. In the present study, we found that mouse embryonic cortical neural progenitor cells exhibit intermittent spontaneous mitochondrial superoxide (SO) flashes that require transient opening of mitochondrial permeability transition pores (mPTPs). The incidence of mitochondria SO flash activity in NPCs increased during the first 6 – 24 hours of exposure to aggregating amyloid β-peptide (Aβ1-42), indicating an increase in transient mPTP opening. Subsequently, the SO flash frequency progressively decreased and ceased between 48 and 72 hours of exposure to Aβ1-42, during which time global cellular ROS increased, mitochondrial membrane potential decreased, cytochrome C was released from mitochondria and the cells degenerated. Inhibition of mPTPs and selective reduction in mitochondrial SO flashes significantly ameliorated the negative effects of Aβ1-42 on NPC proliferation and survival. Our findings suggest that mPTP-mediated bursts of mitochondrial SO production is a relatively early and pivotal event in the adverse effects of Aβ1-42 on NPCs. If Aβ inhibits NPC proliferation in the brains of AD patients by a similar mechanism, then interventions that inhibit mPTP-mediated superoxide flashes would be expected to protect NPCs against the adverse effects of Aβ. PMID:24325797

  13. Biotic interactions mediate the expansion of black mangrove (Avicennia germinans) into salt marshes under climate change.

    PubMed

    Guo, Hongyu; Zhang, Yihui; Lan, Zhenjiang; Pennings, Steven C

    2013-09-01

    Many species are expanding their distributions to higher latitudes due to global warming. Understanding the mechanisms underlying these distribution shifts is critical for better understanding the impacts of climate changes. The climate envelope approach is widely used to model and predict species distribution shifts with changing climates. Biotic interactions between species, however, may also influence species distributions, and a better understanding of biotic interactions could improve predictions based solely on climate envelope models. Along the northern Gulf of Mexico coast, USA, subtropical black mangrove (Avicennia germinans) at the northern limit of its distribution grows sympatrically with temperate salt marsh plants in Florida, Louisiana, and Texas. In recent decades, freeze-free winters have led to an expansion of black mangrove into salt marshes. We examined how biotic interactions between black mangrove and salt marsh vegetation along the Texas coast varied across (i) a latitudinal gradient (associated with a winter-temperature gradient); (ii) the elevational gradient within each marsh (which creates different marsh habitats); and (iii) different life history stages of black mangroves (seedlings vs. juvenile trees). Each of these variables affected the strength or nature of biotic interactions between black mangrove and salt marsh vegetation: (i) Salt marsh vegetation facilitated black mangrove seedlings at their high-latitude distribution limit, but inhibited black mangrove seedlings at lower latitudes; (ii) mangroves performed well at intermediate elevations, but grew and survived poorly in high- and low-marsh habitats; and (iii) the effect of salt marsh vegetation on black mangroves switched from negative to neutral as black mangroves grew from seedlings into juvenile trees. These results indicate that the expansion of black mangroves is mediated by complex biotic interactions. A better understanding of the impacts of climate change on ecological

  14. Reversible control of pore size and surface chemistry of mesoporous silica through dynamic covalent chemistry: philicity mediated catalysis

    NASA Astrophysics Data System (ADS)

    Singh, Dheeraj Kumar; Pavan Kumar, B. V. V. S.; Eswaramoorthy, M.

    2015-08-01

    Here, we report the synthesis of adaptive hybrid mesoporous silica having the ability to reconfigure its pore properties such as pore size and philicity in response to the external environment. Decyl chains were reversibly appended to the pore walls of silica through imine motifs as dynamic covalent modules to switch the pore size and philicity in response to pH. This switching of pore properties was used to gate the access of reactants to the gold nanoparticles immobilized inside the nanopores, thus enabling us to turn-on/turn-off the catalytic reaction. The use of such dynamic covalent modules to govern pore properties would enable the realization of intelligent hybrids capable of controlling many such chemical processes in response to stimuli.Here, we report the synthesis of adaptive hybrid mesoporous silica having the ability to reconfigure its pore properties such as pore size and philicity in response to the external environment. Decyl chains were reversibly appended to the pore walls of silica through imine motifs as dynamic covalent modules to switch the pore size and philicity in response to pH. This switching of pore properties was used to gate the access of reactants to the gold nanoparticles immobilized inside the nanopores, thus enabling us to turn-on/turn-off the catalytic reaction. The use of such dynamic covalent modules to govern pore properties would enable the realization of intelligent hybrids capable of controlling many such chemical processes in response to stimuli. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr02959g

  15. The mitochondrial permeability transition pore regulates nitric oxide-mediated apoptosis of neurons induced by target deprivation.

    PubMed

    Martin, Lee J; Adams, Neal A; Pan, Yan; Price, Ann; Wong, Margaret

    2011-01-01

    Ablation of mouse occipital cortex induces precisely timed and uniform p53-modulated and Bax-dependent apoptosis of thalamocortical projection neurons in the dorsal lateral geniculate nucleus (LGN) by 7 d after lesion. We tested the hypothesis that this neuronal apoptosis is initiated by oxidative stress and the mitochondrial permeability transition pore (mPTP). Preapoptotic LGN neurons accumulate mitochondria, Zn(2+) and Ca(2+), and generate higher levels of reactive oxygen species (ROS), including superoxide, nitric oxide (NO), and peroxynitrite, than LGN neurons with an intact cortical target. Preapoptosis of LGN neurons is associated with increased formation of protein carbonyls, protein nitration, and protein S-nitrosylation. Genetic deletion of nitric oxide synthase 1 (nos1) and inhibition of NOS1 with nitroindazole protected LGN neurons from apoptosis, revealing NO as a mediator. Putative components of the mPTP are expressed in mouse LGN, including the voltage-dependent anion channel (VDAC), adenine nucleotide translocator (ANT), and cyclophilin D (CyPD). Nitration of CyPD and ANT in LGN mitochondria occurs by 2 d after cortical injury. Chemical cross-linking showed that LGN neuron preapoptosis is associated with formation of CyPD and VDAC oligomers, consistent with mPTP formation. Mice without CyPD are rescued from neuron apoptosis as are mice treated with the mPTP inhibitors TRO-19622 (cholest-4-en-3-one oxime) and TAT-Bcl-X(L)-BH4. Manipulation of the mPTP markedly attenuated the early preapoptotic production of reactive oxygen/nitrogen species in target-deprived neurons. Our results demonstrate in adult mouse brain neurons that the mPTP functions to enhance ROS production and the mPTP and NO trigger apoptosis; thus, the mPTP is a target for neuroprotection in vivo. PMID:21209222

  16. Permeability Transition Pore-dependent and PARP-mediated Depletion of Neuronal Pyridine Nucleotides During Anoxia and Glucose Deprivation

    PubMed Central

    Kahraman, Sibel; Siegel, Alex; Polster, Brian M.; Fiskum, Gary

    2015-01-01

    Exposure of rat cortical neurons to combined oxygen and glucose deprivation results in loss of NAD(P)H autofluorescence that is only partially reversible following restoration of oxygen and glucose, suggesting catabolism of pyridine nucleotides. This study tested the hypothesis that metabolic inhibition caused by cyanide-induced chemical anoxia plus glucose deprivation promotes both release of mitochondrial NAD(H) in response to opening of the permeability transition pore (PTP) and NAD(P)(H) degradation through activation of poly(ADP-ribose) polymerase (PARP). The NAD(P)H autofluorescence of rat neonatal cortical neurons was monitored during and following acute (10 – 30 min) exposure to the respiratory inhibitor, cyanide, in the absence and presence of glucose. Because nitric oxide-derived peroxynitrite is a known activator of PARP, we additionally assessed the effect of a nitric oxide generating agent on the NAD(P)H autofluorescence response to chemical anoxia plus glucose deprivation. Cyanide induced a rapid increase in autofluorescence, followed by a steady decline promoted by the presence of nitric oxide. This decline was primarily due to NAD(H) catabolism, as verified by measurements of total NAD(H) present in cellular extracts. Catabolism was partially blocked by an inhibitor of PARP, by a PTP inhibitor, and by either glucose or pyruvate as a source of reducing power. Overall, data suggest that metabolic, oxidative, and nitrosative stress during in vitro neuronal anoxia and glucose deprivation result in release of mitochondrial pyridine nucleotides in response to PTP opening and rapid, extensive NAD(H) degradation mediated by PARP activation. These events may contribute to the metabolic dysfunction that occurs in vivo during cerebral ischemia and reperfusion and therefore represent prime targets for neuroprotection. PMID:25341378

  17. Mediation of Clathrin-Dependent Trafficking during Cytokinesis and Cell Expansion by Arabidopsis STOMATAL CYTOKINESIS DEFECTIVE Proteins[W

    PubMed Central

    McMichael, Colleen M.; Reynolds, Gregory D.; Koch, Lisa M.; Wang, Chao; Jiang, Nan; Nadeau, Jeanette; Sack, Fred D.; Gelderman, Max B.; Pan, Jianwei; Bednarek, Sebastian Y.

    2013-01-01

    STOMATAL CYTOKINESIS DEFECTIVE1 (SCD1) encodes a putative Rab guanine nucleotide exchange factor that functions in membrane trafficking and is required for cytokinesis and cell expansion in Arabidopsis thaliana. Here, we show that the loss of SCD2 function disrupts cytokinesis and cell expansion and impairs fertility, phenotypes similar to those observed for scd1 mutants. Genetic and biochemical analyses showed that SCD1 function is dependent upon SCD2 and that together these proteins are required for plasma membrane internalization. Further specifying the role of these proteins in membrane trafficking, SCD1 and SCD2 proteins were found to be associated with isolated clathrin-coated vesicles and to colocalize with clathrin light chain at putative sites of endocytosis at the plasma membrane. Together, these data suggest that SCD1 and SCD2 function in clathrin-mediated membrane transport, including plasma membrane endocytosis, required for cytokinesis and cell expansion. PMID:24179130

  18. Origin and Expansion of the Yunnan Shoot Borer, Tomicus yunnanensis (Coleoptera: Scolytinae): A Mixture of Historical Natural Expansion and Contemporary Human-Mediated Relocation

    PubMed Central

    Ma, Xue-yu; Chen, Jin-min; Li, Qing-qing; Ye, Hui

    2014-01-01

    The Yunnan shoot borer, Tomicus yunnanensis, is a recently-discovered, aggressive pest of the Yunnan pine stands in southwestern China. Despite many bionomics studies and massive controlling efforts, research on its population genetics is extremely limited. The present study, aimed at investigating the origin and dispersal of this important forestry pest, analyzed the population genetic structure and demographic history using a mitochondrial cox1 gene fragment. Our results showed that T. yunnanensis most likely originated from the Central-Yunnan Altiplano, and the divergence time analysis placed the origin approximately 0.72 million-years ago. Host separation and specialization might have caused the speciation of T. yunnanensis. Genetic structure analyses identified two population groups, with six populations near the origin area forming one group and the remaining six populations from western and eastern Yunnan and southwestern Sichuan comprising the other. Divergence time analysis placed the split of the two groups at approximately 0.60 million-years ago, and haplotype phylogenetic tree, network, as well as migration rate suggested that populations of the latter group were established via a small number of individuals from the former one. Migration analysis also showed a certain degree of recent expansion from southwestern Sichuan to eastern Yunnan. Our findings implied that T. yunnanensis underwent both historical expansion and recent dispersal. The historical expansion may relate to the oscillation of regional climate due to glacial and interglacial periods in the Pleistocene, while human-mediated transportation of pine-wood material might have assisted the relocation and establishment of this pest in novel habitats. PMID:25372458

  19. Origin and expansion of the Yunnan Shoot Borer, Tomicus yunnanensis (coleoptera: scolytinae): a mixture of historical natural expansion and contemporary human-mediated relocation.

    PubMed

    Lü, Jun; Hu, Shao-ji; Ma, Xue-yu; Chen, Jin-min; Li, Qing-qing; Ye, Hui

    2014-01-01

    The Yunnan shoot borer, Tomicus yunnanensis, is a recently-discovered, aggressive pest of the Yunnan pine stands in southwestern China. Despite many bionomics studies and massive controlling efforts, research on its population genetics is extremely limited. The present study, aimed at investigating the origin and dispersal of this important forestry pest, analyzed the population genetic structure and demographic history using a mitochondrial cox1 gene fragment. Our results showed that T. yunnanensis most likely originated from the Central-Yunnan Altiplano, and the divergence time analysis placed the origin approximately 0.72 million-years ago. Host separation and specialization might have caused the speciation of T. yunnanensis. Genetic structure analyses identified two population groups, with six populations near the origin area forming one group and the remaining six populations from western and eastern Yunnan and southwestern Sichuan comprising the other. Divergence time analysis placed the split of the two groups at approximately 0.60 million-years ago, and haplotype phylogenetic tree, network, as well as migration rate suggested that populations of the latter group were established via a small number of individuals from the former one. Migration analysis also showed a certain degree of recent expansion from southwestern Sichuan to eastern Yunnan. Our findings implied that T. yunnanensis underwent both historical expansion and recent dispersal. The historical expansion may relate to the oscillation of regional climate due to glacial and interglacial periods in the Pleistocene, while human-mediated transportation of pine-wood material might have assisted the relocation and establishment of this pest in novel habitats. PMID:25372458

  20. The Interplay between Wnt Mediated Expansion and Negative Regulation of Growth Promotes Robust Intestinal Crypt Structure and Homeostasis

    PubMed Central

    Du, Huijing; Nie, Qing; Holmes, William R.

    2015-01-01

    The epithelium of the small intestinal crypt, which has a vital role in protecting the underlying tissue from the harsh intestinal environment, is completely renewed every 4–5 days by a small pool of stem cells at the base of each crypt. How is this renewal controlled and homeostasis maintained, particularly given the rapid nature of this process? Here, based on the recent observations from in vitro “mini gut” studies, we use a hybrid stochastic model of the crypt to investigate how exogenous niche signaling (from Wnt and BMP) combines with auto-regulation to promote homeostasis. This model builds on the sub-cellular element method to account for the three-dimensional structure of the crypt, external regulation by Wnt and BMP, internal regulation by Notch signaling, as well as regulation by internally generated diffusible signals. Results show that Paneth cell derived Wnt signals, which have been observed experimentally to sustain crypts in cultured organs, have a dramatically different influence on niche dynamics than does mesenchyme derived Wnt. While this signaling can indeed act as a redundant backup to the exogenous gradient, it introduces a positive feedback that destabilizes the niche and causes its uncontrolled expansion. We find that in this setting, BMP has a critical role in constraining this expansion, consistent with observations that its removal leads to crypt fission. Further results also point to a new hypothesis for the role of Ephrin mediated motility of Paneth cells, specifically that it is required to constrain niche expansion and maintain the crypt’s spatial structure. Combined, these provide an alternative view of crypt homeostasis where the niche is in a constant state of expansion and the spatial structure of the crypt arises as a balance between this expansion and the action of various sources of negative regulation that hold it in check. PMID:26288152

  1. Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction.

    PubMed

    Pelassa, Ilaria; Corà, Davide; Cesano, Federico; Monje, Francisco J; Montarolo, Pier Giorgio; Fiumara, Ferdinando

    2014-07-01

    The expansion of homopolymeric glutamine (polyQ) or alanine (polyA) repeats in certain proteins owing to genetic mutations induces protein aggregation and toxicity, causing at least 18 human diseases. PolyQ and polyA repeats can also associate in the same proteins, but the general extent of their association in proteomes is unknown. Furthermore, the structural mechanisms by which their expansion causes disease are not well understood, and these repeats are generally thought to misfold upon expansion into aggregation-prone β-sheet structures like amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) structures in triggering aggregation and toxicity of polyQ-expanded proteins, raising the possibility that polyA repeats may as well form these structures, by themselves or in association with polyQ. We found through bioinformatics screenings that polyA, polyQ and polyQA repeats have a phylogenetically graded association in human and non-human proteomes and associate/overlap with CC domains. Circular dichroism and cross-linking experiments revealed that polyA repeats can form--alone or with polyQ and polyQA--CC structures that increase in stability with polyA length, forming higher-order multimers and polymers in vitro. Using structure-guided mutagenesis, we studied the relevance of polyA CCs to the in vivo aggregation and toxicity of RUNX2--a polyQ/polyA protein associated with cleidocranial dysplasia upon polyA expansion--and found that the stability of its polyQ/polyA CC controls its aggregation, localization and toxicity. These findings indicate that, like polyQ, polyA repeats form CC structures that can trigger protein aggregation and toxicity upon expansion in human genetic diseases. PMID:24497578

  2. Carboxy terminus and pore-forming domain properties specific to Cx37 are necessary for Cx37-mediated suppression of insulinoma cell proliferation

    PubMed Central

    Nelson, Tasha K.; Sorgen, Paul L.

    2013-01-01

    Connexin 37 (Cx37) suppresses cell proliferation when expressed in rat insulinoma (Rin) cells, an effect also manifest in vivo during vascular development and in response to tissue injury. Mutant forms of Cx37 with nonfunctional channels but normally localized, wild-type carboxy termini are not growth suppressive. Here we determined whether the carboxy-terminal (CT) domain is required for Cx37-mediated growth suppression and whether the Cx37 pore-forming domain can be replaced with the Cx43 pore-forming domain and still retain growth-suppressive properties. We show that despite forming functional gap junction channels and hemichannels, Cx37 with residues subsequent to 273 replaced with a V5-epitope tag (Cx37–273tr*V5) had no effect on the proliferation of Rin cells, did not facilitate G1-cell cycle arrest with serum deprivation, and did not prolong cell cycle time comparably to the wild-type protein. The chimera Cx43*CT37, comprising the pore-forming domain of Cx43 and CT of Cx37, also did not suppress proliferation, despite forming functional gap junctions with a permselective profile similar to wild-type Cx37. Differences in channel behavior of both Cx37–273tr*V5 and Cx43*CT37 relative to their wild-type counterparts and failure of the Cx37-CT to interact as the Cx43-CT does with the Cx43 cytoplasmic loop suggest that the Cx37-CT and pore-forming domains are both essential to growth suppression by Cx37. PMID:24133065

  3. Pyroptosis is driven by non-selective gasdermin-D pore and its morphology is different from MLKL channel-mediated necroptosis.

    PubMed

    Chen, Xin; He, Wan-Ting; Hu, Lichen; Li, Jingxian; Fang, Yuan; Wang, Xin; Xu, Xiaozheng; Wang, Zhuo; Huang, Kai; Han, Jiahuai

    2016-09-01

    Necroptosis and pyroptosis are two forms of programmed cell death with a common feature of plasma membrane rupture. Here we studied the morphology and mechanism of pyroptosis in comparison with necroptosis. Different from necroptosis, pyroptosis undergoes membrane blebbing and produces apoptotic body-like cell protrusions (termed pyroptotic bodies) prior to plasma membrane rupture. The rupture in necroptosis is explosion-like, whereas in pyroptosis it leads to flattening of cells. It is known that the execution of necroptosis is mediated by mixed lineage kinase domain-like (MLKL) oligomers in the plasma membrane, whereas gasdermin-D (GSDMD) mediates pyroptosis after its cleavage by caspase-1 or caspase-11. We show that N-terminal fragment of GSDMD (GSDMD-N) generated by caspase cleavage also forms oligomer and migrates to the plasma membrane to kill cells. Both MLKL and GSDMD-N are lipophilic and the N-terminal sequences of both proteins are important for their oligomerization and plasma membrane translocation. Unlike MLKL which forms channels on the plasma membrane that induces influx of selected ions which osmotically swell the cells to burst, GSDMD-N forms non-selective pores and does not rely on increased osmolarity to disrupt cells. Our study reveals the pore-forming activity of GSDMD and channel-forming activity of MLKL determine different ways of plasma membrane rupture in pyroptosis and necroptosis. PMID:27573174

  4. The Serine Protease EspC from Enteropathogenic Escherichia coli Regulates Pore Formation and Cytotoxicity Mediated by the Type III Secretion System

    PubMed Central

    Guignot, Julie; Segura, Audrey; Tran Van Nhieu, Guy

    2015-01-01

    Type III secretion systems (T3SSs) are specialized macromolecular machines critical for bacterial virulence, and allowing the injection of bacterial effectors into host cells. The T3SS-dependent injection process requires the prior insertion of a protein complex, the translocon, into host cell membranes consisting of two-T3SS hydrophobic proteins, associated with pore-forming activity. In all described T3SS to date, a hydrophilic protein connects one hydrophobic component to the T3SS needle, presumably insuring the continuum between the hollow needle and the translocon. In the case of Enteropathogenic Escherichia coli (EPEC), the hydrophilic component EspA polymerizes into a filament connecting the T3SS needle to the translocon composed of the EspB and EspD hydrophobic proteins. Here, we identify EspA and EspD as targets of EspC, a serine protease autotransporter of Enterobacteriaceae (SPATE). We found that in vitro, EspC preferentially targets EspA associated with EspD, but was less efficient at proteolyzing EspA alone. Consistently, we found that EspC did not regulate EspA filaments at the surface of primed bacteria that was devoid of EspD, but controlled the levels of EspD and EspA secreted in vitro or upon cell contact. While still proficient for T3SS-mediated injection of bacterial effectors and cytoskeletal reorganization, an espC mutant showed increased levels of cell-associated EspA and EspD, as well as increased pore formation activity associated with cytotoxicity. EspP from enterohaemorrhagic E. coli (EHEC) also targeted translocator components and its activity was interchangeable with that of EspC, suggesting a common and important function of these SPATEs. These findings reveal a novel regulatory mechanism of T3SS-mediated pore formation and cytotoxicity control during EPEC/EHEC infection. PMID:26132339

  5. The Pore-Domain of TRPA1 Mediates the Inhibitory Effect of the Antagonist 6-Methyl-5-(2-(trifluoromethyl)phenyl)-1H-indazole

    PubMed Central

    Moldenhauer, Hans; Latorre, Ramon; Grandl, Jörg

    2014-01-01

    The transient receptor potential ion channel TRPA1 confers the ability to detect tissue damaging chemicals to sensory neurons and as a result mediates chemical nociception in vivo. Mouse TRPA1 is activated by electrophilic compounds such as mustard-oil and several physical stimuli such as cold temperature. Due to its sensory function inhibition of TRPA1 activity might provide an effective treatment against chronic and inflammatory pain. Therefore, TRPA1 has become a target for the development of analgesic drugs. 6-Methyl-5-(2-(trifluoromethyl)phenyl)-1H-indazole (Compound 31) has been identified by a chemical screen and lead optimization as an inhibitor of chemical activation of TRPA1. However, the structures or domains of TRPA1 that mediate the inhibitory effect of Compound 31 are unknown. Here, we screened 12,000 random mutant clones of mouse TRPA1 for their sensitivity to mustard-oil and the ability of Compound 31 to inhibit chemical activation by mustard-oil. In addition, we separately screened this mutant library while stimulating it with cold temperatures. We found that the single-point mutation I624N in the N-terminus of TRPA1 specifically affects the sensitivity to mustard-oil, but not to cold temperatures. This is evidence that sensitivity of TRPA1 to chemicals and cold temperatures is conveyed by separable mechanisms. We also identified five mutations located within the pore domain that cause loss of inhibition by Compound 31. This result demonstrates that the pore-domain is a regulator of chemical activation and suggests that Compound 31 might be acting directly on the pore-domain. PMID:25181545

  6. Increased tubuloglomerular feed-back mediated suppression of glomerular filtration during acute volume expansion in rats.

    PubMed Central

    Davis, J M; Häberle, D A; Kawata, T; Schmitt, E; Takabatake, T; Wohlfeil, S

    1988-01-01

    1. Volume expansion is currently believed to change the intrinsic properties of the juxtaglomerular apparatus such that the sensitivity of the tubuloglomerular feedback (TGF) mechanism is reduced, thus allowing glomerular filtration rate, and hence salt and water excretion, to rise. Recent studies conflict with this view and indeed the older literature reveals that the rise in glomerular filtration rate (GFR) under these conditions is far more modest than would be expected if TGF control were eliminated. 2. To investigate this problem, TGF control of filtration rate was examined by measuring single-nephron glomerular filtration rate (SNGFR) during loop of Henle perfusion at varying rates in rats under control conditions, after acute, moderate (4% of body weight), iso-oncotic volume expansion and in rats treated with antibodies to atrial natriuretic peptide (ANP) prior to the acute volume expansion. 3. With TGF control of filtration interrupted by filtrate collection from the proximal tubule, SNGFR in the expanded rats was massively increased compared with controls, although SNGFR measured in the distal tubule, and hence with TGF control intact, was only modestly increased, as was whole-kidney filtration rate. Loop perfusion at increasing rates up to 30 nl min-1 progressively decreased SNGFR in controls, and in the expanded rats the range over which control was exerted extended up to 60-80 nl min-1. For changes in loop flow around the spontaneous operating point, the sensitivity of the TGF mechanism, defined as delta SNGFR/delta loop flow, was similar in both groups. Treatment of rats with ANP antibodies prior to volume expansion substantially blunted the changes in renal salt and water excretion and the increase in SNGFR seen in the absence of loop perfusion. 4. These results are not consistent with a diminution of TGF function after volume expansion, rather with an enhancement. The latter is best accounted for by vasodilation of preglomerular resistance vessels on

  7. Association of polyalanine and polyglutamine coiled coils mediates expansion disease-related protein aggregation and dysfunction

    PubMed Central

    Pelassa, Ilaria; Corà, Davide; Cesano, Federico; Monje, Francisco J.; Montarolo, Pier Giorgio; Fiumara, Ferdinando

    2014-01-01

    The expansion of homopolymeric glutamine (polyQ) or alanine (polyA) repeats in certain proteins owing to genetic mutations induces protein aggregation and toxicity, causing at least 18 human diseases. PolyQ and polyA repeats can also associate in the same proteins, but the general extent of their association in proteomes is unknown. Furthermore, the structural mechanisms by which their expansion causes disease are not well understood, and these repeats are generally thought to misfold upon expansion into aggregation-prone β-sheet structures like amyloids. However, recent evidence indicates a critical role for coiled-coil (CC) structures in triggering aggregation and toxicity of polyQ-expanded proteins, raising the possibility that polyA repeats may as well form these structures, by themselves or in association with polyQ. We found through bioinformatics screenings that polyA, polyQ and polyQA repeats have a phylogenetically graded association in human and non-human proteomes and associate/overlap with CC domains. Circular dichroism and cross-linking experiments revealed that polyA repeats can form—alone or with polyQ and polyQA—CC structures that increase in stability with polyA length, forming higher-order multimers and polymers in vitro. Using structure-guided mutagenesis, we studied the relevance of polyA CCs to the in vivo aggregation and toxicity of RUNX2—a polyQ/polyA protein associated with cleidocranial dysplasia upon polyA expansion—and found that the stability of its polyQ/polyA CC controls its aggregation, localization and toxicity. These findings indicate that, like polyQ, polyA repeats form CC structures that can trigger protein aggregation and toxicity upon expansion in human genetic diseases. PMID:24497578

  8. Instrumental Genesis in Technology-Mediated Learning: From Double Stimulation to Expansive Knowledge Practices

    ERIC Educational Resources Information Center

    Ritella, Giuseppe; Hakkarainen, Kai

    2012-01-01

    The purpose of the present paper is to examine the socio-cultural foundations of technology-mediated collaborative learning. Toward that end, we discuss the role of artifacts in knowledge-creating inquiry, relying on the theoretical ideas of Carl Bereiter, Merlin Donald, Pierre Rabardel, Keith Sawyer and L. S. Vygotsky. We argue that epistemic…

  9. Self-expansion as a mediator of relationship improvements in a mindfulness intervention.

    PubMed

    Carson, James W; Carson, Kimberly M; Gil, Karen M; Baucom, Donald H

    2007-10-01

    In a recent randomized controlled trial, couples participating in a mindfulness-based relationship enhancement program demonstrated significant improvements in relationship satisfaction and relationship distress (Carson, Carson, Gil, & Baucom, 2004). Here we report on a multiple mediation analysis of these couples' improvements. Potential mediators included measures of couples' engagement in exciting self-expanding activities, couples' ability to accept one another's difficult characteristics, and individual partners' ability to relax. Results indicate that to a large extent, the mindfulness-related relationship improvements can be attributed to partners' sense that they were participating in exciting self-expanding activities together during the course of the intervention. The implications of these findings for future mindfulness research are discussed. PMID:17935533

  10. Alanine Expansions Associated with Congenital Central Hypoventilation Syndrome Impair PHOX2B Homeodomain-mediated Dimerization and Nuclear Import*

    PubMed Central

    Di Lascio, Simona; Belperio, Debora

    2016-01-01

    Heterozygous mutations of the human PHOX2B gene, a key regulator of autonomic nervous system development, lead to congenital central hypoventilation syndrome (CCHS), a neurodevelopmental disorder characterized by a failure in the autonomic control of breathing. Polyalanine expansions in the 20-residues region of the C terminus of PHOX2B are the major mutations responsible for CCHS. Elongation of the alanine stretch in PHOX2B leads to a protein with altered DNA binding, transcriptional activity, and nuclear localization and the possible formation of cytoplasmic aggregates; furthermore, the findings of various studies support the idea that CCHS is not due to a pure loss of function mechanism but also involves a dominant negative effect and/or toxic gain of function for PHOX2B mutations. Because PHOX2B forms homodimers and heterodimers with its paralogue PHOX2A in vitro, we tested the hypothesis that the dominant negative effects of the mutated proteins are due to non-functional interactions with the wild-type protein or PHOX2A using a co-immunoprecipitation assay and the mammalian two-hybrid system. Our findings show that PHOX2B forms homodimers and heterodimerizes weakly with mutated proteins, exclude the direct involvement of the polyalanine tract in dimer formation, and indicate that mutated proteins retain partial ability to form heterodimers with PHOX2A. Moreover, in this study, we investigated the effects of the longest polyalanine expansions on the homeodomain-mediated nuclear import, and our data clearly show that the expanded C terminus interferes with this process. These results provide novel insights into the effects of the alanine tract expansion on PHOX2B folding and activity. PMID:27129232

  11. Alanine Expansions Associated with Congenital Central Hypoventilation Syndrome Impair PHOX2B Homeodomain-mediated Dimerization and Nuclear Import.

    PubMed

    Di Lascio, Simona; Belperio, Debora; Benfante, Roberta; Fornasari, Diego

    2016-06-17

    Heterozygous mutations of the human PHOX2B gene, a key regulator of autonomic nervous system development, lead to congenital central hypoventilation syndrome (CCHS), a neurodevelopmental disorder characterized by a failure in the autonomic control of breathing. Polyalanine expansions in the 20-residues region of the C terminus of PHOX2B are the major mutations responsible for CCHS. Elongation of the alanine stretch in PHOX2B leads to a protein with altered DNA binding, transcriptional activity, and nuclear localization and the possible formation of cytoplasmic aggregates; furthermore, the findings of various studies support the idea that CCHS is not due to a pure loss of function mechanism but also involves a dominant negative effect and/or toxic gain of function for PHOX2B mutations. Because PHOX2B forms homodimers and heterodimers with its paralogue PHOX2A in vitro, we tested the hypothesis that the dominant negative effects of the mutated proteins are due to non-functional interactions with the wild-type protein or PHOX2A using a co-immunoprecipitation assay and the mammalian two-hybrid system. Our findings show that PHOX2B forms homodimers and heterodimerizes weakly with mutated proteins, exclude the direct involvement of the polyalanine tract in dimer formation, and indicate that mutated proteins retain partial ability to form heterodimers with PHOX2A. Moreover, in this study, we investigated the effects of the longest polyalanine expansions on the homeodomain-mediated nuclear import, and our data clearly show that the expanded C terminus interferes with this process. These results provide novel insights into the effects of the alanine tract expansion on PHOX2B folding and activity. PMID:27129232

  12. BMP4 mediates the interplay between adipogenesis and angiogenesis during expansion of subcutaneous white adipose tissue.

    PubMed

    Tang, Yan; Qian, Shu-Wen; Wu, Meng-Yuan; Wang, Jue; Lu, Ping; Li, Xi; Huang, Hai-Yan; Guo, Liang; Sun, Xia; Xu, Cong-Jian; Tang, Qi-Qun

    2016-08-01

    The expansion of subcutaneous (SC) white adipose tissue (WAT) has beneficial effects on metabolic health. Our previous work showed an increased number of bone morphogenetic protein 4 (BMP4)-activated beige adipocytes in SC WAT, indicating a potential role of BMP4 in adipocyte recruitment. It was also demonstrated that BMP4 committed multipotent mesodermal C3H10T1/2 stem cells to the adipocyte lineage ex vivo However, the mechanism by which BMP4 regulates adipogenesis in vivo has not been clarified. In this study, we found that BMP4 stimulated de novo adipogenesis in SC WAT concomitant with enhanced blood vessel formation, thus promoting adipose tissue angiogenesis. Platelet-derived growth factor receptor-β-positive (PDGFRβ(+)) multipotent stem cells within the neoangiogenic vessels were found to be adipocyte progenitors. Moreover, BMP4 downregulated PDGFRβ by stimulating the lysosome-dependent degradation, which efficiently initiated adipogenic differentiation. These results suggest how BMP4 regulates adipocyte recruitment in SC WAT, and thus promote its beneficial metabolic effects. PMID:27030507

  13. VEGF-induced neoangiogenesis is mediated by NAADP and two-pore channel-2–dependent Ca2+ signaling

    PubMed Central

    Favia, Annarita; Desideri, Marianna; Gambara, Guido; D’Alessio, Alessio; Ruas, Margarida; Esposito, Bianca; Del Bufalo, Donatella; Parrington, John; Ziparo, Elio; Palombi, Fioretta; Galione, Antony; Filippini, Antonio

    2014-01-01

    Vascular endothelial growth factor (VEGF) and its receptors VEGFR1/VEGFR2 play major roles in controlling angiogenesis, including vascularization of solid tumors. Here we describe a specific Ca2+ signaling pathway linked to the VEGFR2 receptor subtype, controlling the critical angiogenic responses of endothelial cells (ECs) to VEGF. Key steps of this pathway are the involvement of the potent Ca2+ mobilizing messenger, nicotinic acid adenine-dinucleotide phosphate (NAADP), and the specific engagement of the two-pore channel TPC2 subtype on acidic intracellular Ca2+ stores, resulting in Ca2+ release and angiogenic responses. Targeting this intracellular pathway pharmacologically using the NAADP antagonist Ned-19 or genetically using Tpcn2−/− mice was found to inhibit angiogenic responses to VEGF in vitro and in vivo. In human umbilical vein endothelial cells (HUVECs) Ned-19 abolished VEGF-induced Ca2+ release, impairing phosphorylation of ERK1/2, Akt, eNOS, JNK, cell proliferation, cell migration, and capillary-like tube formation. Interestingly, Tpcn2 shRNA treatment abolished VEGF-induced Ca2+ release and capillary-like tube formation. Importantly, in vivo VEGF-induced vessel formation in matrigel plugs in mice was abolished by Ned-19 and, most notably, failed to occur in Tpcn2−/− mice, but was unaffected in Tpcn1−/− animals. These results demonstrate that a VEGFR2/NAADP/TPC2/Ca2+ signaling pathway is critical for VEGF-induced angiogenesis in vitro and in vivo. Given that VEGF can elicit both pro- and antiangiogenic responses depending upon the balance of signal transduction pathways activated, targeting specific VEGFR2 downstream signaling pathways could modify this balance, potentially leading to more finely tailored therapeutic strategies. PMID:25331892

  14. VEGF-induced neoangiogenesis is mediated by NAADP and two-pore channel-2-dependent Ca2+ signaling.

    PubMed

    Favia, Annarita; Desideri, Marianna; Gambara, Guido; D'Alessio, Alessio; Ruas, Margarida; Esposito, Bianca; Del Bufalo, Donatella; Parrington, John; Ziparo, Elio; Palombi, Fioretta; Galione, Antony; Filippini, Antonio

    2014-11-01

    Vascular endothelial growth factor (VEGF) and its receptors VEGFR1/VEGFR2 play major roles in controlling angiogenesis, including vascularization of solid tumors. Here we describe a specific Ca(2+) signaling pathway linked to the VEGFR2 receptor subtype, controlling the critical angiogenic responses of endothelial cells (ECs) to VEGF. Key steps of this pathway are the involvement of the potent Ca(2+) mobilizing messenger, nicotinic acid adenine-dinucleotide phosphate (NAADP), and the specific engagement of the two-pore channel TPC2 subtype on acidic intracellular Ca(2+) stores, resulting in Ca(2+) release and angiogenic responses. Targeting this intracellular pathway pharmacologically using the NAADP antagonist Ned-19 or genetically using Tpcn2(-/-) mice was found to inhibit angiogenic responses to VEGF in vitro and in vivo. In human umbilical vein endothelial cells (HUVECs) Ned-19 abolished VEGF-induced Ca(2+) release, impairing phosphorylation of ERK1/2, Akt, eNOS, JNK, cell proliferation, cell migration, and capillary-like tube formation. Interestingly, Tpcn2 shRNA treatment abolished VEGF-induced Ca(2+) release and capillary-like tube formation. Importantly, in vivo VEGF-induced vessel formation in matrigel plugs in mice was abolished by Ned-19 and, most notably, failed to occur in Tpcn2(-/-) mice, but was unaffected in Tpcn1(-/-) animals. These results demonstrate that a VEGFR2/NAADP/TPC2/Ca(2+) signaling pathway is critical for VEGF-induced angiogenesis in vitro and in vivo. Given that VEGF can elicit both pro- and antiangiogenic responses depending upon the balance of signal transduction pathways activated, targeting specific VEGFR2 downstream signaling pathways could modify this balance, potentially leading to more finely tailored therapeutic strategies. PMID:25331892

  15. Glucocorticoid receptor mediates the expansion of splenic late erythroid progenitors during chronic psychological stress.

    PubMed

    Vignjevic, S; Budec, M; Markovic, D; Dikic, D; Mitrovic, O; Diklic, M; Suboticki, T; Cokic, V; Jovcic, G

    2015-02-01

    Stress evokes an integrated neuroendocrine response perturbing the homeostasis of different physiological systems. In contrast to well established physiologica linteractions between neuroendocrine and immune systems during chronic stress, there has been relatively little information on the effects of psychological stress on erythroid cells. Since stress-induced erythropoiesis occurs predominantly in the spleen, in the current study, we investigated the influence of chronic psychological stress on splenic erythroid progenitors and examined a role of glucocorticoid receptor (GR) in observed effect using a mouse model of restraint. The adult male mice were subjected to 2 hours daily restraint stress for 7 or 14 consecutive days and the role of GR in erythropoietic response to stress was assessed by pretreatment of mice with GR antagonist mifepristone 60 min prior to restraint. The results showed that chronic restraint stress induced an increase in spleen weight as well as in the cellularity of red pulp, as compared to controls. Furthermore, 7 and 14 days of restraint stress resulted in markedly increased number of both splenic early (BFU-E) and late (CFU-E) erythroid progenitors. Blockade of GR with mifepristone did not affect the number of BFU-E in stressed mice, but it completely abolished the effect of repeated psychological stress on CFU-E cells. Additionally, plasma corticosterone concentration was enhanced whereas the GR expression was significantly decreased within splenic red pulp after one and two weeks of stress exposure. Obtained findings suggest for the first time an indispensable role for GR in the expansion of CFU-E progenitors in the spleen under conditions of chronic psychological stress. PMID:25716969

  16. Immune-mediated pore-forming pathways induce cellular hypercitrullination and generate citrullinated autoantigens in rheumatoid arthritis*

    PubMed Central

    Romero, Violeta; Fert-Bober, Justyna; Nigrovic, Peter A.; Darrah, Erika; Haque, Uzma J.; Lee, David M.; van Eyk, Jennifer; Rosen, Antony; Andrade, Felipe

    2014-01-01

    Autoantibodies to citrullinated protein antigens are specific markers of rheumatoid arthritis (RA). Although protein citrullination can be activated by numerous stimuli in cells, it remains unclear which of these produce the prominent citrullinated autoantigens targeted in RA. In these studies, we show that RA synovial fluid cells have an unusual pattern of citrullination with marked citrullination of proteins across the broad range of molecular weights, which we term cellular hypercitrullination. Although histone citrullination is a common event during neutrophil activation and death induced by different pathways including apoptosis, NETosis, and necroptosis/autophagy, hypercitrullination is not induced by these stimuli. However, marked hypercitrullination is induced by two immune-mediated membranolytic pathways, mediated by perforin and the membrane attack complex (MAC), which are active in the RA joint and of importance in RA pathogenesis. We further demonstrate that perforin and MAC activity on neutrophils generate the profile of citrullinated autoantigens characteristic of RA. These data suggest that activation of peptidylarginine deiminases during complement and perforin activity may be at the core of citrullinated autoantigen production in RA. These pathways may be amenable to monitoring and therapeutic modulation. PMID:24174326

  17. Syndecan 4 Mediates Nrf2-dependent Expansion of Bronchiolar Progenitors That Protect Against Lung Inflammation

    PubMed Central

    Santoso, Arif; Kikuchi, Toshiaki; Tode, Naoki; Hirano, Taizou; Komatsu, Riyo; Damayanti, Triya; Motohashi, Hozumi; Yamamoto, Masayuki; Kojima, Tetsuhito; Uede, Toshimitsu; Nukiwa, Toshihiro; Ichinose, Masakazu

    2016-01-01

    The use of lung progenitors for regenerative medicine appears promising, but their biology is not fully understood. Here, we found anti-inflammatory attributes in bronchiolar progenitors that were sorted as a multipotent subset of mouse club cells and found to express secretory leukocyte protease inhibitor (SLPI). Notably, the impaired expression of SLPI in mice increased the number of bronchiolar progenitors and decreased the lung inflammation. We determined a transcriptional profile for the bronchiolar progenitors of Slpi-deficient mice and identified syndecan 4, whose expression was markedly elevated as compared to that of wild-type mice. Systemic administration of recombinant syndecan 4 protein caused a substantial increase in the number of bronchiolar progenitors with concomitant attenuation of both airway and alveolar inflammation. The syndecan 4 administration also resulted in activation of the Keap1-Nrf2 antioxidant pathway in lung cells, which is critically involved in the therapeutic responses to the syndecan 4 treatment. Moreover, in 3D culture, the presence of syndecan 4 induced differentiated club cells to undergo Nrf2-dependent transition into bronchiolar progenitors. Our observations reveal that differentiative switches between bronchiolar progenitors and club cells are under the Nrf2-mediated control of SLPI and syndecan 4, suggesting the possibility of new therapeutic approaches in inflammatory lung diseases. PMID:26307669

  18. Astroglial β-Arrestin1-mediated Nuclear Signaling Regulates the Expansion of Neural Precursor Cells in Adult Hippocampus

    PubMed Central

    Tao, Yezheng; Ma, Li; Liao, Zhaohui; Le, Qiumin; Yu, Jialing; Liu, Xing; Li, Haohong; Chen, Yuejun; Zheng, Ping; Yang, Zhengang; Ma, Lan

    2015-01-01

    Adult hippocampal neurogenesis is crucial for preserving normal brain function, but how it is regulated by niche cells is uncertain. Here we show that β-arrestin 1 (β-arr1) in dentate gyrus (DG) regulates neural precursor proliferation. β-arr1 knockout (KO) mice show reduced neural precursor proliferation in subgranular zone (SGZ) which could be rescued by selective viral expression of β-arr1 but not its nuclear-function-deficient mutants under control of hGFAP promotor in DG. Compared with wild type astrocytes, β-arr1 KO astrocytes nurture less neurospheres, and this may be attributed to changed activity of soluble, heat-sensitive excretive factors, such as BMP2. RNA-sequencing reveals that β-arr1 KO DG astrocytes exhibit an aberrant gene expression profile of niche factors, including elevated transcription of Bmp2. Taken together, our data suggest that β-arr1 mediated nuclear signaling regulates the production of excretive factors derived from niche astrocytes and expansion of neural precursors in DG, thus maintaining homeostasis of adult hippocampal neurogenesis. PMID:26500013

  19. Nanoparticle-Mediated Targeting of Cyclosporine A Enhances Cardioprotection Against Ischemia-Reperfusion Injury Through Inhibition of Mitochondrial Permeability Transition Pore Opening

    PubMed Central

    Ikeda, Gentaro; Matoba, Tetsuya; Nakano, Yasuhiro; Nagaoka, Kazuhiro; Ishikita, Ayako; Nakano, Kaku; Funamoto, Daiki; Sunagawa, Kenji; Egashira, Kensuke

    2016-01-01

    Myocardial ischemia-reperfusion (IR) injury limits the therapeutic effects of early reperfusion therapy for acute myocardial infarction (MI), in which mitochondrial permeability transition pore (mPTP) opening plays a critical role. Our aim was to determine whether poly-lactic/glycolic acid (PLGA) nanoparticle-mediated mitochondrial targeting of a molecule that inhibits mPTP opening, cyclosporine A (CsA), enhances CsA-induced cardioprotection. In an in vivo murine IR model, intravenously injected PLGA nanoparticles were located at the IR myocardium mitochondria. Treatment with nanoparticles incorporated with CsA (CsA-NP) at the onset of reperfusion enhanced cardioprotection against IR injury by CsA alone (as indicated by the reduced MI size at a lower CsA concentration) through the inhibition of mPTP opening. Left ventricular remodeling was ameliorated 28 days after IR, but the treatment did not affect inflammatory monocyte recruitment to the IR heart. In cultured rat cardiomyocytes in vitro, mitochondrial PLGA nanoparticle-targeting was observed after the addition of hydrogen peroxide, which represents oxidative stress during IR, and was prevented by CsA. CsA-NP can be developed as an effective mPTP opening inhibitor and may protect organs from IR injury. PMID:26861678

  20. Pore-forming epsilon toxin causes membrane permeabilization and rapid ATP depletion-mediated cell death in renal collecting duct cells.

    PubMed

    Chassin, C; Bens, M; de Barry, J; Courjaret, R; Bossu, J L; Cluzeaud, F; Ben Mkaddem, S; Gibert, M; Poulain, B; Popoff, M R; Vandewalle, A

    2007-09-01

    Clostridium perfringens epsilon toxin (ET) is a potent pore-forming cytotoxin causing fatal enterotoxemia in livestock. ET accumulates in brain and kidney, particularly in the renal distal-collecting ducts. ET binds and oligomerizes in detergent-resistant membranes (DRMs) microdomains and causes cell death. However, the causal linkage between membrane permeabilization and cell death is not clear. Here, we show that ET binds and forms 220-kDa insoluble complexes in plasma membrane DRMs of renal mpkCCD(cl4) collecting duct cells. Phosphatidylinositol-specific phospholipase C did not impair binding or the formation of ET complexes, suggesting that the receptor for ET is not GPI anchored. ET induced a dose-dependent fall in the transepithelial resistance and potential in confluent cells grown on filters, transiently stimulated Na+ absorption, and induced an inward ionic current and a sustained rise in [Ca2+]i. ET also induced rapid depletion of cellular ATP, and stimulated the AMP-activated protein kinase, a metabolic-sensing Ser/Thr kinase. ET also induced mitochondrial membrane permeabilization and mitochondrial-nuclear translocation of apoptosis-inducing factor, a potent caspase-independent cell death effector. Finally, ET induced cell necrosis characterized by a marked reduction in nucleus size without DNA fragmentation. DRM disruption by methyl-beta-cyclodextrin impaired ET oligomerization, and significantly reduced the influx of Na+ and [Ca2+]i, but did not impair ATP depletion and cell death caused by the toxin. These findings indicate that ET causes rapid necrosis of renal collecting duct cells and establish that ATP depletion-mediated cell death is not strictly correlated with the plasma membrane permeabilization and ion diffusion caused by the toxin. PMID:17567938

  1. A BTLA-mediated bait and switch strategy permits Listeria expansion in CD8α(+) DCs to promote long-term T cell responses.

    PubMed

    Yang, Xuanming; Zhang, Xunmin; Sun, Yonglian; Tu, Tony; Fu, May Lynne; Miller, Mendy; Fu, Yang-Xin

    2014-07-01

    Listeria monocytogenes infected CD8α(+) DCs in the spleen are essential for CD8(+) T cell generation. CD8α(+) DCs are also necessary for Listeria expansion and dissemination within the host. The mechanisms that regulate CD8α(+) DCs to allow Listeria expansion are unclear. We find that activating the B and T lymphocyte attenuator (BTLA), a coinhibitory receptor for T cells, suppresses, while blocking BTLA enhances, both the primary and memory CD8 T cell responses against Listeria. Btla(-/-) mice have lower effector and memory CD8(+) T cells while paradoxically also being more resistant to Listeria. Although bacterial entry into Btla(-/-) CD8α(+) DCs is unaffected, Listeria fails to expand within these cells. BTLA signaling limits Fas/FasL-mediated suppression of Listeria expansion within CD8α(+) DCs to more effectively alert adaptive immune cells. This study uncovers a BTLA-mediated strategy used by the host that permits Listeria proliferation to enable increasing T cell responses for long-term protection. PMID:25011109

  2. NOTCH-Mediated Maintenance and Expansion of Human Bone Marrow Stromal/Stem Cells: A Technology Designed for Orthopedic Regenerative Medicine

    PubMed Central

    Dong, Yufeng; Long, Teng; Wang, Cuicui; Mirando, Anthony J.; Chen, Jianquan; O’Keefe, Regis J.

    2014-01-01

    Human bone marrow-derived stromal/stem cells (BMSCs) have great therapeutic potential for treating skeletal disease and facilitating skeletal repair, although maintaining their multipotency and expanding these cells ex vivo have proven difficult. Because most stem cell-based applications to skeletal regeneration and repair in the clinic would require large numbers of functional BMSCs, recent research has focused on methods for the appropriate selection, expansion, and maintenance of BMSC populations during long-term culture. We describe here a novel biological method that entails selection of human BMSCs based on NOTCH2 expression and activation of the NOTCH signaling pathway in cultured BMSCs via a tissue culture plate coated with recombinant human JAGGED1 (JAG1) ligand. We demonstrate that transient JAG1-mediated NOTCH signaling promotes human BMSC maintenance and expansion while increasing their skeletogenic differentiation capacity, both ex vivo and in vivo. This study is the first of its kind to describe a NOTCH-mediated methodology for the maintenance and expansion of human BMSCs and will serve as a platform for future clinical or translational studies aimed at skeletal regeneration and repair. PMID:25368376

  3. Epithelial cell-specific Act1 adaptor mediates interleukin-25-dependent helminth expulsion through expansion of Lin−c-Kit+ innate cell population

    PubMed Central

    Kang, Zizhen; Swaidani, Shadi; Yin, Weiguo; Wang, Chenhui; Barlow, Jillian L.; Gulen, Muhammet Fatih; Bulek, Katarzyna; Do, Jeong-su; Aronica, Mark; McKenzie, Andrew N. J.; Min, Booki; Li, Xiaoxia

    2012-01-01

    SUMMARY Interleukin-25 (IL-25 or IL-17E), a member of the structurally related IL-17 family, functions as an important mediator of T helper 2 cell-type (type 2) responses. We examined the cell-type specific role of IL-25-induced Act1-mediated signaling in protective immunity against helminth infection. Targeted Act1 deficiency in epithelial cells resulted in a marked delay in worm expulsion and abolished the expansion of the Lin−c-kit+ innate cell population in the mesenteric lymph node, lung and liver. Th2 cell-inducing cytokines (IL-25 and IL-33) expression were reduced in the intestinal epithelial cells from the infected and IL-25-injected epithelial-specific Act1-deficient mice. Adoptive transfer of Lin−c-kit+ cells or combined injection of IL-25 and IL-33 restored the type 2 responses in these mice. Taken together, these results suggest that epithelial-specific Act1 mediates the expansion of the Lin−c-kit+ innate cell population through the positive feedback loop of IL-25, initiating the type 2 immunity against helminth infection. PMID:22608496

  4. Epithelial cell-specific Act1 adaptor mediates interleukin-25-dependent helminth expulsion through expansion of Lin(-)c-Kit(+) innate cell population.

    PubMed

    Kang, Zizhen; Swaidani, Shadi; Yin, Weiguo; Wang, Chenhui; Barlow, Jillian L; Gulen, Muhammet Fatih; Bulek, Katarzyna; Do, Jeong-su; Aronica, Mark; McKenzie, Andrew N J; Min, Booki; Li, Xiaoxia

    2012-05-25

    Interleukin-25 (IL-25 or IL-17E), a member of the structurally related IL-17 family, functions as an important mediator of T helper 2 cell-type (type 2) responses. We examined the cell type-specific role of IL-25-induced Act1-mediated signaling in protective immunity against helminth infection. Targeted Act1 deficiency in epithelial cells resulted in a marked delay in worm expulsion and abolished the expansion of the Lin(-)c-Kit(+) innate cell population in the mesenteric lymph node, lung, and liver. Th2 cell-inducing cytokine (IL-25 and IL-33) expression were reduced in the intestinal epithelial cells from the infected and IL-25-injected epithelial-specific Act1-deficient mice. Adoptive transfer of Lin(-)c-Kit(+) cells or combined injection of IL-25 and IL-33 restored the type 2 responses in these mice. Taken together, these results suggest that epithelial-specific Act1 mediates the expansion of the Lin(-)c-Kit(+) innate cell population through the positive-feedback loop of IL-25, initiating the type 2 immunity against helminth infection. PMID:22608496

  5. Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development.

    PubMed

    Hampoelz, Bernhard; Mackmull, Marie-Therese; Machado, Pedro; Ronchi, Paolo; Bui, Khanh Huy; Schieber, Nicole; Santarella-Mellwig, Rachel; Necakov, Aleksandar; Andrés-Pons, Amparo; Philippe, Jean Marc; Lecuit, Thomas; Schwab, Yannick; Beck, Martin

    2016-07-28

    Nuclear pore complexes (NPCs) span the nuclear envelope (NE) and mediate nucleocytoplasmic transport. In metazoan oocytes and early embryos, NPCs reside not only within the NE, but also at some endoplasmic reticulum (ER) membrane sheets, termed annulate lamellae (AL). Although a role for AL as NPC storage pools has been discussed, it remains controversial whether and how they contribute to the NPC density at the NE. Here, we show that AL insert into the NE as the ER feeds rapid nuclear expansion in Drosophila blastoderm embryos. We demonstrate that NPCs within AL resemble pore scaffolds that mature only upon insertion into the NE. We delineate a topological model in which NE openings are critical for AL uptake that nevertheless occurs without compromising the permeability barrier of the NE. We finally show that this unanticipated mode of pore insertion is developmentally regulated and operates prior to gastrulation. PMID:27397507

  6. Membrane pores induced by magainin.

    PubMed

    Ludtke, S J; He, K; Heller, W T; Harroun, T A; Yang, L; Huang, H W

    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. PMID:8901513

  7. Poring over two-pore channel pore mutants

    PubMed Central

    Penny, Christopher J.; Patel, Sandip

    2016-01-01

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

  8. Genistein-mediated inhibition of mammary stromal adipocyte differentiation limits expansion of mammary stem/progenitor cells by paracrine signaling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mammary adiposity may contribute to breast cancer development and progression by releasing cytokines and other inflammatory mediators that promote mammary epithelial proliferation. We evaluated the effects of soy isoflavone genistein (GEN) on the adipogenic differentiation of a SV40-immortalized mou...

  9. Ndfip-mediated degradation of Jak1 tunes cytokine signalling to limit expansion of CD4+ effector T cells

    PubMed Central

    O'Leary, Claire E.; Riling, Christopher R.; Spruce, Lynn A.; Ding, Hua; Kumar, Suresh; Deng, Guoping; Liu, Yuhong; Seeholzer, Steven H.; Oliver, Paula M.

    2016-01-01

    Nedd4 family E3 ubiquitin ligases have been shown to restrict T-cell function and impact T-cell differentiation. We show here that Ndfip1 and Ndfip2, activators of Nedd4 family ligases, together limit accumulation and function of effector CD4+ T cells. Using a three-part proteomics approach in primary T cells, we identify stabilization of Jak1 in Ndfip1/2-deficient T cells stimulated through the TCR. Jak1 degradation is aborted in activated T cells that lack Ndfips. In wild-type cells, Jak1 degradation lessens CD4+ cell sensitivity to cytokines during TCR stimulation, while in Ndfip-deficient cells cytokine responsiveness persists, promoting increased expansion and survival of pathogenic effector T cells. Thus, Ndfip1/Ndfip2 regulate the cross talk between the T-cell receptor and cytokine signalling pathways to limit inappropriate T-cell responses. PMID:27088444

  10. IL-27 and TGFβ mediated expansion of Th1 and adaptive regulatory T cells expressing IL-10 correlates with bacterial burden and disease severity in pulmonary tuberculosis

    PubMed Central

    Kumar, Nathella P; Moideen, Kadar; Banurekha, Vaithilingam V; Nair, Dina; Sridhar, Rathinam; Nutman, Thomas B; Babu, Subash

    2015-01-01

    CD4+ T cell expression of IL-10 is an important mechanism controlling immunity to tuberculosis (TB). To identify the CD4+ T cell subsets producing IL-10 in human TB, we enumerated the frequencies of IL-10 expressing CD4+ T cell subsets following TB—antigen stimulation of cells from individuals with pulmonary (PTB) and latent TB (LTB). We first demonstrate that TB antigens induce an expansion of IL-10 expressing Th1 (IL-10+, IFNγ+, T-bet+), Th2 (IL-10+, IL-4+, GATA-3+), Th9 (IL-10+, IL-9+, IL-4−), Th17 (IL-10+, IL-17+, IFNγ−), and natural and adaptive regulatory T cells [nTregs; IL-10+, CD4+, CD25+, Foxp3+ and aTregs; IL-10 single+, CD4+, CD25−, Foxp3−] in PTB and LTB individuals, with frequencies being significantly higher in the former. However, only Th1 cells and adaptive Tregs expressing IL-10 exhibit a positive relationship with bacterial burdens and extent of disease in PTB. Finally, we show that IL-27 and TGFβ play an important role in the regulation of IL-10+ Th cell subsets. Thus, active PTB is characterized by an IL-27 and TGFβ mediated expansion of IL-10 expressing CD4+ T cell subsets, with IL-10+ Th1 and IL-10+ aTreg cells playing a potentially pivotal role in the pathogenesis of active disease. PMID:26417443

  11. IRF-5-Mediated Inflammation Limits CD8+ T Cell Expansion by Inducing HIF-1α and Impairing Dendritic Cell Functions during Leishmania Infection

    PubMed Central

    Hammami, Akil; Charpentier, Tania; Smans, Mélina; Stäger, Simona

    2015-01-01

    Inflammation is known to be necessary for promoting, sustaining, and tuning CD8+ T cell responses. Following experimental Leishmania donovani infection, the inflammatory response is mainly induced by the transcription factor IRF-5. IRF-5 is responsible for the activation of several genes encoding key pro-inflammatory cytokines, such as IL-6 and TNF. Here, we investigate the role of IRF-5-mediated inflammation in regulating antigen-specific CD8+ T cell responses during L. donovani infection. Our data demonstrate that the inflammatory response induced by IRF-5 limits CD8+ T cell expansion and induces HIF-1α in dendritic cells. Ablation of HIF-1α in CD11c+ cells resulted into a higher frequency of short-lived effector cells (SLEC), enhanced CD8+ T cell expansion, and increased IL-12 expression by splenic DCs. Moreover, mice with a targeted depletion of HIF-1α in CD11c+ cells had a significantly lower splenic parasite burden, suggesting that induction of HIF-1α may represent an immune evasive mechanism adopted by Leishmania parasites to establish persistent infections. PMID:26046638

  12. IL-27 and TGFβ mediated expansion of Th1 and adaptive regulatory T cells expressing IL-10 correlates with bacterial burden and disease severity in pulmonary tuberculosis.

    PubMed

    Kumar, Nathella P; Moideen, Kadar; Banurekha, Vaithilingam V; Nair, Dina; Sridhar, Rathinam; Nutman, Thomas B; Babu, Subash

    2015-09-01

    CD4(+) T cell expression of IL-10 is an important mechanism controlling immunity to tuberculosis (TB). To identify the CD4(+) T cell subsets producing IL-10 in human TB, we enumerated the frequencies of IL-10 expressing CD4(+) T cell subsets following TB-antigen stimulation of cells from individuals with pulmonary (PTB) and latent TB (LTB). We first demonstrate that TB antigens induce an expansion of IL-10 expressing Th1 (IL-10(+), IFNγ(+), T-bet(+)), Th2 (IL-10(+), IL-4(+), GATA-3(+)), Th9 (IL-10(+), IL-9(+), IL-4(-)), Th17 (IL-10(+), IL-17(+), IFNγ(-)), and natural and adaptive regulatory T cells [nTregs; IL-10(+), CD4(+), CD25(+), Foxp3(+) and aTregs; IL-10 single(+), CD4(+), CD25(-), Foxp3(-)] in PTB and LTB individuals, with frequencies being significantly higher in the former. However, only Th1 cells and adaptive Tregs expressing IL-10 exhibit a positive relationship with bacterial burdens and extent of disease in PTB. Finally, we show that IL-27 and TGFβ play an important role in the regulation of IL-10(+) Th cell subsets. Thus, active PTB is characterized by an IL-27 and TGFβ mediated expansion of IL-10 expressing CD4(+) T cell subsets, with IL-10(+) Th1 and IL-10(+) aTreg cells playing a potentially pivotal role in the pathogenesis of active disease. PMID:26417443

  13. Mitochondrial Dysfunction Induced by Different Organochalchogens Is Mediated by Thiol Oxidation and Is Not Dependent of the Classical Mitochondrial Permeability Transition Pore Opening

    PubMed Central

    Puntel, Robson L.; Roos, Daniel H.; Folmer, Vanderlei; Nogueira, Cristina W.; Galina, Antonio; Aschner, Michael; Rocha, João B. T.

    2010-01-01

    Ebselen (Ebs) and diphenyl diselenide [(PhSe)2] readily oxidize thiol groups. Here we studied mitochondrial swelling changes in mitochondrial potential (Δψm), NAD(P)H oxidation, reactive oxygen species production, protein aggregate formation, and oxygen consumption as ending points of their in vitro toxicity. Specifically, we tested the hypothesis that organochalchogens toxicity could be associated with mitochondrial dysfunction via oxidation of vicinal thiol groups that are known to be involved in the regulation of mitochondrial permeability (Petronilli et al. J. Biol. Chem., 269; 16638; 1994). Furthermore, we investigated the possible mechanism(s) by which these organochalchogens could disrupt liver mitochondrial function. Ebs and (PhSe)2 caused mitochondrial depolarization and swelling in a concentration-dependent manner. Furthermore, both organochalchogens caused rapid oxidation of the mitochondrial pyridine nucleotides (NAD(P)H) pool, likely reflecting the consequence and not the cause of increased mitochondrial permeability (Costantini, P., Chernyak, B. V., Petronilli, V., and Bernardi, P. (1996). Modulation of the mitochondrial permeability transition pore (PTP) by pyridine nucleotides and dithiol oxidation at two separate sites. J. Biol. Chem. 271, 6746–6751). The organochalchogens-induced mitochondrial dysfunction was prevented by the reducing agent dithiothreitol (DTT). Ebs- and (PhSe)2-induced mitochondrial depolarization and swelling were unchanged by ruthenium red (4μM), butylated hydroxytoluene (2.5μM), or cyclosporine A (1μM). N-ethylmaleimide enhanced the organochalchogens-induced mitochondrial depolarization, without affecting the magnitude of the swelling response. In contrast, iodoacetic acid did not modify the effects of Ebs or (PhSe)2 on the mitochondria. Additionally, Ebs and (PhSe)2 decreased the basal 2' 7' dichlorofluorescin diacetate (H2-DCFDA) oxidation and oxygen consumption rate in state 3 and increased it during the state 4 of

  14. GPER mediates the inhibitory actions of estrogen on adipogenesis in 3T3-L1 cells through perturbation of mitotic clonal expansion.

    PubMed

    Zhu, Pei; Yuen, Jacky M L; Sham, Kathy W Y; Cheng, Christopher H K

    2013-11-01

    G-protein-coupled estrogen receptor 1 (GPER) mediates non-genomic signaling of estrogenic events. Here we showed for the first time that Gper/GPER is expressed in Swiss 3T3 mouse embryo preadipocytes 3T3-L1, and that Gper/GPER is up-regulated during differentiation of the cells induced by monocyte differentiation-inducing (MDI) cocktail. Activation of GPER by the natural ligand 17β-estradiol (E2), and the specific agonist G1, was shown to inhibit lipid accumulation in 3T3-L1 cells, while such inhibition was reversed upon knockdown of GPER using specific siRNA. GPER was also found to mediate perturbation of mitotic clonal expansion (MCE) in these cells by inhibiting cell cycle arrest during MDI cocktail-induced differentiation. Persistent activation of cell cycle regulating factors cyclin-dependant kinase (CDK) 4, CDK6 and cyclin D1, and phosphorylation of retinoblastoma (Rb) protein at serine 795 was observed in the G1-treated cells. Taken together, our results indicate that E2-GPER signaling leads to an inhibition of adipogenesis in 3T3-L1 cells via perturbation of MCE. PMID:23871778

  15. Precise Modulation of the Breathing Behavior and Pore Surface in Zr-MOFs by Reversible Post-Synthetic Variable-Spacer Installation to Fine-Tune the Expansion Magnitude and Sorption Properties.

    PubMed

    Chen, Cheng-Xia; Wei, Zhangwen; Jiang, Ji-Jun; Fan, Yan-Zhong; Zheng, Shao-Ping; Cao, Chen-Chen; Li, Yu-Hao; Fenske, Dieter; Su, Cheng-Yong

    2016-08-16

    To combine flexibility and modifiability towards a more controllable complexity of MOFs, a post-synthetic variable-spacer installation (PVSI) strategy is used to implement kinetic installation/ uninstallation of secondary ligands into/from a robust yet flexible proto-Zr-MOF. This PVSI process features precise positioning of spacers with different length, size, number, and functionality, enabling accurate fixation of successive breathing stages and fine-tuning of pore surface. It shows unprecedented synthetic tailorability to create complicated MOFs in a predictable way for property modification, for example, CO2 and R22 adsorption/separation, thermal/chemical stability, and extended breathing behavior. PMID:27405047

  16. Cysteine protease antigens cleave CD123, the α subunit of murine IL-3 receptor, on basophils and suppress IL-3-mediated basophil expansion

    SciTech Connect

    Nishikado, Hideto; Fujimura, Tsutomu; Taka, Hikari; Mineki, Reiko; Ogawa, Hideoki; Okumura, Ko; Takai, Toshiro

    2015-05-01

    Th2 type immune responses are essential for protective immunity against parasites and play crucial roles in allergic disorders. Helminth parasites secrete a variety of proteases for their infectious cycles including for host entry, tissue migration, and suppression of host immune effector cell function. Furthermore, a number of pathogen-derived antigens, as well as allergens such as papain, belong to the family of cysteine proteases. Although the link between protease activity and Th2 type immunity is well documented, the mechanisms by which proteases regulate host immune responses are largely unknown. Here, we demonstrate that the cysteine proteases papain and bromelain selectively cleave the α subunit of the IL-3 receptor (IL-3Rα/CD123) on the surface of murine basophils. The decrease in CD123 expression on the cell surface, and the degradation of the extracellular domain of recombinant CD123 were dependent on the protease activity of papain and bromelain. Pre-treatment of murine basophils with papain resulted in inhibition of IL-3-IL-3R signaling and suppressed IL-3- but not thymic stromal lymphopoietin-induced expansion of basophils in vitro. Our unexpected findings illuminate a novel mechanism for the regulation of basophil functions by protease antigens. Because IL-3 plays pivotal roles in the activation and proliferation of basophils and in protective immunity against helminth parasites, pathogen-derived proteases might contribute to the pathogenesis of infections by regulating IL-3-mediated functions in basophils. - Highlights: • We identified the murine IL3R as a novel target of papain-family cysteine proteases. • Papain-family cysteine proteases cleaved IL3Rα/CD123 on murine basophils. • Papain suppressed IL3- but not TSLP-induced expansion of murine basophils. • The inactivation of IL3R might be a strategy for pathogens to suppress host immunity.

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

    SciTech Connect

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

    2006-04-15

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

  18. PEDF-Deficient Mice Exhibit an Enhanced Rate of Retinal Vascular Expansion and are More Sensitive to Hyperoxia-Mediated Vessel Obliteration

    PubMed Central

    Huang, Qiong; Wang, Shoujian; Sorenson, Christine M.; Sheibani, Nader

    2008-01-01

    Pigment epithelium derived factor (PEDF) is an endogenous inhibitor of angiogenesis. However, its physiological role during vascular development and neovascularization remains elusive. Here we investigated the role of PEDF in normal postnatal vascularization of retina and retinal neovascularization during oxygen-induced ischemic retinopathy (OIR) using PEDF-deficient (PEDFminus;/minus;) mice. The β-galactosidase staining of eye sections from PEDFminus;/minus; mice confirmed the expression pattern of endogenous PEDF previously reported in mouse retina. However, strongest staining was observed in the retinal outer plexiform layer. Retinal trypsin digests indicated that the ratio of endothelial cells (EC) to pericytes (PC) was significantly higher in PEDFminus;/minus; mice compared to wild type (PEDF+/+) mice at postnatal day 21 (P21). This was mainly attributed to increased number of EC in the absence of PEDF. There was no significant difference in the number of PC. We observed increased rate of proliferation in retinal vasculature of PEDFminus;/minus; mice, which was somewhat compensated for by an increase in the rate of apoptosis. Staining of the retinal wholemounts and eye frozen sections indicated postnatal retinal vascularization expansion occurred at a faster rate in the absence of PEDF, and was more prominent at early time points (prior to P21). The retinal vascularization in PEDF+/+ mice reaches that of PEDFminus;/minus; mice such that no significant difference in vascular densities was observed by P42. Lack of PEDF had minimal effect on the regression of hyaloid vasculature and VEGF levels. PEDFminus;/minus; mice also exhibited enhanced sensitivity to hyperoxia-mediated vessel obliteration during OIR compared to PEDF+/+ mice despite higher levels of VEGF. However, there was no significant difference in the degree of retinal neovascularization. Our studies indicate that PEDF is an important modulator of early postnatal retinal vascularization and in its

  19. Caspase-11 requires the pannexin-1 channel and the purinergic P2X7 pore to mediate pyroptosis and endotoxic shock

    PubMed Central

    Yang, Dahai; He, Yuan; Muñoz-Planillo, Raul; Liu, Qin; Núñez, Gabriel

    2016-01-01

    SUMMARY The noncanonical inflammasome induced by intracellular lipopolysaccharide (LPS) leads to caspase-11-dependent pyroptosis which is critical for induction of endotoxic shock in mice. However, the signaling pathway downstream of caspase-11 is unknown. We found that cytosolic LPS stimulation induced caspase-11-dependent cleavage of the pannexin-1 channel and ATP release, which in turn activated the purinergic P2X7 receptor to mediate cytotoxicity. In the absence of P2X7 or pannexin-1, pyroptosis induced by LPS transfection or treatment with cholera toxin B and LPS was abrogated. Cleavage of pannexin-1 required the catalytic activity of caspase-11 and was essential for ATP release and P2X7-mediated pyroptosis. Priming the caspase-11 pathway in vivo with LPS or toll-like receptor-3 (TLR3) agonist resulted in high mortality in wild-type mice after secondary LPS challenge, but not in Casp11−/−, Panx1−/− or P2x7−/− mice. These results reveal a critical role for pannexin-1 and P2X7 downstream of caspase-11 for pyroptosis and susceptibility to sepsis induced by the noncanonical inflammasome. PMID:26572062

  20. Caspase-11 Requires the Pannexin-1 Channel and the Purinergic P2X7 Pore to Mediate Pyroptosis and Endotoxic Shock.

    PubMed

    Yang, Dahai; He, Yuan; Muñoz-Planillo, Raul; Liu, Qin; Núñez, Gabriel

    2015-11-17

    The noncanonical inflammasome induced by intracellular lipopolysaccharide (LPS) leads to caspase-11-dependent pyroptosis, which is critical for induction of endotoxic shock in mice. However, the signaling pathway downstream of caspase-11 is unknown. We found that cytosolic LPS stimulation induced caspase-11-dependent cleavage of the pannexin-1 channel followed up by ATP release, which in turn activated the purinergic P2X7 receptor to mediate cytotoxicity. In the absence of P2X7 or pannexin-1, pyroptosis induced by cytosolic LPS was abrogated. Cleavage of pannexin-1 required the catalytic activity of caspase-11 and was essential for ATP release and P2X7-mediated pyroptosis. Priming the caspase-11 pathway in vivo with LPS or Toll-like receptor-3 (TLR3) agonist resulted in high mortality in wild-type mice after secondary LPS challenge, but not in Casp11(-/-), Panx1(-/-), or P2x7(-/-) mice. These results reveal a critical role for pannexin-1 and P2X7 downstream of caspase-11 for pyroptosis and susceptibility to sepsis induced by the noncanonical inflammasome. PMID:26572062

  1. Cysteine protease antigens cleave CD123, the α subunit of murine IL-3 receptor, on basophils and suppress IL-3-mediated basophil expansion.

    PubMed

    Nishikado, Hideto; Fujimura, Tsutomu; Taka, Hikari; Mineki, Reiko; Ogawa, Hideoki; Okumura, Ko; Takai, Toshiro

    2015-05-01

    Th2 type immune responses are essential for protective immunity against parasites and play crucial roles in allergic disorders. Helminth parasites secrete a variety of proteases for their infectious cycles including for host entry, tissue migration, and suppression of host immune effector cell function. Furthermore, a number of pathogen-derived antigens, as well as allergens such as papain, belong to the family of cysteine proteases. Although the link between protease activity and Th2 type immunity is well documented, the mechanisms by which proteases regulate host immune responses are largely unknown. Here, we demonstrate that the cysteine proteases papain and bromelain selectively cleave the α subunit of the IL-3 receptor (IL-3Rα/CD123) on the surface of murine basophils. The decrease in CD123 expression on the cell surface, and the degradation of the extracellular domain of recombinant CD123 were dependent on the protease activity of papain and bromelain. Pre-treatment of murine basophils with papain resulted in inhibition of IL-3-IL-3R signaling and suppressed IL-3- but not thymic stromal lymphopoietin-induced expansion of basophils in vitro. Our unexpected findings illuminate a novel mechanism for the regulation of basophil functions by protease antigens. Because IL-3 plays pivotal roles in the activation and proliferation of basophils and in protective immunity against helminth parasites, pathogen-derived proteases might contribute to the pathogenesis of infections by regulating IL-3-mediated functions in basophils. PMID:25778870

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

    PubMed Central

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

    2004-01-01

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

  3. Universal Expansion.

    ERIC Educational Resources Information Center

    McArdle, Heather K.

    1997-01-01

    Describes a week-long activity for general to honors-level students that addresses Hubble's law and the universal expansion theory. Uses a discrepant event-type activity to lead up to the abstract principles of the universal expansion theory. (JRH)

  4. Membrane mechanics can account for fusion pore dilation in stages.

    PubMed Central

    Chizmadzhev, Y A; Cohen, F S; Shcherbakov, A; Zimmerberg, J

    1995-01-01

    Once formed, fusion pores rapidly enlarge to semi-stable conductance values. The membranes lining the fusion pore are continuous bilayer structures, so variations of conductance in time reflect bending and stretching of membranes. We therefore modeled the evolution of fusion pores using the theory of the mechanics of deforming homogeneous membranes. We calculated the changes in length and width of theoretical fusion pores according to standard dynamical equations of motion. Theoretical fusion pores quickly achieve semi-stable dimensions, which correspond to energy minima located in a canyon between energy barriers. The height of the barrier preventing pore expansion diminishes along the dimensions of length and width. The bottom of the canyon slopes gently downward along increasing length. As a consequence, theoretical fusion pores slowly lengthen and widen as the dimensions migrate along the bottom of the canyon, until the barrier vanishes and the pore rapidly enlarges. The dynamics of growth is sensitive to tension, spontaneous curvature, bending elasticity, and mobilities. This sensitivity can account for the quantitative differences in pore evolution observed in two experimental systems: HA-expressing cells fusing to planar bilayer membranes and beige mouse mast cell degranulation. We conclude that the mechanics of membranes could cause the phenomenon of stagewise growth of fusion pores. Images FIGURE 9 PMID:8599655

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

    PubMed Central

    Miller, Brian R.; Forbes, Douglass J.

    2015-01-01

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

  6. Enhanced membrane pore formation by multimeric/oligomeric antimicrobial peptides.

    PubMed

    Arnusch, Christopher J; Branderhorst, Hilbert; de Kruijff, Ben; Liskamp, Rob M J; Breukink, Eefjan; Pieters, Roland J

    2007-11-20

    The pore-forming antibacterial peptide magainin 2 was made divalent, tetravalent, and octavalent via a copper(I)-mediated 1-3 dipolar cycloaddition reaction ("click" chemistry). This series of pore-forming compounds was tested in vitro for their ability to form pores in large unilamillar vesicles (LUVs). A large increase in the pore-forming capability was especially observed with the tetravalent and octavalent magainin compounds in the LUVs consisting of DOPC, and the octavalent magainin compound showed a marked increase with the DOPC/DOPG LUVs. Activity was observed in the low nanomolar range for these compounds. PMID:17944489

  7. A new view of the lethal apoptotic pore.

    PubMed

    Basañez, Gorka; Soane, Lucian; Hardwick, J Marie

    2012-01-01

    Cell death by apoptosis is indispensable for proper development and tissue homeostasis in all multicellular organisms, and its deregulation plays a key role in cancer and many other diseases. A crucial event in apoptosis is the formation of protein-permeable pores in the outer mitochondrial membrane that release cytochrome c and other apoptosis-promoting factors into the cytosol. Research efforts over the past two decades have established that apoptotic pores require BCL-2 family proteins, with the proapoptotic BAX-type proteins being direct effectors of pore formation. Accumulating evidence indicates that other cellular components also cooperate with BCL-2 family members to regulate the apoptotic pore. Despite this knowledge, the molecular pathway leading to apoptotic pore formation at the outer mitochondrial membrane and the precise nature of this outer membrane pore remain enigmatic. In this issue of PLOS Biology, Kushnareva and colleagues describe a novel kinetic analysis of the dynamics of BAX-dependent apoptotic pore formation recapitulated in native mitochondrial outer membranes. Their study reveals the existence of a hitherto unknown outer mitochondrial membrane factor that is critical for BAX-mediated apoptotic pore formation, and challenges the currently popular view that the apoptotic pore is a purely proteinaceous multimeric assembly of BAX proteins. It also supports the notion that membrane remodeling events are implicated in the formation of a lipid-containing apoptotic pore. PMID:23049484

  8. Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers

    PubMed Central

    Leontiadou, Hari; Mark, Alan E.; Marrink, Siewert J.

    2004-01-01

    Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer have been conducted. The system was simulated in two different states; first, as a bilayer containing a meta-stable pore and second, as an equilibrated bilayer without a pore. Surface tension in both cases was applied to study the formation and stability of hydrophilic pores inside the bilayers. It is observed that below a critical threshold tension of ∼38 mN/m the pores are stabilized. The minimum radius at which a pore can be stabilized is 0.7 nm. Based on the critical threshold tension the line tension of the bilayer was estimated to be ∼3 × 10−11 N, in good agreement with experimental measurements. The flux of water molecules through these stabilized pores was analyzed, and the structure and size of the pores characterized. When the lateral pressure exceeds the threshold tension, the pores become unstable and start to expand causing the rupture of the membrane. In the simulations the mechanical threshold tension necessary to cause rupture of the membrane on a nanosecond timescale is much higher in the case of the equilibrated bilayers, as compared with membranes containing preexisting pores. PMID:15041656

  9. Mycobacteria-responsive sonic hedgehog signaling mediates programmed death-ligand 1- and prostaglandin E2-induced regulatory T cell expansion.

    PubMed

    Holla, Sahana; Stephen-Victor, Emmanuel; Prakhar, Praveen; Sharma, Meenu; Saha, Chaitrali; Udupa, Vibha; Kaveri, Srinivas V; Bayry, Jagadeesh; Balaji, Kithiganahalli Narayanaswamy

    2016-01-01

    CD4(+)CD25(+)FoxP3(+) regulatory T cells (Tregs) are exploited by mycobacteria to subvert the protective host immune responses. The Treg expansion in the periphery requires signaling by professional antigen presenting cells and in particularly dendritic cells (DC). However, precise molecular mechanisms by which mycobacteria instruct Treg expansion via DCs are not established. Here we demonstrate that mycobacteria-responsive sonic hedgehog (SHH) signaling in human DCs leads to programmed death ligand-1 (PD-L1) expression and cyclooxygenase (COX)-2-catalyzed prostaglandin E2 (PGE2) that orchestrate mycobacterial infection-induced expansion of Tregs. While SHH-responsive transcription factor GLI1 directly arbitrated COX-2 transcription, specific microRNAs, miR-324-5p and miR-338-5p, which target PD-L1 were downregulated by SHH signaling. Further, counter-regulatory roles of SHH and NOTCH1 signaling during mycobacterial-infection of human DCs was also evident. Together, our results establish that Mycobacterium directs a fine-balance of host signaling pathways and molecular regulators in human DCs to expand Tregs that favour immune evasion of the pathogen. PMID:27080341

  10. Mycobacteria-responsive sonic hedgehog signaling mediates programmed death-ligand 1- and prostaglandin E2-induced regulatory T cell expansion

    PubMed Central

    Holla, Sahana; Stephen-Victor, Emmanuel; Prakhar, Praveen; Sharma, Meenu; Saha, Chaitrali; Udupa, Vibha; Kaveri, Srinivas V.; Bayry, Jagadeesh; Balaji, Kithiganahalli Narayanaswamy

    2016-01-01

    CD4+CD25+FoxP3+ regulatory T cells (Tregs) are exploited by mycobacteria to subvert the protective host immune responses. The Treg expansion in the periphery requires signaling by professional antigen presenting cells and in particularly dendritic cells (DC). However, precise molecular mechanisms by which mycobacteria instruct Treg expansion via DCs are not established. Here we demonstrate that mycobacteria-responsive sonic hedgehog (SHH) signaling in human DCs leads to programmed death ligand-1 (PD-L1) expression and cyclooxygenase (COX)-2-catalyzed prostaglandin E2 (PGE2) that orchestrate mycobacterial infection-induced expansion of Tregs. While SHH-responsive transcription factor GLI1 directly arbitrated COX-2 transcription, specific microRNAs, miR-324-5p and miR-338-5p, which target PD-L1 were downregulated by SHH signaling. Further, counter-regulatory roles of SHH and NOTCH1 signaling during mycobacterial-infection of human DCs was also evident. Together, our results establish that Mycobacterium directs a fine-balance of host signaling pathways and molecular regulators in human DCs to expand Tregs that favour immune evasion of the pathogen. PMID:27080341

  11. Low thermal expansion poreless ceramics

    NASA Astrophysics Data System (ADS)

    Sugawara, Jun; Abe, Kozo; Mukai, Toshio

    2003-05-01

    Low thermal expansion ceramics have been required for ultra precision nanometer positioning stage in the semiconductor equipments. Especially pore-less advanced ceramics have been playng an important part as mirror materials in the optical equipments. Nippon Steel produces Sialon and NEXCERA as the solutions for these demands. Sialon based on silicon nitride shows a thermal expansion of 1.3 x 10-6/K with a high Young's modulus of 300 GPa. Newly-developed NEXCERA based on cordierite ceramics shows near-zero thermal expansion around the room temperature with a Young's modulus of 130 GPa. For these advanced ceramics, near-net shape sintering, direct bonding and mirror polishing are available. These technologies will provide us new design possibilities in precision engineering fields like optical system.

  12. Characterisation of Weibel–Palade body fusion by amperometry in endothelial cells reveals fusion pore dynamics and the effect of cholesterol on exocytosis

    PubMed Central

    Cookson, Emma A.; Conte, Ianina L.; Dempster, John; Hannah, Matthew J.; Carter, Tom

    2013-01-01

    Summary Regulated secretion from endothelial cells is mediated by Weibel–Palade body (WPB) exocytosis. Plasma membrane cholesterol is implicated in regulating secretory granule exocytosis and fusion pore dynamics; however, its role in modulating WPB exocytosis is not clear. To address this we combined high-resolution electrochemical analysis of WPB fusion pore dynamics, by amperometry, with high-speed optical imaging of WPB exocytosis following cholesterol depletion or supplementation in human umbilical vein endothelial cells. We identified serotonin (5-HT) immunoreactivity in WPBs, and VMAT1 expression allowing detection of secreted 5-HT as discrete current spikes during exocytosis. A high proportion of spikes (∼75%) had pre-spike foot signals, indicating that WPB fusion proceeds via an initial narrow pore. Cholesterol depletion significantly reduced pre-spike foot signal duration and increased the rate of fusion pore expansion, whereas cholesterol supplementation had broadly the reverse effect. Cholesterol depletion slowed the onset of hormone-evoked WPB exocytosis, whereas its supplementation increased the rate of WPB exocytosis and hormone-evoked proregion secretion. Our results provide the first analysis of WPB fusion pore dynamics and highlight an important role for cholesterol in the regulation of WPB exocytosis. PMID:24127569

  13. 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

  14. Amino-Biphosphonate–Mediated MMP-9 Inhibition Breaks the Tumor-Bone Marrow Axis Responsible for Myeloid-Derived Suppressor Cell Expansion and Macrophage Infiltration in Tumor Stroma

    PubMed Central

    Melani, Cecilia; Sangaletti, Sabina; Barazzetta, Francesca M.; Werb, Zena; Colombo, Mario P.

    2009-01-01

    BALB-neuT mice expressing an activated rat c-erbB-2/neu transgene under the mouse mammary tumor virus long terminal repeat show enhanced hematopoiesis with hyperproduction of myeloid-derived suppressor cells (MDSC) because of vascular endothelial growth factor (VEGF) secreted by the tumor. Here, we show that both tumor and stromal cells express matrix metalloproteinase-9 (MMP-9), thereby increasing the levels of pro–MMP-9 in the sera of tumor-bearing mice. Treatment with amino-biphosphonates impaired tumor growth, significantly decreased MMP-9 expression and the number of macrophages in tumor stroma, and reduced MDSC expansion both in bone marrow and peripheral blood by dropping serum pro–MMP-9 and VEGF. We dissected the role of tumor-derived MMP-9 from that secreted by stromal leukocytes by transplanting bone marrow from MMP-9 knockout mice into BALB-neuT mice. Although bone marrow progenitor–derived MMP-9 had a major role in driving MDSC expansion, amino-biphosphonate treatment of bone marrow chimeras further reduced both myelopoiesis and the supportive tumor stroma, thus enhancing tumor necrosis. Moreover, by reducing MDSC, amino-biphosphonates overcome the tumor-induced immune suppression and improved the generation and maintenance of antitumor immune response induced by immunization against the p185/HER-2. Our data reveal that suppression of MMP-9 activity breaks the vicious loop linking tumor growth and myeloid cell expansion, thus reducing immunosuppression. Amino-biphosphonates disclose a specific MMP-9 inhibitory activity that may broaden their application above their current usage. PMID:18056472

  15. Open–closed switching of synthetic tubular pores

    PubMed Central

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

    2015-01-01

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

  16. 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.

  17. Dynamin-mediated endocytosis is required for tube closure, cell intercalation, and biased apical expansion during epithelial tubulogenesis in the Drosophila ovary.

    PubMed

    Peters, Nathaniel C; Berg, Celeste A

    2016-01-01

    Most metazoans are able to grow beyond a few hundred cells and to support differentiated tissues because they elaborate multicellular, epithelial tubes that are indispensable for nutrient and gas exchange. To identify and characterize the cellular behaviors and molecular mechanisms required for the morphogenesis of epithelial tubes (i.e., tubulogenesis), we have turned to the D. melanogaster ovary. Here, epithelia surrounding the developing egg chambers first pattern, then form and extend a set of simple, paired, epithelial tubes, the dorsal appendage (DA) tubes, and they create these structures in the absence of cell division or cell death. This genetically tractable system lets us assess the relative contributions that coordinated changes in cell shape, adhesion, orientation, and migration make to basic epithelial tubulogenesis. We find that Dynamin, a conserved regulator of endocytosis and the cytoskeleton, serves a key role in DA tubulogenesis. We demonstrate that Dynamin is required for distinct aspects of DA tubulogenesis: DA-tube closure, DA-tube-cell intercalation, and biased apical-luminal cell expansion. We provide evidence that Dynamin promotes these processes by facilitating endocytosis of cell-cell and cell-matrix adhesion complexes, and we find that precise levels and sub-cellular distribution of E-Cadherin and specific Integrin subunits impact DA tubulogenesis. Thus, our studies identify novel morphogenetic roles (i.e., tube closure and biased apical expansion), and expand upon established roles (i.e., cell intercalation and adhesion remodeling), for Dynamin in tubulogenesis. PMID:26542010

  18. 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

  19. Pore-expanded SBA-15 sulfonic acid silicas for biodiesel synthesis.

    PubMed

    Dacquin, J P; Lee, A F; Pirez, C; Wilson, K

    2012-01-01

    Here we present the first application of pore-expanded SBA-15 in heterogeneous catalysis. Pore expansion over the range 6-14 nm confers a striking activity enhancement towards fatty acid methyl ester (FAME) synthesis from triglycerides (TAG), and free fatty acid (FFA), attributed to improved mass transport and acid site accessibility. PMID:22089025

  20. Combined climate- and prey-mediated range expansion of Humboldt squid (Dosidicus gigas), a large marine predator in the California Current System.

    PubMed

    Stewart, Julia S; Hazen, Elliott L; Bograd, Steven J; Byrnes, Jarrett E K; Foley, David G; Gilly, William F; Robison, Bruce H; Field, John C

    2014-06-01

    Climate-driven range shifts are ongoing in pelagic marine environments, and ecosystems must respond to combined effects of altered species distributions and environmental drivers. Hypoxic oxygen minimum zones (OMZs) in midwater environments are shoaling globally; this can affect distributions of species both geographically and vertically along with predator-prey dynamics. Humboldt (jumbo) squid (Dosidicus gigas) are highly migratory predators adapted to hypoxic conditions that may be deleterious to their competitors and predators. Consequently, OMZ shoaling may preferentially facilitate foraging opportunities for Humboldt squid. With two separate modeling approaches using unique, long-term data based on in situ observations of predator, prey, and environmental variables, our analyses suggest that Humboldt squid are indirectly affected by OMZ shoaling through effects on a primary food source, myctophid fishes. Our results suggest that this indirect linkage between hypoxia and foraging is an important driver of the ongoing range expansion of Humboldt squid in the northeastern Pacific Ocean. PMID:24443361

  1. Egr-1 is a critical regulator of EGF-receptor-mediated expansion of subventricular zone neural stem cells and progenitors during recovery from hypoxia–hypoglycemia

    PubMed Central

    Alagappan, Dhivyaa; Balan, Murugabaskar; Jiang, Yuhui; Cohen, Rachel B.; Kotenko, Sergei V.; Levison, Steven W.

    2013-01-01

    We recently established that the EGF-R (epidermal growth factor receptor) (EGF-R) is an essential regulator of the reactive expansion of SVZ (subventricular zone) NPs (neural precursors) that occurs during recovery from hypoxic-ischemic brain injury. The purpose of the current studies was to identify the conditions and the transcription factor (s) responsible for inducing the EGF-R. Here, we show that the increase in EGF-R expression and the more rapid division of the NPs can be recapitulated in in vitro by exposing SVZ NPs to hypoxia and hypoglycemia simultaneously, but not separately. The EGF-R promoter has binding sites for multiple transcription factors that includes the zinc finger transcription factor, Egr-1. We show that Egr-1 expression increases in NPs, but not astrocytes, following hypoxia and hypoglycemia where it accumulates in the nucleus. To determine whether Egr-1 is necessary for EGF-R expression, we used SiRNAs (small interfering RNA) specific for Egr-1 to decrease Egr-1 expression. Knocking-down Egr-1 decreased basal levels of EGF-R and it abolished the stress-induced increase in EGF-R expression. By contrast, HIF-1 accumulation did not contribute to EGF-R expression and FGF-2 only modestly induced EGF-R. These studies establish a new role for Egr-1 in regulating the expression of the mitogenic EGF-R. They also provide new information into mechanisms that promote NP expansion and provide insights into strategies for amplifying the numbers of stem cells for CNS (central nervous system) regeneration. PMID:23763269

  2. 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.

  3. Assembly of the Bak Apoptotic Pore

    PubMed Central

    Ma, Stephen; Hockings, Colin; Anwari, Khatira; Kratina, Tobias; Fennell, Stephanie; Lazarou, Michael; Ryan, Michael T.; Kluck, Ruth M.; Dewson, Grant

    2013-01-01

    Bak and Bax are the essential effectors of the intrinsic pathway of apoptosis. Following an apoptotic stimulus, both undergo significant changes in conformation that facilitates their self-association to form pores in the mitochondrial outer membrane. However, the molecular structures of Bak and Bax oligomeric pores remain elusive. To characterize how Bak forms pores during apoptosis, we investigated its oligomerization under native conditions using blue native PAGE. We report that, in a healthy cell, inactive Bak is either monomeric or in a large complex involving VDAC2. Following an apoptotic stimulus, activated Bak forms BH3:groove homodimers that represent the basic stable oligomeric unit. These dimers multimerize to higher-order oligomers via a labile interface independent of both the BH3 domain and groove. Linkage of the α6:α6 interface is sufficient to stabilize higher-order Bak oligomers on native PAGE, suggesting an important role in the Bak oligomeric pore. Mutagenesis of the α6 helix disrupted apoptotic function because a chimera of Bak with the α6 derived from Bcl-2 could be activated by truncated Bid (tBid) and could form BH3:groove homodimers but could not form high molecular weight oligomers or mediate cell death. An α6 peptide could block Bak function but did so upstream of dimerization, potentially implicating α6 as a site for activation by BH3-only proteins. Our examination of native Bak oligomers indicates that the Bak apoptotic pore forms by the multimerization of BH3:groove homodimers and reveals that Bak α6 is not only important for Bak oligomerization and function but may also be involved in how Bak is activated by BH3-only proteins. PMID:23893415

  4. Expansion Microscopy

    PubMed Central

    Chen, Fei; Tillberg, Paul W.; Boyden, Edward S.

    2014-01-01

    In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. Here we report the discovery that, by synthesizing a swellable polymer network within a specimen, it can be physically expanded, resulting in physical magnification. By covalently anchoring specific labels located within the specimen directly to the polymer network, labels spaced closer than the optical diffraction limit can be isotropically separated and optically resolved, a process we call expansion microscopy (ExM). Thus, this process can be used to perform scalable super-resolution microscopy with diffraction-limited microscopes. We demonstrate ExM with effective ~70 nm lateral resolution in both cultured cells and brain tissue, performing three-color super-resolution imaging of ~107 μm3 of the mouse hippocampus with a conventional confocal microscope. PMID:25592419

  5. PARP1 Links CHD2-Mediated Chromatin Expansion and H3.3 Deposition to DNA Repair by Non-homologous End-Joining.

    PubMed

    Luijsterburg, Martijn S; de Krijger, Inge; Wiegant, Wouter W; Shah, Rashmi G; Smeenk, Godelieve; de Groot, Anton J L; Pines, Alex; Vertegaal, Alfred C O; Jacobs, Jacqueline J L; Shah, Girish M; van Attikum, Haico

    2016-02-18

    The response to DNA double-strand breaks (DSBs) requires alterations in chromatin structure to promote the assembly of repair complexes on broken chromosomes. Non-homologous end-joining (NHEJ) is the dominant DSB repair pathway in human cells, but our understanding of how it operates in chromatin is limited. Here, we define a mechanism that plays a crucial role in regulating NHEJ in chromatin. This mechanism is initiated by DNA damage-associated poly(ADP-ribose) polymerase 1 (PARP1), which recruits the chromatin remodeler CHD2 through a poly(ADP-ribose)-binding domain. CHD2 in turn triggers rapid chromatin expansion and the deposition of histone variant H3.3 at sites of DNA damage. Importantly, we find that PARP1, CHD2, and H3.3 regulate the assembly of NHEJ complexes at broken chromosomes to promote efficient DNA repair. Together, these findings reveal a PARP1-dependent process that couples ATP-dependent chromatin remodeling with histone variant deposition at DSBs to facilitate NHEJ and safeguard genomic stability. PMID:26895424

  6. Expansion of CMV-mediated NKG2C+ NK cells associates with the development of specific de novo malignancies in liver-transplanted patients.

    PubMed

    Achour, Abla; Baychelier, Florence; Besson, Caroline; Arnoux, Armelle; Marty, Michel; Hannoun, Laurent; Samuel, Didier; Debré, Patrice; Vieillard, Vincent

    2014-01-01

    Solid cancers are a major adverse outcome of orthotopic liver transplantation (OLT). Although the use of chronic immunosuppression is known to play a role in T cell impairment, recent insights into the specificities of NK cells led us to reassess the potential modulation of this innate immune cell compartment after transplantation. Our extensive phenotypic and functional study reveals that the development of specific de novo noncutaneous tumors post-OLT is linked to unusual NK cell subsets with maturation defects and to uncommon cytokine production associated with the development of specific cancers. Remarkably, in CMV(+) patients, the development de novo head/neck or colorectal tumors is linked to an aberrant expansion of NK cells expressing NKG2C and a high level of intracellular TNF-α, which impact on their polyfunctional capacities. In contrast, NK cells from patients diagnosed with genitourinary tumors possessed a standard immature signature, including high expression of NKG2A and a robust production of IFN-γ. Taken together, our results suggest that under an immunosuppressive environment, the interplay between the modulation of NK repertoire and CMV status may greatly hamper the spectrum of immune surveillance and thus favor outgrowth and the development of specific de novo tumors after OLT. PMID:24307732

  7. PARP1 Links CHD2-Mediated Chromatin Expansion and H3.3 Deposition to DNA Repair by Non-homologous End-Joining

    PubMed Central

    Luijsterburg, Martijn S.; de Krijger, Inge; Wiegant, Wouter W.; Shah, Rashmi G.; Smeenk, Godelieve; de Groot, Anton J.L.; Pines, Alex; Vertegaal, Alfred C.O.; Jacobs, Jacqueline J.L.; Shah, Girish M.; van Attikum, Haico

    2016-01-01

    Summary The response to DNA double-strand breaks (DSBs) requires alterations in chromatin structure to promote the assembly of repair complexes on broken chromosomes. Non-homologous end-joining (NHEJ) is the dominant DSB repair pathway in human cells, but our understanding of how it operates in chromatin is limited. Here, we define a mechanism that plays a crucial role in regulating NHEJ in chromatin. This mechanism is initiated by DNA damage-associated poly(ADP-ribose) polymerase 1 (PARP1), which recruits the chromatin remodeler CHD2 through a poly(ADP-ribose)-binding domain. CHD2 in turn triggers rapid chromatin expansion and the deposition of histone variant H3.3 at sites of DNA damage. Importantly, we find that PARP1, CHD2, and H3.3 regulate the assembly of NHEJ complexes at broken chromosomes to promote efficient DNA repair. Together, these findings reveal a PARP1-dependent process that couples ATP-dependent chromatin remodeling with histone variant deposition at DSBs to facilitate NHEJ and safeguard genomic stability. PMID:26895424

  8. Viral Subversion of the Nuclear Pore Complex

    PubMed Central

    Le Sage, Valerie; Mouland, Andrew J.

    2013-01-01

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

  9. Inspection of the grapevine BURP superfamily highlights an expansion of RD22 genes with distinctive expression features in berry development and ABA-mediated stress responses.

    PubMed

    Matus, José Tomás; Aquea, Felipe; Espinoza, Carmen; Vega, Andrea; Cavallini, Erika; Dal Santo, Silvia; Cañón, Paola; Rodríguez-Hoces de la Guardia, Amparo; Serrano, Jennifer; Tornielli, Giovanni Battista; Arce-Johnson, Patricio

    2014-01-01

    The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of polygalacturonases. In grapevine, a RD22 gene has been identified but putative paralogs are also found in the grape genome, possibly forming a large RD22 family in this species. In this work, we searched for annotations containing BURP domains in the Vitis vinifera genome. Nineteen proteins were defined by a comparative analysis between the two genome predictions and RNA-Seq data. These sequences were compared to other plant BURPs identified in previous genome surveys allowing us to reconceive group classifications based on phylogenetic relationships and protein motif occurrence. We observed a lineage-specific evolution of the RD22 family, with the biggest expansion in grapevine and poplar. In contrast, rice, sorghum and maize presented highly expanded monocot-specific groups. The Vitis RD22 group may have expanded from segmental duplications as most of its members are confined to a region in chromosome 4. The inspection of transcriptomic data revealed variable expression of BURP genes in vegetative and reproductive organs. Many genes were induced in specific tissues or by abiotic and biotic stresses. Three RD22 genes were further studied showing that they responded oppositely to ABA and to stress conditions. Our results show that the inclusion of RNA-Seq data is essential while describing gene families and improving gene annotations. Robust phylogenetic analyses including all BURP members from other sequenced species helped us redefine previous relationships that were erroneously established. This work provides additional evidence for RD22 genes serving as marker genes for different organs or stresses in grapevine. PMID

  10. Inspection of the Grapevine BURP Superfamily Highlights an Expansion of RD22 Genes with Distinctive Expression Features in Berry Development and ABA-Mediated Stress Responses

    PubMed Central

    Matus, José Tomás; Aquea, Felipe; Espinoza, Carmen; Vega, Andrea; Cavallini, Erika; Santo, Silvia Dal; Cañón, Paola; de la Guardia, Amparo Rodríguez-Hoces; Serrano, Jennifer; Tornielli, Giovanni Battista; Arce-Johnson, Patricio

    2014-01-01

    The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of polygalacturonases. In grapevine, a RD22 gene has been identified but putative paralogs are also found in the grape genome, possibly forming a large RD22 family in this species. In this work, we searched for annotations containing BURP domains in the Vitis vinifera genome. Nineteen proteins were defined by a comparative analysis between the two genome predictions and RNA-Seq data. These sequences were compared to other plant BURPs identified in previous genome surveys allowing us to reconceive group classifications based on phylogenetic relationships and protein motif occurrence. We observed a lineage-specific evolution of the RD22 family, with the biggest expansion in grapevine and poplar. In contrast, rice, sorghum and maize presented highly expanded monocot-specific groups. The Vitis RD22 group may have expanded from segmental duplications as most of its members are confined to a region in chromosome 4. The inspection of transcriptomic data revealed variable expression of BURP genes in vegetative and reproductive organs. Many genes were induced in specific tissues or by abiotic and biotic stresses. Three RD22 genes were further studied showing that they responded oppositely to ABA and to stress conditions. Our results show that the inclusion of RNA-Seq data is essential while describing gene families and improving gene annotations. Robust phylogenetic analyses including all BURP members from other sequenced species helped us redefine previous relationships that were erroneously established. This work provides additional evidence for RD22 genes serving as marker genes for different organs or stresses in grapevine. PMID

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

    PubMed

    Obado, Samson O; Rout, Michael P

    2016-09-12

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

  12. Thermal Expansion

    NASA Astrophysics Data System (ADS)

    Ventura, Guglielmo; Perfetti, Mauro

    All solid materials, when cooled to low temperatures experience a change in physical dimensions which called "thermal contraction" and is typically lower than 1 % in volume in the 4-300 K temperature range. Although the effect is small, it can have a heavy impact on the design of cryogenic devices. The thermal contraction of different materials may vary by as much as an order of magnitude: since cryogenic devices are constructed at room temperature with a lot of different materials, one of the major concerns is the effect of the different thermal contraction and the resulting thermal stress that may occur when two dissimilar materials are bonded together. In this chapter, theory of thermal contraction is reported in Sect. 1.2 . Section 1.3 is devoted to the phenomenon of negative thermal expansion and its applications.

  13. 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

  14. Silicon Pore Optics Technology

    NASA Astrophysics Data System (ADS)

    Beijersbergen, Marco; Collon, M. J.; Günther, R.; Partapsing, R.; Ackermann, M.; Olde Riekerink, M.; Cooper-Jensen, C.; Christensen, F.; Freyberg, M.; Krumrey, M.; Erhard, M.; van Baren, C.; Wallace, K.; Bavdaz, M.

    2009-01-01

    Silicon pore optics have been developed over the last years to enable future astrophysical X-ray telescopes and have now become a candidate mirror technology for the IXO mission. Scientific requirements demand an angular resolution better than 5” and a large effective area of several square meters at photon energies of 1 keV. This paper discusses the performance of the latest generation of these novel light, stiff and modular X-ray optics, based on ribbed plates made from commercial high grade 12” silicon wafers. Stacks with several tens of silicon plates have been assembled in the course of an ESA technology development program, by bending the plates into an accurate shape and directly bonding them on top of each other. Several mirror modules, using two stacks each, have been aligned and integrated to form the conical approximation of a Wolter-I design. This paper presents the status of the technology, addresses and discusses a number of activities in the ongoing ESA technology development and shows the latest results of full area measurements at the long-beamline MPE X-ray test facility (PANTER) and the PTB beam line at the BESSY electron storage ring in Berlin.

  15. The Tobacco BLADE-ON-PETIOLE2 Gene Mediates Differentiation of the Corolla Abscission Zone by Controlling Longitudinal Cell Expansion1[C][W

    PubMed Central

    Wu, Xiao-Min; Yu, Yi; Han, Li-Bo; Li, Chun-Li; Wang, Hai-Yun; Zhong, Nai-Qin; Yao, Yuan; Xia, Gui-Xian

    2012-01-01

    The BLADE-ON-PETIOLE (BOP) genes of Arabidopsis (Arabidopsis thaliana) have been shown to play an essential role in floral abscission by specializing the abscission zone (AZ) anatomy. However, the molecular and cellular mechanisms that underlie differentiation of the AZ are largely unknown. In this study, we identified a tobacco (Nicotiana tabacum) homolog of BOP (designated NtBOP2) and characterized its cellular function. In tobacco plants, the NtBOP2 gene is predominantly expressed at the base of the corolla in an ethylene-independent manner. Both antisense suppression of NtBOP genes and overexpression of NtBOP2 in tobacco plants caused a failure in corolla shedding. Histological analysis revealed that the differentiation of the corolla AZ was blocked in the transgenic flowers. This blockage was due to uncontrolled cell elongation at the region corresponding to wild-type AZ. The role of NtBOP2 in regulating cell elongation was further demonstrated in Bright Yellow 2 single cells: perturbation of NtBOP2 function by a dominant negative strategy led to the formation of abnormally elongated cells. Subcellular localization analysis showed that NtBOP2-green fluorescent protein fusion proteins were targeted to both the nucleus and cytoplasm. Yeast two-hybrid, firefly luciferase complementation imaging, and in vitro pull-down assays demonstrated that NtBOP2 proteins interacted with TGA transcription factors. Taken together, these results indicated that NtBOP2 mediated the differentiation of AZ architecture by controlling longitudinal cell growth. Furthermore, NtBOP2 may achieve this outcome through interaction with the TGA transcription factors and via an ethylene-independent signaling pathway. PMID:22492844

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

    PubMed Central

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

    2015-01-01

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

  17. Cdc42 controls the dilation of the exocytotic fusion pore by regulating membrane tension

    PubMed Central

    Bretou, Marine; Jouannot, Ouardane; Fanget, Isabelle; Pierobon, Paolo; Larochette, Nathanaël; Gestraud, Pierre; Guillon, Marc; Emiliani, Valentina; Gasman, Stéphane; Desnos, Claire; Lennon-Duménil, Ana-Maria; Darchen, François

    2014-01-01

    Membrane fusion underlies multiple processes, including exocytosis of hormones and neurotransmitters. Membrane fusion starts with the formation of a narrow fusion pore. Radial expansion of this pore completes the process and allows fast release of secretory compounds, but this step remains poorly understood. Here we show that inhibiting the expression of the small GTPase Cdc42 or preventing its activation with a dominant negative Cdc42 construct in human neuroendocrine cells impaired the release process by compromising fusion pore enlargement. Consequently the mode of vesicle exocytosis was shifted from full-collapse fusion to kiss-and-run. Remarkably, Cdc42-knockdown cells showed reduced membrane tension, and the artificial increase of membrane tension restored fusion pore enlargement. Moreover, inhibiting the motor protein myosin II by blebbistatin decreased membrane tension, as well as fusion pore dilation. We conclude that membrane tension is the driving force for fusion pore dilation and that Cdc42 is a key regulator of this force. PMID:25143404

  18. Membrane electroporation: The absolute rate equation and nanosecond time scale pore creation

    NASA Astrophysics Data System (ADS)

    Vasilkoski, Zlatko; Esser, Axel T.; Gowrishankar, T. R.; Weaver, James C.

    2006-08-01

    The recent applications of nanosecond, megavolt-per-meter electric field pulses to biological systems show striking cellular and subcellular electric field induced effects and revive the interest in the biophysical mechanism of electroporation. We first show that the absolute rate theory, with experimentally based parameter input, is consistent with membrane pore creation on a nanosecond time scale. Secondly we use a Smoluchowski equation-based model to formulate a self-consistent theoretical approach. The analysis is carried out for a planar cell membrane patch exposed to a 10ns trapezoidal pulse with 1.5ns rise and fall times. Results demonstrate reversible supraelectroporation behavior in terms of transmembrane voltage, pore density, membrane conductance, fractional aqueous area, pore distribution, and average pore radius. We further motivate and justify the use of Krassowska’s asymptotic electroporation model for analyzing nanosecond pulses, showing that pore creation dominates the electrical response and that pore expansion is a negligible effect on this time scale.

  19. Pore-forming activity of clostridial binary toxins.

    PubMed

    Knapp, O; Benz, R; Popoff, M R

    2016-03-01

    Clostridial binary toxins (Clostridium perfringens Iota toxin, Clostridium difficile transferase, Clostridium spiroforme toxin, Clostridium botulinum C2 toxin) as Bacillus binary toxins, including Bacillus anthracis toxins consist of two independent proteins, one being the binding component which mediates the internalization into cell of the intracellularly active component. Clostridial binary toxins induce actin cytoskeleton disorganization through mono-ADP-ribosylation of globular actin and are responsible for enteric diseases. Clostridial and Bacillus binary toxins share structurally and functionally related binding components which recognize specific cell receptors, oligomerize, form pores in endocytic vesicle membrane, and mediate the transport of the enzymatic component into the cytosol. Binding components retain the global structure of pore-forming toxins (PFTs) from the cholesterol-dependent cytotoxin family such as perfringolysin. However, their pore-forming activity notably that of clostridial binding components is more related to that of heptameric PFT family including aerolysin and C. perfringens epsilon toxin. This review focuses upon pore-forming activity of clostridial binary toxins compared to other related PFTs. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale. PMID:26278641

  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. Gas Hydrate and Pore Pressure

    NASA Astrophysics Data System (ADS)

    Tinivella, Umberta; Giustiniani, Michela

    2014-05-01

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

  2. Can ash clog soil pores?

    NASA Astrophysics Data System (ADS)

    Stoof, Cathelijne; Stoof, Cathelijne; Gevaert, Anouk; Gevaert, Anouk; Baver, Christine; Baver, Christine; Hassanpour, Bahareh; Hassanpour, Bahareh; Morales, Veronica; Morales, Veronica; Zhang, Wei; Zhang, Wei; Martin, Deborah; Martin, Deborah; Steenhuis, Tammo; Steenhuis, Tammo

    2015-04-01

    Wildfire can greatly increase a landscape's vulnerability to flooding and erosion events, and ash is thought to play a large role in controlling runoff and erosion processes after wildfire. Although ash can store rainfall and thereby reduce runoff and erosion for a limited period after wildfires, it has also been hypothesized to clog soil pores and reduce infiltration. Several researchers have attributed the commonly observed increase in runoff and erosion after fire to the potential pore-clogging effect of ash. Evidence is however incomplete, as to date, research has solely focused on identifying the presence of ash in the soil, with the actual flow processes associated with the infiltration and pore-clogging of ash remaining a major unknown. In several laboratory experiments, we tested the hypothesis that ash causes pore clogging to the point that infiltration is hampered and ponding occurs. We first visualized and quantified pore-scale infiltration of water and ash in sand of a range of textures and at various infiltration rates, using a digital bright field microscope capturing both photo and video. While these visualization experiments confirm field and lab observation of ash washing into soil pores, we did not observe any clogging of pores, and have not been able to create conditions for which this does occur. Additional electrochemical analysis and measurement of saturated hydraulic conductivity indicate that pore clogging by ash is not plausible. Electrochemical analysis showed that ash and sand are both negatively charged, showing that attachment of ash to sand and any resulting clogging is unlikely. Ash also had quite high saturated conductivity, and systems where ash was mixed in or lying on top of sand had similarly high hydraulic conductivity. Based on these various experiments, we cannot confirm the hypothesis that pore clogging by ash contributes to the frequently observed increase in post-fire runoff, at least for the medium to coarse sands

  3. 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.

  4. 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

  5. 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.

  6. Tight dual models of pore spaces

    NASA Astrophysics Data System (ADS)

    Glantz, Roland; Hilpert, Markus

    2008-05-01

    The pore throats in a porous medium control permeability, drainage, and straining through their pore scale geometry and through the way they are connected via pore bodies on the macroscale. Likewise, imbibition is controlled through the geometry of the pore bodies (pore scale) and through the way the pore bodies are connected via pore throats on the macroscale. In an effort to account for both scales at the same time we recently introduced an image-based model for pore spaces that consists of two parts related by duality: (1) a decomposition of a polyhedral pore space into polyhedral pore bodies separated by polygonal pore throats and (2) a polygonal pore network that is homotopy equivalent to the pore space. In this paper we stick to the dual concept while amending the definition of the pore throats and, as a consequence, the other elements of the dual model. Formerly, the pore throats consisted of single two-dimensional Delaunay cells, while they now usually consist of more than one two-dimensional Delaunay cell and extend all the way into the narrowing ends of the pore channel cross sections. This is the first reason for naming the amended dual model "tight". The second reason is that the formation of the pore throats is now guided by an objective function that always attains its global optimum (tight optimization). At the end of the paper we report on simulations of drainage performed on tight dual models derived from simulated sphere packings and 3D gray-level images. The C-code for the generation of the tight dual model and the simulation of drainage is publicly available at https://jshare.johnshopkins.edu/mhilper1/public_html/tdm.html.

  7. Defeating the pores of Kohn.

    PubMed

    Ng, Calvin S H; Lau, Rainbow W H; Lau, Kelvin K W; Underwood, Malcolm J; Yim, Anthony P C

    2014-01-01

    In the treatment of emphysema with an endobronchial valve, entire lobar treatment is important in achieving adequate atelectasis. This case illustrates that without treatment of the entire lobe, it can fail to collapse even after several years, leading to treatment failure. Intralobar collateral ventilation through the pores of Kohn is demonstrated in this case, as endobronchial valve blockage of the remaining patent anterior segment resulted in the desired atelectasis and significant improvements in pulmonary function. PMID:24585656

  8. 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 ...

  9. Pore structure modification of diatomite as sulfuric acid catalyst support by high energy electron beam irradiation and hydrothermal treatment

    NASA Astrophysics Data System (ADS)

    Li, Chong; Zhang, Guilong; Wang, Min; Chen, Jianfeng; Cai, Dongqing; Wu, Zhengyan

    2014-08-01

    High energy electron beam (HEEB) irradiation and hydrothermal treatment (HT), were applied in order to remove the impurities and enlarge the pore size of diatomite, making diatomite more suitable to be a catalyst support. The results demonstrated that, through thermal, charge, impact and etching effects, HEEB irradiation could make the impurities in the pores of diatomite loose and remove some of them. Then HT could remove rest of them from the pores and contribute significantly to the modification of the pore size distribution of diatomite due to thermal expansion, water swelling and thermolysis effects. Moreover, the pore structure modification improved the properties (BET (Brunauer-Emmett-Teller) specific surface area, bulk density and pore volume) of diatomite and the catalytic efficiency of the catalyst prepared from the treated diatomite.

  10. Mechanism and kinetics of pore formation in membranes by water-soluble amphipathic peptides

    PubMed Central

    Lee, Ming-Tao; Hung, Wei-Chin; Chen, Fang-Yu; Huang, Huey W.

    2008-01-01

    How antimicrobial peptides form pores in membranes is of interest as a fundamental membrane process. However, the underlying molecular mechanism, which has potential applications in therapeutics, nonviral gene transfer, and drug delivery, has been in dispute. We have resolved this mechanism by observing the time-dependent process of pore formation in individual giant unilamellar vesicles (GUVs) exposed to a melittin solution. An individual GUV first expanded its surface area at constant volume and then suddenly reversed to expanding its volume at constant area. The area expansion, the volume expansion, and the point of reversal all match the results of equilibrium measurements performed on peptide–lipid mixtures. The mechanism includes a negative feedback that makes peptide-induced pores stable with a well defined size, contrary to the suggestion that peptides disintegrate the membrane in a detergent-like manner. PMID:18375755

  11. Synthetic ion channels: from pores to biological applications.

    PubMed

    Gokel, George W; Negin, Saeedeh

    2013-12-17

    In this Account, we describe the development of several diverse families of synthetic, membrane-active amphiphiles that form pores and facilitate transport within membrane bilayers. For the most part, the compounds are amphiphiles that insert into the bilayer and form pores either on their own or by self-assembly. The first family of synthetic ion channels prepared in our lab, the hydraphiles, used crown ethers as head groups and as a polar central element. In a range of biophysical studies, we showed that the hydraphiles formed unimolecular pores that spanned the bilayer. They mediated the transport of Na(+) and K(+) but were blocked by Ag(+). The hydraphiles are nonrectifying and disrupt ion homeostasis. As a result, these synthetic ion channels are toxic to various bacteria and yeast, a feature that has been used therapeutically in direct injection chemotherapy. We also developed a family of amphiphilic heptapeptide ion transporters that selected Cl(-) >10-fold over K(+) and showed voltage dependent gating. The formed pores were approximately dimeric, and variations in the N- and C-terminal anchor chains and the acids affected transport rates. Surprisingly, the longer N-terminal anchor chains led to less transport but greater Cl(-) selectivity. A proline residue, which is present in the ClC protein channel's conductance pore, proved to be critical for Cl(-) transport selectivity. Pyrogallol[4]arenes are macrocycles formed by acid-catalyzed condensation of four 1,2,3- trihydroxybenzenes with four aldehydes. The combination of 12 hydroxyl groups on one face of the macrocycle and four pendant alkyl chains conferred considerable amphiphilicity to these compounds. The pyrogallol[4]arenes inserted into bilayer membranes and conducted ions. Based on our experimental evidence, the ions passed through a self-assembled pore comprising four or five amphiphiles rather than passing through the central opening of a single macrocycle. Pyrogallol[4]arenes constructed with

  12. Trapping and release of bubbles from a linear pore

    NASA Astrophysics Data System (ADS)

    Juel, Anne; Dawson, Geoffrey; Lee, Sungyon

    2012-11-01

    Multiphase flows of practical interest are characterized by complex vessel geometries ranging from natural porous media to man-made lab-on-a-chip devices. Models based on the over-simplification of the pore geometry often suppress fundamental physical behavior. We study the effect on bubble motion of a sudden streamwise expansion of a square tube. The extent to which a bubble driven by constant flux flow broadens to partially fill the expansion depends on the balance between viscous and surface tension stresses, measured by the capillary number Ca . This broadening is accompanied by the slowing and momentary arrest of the bubble as Ca is reduced towards its critical value for trapping. For Ca < Cac the pressure drag forces on the quasi-arrested bubble are insufficient to force the bubble out of the expansion so it remains trapped. We examine the conditions for trapping by varying bubble volume, flow rate of the carrier fluid, and length of expanded region, and find that Cac depends non-monotonically on the size of the bubble. We verify with experiments and a capillary static model that a bubble is released if the work of the pressure forces over the length of the expansion exceeds the surface energy required for the trapped bubble to reenter the constricted square tube.

  13. Measuring kinetic drivers of pneumolysin pore structure.

    PubMed

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

    2016-05-01

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

  14. Pore-scale spectral induced polarization signatures associated with FeS biomineral transformations

    NASA Astrophysics Data System (ADS)

    Slater, Lee; Ntarlagiannis, Dimitrios; Personna, Yves R.; Hubbard, Susan

    2007-11-01

    We measured spectral induced polarization (SIP) signatures in sand columns during (1) FeS biomineralization produced by sulfate reducing bacteria (Desulfovibrio vulgaris) under anaerobic conditions, and (2) subsequent biomineral dissolution upon return to an aerobic state. The low-frequency (0.1-10 Hz peak) relaxations produced during biomineralization can be modeled with a Cole-Cole formulation, from which the evolution of the polarization magnitude and relaxation length scale can be estimated. We find that the modeled time constant is consistent with the polarizable elements being biomineral encrusted pores. Evolution of the model parameters is consistent with FeS surface area increases and pore-size reduction during biomineral growth, and subsequent biomineral dissolution (FeS surface area decreases and pore expansion) upon return to the aerobic state. We conclude that SIP signatures are diagnostic of pore-scale geometrical changes associated with FeS biomineralization by sulfate reducing bacteria.

  15. Properties and hydration products of lightweight and expansive cements. Part I: Physical and mechanical properties

    SciTech Connect

    Lilkov, V.; Djabarov, N.; Bechev, G.; Kolev, K.

    1999-10-01

    Results from studies on the physical and mechanical properties of lightweight and expansive cements cured at 20 and 75 C are presented. Lightweight additive (cenospheres from thermoelectric power station Bobov Dol, Bulgaria) and expansive additive (Bulexa with hydroxide type of expansion) were used. The compressive and flexural strength, the gas and water impermeability, and the pore structure of the cement stone of lightweight and expansive cements were investigated. The results are compared with corresponding parameters of cement stone without additives. It was found that the cenospheres are appropriate lightweight additives. The use of expansive additive helps overcome the dry shrinkage of cement stone and strengthens the bond with the bounding surfaces.

  16. A DELLA gene, RhGAI1, is a direct target of EIN3 and mediates ethylene-regulated rose petal cell expansion via repressing the expression of RhCesA2.

    PubMed

    Luo, Jing; Ma, Nan; Pei, Haixia; Chen, Jiwei; Li, Jing; Gao, Junping

    2013-11-01

    Ethylene plays an important role in organ growth. In Arabidopsis, ethylene can inhibit root elongation by stabilizing DELLA proteins. In previous work, it was found that ethylene suppressed cell expansion in rose petals, and five unisequences of DELLA genes are induced by ethylene. However, the mechanism of transcriptional regulation of DELLA genes by ethylene is still not clear. The results showed that the expression of RhGAI1 was induced in both ethylene-treated and ETR gene-silenced rose petals, and the promoter activity of RhGAI1 was strongly induced by RhEIN3-3 in Arabidopsis protoplasts. What is more, RhEIN3-3 could bind to the promoter of RhGAI1 directly in an electrophoretic mobility shift assay (EMSA). Cell expansion was suppressed in RhGAI1-Δ17-overexpressed Arabidopsis petals and promoted in RhGAI1-silenced rose petals. Moreover, in RhGAI1-silenced petals, the expression of nine cell expansion-related genes was clearly changed, and RhGAI1 can bind to the promoter of RhCesA2 in an EMSA. These results suggested that RhGAI1 was regulated by ethylene at the transcriptional level, and RhGAI1 was a direct target of RhEIN3-3. Also, RhGAI1 was shown to be involved in cell expansion partially through regulating the expression of cell expansion-related genes. Furthermore, RhCesA2 was a direct target of RhGAI1. This work uncovers the transcriptional regulation of RhGAI1 by ethylene and provides a better understanding of how ethylene regulates petal expansion in roses. PMID:24014864

  17. USING A NEW FINITE SLIT PORE MODEL FOR NLDFT ANALYSIS OF CARBON PORE STRUCTURE

    SciTech Connect

    Jagiello, Jacek; Kenvin, Jeffrey; Oliver, James P; Lupini, Andrew R; Contescu, Cristian I

    2011-01-01

    In this work, we present a model for analyzing activated carbon micropore structures based on graphene sheet walls of finite thickness and extent. This is a two-dimensional modification of the widely used infinite slit pore model that assumes graphite-like infinitely extended pore walls. The proposed model has two versions: (1) a strip pore constructed with graphene strip walls that have finite length L in the x direction and are infinite in the y direction. Strip pores are open on both sides in the x direction. (2) A channel pore is a strip pore partially closed along one edge by a perpendicularly oriented graphene wall. This more realistic model allows pore termination via both physical pore entrances and pore blockage. The model consequently introduces heterogeneity of the adsorption potential that is reduced near pore entrances and enhanced near corners of pore walls. These energetically heterogeneous structures fill with adsorbate more gradually than homogeneous pores of the same width. As a result, the calculated adsorption isotherms are smoother and less steep for the finite versus the infinite pore model. In the application of this model for carbon characterization it is necessary to make an assumption about the pore length. In this work we made this assumption based on the high resolution scanning transmission electron microscopy (STEM) results. We find the agreement between the experiment and the model significantly better for the finite than for the infinite pore model.

  18. Translocation of flexible polymersomes across pores at the nanoscale.

    PubMed

    Pegoraro, Carla; Cecchin, Denis; Madsen, Jeppe; Warren, Nicholas; Armes, Steven P; MacNeil, Sheila; Lewis, Andrew; Battaglia, Giuseppe

    2014-04-01

    Hierarchical biological systems such as tissues and organs are often characterised by highly crowded and packed environments with nanoscopic interconnections between them. Engineering nanovectors that can penetrate and diffuse across these is critical to ensure enhanced delivery and targeting. Here we demonstrate that flexible polymeric vesicles, known as polymersomes, enable the translocation of large macromolecules across both synthetic and biological porous systems. We compare the translocation across narrow pores of different polymersome formulations. We demonstrate that effective translocation depends on the right combination of mechanical properties and surface lubrication. We prove that with the effect of external gradients (e.g. osmotic pressure, capillarity, hydration, etc.) polymersomes can translocate across pores with diameters one order of magnitude smaller without breaking. We demonstrate that these properties are essential to develop effective tissue penetration and show polymersome mediated transdermal delivery of large macromolecules such as dextran and antibodies using human ex vivo skin. PMID:26828800

  19. High-pressure alchemy on a small-pore zeolite

    NASA Astrophysics Data System (ADS)

    Lee, Y.

    2011-12-01

    While an ever-expanding variety of zeolites with a wide range of framework topology is available, it is desirable to have a way to tailor the chemistry of the zeolitic nanopores for a given framework topology via controlling both the coordination-inclusion chemistry and framework distortion/relaxation. This is, however, subjected to the ability of a zeolitic nanopore to allow the redistribution of cations-water assembly and/or insertion of foreign molecules into the pores and channels. Small-pore zeolites such as natrolite (Na16Al16Si24O80x16H2O), however, have been known to show very limited capacity for any changes in the confinement chemistry. We have recently shown that various cation-exchanged natrolites can be prepared under modest conditions from natural sodium natrolite and exhibit cation-dependent volume expansions by up to 18.5% via converting the elliptical channels into progressively circular ones. Here, we show that pressure can be used as a unique and clean tool to further manipulate the chemistry of the natrolite nanopores. Our recent crystallographic and spectroscopic studies of pressure-insertion of foreign molecules, trivalent-cation exchange under pressure, and pressure-induced inversion of cation-water coordination and pore geometry in various cation-exchanged natrolites will be presented.

  20. 2-Aminoethoxydiphenyl Borate Potentiates CRAC Current by Directly Dilating the Pore of Open Orai1

    PubMed Central

    Xu, Xiaolan; Ali, Sher; Li, Yufeng; Yu, Haijie; Zhang, Mingshu; Lu, Jingze; Xu, Tao

    2016-01-01

    2-Aminoethoxydiphenyl borate (2-APB) elicits potentiation current (Ip) on Ca2+ release-activated Ca2+ (CRAC) channels. An accurate investigation into this modulation mechanism would reveal how STIM1-dependent channel gating is enhanced, and benefit the future immune enhancer development. Here, we directly probed the pore diameter of CRAC channels and found that 2-APB enlarged the pore size of STIM1-activated Orai1 from 3.8 to 4.6 Å. We demonstrated that ions with small sizes, i.e., Ca2+ and Na+, mediated prominent 2-APB-induced Ip on the wildtype (WT) Orai1 channels of narrow pore sizes, while conducted decreased or no Ip on Orai1-V102C/A/G mutant channels with enlarged pore diameters. On the contrary, large Cs+ ions blocked the WT channels, while displayed large 2-APB induced Ip on pore-enlarged Orai1-V102C/A/G mutant channels, and the potentiation ratio was highest on Orai1-V102C with an intermediate pore size. Furthermore, we showed that 2-APB potentiated Cs+ current on constitutively active Orai1-V102C/A/G mutants independent of STIM1. Our data suggest that 2-APB directly dilates the pore of open Orai1 channels, both ion size and pore diameter jointly determine the amplitude of Ip on CRAC channels, and the generation of Ip requires the open state of Orai1, not STIM1 itself. PMID:27373367

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

    PubMed

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

    2015-03-01

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

  2. Incomplete pneumolysin oligomers form membrane pores.

    PubMed

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

    2014-01-01

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

  3. 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)

  4. Atomic Structure of Graphene Subnanometer Pores.

    PubMed

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

    2015-12-22

    The atomic structure of subnanometer pores in graphene, of interest due to graphene's potential as a desalination and gas filtration membrane, is demonstrated by atomic resolution aberration corrected transmission electron microscopy. High temperatures of 500 °C and over are used to prevent self-healing of the pores, permitting the successful imaging of open pore geometries consisting of between -4 to -13 atoms, all exhibiting subnanometer diameters. Picometer resolution bond length measurements are used to confirm reconstruction of five-membered ring projections that often decorate the pore perimeter, knowledge which is used to explore the viability of completely self-passivated subnanometer pore structures; bonding configurations where the pore would not require external passivation by, for example, hydrogen to be chemically inert. PMID:26524121

  5. Pore formation and translocation of melittin.

    PubMed Central

    Matsuzaki, K; Yoneyama, S; Miyajima, K

    1997-01-01

    Melittin, a bee venom, is a basic amphiphilic peptide, which mainly acts on the lipid matrix of membranes, lysing various cells. To elucidate the molecular mechanism, we investigated its interactions with phospholipid vesicles. The peptide formed a pore with a short lifetime in the membrane, as revealed by the release of an anionic fluorescent dye, calcein, from the liposomes. Our new double-labeling method clarified that the pore size increased with the peptide-to-lipid ratio. Upon the disintegration of the pore, a fraction of the peptides translocated across the bilayer. The pore formation was coupled with the translocation, which was proved by three fluorescence experiments recently developed by our laboratory. A novel model for the melittin pore formation was discussed in comparison with other pore-forming peptides. PMID:9251799

  6. 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.

  7. Weakly relativistic plasma expansion

    SciTech Connect

    Fermous, Rachid Djebli, Mourad

    2015-04-15

    Plasma expansion is an important physical process that takes place in laser interactions with solid targets. Within a self-similar model for the hydrodynamical multi-fluid equations, we investigated the expansion of both dense and under-dense plasmas. The weakly relativistic electrons are produced by ultra-intense laser pulses, while ions are supposed to be in a non-relativistic regime. Numerical investigations have shown that relativistic effects are important for under-dense plasma and are characterized by a finite ion front velocity. Dense plasma expansion is found to be governed mainly by quantum contributions in the fluid equations that originate from the degenerate pressure in addition to the nonlinear contributions from exchange and correlation potentials. The quantum degeneracy parameter profile provides clues to set the limit between under-dense and dense relativistic plasma expansions at a given density and temperature.

  8. Thermal Expansion "Paradox."

    ERIC Educational Resources Information Center

    Fakhruddin, Hasan

    1993-01-01

    Describes a paradox in the equation for thermal expansion. If the calculations for heating a rod and subsequently cooling a rod are determined, the new length of the cool rod is shorter than expected. (PR)

  9. Pen Branch delta expansion

    SciTech Connect

    Nelson, E.A.; Christensen, E.J.; Mackey, H.E.; Sharitz, R.R.; Jensen, J.R.; Hodgson, M.E.

    1984-02-01

    Since 1954, cooling water discharges from K Reactor ({anti X} = 370 cfs {at} 59 C) to Pen Branch have altered vegetation and deposited sediment in the Savannah River Swamp forming the Pen Branch delta. Currently, the delta covers over 300 acres and continues to expand at a rate of about 16 acres/yr. Examination of delta expansion can provide important information on environmental impacts to wetlands exposed to elevated temperature and flow conditions. To assess the current status and predict future expansion of the Pen Branch delta, historic aerial photographs were analyzed using both basic photo interpretation and computer techniques to provide the following information: (1) past and current expansion rates; (2) location and changes of impacted areas; (3) total acreage presently affected. Delta acreage changes were then compared to historic reactor discharge temperature and flow data to see if expansion rate variations could be related to reactor operations.

  10. The origin of early age expansions induced in cementitious materials containing shrinkage reducing admixtures

    SciTech Connect

    Sant, Gaurav; Lothenbach, Barbara; Juilland, Patrick; Le Saout, Gwenn; Weiss, Jason; Scrivener, Karen

    2011-03-15

    Studies on the early-age shrinkage behavior of cement pastes, mortars, and concretes containing shrinkage reducing admixtures (SRAs) have indicated these mixtures frequently exhibit an expansion shortly after setting. While the magnitude of the expansion has been noted to be a function of the chemistry of the cement and the admixture dosage; the cause of the expansion is not clearly understood. This investigation uses measurements of autogenous deformation, X-ray diffraction, pore solution analysis, thermogravimetry, and scanning electron microscopy to study the early-age properties and describe the mechanism of the expansion in OPC pastes made with and without SRA. The composition of the pore solution indicates that the presence of the SRA increases the portlandite oversaturation level in solution which can result in higher crystallization stresses which could lead to an expansion. This observation is supported by deformation calculations for the systems examined.

  11. DNA Triplet Repeat Expansion and Mismatch Repair

    PubMed Central

    Iyer, Ravi R.; Pluciennik, Anna; Napierala, Marek; Wells, Robert D.

    2016-01-01

    DNA mismatch repair is a conserved antimutagenic pathway that maintains genomic stability through rectification of DNA replication errors and attenuation of chromosomal rearrangements. Paradoxically, mutagenic action of mismatch repair has been implicated as a cause of triplet repeat expansions that cause neurological diseases such as Huntington disease and myotonic dystrophy. This mutagenic process requires the mismatch recognition factor MutSβ and the MutLα (and/or possibly MutLγ) endonuclease, and is thought to be triggered by the transient formation of unusual DNA structures within the expanded triplet repeat element. This review summarizes the current knowledge of DNA mismatch repair involvement in triplet repeat expansion, which encompasses in vitro biochemical findings, cellular studies, and various in vivo transgenic animal model experiments. We present current mechanistic hypotheses regarding mismatch repair protein function in mediating triplet repeat expansions and discuss potential therapeutic approaches targeting the mismatch repair pathway. PMID:25580529

  12. Cationic PAMAM Dendrimers as Pore-Blocking Binary Toxin Inhibitors

    PubMed Central

    2015-01-01

    Dendrimers are unique highly branched macromolecules with numerous groundbreaking biomedical applications under development. Here we identified poly(amido amine) (PAMAM) dendrimers as novel blockers for the pore-forming B components of the binary anthrax toxin (PA63) and Clostridium botulinum C2 toxin (C2IIa). These pores are essential for delivery of the enzymatic A components of the internalized toxins from endosomes into the cytosol of target cells. We demonstrate that at low μM concentrations cationic PAMAM dendrimers block PA63 and C2IIa to inhibit channel-mediated transport of the A components, thereby protecting HeLa and Vero cells from intoxication. By channel reconstitution and high-resolution current recording, we show that the PAMAM dendrimers obstruct transmembrane PA63 and C2IIa pores in planar lipid bilayers at nM concentrations. These findings suggest a new potential role for the PAMAM dendrimers as effective polyvalent channel-blocking inhibitors, which can protect human target cells from intoxication with binary toxins from pathogenic bacteria. PMID:24954629

  13. Nanofiltration membranes with narrowed pore size distribution via pore wall modification.

    PubMed

    Du, Yong; Lv, Yan; Qiu, Wen-Ze; Wu, Jian; Xu, Zhi-Kang

    2016-06-30

    We propose a novel strategy for narrowing down the pore size distribution of ready-made nanofiltration membranes (NFMs) via pore wall modification. NFMs were subjected to the filtration of a highly reactive molecule solution, during which large pores were selectively reduced in size. The as-treated NFMs have high monovalent ion/divalent ion selectivity. PMID:27321407

  14. Undrained heating and anomalous pore-fluid pressurization of a hardened cement paste

    NASA Astrophysics Data System (ADS)

    Ghabezloo, S.; Sulem, J.; Saint-Marc, J.

    2009-04-01

    Temperature increase in a fluid-saturated porous material in undrained condition leads to volume change and pore pressure increase due to the discrepancy between the thermal expansion coefficients of the pore fluid and of the pore volume. This increase of the pore fluid pressure induces a reduction of the effective mean stress, and can lead to shear failure or hydraulic fracturing. This phenomenon is important is important in environmental engineering for radioactive (exothermal) waste disposal in deep clay geological formations as well as in geophysics in the studies of rapid fault slip events when shear heating tends to increase the pore pressure and to decrease the effective compressive stress and the shearing resistance of the fault material (Sulem et al. 2007). This is also important in petroleum engineering where the reservoir rock and the well cement lining undergo sudden temperature changes for example when extracting heavy oils by steam injection methods. This rapid increase of temperature could damage cement sheath integrity of wells and lead to loss of zonal isolation. The values of the thermal pressurization coefficient, defined as the pore pressure increase due to a unit temperature increase in undrained condition, is largely dependent upon the nature of the material, the state of stress, the range of temperature change, the induced damage. The large variability of the thermal pressurization coefficient reported in the literature for different porous materials with values from 0.01MPa/°C to 1.5MPa/°C highlights the necessity of laboratory studies. This phenomenon of thermal pressurization is studied experimentally for a fluid-saturated hardened cement paste in an undrained heating test. Careful analysis of the effect of the dead volume of the drainage system of the triaxial cell has been performed based on a simple correction method proposed by Ghabezloo and Sulem (2008, 2009). The drained and undrained thermal expansion coefficients of the hardened

  15. Using ApoE Nanolipoprotein Particles To Analyze SNARE-Induced Fusion Pores.

    PubMed

    Bello, Oscar D; Auclair, Sarah M; Rothman, James E; Krishnakumar, Shyam S

    2016-03-29

    Here we introduce ApoE-based nanolipoprotein particle (NLP)-a soluble, discoidal bilayer mimetic of ∼23 nm in diameter, as fusion partners to study the dynamics of fusion pores induced by SNARE proteins. Using in vitro lipid mixing and content release assays, we report that NLPs reconstituted with synaptic v-SNARE VAMP2 (vNLP) fuse with liposomes containing the cognate t-SNARE (Syntaxin1/SNAP25) partner, with the resulting fusion pore opening directly to the external buffer. Efflux of encapsulated fluorescent dextrans of different sizes show that unlike the smaller nanodiscs, these larger NLPs accommodate the expansion of the fusion pore to at least ∼9 nm, and dithionite quenching of fluorescent lipid introduced in vNLP confirms that the NLP fusion pores are short-lived and eventually reseal. The NLPs also have capacity to accommodate larger number of proteins and using vNLPs with defined number of VAMP2 protein, including physiologically relevant copy numbers, we find that 3-4 copies of VAMP2 (minimum 2 per face) are required to keep a nascent fusion pore open, and the SNARE proteins act cooperatively to dilate the nascent fusion pore. PMID:26972604

  16. A melanosomal two-pore sodium channel regulates pigmentation.

    PubMed

    Bellono, Nicholas W; Escobar, Iliana E; Oancea, Elena

    2016-01-01

    Intracellular organelles mediate complex cellular functions that often require ion transport across their membranes. Melanosomes are organelles responsible for the synthesis of the major mammalian pigment melanin. Defects in melanin synthesis result in pigmentation defects, visual deficits, and increased susceptibility to skin and eye cancers. Although genes encoding putative melanosomal ion transporters have been identified as key regulators of melanin synthesis, melanosome ion transport and its contribution to pigmentation remain poorly understood. Here we identify two-pore channel 2 (TPC2) as the first reported melanosomal cation conductance by directly patch-clamping skin and eye melanosomes. TPC2 has been implicated in human pigmentation and melanoma, but the molecular mechanism mediating this function was entirely unknown. We demonstrate that the vesicular signaling lipid phosphatidylinositol bisphosphate PI(3,5)P2 modulates TPC2 activity to control melanosomal membrane potential, pH, and regulate pigmentation. PMID:27231233

  17. A melanosomal two-pore sodium channel regulates pigmentation

    PubMed Central

    Bellono, Nicholas W.; Escobar, Iliana E.; Oancea, Elena

    2016-01-01

    Intracellular organelles mediate complex cellular functions that often require ion transport across their membranes. Melanosomes are organelles responsible for the synthesis of the major mammalian pigment melanin. Defects in melanin synthesis result in pigmentation defects, visual deficits, and increased susceptibility to skin and eye cancers. Although genes encoding putative melanosomal ion transporters have been identified as key regulators of melanin synthesis, melanosome ion transport and its contribution to pigmentation remain poorly understood. Here we identify two-pore channel 2 (TPC2) as the first reported melanosomal cation conductance by directly patch-clamping skin and eye melanosomes. TPC2 has been implicated in human pigmentation and melanoma, but the molecular mechanism mediating this function was entirely unknown. We demonstrate that the vesicular signaling lipid phosphatidylinositol bisphosphate PI(3,5)P2 modulates TPC2 activity to control melanosomal membrane potential, pH, and regulate pigmentation. PMID:27231233

  18. Sulfate attack expansion mechanisms

    SciTech Connect

    Müllauer, Wolfram Beddoe, Robin E.; Heinz, Detlef

    2013-10-15

    A specially constructed stress cell was used to measure the stress generated in thin-walled Portland cement mortar cylinders caused by external sulfate attack. The effects of sulfate concentration of the storage solution and C{sub 3}A content of the cement were studied. Changes in mineralogical composition and pore size distribution were investigated by X-ray diffraction and mercury intrusion porosimetry, respectively. Damage is due to the formation of ettringite in small pores (10–50 nm) which generates stresses up to 8 MPa exceeding the tensile strength of the binder matrix. Higher sulfate concentrations and C{sub 3}A contents result in higher stresses. The results can be understood in terms of the effect of crystal surface energy and size on supersaturation and crystal growth pressure.

  19. Accelerating the loop expansion

    SciTech Connect

    Ingermanson, R.

    1986-07-29

    This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi/sup 4/ theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs.

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

    PubMed

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

    2015-10-01

    Nuclear pore complexes are fundamental components of all eukaryotic cells that mediate nucleocytoplasmic exchange. Determining their 110-megadalton structure imposes a formidable challenge and requires in situ structural biology approaches. Of approximately 30 nucleoporins (Nups), 15 are structured and form the Y and inner-ring complexes. These two major scaffolding modules assemble in multiple copies into an eight-fold rotationally symmetric structure that fuses the inner and outer nuclear membranes to form a central channel of ~60 nm in diameter. The scaffold is decorated with transport-channel Nups that often contain phenylalanine-repeat sequences and mediate the interaction with cargo complexes. Although the architectural arrangement of parts of the Y complex has been elucidated, it is unclear how exactly it oligomerizes in situ. Here we combine cryo-electron tomography with mass spectrometry, biochemical analysis, perturbation experiments and structural modelling to generate, to our knowledge, the most comprehensive architectural model of the human nuclear pore complex to date. Our data suggest previously unknown protein interfaces across Y complexes and to inner-ring complex members. We show that the transport-channel Nup358 (also known as Ranbp2) has a previously unanticipated role in Y-complex oligomerization. Our findings blur the established boundaries between scaffold and transport-channel Nups. We conclude that, similar to coated vesicles, several copies of the same structural building block--although compositionally identical--engage in different local sets of interactions and conformations. PMID:26416747

  1. Role of Pore-Forming Toxins in Bacterial Infectious Diseases

    PubMed Central

    Los, Ferdinand C. O.; Randis, Tara M.

    2013-01-01

    SUMMARY Pore-forming toxins (PFTs) are the most common bacterial cytotoxic proteins and are required for virulence in a large number of important pathogens, including Streptococcus pneumoniae, group A and B streptococci, Staphylococcus aureus, Escherichia coli, and Mycobacterium tuberculosis. PFTs generally disrupt host cell membranes, but they can have additional effects independent of pore formation. Substantial effort has been devoted to understanding the molecular mechanisms underlying the functions of certain model PFTs. Likewise, specific host pathways mediating survival and immune responses in the face of toxin-mediated cellular damage have been delineated. However, less is known about the overall functions of PFTs during infection in vivo. This review focuses on common themes in the area of PFT biology, with an emphasis on studies addressing the roles of PFTs in in vivo and ex vivo models of colonization or infection. Common functions of PFTs include disruption of epithelial barrier function and evasion of host immune responses, which contribute to bacterial growth and spreading. The widespread nature of PFTs make this group of toxins an attractive target for the development of new virulence-targeted therapies that may have broad activity against human pathogens. PMID:23699254

  2. MNK1-induced eIF-4E phosphorylation in myeloma cells: a pathway mediating IL-6-induced expansion and expression of genes involved in metabolic and proteotoxic responses.

    PubMed

    Shi, Yijiang; Frost, Patrick; Hoang, Bao; Yang, Yonghui; Bardeleben, Carolyne; Gera, Joseph; Lichtenstein, Alan

    2014-01-01

    Because multiple myeloma (MM) cells are at risk for endoplasmic reticulum (ER) stress, they require a carefully regulated mechanism to promote protein translation of selected transcripts when proliferation is stimulated. MAPK-interacting kinases (MNKs) may provide this mechanism by enhancing cap-dependent translation of a small number of critical transcripts. We, thus, tested whether MNKs played a role in MM responses to the myeloma growth factor interleukin-6 (IL-6). IL-6 activated MNK1 phosphorylation and induced phosphorylation of its substrate, eIF-4E, in MM lines and primary specimens. MNK paralysis, achieved pharmacologically or by shRNA, prevented MM expansion stimulated by IL-6. A phosphodefective eIF-4E mutant also prevented the IL-6 response, supporting the notion that MNK's role was via phosphorylation of eIF-4E. Both pharmacological MNK inhibition and expression of the phosphodefective eIF-4E mutant inhibited MM growth in mice. Although critical for IL-6-induced expansion, eIF-4E phosphorylation had no significant effect on global translation or Ig expression. Deep sequencing of ribosome-protected mRNAs revealed a repertoire of genes involved in metabolic processes and ER stress modulation whose translation was regulated by eIF-4E phosphorylation. These data indicate MM cells exploit the MNK/eIF-4E pathway for selective mRNA translation without enhancing global translation and risking ER stress. PMID:24714040

  3. Thermal expansion in nanoresonators

    NASA Astrophysics Data System (ADS)

    Mancardo Viotti, Agustín; Monastra, Alejandro G.; Moreno, Mariano F.; Florencia Carusela, M.

    2016-08-01

    Inspired by some recent experiments and numerical works related to nanoresonators, we perform classical molecular dynamics simulations to investigate the thermal expansion and the ability of the device to act as a strain sensor assisted by thermally-induced vibrations. The proposed model consists in a chain of atoms interacting anharmonically with both ends clamped to thermal reservoirs. We analyze the thermal expansion and resonant frequency shifts as a function of temperature and the applied strain. For the transversal modes the shift is approximately linear with strain. We also present analytical results from canonical calculations in the harmonic approximation showing that thermal expansion is uniform along the device. This prediction also works when the system operates in a nonlinear oscillation regime at moderate and high temperatures.

  4. Novel Foraminal Expansion Technique

    PubMed Central

    Senturk, Salim; Ciplak, Mert; Oktenoglu, Tunc; Sasani, Mehdi; Egemen, Emrah; Yaman, Onur; Suzer, Tuncer

    2016-01-01

    The technique we describe was developed for cervical foraminal stenosis for cases in which a keyhole foraminotomy would not be effective. Many cervical stenosis cases are so severe that keyhole foraminotomy is not successful. However, the technique outlined in this study provides adequate enlargement of an entire cervical foraminal diameter. This study reports on a novel foraminal expansion technique. Linear drilling was performed in the middle of the facet joint. A small bone graft was placed between the divided lateral masses after distraction. A lateral mass stabilization was performed with screws and rods following the expansion procedure. A cervical foramen was linearly drilled medially to laterally, then expanded with small bone grafts, and a lateral mass instrumentation was added with surgery. The patient was well after the surgery. The novel foraminal expansion is an effective surgical method for severe foraminal stenosis. PMID:27559460

  5. Optimal Electric Utility Expansion

    Energy Science and Technology Software Center (ESTSC)

    1989-10-10

    SAGE-WASP is designed to find the optimal generation expansion policy for an electrical utility system. New units can be automatically selected from a user-supplied list of expansion candidates which can include hydroelectric and pumped storage projects. The existing system is modeled. The calculational procedure takes into account user restrictions to limit generation configurations to an area of economic interest. The optimization program reports whether the restrictions acted as a constraint on the solution. All expansionmore » configurations considered are required to pass a user supplied reliability criterion. The discount rate and escalation rate are treated separately for each expansion candidate and for each fuel type. All expenditures are separated into local and foreign accounts, and a weighting factor can be applied to foreign expenditures.« less

  6. Novel Foraminal Expansion Technique.

    PubMed

    Ozer, Ali Fahir; Senturk, Salim; Ciplak, Mert; Oktenoglu, Tunc; Sasani, Mehdi; Egemen, Emrah; Yaman, Onur; Suzer, Tuncer

    2016-08-01

    The technique we describe was developed for cervical foraminal stenosis for cases in which a keyhole foraminotomy would not be effective. Many cervical stenosis cases are so severe that keyhole foraminotomy is not successful. However, the technique outlined in this study provides adequate enlargement of an entire cervical foraminal diameter. This study reports on a novel foraminal expansion technique. Linear drilling was performed in the middle of the facet joint. A small bone graft was placed between the divided lateral masses after distraction. A lateral mass stabilization was performed with screws and rods following the expansion procedure. A cervical foramen was linearly drilled medially to laterally, then expanded with small bone grafts, and a lateral mass instrumentation was added with surgery. The patient was well after the surgery. The novel foraminal expansion is an effective surgical method for severe foraminal stenosis. PMID:27559460

  7. Evaporative modeling for idealized lithographic pores

    NASA Astrophysics Data System (ADS)

    Oinuma, Ryoji; Best, Frederick

    2002-01-01

    As a demand for the high performance and small size electronics devices increased, the heat removal from those electronic devices for space use is getting critical factor more than devices on the earth due to the limitation of the size. The purpose of this paper is to show a study of optimized size of coherent pores or slits in the evaporative wick of a heat pipe to cool down the high heat flux density heat source. Our system considered in this paper consists of a plate heat source, the evaporative wick with coherent pores and conducting walls connecting between the heat source and the evaporator. The evaporation rate of working fluid along the meniscus interface in a micro-order pore or slit was calculated based on the kinetic theory and the statistical rate theory to find a proper diameter of pores to cool down the heat source effectively. The results show the smaller diameter of pores is preferred to achieve the smallest total size of the evaporator although it will involve the cost issue. As a demand for the high performance and small size electronics devices increased, the heat removal from those electronic devices for space use is getting critical factor more than devices on the earth due to the limitation of the size. The purpose of this paper is to show a study of optimized size of coherent pores or slits in the evaporative wick of a heat pipe to cool down the high heat flux density heat source. Our system considered in this paper consists of a plate heat source, the evaporative wick with coherent pores and conducting walls connecting between the heat source and the evaporator. The evaporation rate of working fluid along the meniscus interface in a micro-order pore or slit was calculated based on the kinetic theory and the statistical rate theory to find a proper diameter of pores to cool down the heat source effectively. The results show that the smaller diameter of pores uses the pore for evaporation effectively and is preferred to achieve the smallest

  8. Molecular mechanism of pore formation by actinoporins.

    PubMed

    Kristan, Katarina Crnigoj; Viero, Gabriella; Dalla Serra, Mauro; Macek, Peter; Anderluh, Gregor

    2009-12-15

    Actinoporins are effective pore-forming toxins produced by sea anemones. These extremely potent, basic 20 kDa proteins readily form pores in membranes that contain sphingomyelin. Much has been learned about the molecular basis of their pore-forming mechanism in recent years. Pore formation is a multi-step process that involves recognition of membrane sphingomyelin, firm binding to the membrane accompanied by the transfer of the N-terminal region to the lipid-water interface and finally pore formation after oligomerisation of three to four monomers. The final conductive pathway is formed by amphipathic alpha-helices, hence actinoporins are an important example of so-called alpha-helical pore-forming toxins. Actinoporins have become useful model proteins to study protein-membrane interactions, specific recognition of lipids in the membrane, and protein oligomerisation in the lipid milieu. Recent sequence and structural data of proteins similar to actinoporins indicate that they are not a unique family restricted to sea anemones as was long believed. An AF domain superfamily (abbreviated from actinoporin-like proteins and fungal fruit-body lectins) was defined and shown to contain members from three animal and two plant phyla. On the basis of functional properties of some members we hypothesise that AF domain proteins are peripheral membrane proteins. Finally, ability of actinoporins to form transmembrane pores has been exploited in some novel biomedical applications. PMID:19268680

  9. The N-terminal half of the connexin protein contains the core elements of the pore and voltage gates

    PubMed Central

    Kronengold, Jack; Srinivas, Miduturu; Verselis, Vytas K.

    2013-01-01

    Connexins form channels with large aqueous pores that mediate fluxes of inorganic ions and biological signaling molecules. Studies aimed at identifying the connexin pore now include a crystal structure that provides details of putative pore-lining residues that need to be verified using independent biophysical approaches. Here we extended our initial cysteine-scanning studies of the TM1/E1 region of Cx46 hemichannels to include TM2 and TM3 transmembrane segments. No evidence of reactivity was observed in either TM2 or TM3 probed with small or large thiol-modifying reagents. Several identified pore residues in E1 of Cx46 have been verified in different Cx isoforms. Use of variety of thiol reagents indicates that the connexin hemichannel pore is large and flexible enough, at least in the extracellular part of the pore funnel, to accommodate uncommonly large side chains. We also find that that gating characteristics are largely determined by the same domains that constitute the pore. These data indicate that biophysical and structural studies are converging towards a view that the N-terminal half of the Cx protein contains the principal components of the pore and gating elements, with NT, TM1 and E1 forming the pore funnel. PMID:22825713

  10. 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. PMID:26431785

  11. 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.

  12. 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.

  13. Enlarged facial pores: an update on treatments.

    PubMed

    Dong, Joanna; Lanoue, Julien; Goldenberg, Gary

    2016-07-01

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

  14. Surface chemistry, reactivity, and pore structure of porous silicon oxidized by various methods.

    PubMed

    Riikonen, Joakim; Salomäki, Mikko; van Wonderen, Jessica; Kemell, Marianna; Xu, Wujun; Korhonen, Ossi; Ritala, Mikko; MacMillan, Fraser; Salonen, Jarno; Lehto, Vesa-Pekka

    2012-07-17

    Oxidation is the most commonly used method of passivating porous silicon (PSi) surfaces against unwanted reactions with guest molecules and temporal changes during storage or use. In the present study, several oxidation methods were compared in order to find optimal methods able to generate inert surfaces free of reactive hydrides but would cause minimal changes in the pore structure of PSi. The studied methods included thermal oxidations, liquid-phase oxidations, annealings, and their combinations. The surface-oxidized samples were studied by Fourier transform infrared spectroscopy, isothermal titration microcalorimetry, nitrogen sorption, ellipsometry, X-ray diffraction, electron paramagnetic resonance spectroscopy, and scanning electron microscopy imaging. Treatment at high temperature was found to have two advantages. First, it enables the generation of surfaces free of hydrides, which is not possible at low temperatures in a liquid or a gas phase. Second, it allows the silicon framework to partially accommodate a volume expansion because of oxidation, whereas at low temperature the volume expansion significantly consumes the free pore volume. The most promising methods were further optimized to minimize the negative effects on the pore structure. Simple thermal oxidation at 700 °C was found to be an effective oxidation method although it causes a large decrease in the pore volume. A novel combination of thermal oxidation, annealing, and liquid-phase oxidation was also effective and caused a smaller decrease in the pore volume with no significant change in the pore diameter but was more complicated to perform. Both methods produced surfaces that were not found to react with a model drug cinnarizine in isothermal titration microcalorimetry experiments. The study enables a reasonable choice of oxidation method for PSi applications. PMID:22671967

  15. A Special Trinomial Expansion

    ERIC Educational Resources Information Center

    Ayoub, Ayoub B.

    2006-01-01

    In this article, the author takes up the special trinomial (1 + x + x[squared])[superscript n] and shows that the coefficients of its expansion are entries of a Pascal-like triangle. He also shows how to calculate these entries recursively and explicitly. This article could be used in the classroom for enrichment. (Contains 1 table.)

  16. Static gas expansion cooler

    DOEpatents

    Guzek, J.C.; Lujan, R.A.

    1984-01-01

    Disclosed is a cooler for television cameras and other temperature sensitive equipment. The cooler uses compressed gas ehich is accelerated to a high velocity by passing it through flow passageways having nozzle portions which expand the gas. This acceleration and expansion causes the gas to undergo a decrease in temperature thereby cooling the cooler body and adjacent temperature sensitive equipment.

  17. Urban Expansion Study

    NASA Technical Reports Server (NTRS)

    1985-01-01

    Under an Egyptian government contract, PADCO studies urban growth in the Nile Area. They were assisted by LANDSAT survey maps and measurements provided by TAC. TAC had classified the raw LANDSAT data and processed it into various categories to detail urban expansion. PADCO crews spot checked the results, and correlations were established.

  18. AUTO-EXPANSIVE FLOW

    EPA Science Inventory

    Physics suggests that the interplay of momentum, continuity, and geometry in outward radial flow must produce density and concomitant pressure reductions. In other words, this flow is intrinsically auto-expansive. It has been proposed that this process is the key to understanding...

  19. Expansion of Pannes

    EPA Science Inventory

    For the Long Island, New Jersey, and southern New England region, one facet of marsh drowning as a result of accelerated sea level rise is the expansion of salt marsh ponds and pannes. Over the past century, marsh ponds and pannes have formed and expanded in areas of poor drainag...

  20. 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).

  1. The open pore conformation of potassium channels

    NASA Astrophysics Data System (ADS)

    Jiang, Youxing; Lee, Alice; Chen, Jiayun; Cadene, Martine; Chait, Brian T.; MacKinnon, Roderick

    2002-05-01

    Living cells regulate the activity of their ion channels through a process known as gating. To open the pore, protein conformational changes must occur within a channel's membrane-spanning ion pathway. KcsA and MthK, closed and opened K+ channels, respectively, reveal how such gating transitions occur. Pore-lining `inner' helices contain a `gating hinge' that bends by approximately 30°. In a straight conformation four inner helices form a bundle, closing the pore near its intracellular surface. In a bent configuration the inner helices splay open creating a wide (12Å) entryway. Amino-acid sequence conservation suggests a common structural basis for gating in a wide range of K+ channels, both ligand- and voltage-gated. The open conformation favours high conduction by compressing the membrane field to the selectivity filter, and also permits large organic cations and inactivation peptides to enter the pore from the intracellular solution.

  2. DESIGN MANUAL: FINE PORE AERATION SYSTEMS

    EPA Science Inventory

    This manual presents the best current practices for selecting, designing, operating, maintaining, and controlling fine pore aeration systems used in the treatment of municipal wastewater. It was prepared by the American Society of Civil Engineers Committee on Oxygen Transfer unde...

  3. Small-pore, big opportunity: searching for novel applications of small-pore zeolites by means of pressure and temperature

    NASA Astrophysics Data System (ADS)

    Im, J.; Lee, Y.

    2013-12-01

    Pressure-induced structural and chemical changes observed in small-pore zeolite natrolites are especially encouraging in terms of finding appropriate applications as they occur in the industrially-achievable low-pressure regime, i.e., as low as a few kilobars. After identifying the systematics of structural and chemical behaviors of natrolites in relation to the composition of pressure media, we have developed a procedure to exchange and sequestrate both Cs cation and I anion under intermediate pressure and temperature conditions. This result points towards the possibility of designing novel storage means for important radionuclides. Another avenue to utilize the unique pressure-induced chemistry of small-pore zeolite natrolite is to trap nominally non-adsorbable gas molecules via auxetic expansion under pressure. We have recently succeeded in pressure-induced insertion of Xe into silver-natrolite. Intriguingly, Xe adsorption occurs concomitant with charge disproportionation of silver cations to form silver nano-blobs on the surface of natrolite crystals. We will also present here various usages of laboratory-based high-pressure devices and characterization tools, which play important roles to confirm the synchrotron-based high-pressure experiments involving synthesis of new materials.

  4. Inter-Subunit Interactions across the Upper Voltage Sensing-Pore Domain Interface Contribute to the Concerted Pore Opening Transition of Kv Channels

    PubMed Central

    Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

    2013-01-01

    The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels. PMID:24340010

  5. Dual modes of membrane binding direct pore formation by Streptolysin O.

    PubMed

    Mozola, Cara C; Caparon, Michael G

    2015-09-01

    Effector translocation is central to the virulence of many bacterial pathogens, including Streptococcus pyogenes, which utilizes the cholesterol-dependent cytolysin Streptolysin O (SLO) to translocate the NAD(+) glycohydrolase SPN into host cells during infection. SLO's translocation activity does not require host cell membrane cholesterol or pore formation by SLO, yet SLO does form pores during infection via a cholesterol-dependent mechanism. Although cholesterol was considered the primary receptor for SLO, SLO's membrane-binding domain also encodes a putative carbohydrate-binding site, implicating a potential glycan receptor in binding and pore formation. Analysis of carbohydrate-binding site SLO mutants and carbohydrate-defective cell lines revealed that glycan recognition is involved in SLO's pore formation pathway and is an essential step when SLO is secreted by non-adherent bacteria, as occurs during lysis of erythrocytes. However, SLO also recognizes host cell membranes via a second mechanism when secreted from adherent bacteria, which requires co-secretion of SPN but not glycan binding by SLO. This SPN-mediated membrane binding of SLO correlates with SPN translocation, and requires SPN's non-enzymatic domain, which is predicted to adopt the structure of a carbohydrate-binding module. SPN-dependent membrane binding also promotes pore formation by SLO, demonstrating that pore formation can occur by distinct pathways during infection. PMID:26059530

  6. Two-pore channels: Regulation by NAADP and customized roles in triggering calcium signals.

    PubMed

    Patel, Sandip; Marchant, Jonathan S; Brailoiu, Eugen

    2010-06-01

    NAADP is a potent regulator of cytosolic calcium levels. Much evidence suggests that NAADP activates a novel channel located on an acidic (lysosomal-like) calcium store, the mobilisation of which results in further calcium release from the endoplasmic reticulum. Here, we discuss the recent identification of a family of poorly characterized ion channels (the two-pore channels) as endo-lysosomal NAADP receptors. The generation of calcium signals by these channels is likened to those evoked by depolarisation during excitation-contraction coupling in muscle. We discuss the idea that two-pore channels can mediate a trigger release of calcium which is then amplified by calcium-induced calcium release from the endoplasmic reticulum. This is similar to the activation of voltage-sensitive calcium channels and subsequent mobilisation of sarcoplasmic reticulum calcium stores in cardiac tissue. We suggest that two-pore channels may physically interact with ryanodine receptors to account for more direct release of calcium from the endoplasmic reticulum in analogy with the conformational coupling of voltage-sensitive calcium channels and ryanodine receptors in skeletal muscle. Interaction of two-pore channels with other calcium release channels likely occurs between stores "trans-chatter" and possibly within the same store "cis-chatter". We also speculate that trafficking of two-pore channels through the endo-lysosomal system facilitates interactions with calcium entry channels. Strategic placing of two-pore channels thus provides a versatile means of generating spatiotemporally complex cellular calcium signals. PMID:20621760

  7. 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.

  8. Expansion tube test time predictions

    NASA Technical Reports Server (NTRS)

    Gourlay, Christopher M.

    1988-01-01

    The interaction of an interface between two gases and strong expansion is investigated and the effect on flow in an expansion tube is examined. Two mechanisms for the unsteady Pitot-pressure fluctuations found in the test section of an expansion tube are proposed. The first mechanism depends on the Rayleigh-Taylor instability of the driver-test gas interface in the presence of a strong expansion. The second mechanism depends on the reflection of the strong expansion from the interface. Predictions compare favorably with experimental results. The theory is expected to be independent of the absolute values of the initial expansion tube filling pressures.

  9. Bigravity from gradient expansion

    NASA Astrophysics Data System (ADS)

    Yamashita, Yasuho; Tanaka, Takahiro

    2016-05-01

    We discuss how the ghost-free bigravity coupled with a single scalar field can be derived from a braneworld setup. We consider DGP two-brane model without radion stabilization. The bulk configuration is solved for given boundary metrics, and it is substituted back into the action to obtain the effective four-dimensional action. In order to obtain the ghost-free bigravity, we consider the gradient expansion in which the brane separation is supposed to be sufficiently small so that two boundary metrics are almost identical. The obtained effective theory is shown to be ghost free as expected, however, the interaction between two gravitons takes the Fierz-Pauli form at the leading order of the gradient expansion, even though we do not use the approximation of linear perturbation. We also find that the radion remains as a scalar field in the four-dimensional effective theory, but its coupling to the metrics is non-trivial.

  10. China petrochemical expansion progressing

    SciTech Connect

    Not Available

    1991-08-05

    This paper reports on China's petrochemical expansion surge which is picking up speed. A worldscale petrochemical complex is emerging at Shanghai with an eye to expanding China's petrochemical exports, possibly through joint ventures with foreign companies, China Features reported. In other action, Beijing and Henan province have approved plans for a $1.2 billion chemical fibers complex at the proposed Luoyang refinery, China Daily reported.

  11. The Impact of Expansion

    PubMed Central

    Yaffe, Mark J.; Steinert, Yvonne

    1990-01-01

    Postgraduate training for family physicians has become increasingly centred on 2-year residency programs. The expansion of family medicine residency programs in Quebec raises challenges: to uphold program standards, to recruit and develop new teachers, to recognize and respect the needs of students, to balance program objectives with service requirements for house staff, and to adapt to change within family medicine centers and their affiliated hospitals. Imagesp2054-ap2057-a PMID:21233950

  12. Mechanical properties, pore size distribution, and pore solution of fly ash-belite cement mortars

    SciTech Connect

    Guerrero, A.; Goni, S.; Macias, A.; Luxan, M.P.

    1999-11-01

    The mechanical properties, pore size distribution, and extracted pore solution of fly ash-belite cement (FABC) mortars were studied for a period of 200 days. The influence of the calcination temperature, which ranged from 700 to 900 C, of the fly ash-belite cement was discussed. The evolution with hydration time of the pore size distribution was followed by mercury intrusion porosimetry, and the results correlated with those of flexural and compressive strength. The pore solution was expressed and analyzed at different times of hydration.

  13. Active pore space utilization in nanoporous carbon-based supercapacitors: Effects of conductivity and pore accessibility

    NASA Astrophysics Data System (ADS)

    Seredych, Mykola; Koscinski, Mikolaj; Sliwinska-Bartkowiak, Malgorzata; Bandosz, Teresa J.

    2012-12-01

    Composites of commercial graphene and nanoporous sodium-salt-polymer-derived carbons were prepared with 5 or 20 weight% graphene. The materials were characterized using the adsorption of nitrogen, SEM/EDX, thermal analysis, Raman spectroscopy and potentiometric titration. The samples' conductivity was also measured. The performance of the carbon composites in energy storage was linked to their porosity and electronic conductivity. The small pores (<0.7) were found as very active for double layer capacitance. It was demonstrated that when double layer capacitance is a predominant mechanism of charge storage, the degree of the pore space utilization for that storage can be increased by increasing the conductivity of the carbons. That active pore space utilization is defined as gravimetric capacitance per unit pore volume in pores smaller than 0.7 nm. Its magnitude is affected by conductivity of the carbon materials. The functional groups, besides pseudocapacitive contribution, increased the wettability and thus the degree of the pore space utilization. Graphene phase, owing to its conductivity, also took part in an insitu increase of the small pore accessibility and thus the capacitance of the composites via enhancing an electron transfer to small pores and thus imposing the reduction of groups blocking the pores for electrolyte ions.

  14. 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

  15. Ultraprecise thermal expansion measurements of seven low expansion materials

    NASA Technical Reports Server (NTRS)

    Berthold, J. W., III; Jacobs, S. F.

    1976-01-01

    We summarize a large number of ultraprecise thermal expansion measurements made on seven different low expansivity materials. Expansion coefficients in the -150-300 C temperature range are shown for Owens-Illinois Cer-Vit C-101, Corning ULE 7971 (titanium silicate) and fused silica 7940, Heraeus-Schott Zerodur low-expansion material and Homosil fused silica, Universal Cyclops Invar LR-35, and Simonds Saw and Steel Super Invar.

  16. Facial skin pores: a multiethnic study.

    PubMed

    Flament, Frederic; Francois, Ghislain; Qiu, Huixia; Ye, Chengda; Hanaya, Tomoo; Batisse, Dominique; Cointereau-Chardon, Suzy; Seixas, Mirela Donato Gianeti; Dal Belo, Susi Elaine; Bazin, Roland

    2015-01-01

    Skin pores (SP), as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc) that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage) on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 μm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm(2)) and determination of their respective sizes in mm(2). Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage) that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1) were recorded in all studied subjects; 2) varied greatly with ethnicity; 3) plateaued with age in most cases; and 4) globally refected self-assessment by subjects, in particular those who self-declare having "enlarged pores" like Brazilian women. Inversely, Chinese women were clearly distinct from other ethnicities in having very low density and sizes. Analyzing the present results suggests that facial skin pore's morphology as perceived by human eye less result from functional criteria of associated appendages such as sebaceous glands. To what extent skin pores may be viewed as additional criteria of a photo-altered skin is an issue to be further addressed. PMID:25733918

  17. Low pore connectivity in natural rock

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

    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.

  18. The Arabidopsis Nuclear Pore and Nuclear Envelope

    PubMed Central

    Meier, Iris; Brkljacic, Jelena

    2010-01-01

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

  19. Soil pore structure and substrate C mineralization

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  20. 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. PMID:22507286

  1. 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.

  2. Studies on counterstreaming plasma expansion

    NASA Technical Reports Server (NTRS)

    Singh, N.; Thiemann, H.; Schunk, R. W.

    1986-01-01

    Recent studies on counterstreaming plasma expansions are summarized. The basic phenomenon of plasma expansion is reviewed, and results from one-dimensional simulations of counterstreaming plasma expansion are discussed. Results from simulations based on an electrostatic particle-in-cell code, in which the dynamics of both the electrons and ions are exactly followed, are discussed. The formation of electrostatic shocks is addressed. Finally, results are presented on the ionospheric plasma expansion along the geomagnetic flux tubes by solving the hydrodynamic equations.

  3. Magnetic expansion of cosmic plasmas

    NASA Technical Reports Server (NTRS)

    Yang, Wei-Hong

    1995-01-01

    Plasma expansion is common in many astrophysical phenomena. The understanding of the driving mechanism has usually been focused on the gas pressure that implies conversion of thermal energy into flow kinetic energy. However, 'cool' expansions have been indicated in stellar/solar winds and other expanding processes. Magnetic expansion may be the principal driving mechanism. Magnetic energy in the potential form can be converted into kinetic energy during global expansion of magnetized plasmas.

  4. 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

  5. A nonlinear electromechanical coupling model for electropore expansion in cell electroporation

    NASA Astrophysics Data System (ADS)

    Deng, Peigang; Lee, Yi-Kuen; Zhang, Tong-Yi

    2014-11-01

    Under an electric field, the electric tractions acting on a cell membrane containing a pore-nucleus are investigated by using a nonlinear electromechanical coupling model, in which the cell membrane is treated as a hyperelastic material. Iterations between the electric field and the structure field are performed to reveal the electrical forces exerting on the pore region and the subsequent pore expansion process. An explicit exponential decay of the membrane’s edge energy as a function of pore radius is defined for a hydrophilic pore and the transition energy as a hydrophobic pore converts to a hydrophilic pore during the initial stage of pore formation is investigated. It is found that the edge energy for the creation of an electropore edge plays an important role at the atomistic scale and it determines the hydrophobic-hydrophilic transition energy barrier. Various free energy evolution paths are exhibited, depending on the applied electric field, which provides further insight towards the electroporation (EP) phenomenon. In comparison with previous EP models, the proposed model has the ability to predict the metastable point on the free energy curve that is relevant to the lipid ion channel. In addition, the proposed model can also predict the critical transmembrane potential for the activation of an effective electroporation that is in a good agreement with previously published experimental data.

  6. 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.

  7. Analysis of a spatially deconvolved solar pore

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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 LOS 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.

  8. 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.

  9. Organization of the Mitochondrial Apoptotic BAK Pore

    PubMed Central

    Aluvila, Sreevidya; Mandal, Tirtha; Hustedt, Eric; Fajer, Peter; Choe, Jun Yong; Oh, Kyoung Joon

    2014-01-01

    The multidomain pro-apoptotic Bcl-2 family proteins BAK and BAX are believed to form large oligomeric pores in the mitochondrial outer membrane during apoptosis. Formation of these pores results in the release of apoptotic factors including cytochrome c from the intermembrane space into the cytoplasm, where they initiate the cascade of events that lead to cell death. Using the site-directed spin labeling method of electron paramagnetic resonance (EPR) spectroscopy, we have determined the conformational changes that occur in BAK when the protein targets to the membrane and forms pores. The data showed that helices α1 and α6 disengage from the rest of the domain, leaving helices α2-α5 as a folded unit. Helices α2-α5 were shown to form a dimeric structure, which is structurally homologous to the recently reported BAX “BH3-in-groove homodimer.” Furthermore, the EPR data and a chemical cross-linking study demonstrated the existence of a hitherto unknown interface between BAK BH3-in-groove homodimers in the oligomeric BAK. This novel interface involves the C termini of α3 and α5 helices. The results provide further insights into the organization of the BAK oligomeric pores by the BAK homodimers during mitochondrial apoptosis, enabling the proposal of a BAK-induced lipidic pore with the topography of a “worm hole.” PMID:24337568

  10. Modeling Tissue Growth Within Nonwoven Scaffolds Pores

    PubMed Central

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

    2011-01-01

    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. PMID:20687775

  11. Expansion: A Plan for Success.

    ERIC Educational Resources Information Center

    Callahan, A.P.

    This report provides selling brokers' guidelines for the successful expansion of their operations outlining a basic method of preparing an expansion plan. Topic headings are: The Pitfalls of Expansion (The Language of Business, Timely Financial Reporting, Regulatory Agencies of Government, Preoccupation with the Facade of Business, A Business Is a…

  12. The pore-forming haemolysins of bacillus cereus: a review.

    PubMed

    Ramarao, Nalini; Sanchis, Vincent

    2013-06-01

    The Bacillus cereus sensu lato group contains diverse Gram-positive spore-forming bacteria that can cause gastrointestinal diseases and severe eye infections in humans. They have also been incriminated in a multitude of other severe, and frequently fatal, clinical infections, such as osteomyelitis, septicaemia, pneumonia, liver abscess and meningitis, particularly in immuno-compromised patients and preterm neonates. The pathogenic properties of this organism are mediated by the synergistic effects of a number of virulence products that promote intestinal cell destruction and/or resistance to the host immune system. This review focuses on the pore-forming haemolysins produced by B. cereus: haemolysin I (cereolysin O), haemolysin II, haemolysin III and haemolysin IV (CytK). Haemolysin I belongs to the cholesterol-dependent cytolysin (CDC) family whose best known members are listeriolysin O and perfringolysin O, produced by L. monocytogenes and C. perfringens respectively. HlyII and CytK are oligomeric ß-barrel pore-forming toxins related to the α-toxin of S. aureus or the ß-toxin of C. perfringens. The structure of haemolysin III, the least characterized haemolytic toxin from the B. cereus, group has not yet been determined. PMID:23748204

  13. Energetics of Transport through the Nuclear Pore Complex.

    PubMed

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

    2016-01-01

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

  14. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    NASA Astrophysics Data System (ADS)

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

    2016-07-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation.

  15. The RTX pore-forming toxin α-hemolysin of uropathogenic Escherichia coli: progress and perspectives

    PubMed Central

    Wiles, Travis J; Mulvey, Matthew A

    2013-01-01

    Members of the RTX family of protein toxins are functionally conserved among an assortment of bacterial pathogens. By disrupting host cell integrity through their pore-forming and cytolytic activities, this class of toxins allows pathogens to effectively tamper with normal host cell processes, promoting pathogenesis. Here, we focus on the biology of RTX toxins by describing salient properties of a prototype member, α-hemolysin, which is of ten encoded by strains of uropathogenic Escherichia coli. It has long been appreciated that RTX toxins can have distinct effects on host cells aside from outright lysis. Recently, advances in modeling and analysis of host–pathogen interactions have led to novel findings concerning the consequences of pore formation during host–pathogen interactions. We discuss current progress on longstanding questions concerning cell specificity and pore formation, new areas of investigation that involve toxin-mediated perturbations of host cell signaling cascades and perspectives on the future of RTX toxin investigation. PMID:23252494

  16. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation

    PubMed Central

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W.; Lin, Jialing; Li, Jianing

    2016-01-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model — using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation. PMID:27381287

  17. Conformational Heterogeneity of Bax Helix 9 Dimer for Apoptotic Pore Formation.

    PubMed

    Liao, Chenyi; Zhang, Zhi; Kale, Justin; Andrews, David W; Lin, Jialing; Li, Jianing

    2016-01-01

    Helix α9 of Bax protein can dimerize in the mitochondrial outer membrane (MOM) and lead to apoptotic pores. However, it remains unclear how different conformations of the dimer contribute to the pore formation on the molecular level. Thus we have investigated various conformational states of the α9 dimer in a MOM model - using computer simulations supplemented with site-specific mutagenesis and crosslinking of the α9 helices. Our data not only confirmed the critical membrane environment for the α9 stability and dimerization, but also revealed the distinct lipid-binding preference of the dimer in different conformational states. In our proposed pathway, a crucial iso-parallel dimer that mediates the conformational transition was discovered computationally and validated experimentally. The corroborating evidence from simulations and experiments suggests that, helix α9 assists Bax activation via the dimer heterogeneity and interactions with specific MOM lipids, which eventually facilitate proteolipidic pore formation in apoptosis regulation. PMID:27381287

  18. Ion transport through chemically induced pores in protein-free phospholipid membranes.

    PubMed

    Gurtovenko, Andrey A; Anwar, Jamshed

    2007-11-29

    We address the possibility of being able to induce the trafficking of salt ions and other solutes across cell membranes without the use of specific protein-based transporters or pumps. On the basis of realistic atomic-scale molecular dynamics simulations, we demonstrate that transmembrane ionic leakage can be initiated by chemical means, in this instance through addition of dimethyl sulfoxide (DMSO), a solvent widely used in cell biology. Our results provide compelling evidence that the small amphiphilic solute DMSO is able to induce transient defects (water pores) in membranes and to promote a subsequent diffusive pore-mediated transport of salt ions. The findings are consistent with available experimental data and offer a molecular-level explanation for the experimentally observed activities of DMSO solvent as an efficient penetration enhancer and a cryoprotectant, as well as an analgesic. Our findings suggest that transient pore formation by chemical means could emerge as an important general principle for therapeutics. PMID:17983219

  19. Function and dysfunction of two-pore channels.

    PubMed

    Patel, Sandip

    2015-07-01

    Two-pore channels (TPCs) are evolutionarily important members of the voltage-gated ion channel superfamily. TPCs localize to acidic Ca(2+) stores within the endolysosomal system. Most evidence indicate that TPCs mediate Ca(2+) signals through the Ca(2+)-mobilizing messenger nicotinic acid adenine dinucleotide phosphate (NAADP) to control a range of Ca(2+)-dependent events. Recent studies clarify the mechanism of TPC activation and identify roles for TPCs in disease, highlighting the regulation of endolysosomal membrane traffic by local Ca(2+) fluxes. Chemical targeting of TPCs to maintain endolysosomal "well-being" may be beneficial in disorders as diverse as Parkinson's disease, fatty liver disease, and Ebola virus infection. PMID:26152696

  20. 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. PMID:27081075

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

    PubMed

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

    2015-10-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kilodalton inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin heterotrimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three-dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation. PMID:26316600

  2. Tailoring particle translocation via dielectrophoresis in pore channels.

    PubMed

    Tanaka, Shoji; Tsutsui, Makusu; Theodore, Hu; Yuhui, He; Arima, Akihide; Tsuji, Tetsuro; Doi, Kentaro; Kawano, Satoyuki; Taniguchi, Masateru; Kawai, Tomoji

    2016-01-01

    Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification. PMID:27527126

  3. Architecture of the nuclear pore inner ring complex

    PubMed Central

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

    2016-01-01

    The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. We present the reconstitution and interdisciplinary analyses of the ~425-kDa inner ring complex (IRC), which forms the central transport channel and diffusion barrier of the NPC, revealing its interaction network and equimolar stoichiometry. The Nsp1•Nup49•Nup57 channel nucleoporin hetero-trimer (CNT) attaches to the IRC solely through the adaptor nucleoporin Nic96. The CNT•Nic96 structure reveals that Nic96 functions as an assembly sensor that recognizes the three dimensional architecture of the CNT, thereby mediating the incorporation of a defined CNT state into the NPC. We propose that the IRC adopts a relatively rigid scaffold that recruits the CNT to primarily form the diffusion barrier of the NPC, rather than enabling channel dilation. PMID:26316600

  4. Tailoring particle translocation via dielectrophoresis in pore channels

    PubMed Central

    Tanaka, Shoji; Tsutsui, Makusu; Theodore, Hu; Yuhui, He; Arima, Akihide; Tsuji, Tetsuro; Doi, Kentaro; Kawano, Satoyuki; Taniguchi, Masateru; Kawai, Tomoji

    2016-01-01

    Understanding and controlling electrophoretic motions of nanoscopic objects in fluidic channels are a central challenge in developing nanopore technology for molecular analyses. Although progress has been made in slowing the translocation velocity to meet the requirement for electrical detections of analytes via picoampere current measurements, there exists no method useful for regulating particle flows in the transverse directions. Here, we report the use of dielectrophoresis to manipulate the single-particle passage through a solid-state pore. We created a trap field by applying AC voltage between electrodes embedded in a low-aspect-ratio micropore. We demonstrated a traffic control of particles to go through center or near side surface via the voltage frequency. We also found enhanced capture efficiency along with faster escaping speed of particles by virtue of the AC-mediated electroosmosis. This method is compatible with nanopore sensing and would be widely applied for reducing off-axis effects to achieve single-molecule identification. PMID:27527126

  5. The mitochondrial permeability transition pore: a mystery solved?

    PubMed Central

    Bernardi, Paolo

    2013-01-01

    The permeability transition (PT) denotes an increase of the mitochondrial inner membrane permeability to solutes with molecular masses up to about 1500 Da. It is presumed to be mediated by opening of a channel, the permeability transition pore (PTP), whose molecular nature remains a mystery. Here I briefly review the history of the PTP, discuss existing models, and present our new results indicating that reconstituted dimers of the FOF1 ATP synthase form a channel with properties identical to those of the mitochondrial megachannel (MMC), the electrophysiological equivalent of the PTP. Open questions remain, but there is now promise that the PTP can be studied by genetic methods to solve the large number of outstanding problems. PMID:23675351

  6. Expansion in condensates

    SciTech Connect

    Chakrabarti, J.; Sajjad Zahir, M.

    1985-03-01

    We show that the product of local current operators in quantum chromodynamics (QCD), when expanded in terms of condensates, such as psi-barpsi, G/sup a//sub munu/ G/sup a//sub munu/, psi-barGAMMA psipsi-barGAMMApsi, f/sub a/bcG/sup a//sub munu/G/sup b//sub nualpha/ x G/sup c//sub alphamu/, etc., yields a series in Planck's constant. This, however, provides no hint that the higher terms in such an expansion may be less significant.

  7. Load regulating expansion fixture

    DOEpatents

    Wagner, Lawrence M.; Strum, Michael J.

    1998-01-01

    A free standing self contained device for bonding ultra thin metallic films, such as 0.001 inch beryllium foils. The device will regulate to a predetermined load for solid state bonding when heated to a bonding temperature. The device includes a load regulating feature, whereby the expansion stresses generated for bonding are regulated and self adjusting. The load regulator comprises a pair of friction isolators with a plurality of annealed copper members located therebetween. The device, with the load regulator, will adjust to and maintain a stress level needed to successfully and economically complete a leak tight bond without damaging thin foils or other delicate components.

  8. Load regulating expansion fixture

    DOEpatents

    Wagner, L.M.; Strum, M.J.

    1998-12-15

    A free standing self contained device for bonding ultra thin metallic films, such as 0.001 inch beryllium foils is disclosed. The device will regulate to a predetermined load for solid state bonding when heated to a bonding temperature. The device includes a load regulating feature, whereby the expansion stresses generated for bonding are regulated and self adjusting. The load regulator comprises a pair of friction isolators with a plurality of annealed copper members located therebetween. The device, with the load regulator, will adjust to and maintain a stress level needed to successfully and economically complete a leak tight bond without damaging thin foils or other delicate components. 1 fig.

  9. PORE STRUCTURE MODEL OF CEMENT HYDRATES CONSIDERING PORE WATER CONTENT AND REACTION PROCESS UNDER ARBITRARY HUMIDITY

    NASA Astrophysics Data System (ADS)

    Fujikura, Yusuke; Oshita, Hideki

    A simulation model to estimate the pore structure of cement hydrates by curing in arbitrary relative humidity is presented. This paper describes procedures for predicting phase compositions based on the classical hydration model of Portland cement, calculating the particle size distribution of constituent phases and evaluating the pore size distribution by stereological and statistical considerations. And to estimate the water content in pore structure under any relative humidity, we proposed the simulation model of adsorption isotherm model based on the pore structure. To evaluate the effectiveness of this model, simulation results were compared with experimental results of the pore size distribution measured by mercury porosimetry. As a result, it was found that the experimental and simulated results were in close agreement, and the simulated results indicated characterization of the po re structure of cement hydrates.

  10. Emulsion formation at the Pore-Scale

    NASA Astrophysics Data System (ADS)

    Armstrong, R. T.; Van Den Bos, P.; Berg, S.

    2012-12-01

    The use of surfactant cocktails to produce ultra-low interfacial tension between water and oil is an enhanced oil recovery method. In phase behavior tests three distinct emulsion phases are observed: (1) oil-in-water emulsion; (2) microemulsion; and (3) water-in-oil emulsion. However, it is unknown how phase behavior manifests at the pore-scale in a porous media system. What is the time scale needed for microemulsion formation? Where in the pore-space do the microemulsions form? And in what order do the different emulsion phases arrange during oil bank formation? To answer these questions micromodel experiments were conducted. These experiments are used to build a conceptual model for phase behavior at the pore-scale.

  11. Modeling Soil Pore Oxygen in Restored Wetlands

    NASA Astrophysics Data System (ADS)

    Rubol, S.; Loecke, T.; Burgin, A. J.; Franz, T.

    2015-12-01

    Soil pore oxygen (O2) is usually modeled indirectly as a function of soil moisture. However, using soil moisture to describe the oxic /anoxic status of a soil may not be sufficient accurate, especially when soil pore O2 rapidly changes, as following hydrological forcing. As first step, we use the dataset collected in the constructed wetland near Dayton, OH, by Loecke and Burgin, to reconstruct the environmental functions and re-aeration status of the soil. The dataset consist of 24 Apogee sensors and 24 soil moisture and temperature sensors located at 10 cm depth in upland, transitional and submerged zone (see Figure 1). Data were recorded over two years at temporal interval of 30 minutes. Then, we explore the capability of existing biogeochemical models to predict metabolic activity and the soil pore O2. Figure1: Restored wetland field site with soil O2 sensors (yellow stars) in upland (red), transitional (green) and submerged (blue) zones.

  12. Optical detection of pores in adipocyte membrane

    NASA Astrophysics Data System (ADS)

    Yanina, I. Yu.; Doubrovski, V. A.; Tuchin, V. V.

    2013-08-01

    Structures that can be interpreted as cytoplasm droplets leaking through the membrane are experimentally detected on the membranes of adipocytes using optical digital microscopy. The effect of an aqueous alcohol solution of brilliant green on the amount and sizes of structures is studied. It is demonstrated that the optical irradiation of the adipocytes that are sensitized with the aid of the brilliant green leads to an increase in the amount of structures (pores) after the irradiation. The experimental results confirm the existence of an earlier-proposed effect of photochemical action on the sensitized cells of adipose tissue that involves additional formation of pores in the membrane of the sensitized cell under selective optical irradiation. The proposed method for the detection of micropores in the membrane of adipose tissue based on the detection of the cytoplasm droplets leaking from the cell can be considered as a method for the optical detection of nanosized pores.

  13. Pore structure analysis of American coals

    SciTech Connect

    Gallegos, D.P.; Smith, D.M.; Stermer, D.L.

    1987-01-01

    The pore structure of 19 American coals, representing a wide range of rank and geographic origin, has been studied via gas adsorption, mercury porosimetry, helium displacement and NMR spin-lattice relaxation measurements. Nitrogen adsorption at 77 K was used to determine surface area in the pore range of r/sub p/ > approx. = 1nm and carbon dioxide adsorption at 273 K was used to obtain the total surface area. Porosimetry results were complicated by inter-particle void filling, surface roughness/porosity and sample compression. By employing a range of particle sizes, information concerning the relative magnitude of these mechanisms was ascertained as a function of pressure. Spin-lattice relaxation measurements of water contained in saturated coal were used to find pore size distributions over a broad range of T/sub 1/, the spin-lattice relaxation time. Good qualitative agreement was obtained between these measurements and gas adsorption/condensation results. 13 refs., 3 figs., 1 tab.

  14. Expansible quantum secret sharing network

    NASA Astrophysics Data System (ADS)

    Sun, Ying; Xu, Sheng-Wei; Chen, Xiu-Bo; Niu, Xin-Xin; Yang, Yi-Xian

    2013-08-01

    In the practical applications, member expansion is a usual demand during the development of a secret sharing network. However, there are few consideration and discussion on network expansibility in the existing quantum secret sharing schemes. We propose an expansible quantum secret sharing scheme with relatively simple and economical quantum resources and show how to split and reconstruct the quantum secret among an expansible user group in our scheme. Its trait, no requirement of any agent's assistant during the process of member expansion, can help to prevent potential menaces of insider cheating. We also give a discussion on the security of this scheme from three aspects.

  15. The pore dimensions of gramicidin A.

    PubMed Central

    Smart, O S; Goodfellow, J M; Wallace, B A

    1993-01-01

    The ion channel forming peptide gramicidin A adopts a number of distinct conformations in different environments. We have developed a new method to analyze and display the pore dimensions of ion channels. The procedure is applied to two x-ray crystal structures of gramicidin that adopt distinct antiparallel double helical dimer conformations and a nuclear magnetic resonance (NMR) structure for the beta6.3 NH2-terminal to NH2-terminal dimer. The results are discussed with reference to ion conductance properties and dependence of pore dimensions on the environment. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:7508762

  16. Immediate versus chronic tissue expansion.

    PubMed

    Machida, B K; Liu-Shindo, M; Sasaki, G H; Rice, D H; Chandrasoma, P

    1991-03-01

    A quantitative comparison of the effects on tissues is performed between chronic tissue expansion, intraoperative expansion, and load cycling in a guinea pig model. Intra-operative expansion, which was developed by Sasaki as a method of immediate tissue expansion for small- to medium-sized defects, and load cycling, which was described by Gibson as a method using intraoperative pull, are compared with chronic tissue expansion on the basis of the following four parameters: amount of skin produced, flap viability, intraoperative tissue pressures, and histological changes. The chronically expanded group, which included booster and nonbooster expansions, produced a 137% increase in surface area, or a 52% increase in flap arc length, whereas intraoperative expansion resulted in a 31% increase in surface area, or a 15% increase in flap arc length. The load-cycled group, however, resulted in an almost negligible amount of skin increase. All three techniques exhibit immediate postexpansion stretchback. Flap viability is not impaired by any of the three techniques, in spite of the elevated pressures observed during expansion. Therefore, intraoperative expansion is effective primarily for limited expansion of small defects, whereas chronic tissue expansion still provides the greatest amount of skin increase when compared with other techniques. PMID:2029132

  17. Sequential protein unfolding through a carbon nanotube pore

    NASA Astrophysics Data System (ADS)

    Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K.; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

    2016-06-01

    An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable ``unfoldon'' motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability.An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of

  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. PMID:25961729

  20. Antibacterial membrane attack by a pore-forming intestinal C-type lectin

    PubMed Central

    Mukherjee, Sohini; Zheng, Hui; Derebe, Mehabaw; Callenberg, Keith; Partch, Carrie L.; Rollins, Darcy; Propheter, Daniel C.; Rizo, Josep; Grabe, Michael; Jiang, Qiu-Xing; Hooper, Lora V.

    2014-01-01

    Summary Human body surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota1,2. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate1,3 but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. Here we show that human RegIIIα (hRegIIIα, also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the hRegIIIα pore by docking the hRegIIIα crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits hRegIIIα pore-forming activity, explaining why hRegIIIα is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota. PMID:24256734

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

    SciTech Connect

    Teufel, L.W.

    1996-02-01

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

  2. Pore-scale imaging and modelling

    NASA Astrophysics Data System (ADS)

    Blunt, Martin J.; Bijeljic, Branko; Dong, Hu; Gharbi, Oussama; Iglauer, Stefan; Mostaghimi, Peyman; Paluszny, Adriana; Pentland, Christopher

    2013-01-01

    Pore-scale imaging and modelling - digital core analysis - is becoming a routine service in the oil and gas industry, and has potential applications in contaminant transport and carbon dioxide storage. This paper briefly describes the underlying technology, namely imaging of the pore space of rocks from the nanometre scale upwards, coupled with a suite of different numerical techniques for simulating single and multiphase flow and transport through these images. Three example applications are then described, illustrating the range of scientific problems that can be tackled: dispersion in different rock samples that predicts the anomalous transport behaviour characteristic of highly heterogeneous carbonates; imaging of super-critical carbon dioxide in sandstone to demonstrate the possibility of capillary trapping in geological carbon storage; and the computation of relative permeability for mixed-wet carbonates and implications for oilfield waterflood recovery. The paper concludes by discussing limitations and challenges, including finding representative samples, imaging and simulating flow and transport in pore spaces over many orders of magnitude in size, the determination of wettability, and upscaling to the field scale. We conclude that pore-scale modelling is likely to become more widely applied in the oil industry including assessment of unconventional oil and gas resources. It has the potential to transform our understanding of multiphase flow processes, facilitating more efficient oil and gas recovery, effective contaminant removal and safe carbon dioxide storage.

  3. Pore Water Geochemistry of IODP Exp 315 and 316: The NanTroSEIZE Transect

    NASA Astrophysics Data System (ADS)

    Wheat, C. G.; Hulme, S.; Tomaru, H.; Liljedahl, L. C.; Solomon, E.

    2008-12-01

    IODP Exp 315 and 316 drilled six sites as part of the first stage of NanTroSEIZE, an international, multi-year endeavor to elucidate earthquake-related processes. These six sites form a transect southeast of the Kumano Basin, Japan with boreholes that penetrated the Kumano forarc basin (C0002), the megasplay fault region (C0001, C0004, and C0008) and the frontal thrust including sediment from the subducting plate (C0006 and C0007). One element of this drilling is to evaluate the relationship between pore fluid behavior and slip and deformation in the crust. To help address this relationship 322 pore water samples were extracted from sediment whole rounds. Each of the whole rounds was scanned (CT) before it was processed within a nitrogen-filled glove bag and squeezed to express the pore fluid. In addition, 15 samples from C0002 underwent the GRIND technique to gather baseline pore water chemical data for future deep drilling where highly indurated sediments likely exist. Each of these pore water samples underwent a range of analytical procedures at sea. Additional procedures were conducted ashore. Combined, these procedures resulted in data for 30 chemical species including the stable isotopic composition of O and H in water. These data provide the most thorough preliminary reports tables in the history of DSDP, ODP and IODP, and ongoing measurements include a range of isotopic (e.g., I, B, Sr, Li, C), ionic (e.g., REE), and organic measurements. We will present all of the data that appear in the preliminary reports including GRIND samples for comparison to squeezed samples. Our presentation will highlight changes in pore water composition along the transect of boreholes, putting individual site-related pore water chemical profiles in a broader context. Pore water profiles in the upper about 30 m of the sediment column are dominated by microbially mediated reactions with a highly defined sulfate-methane transition. Deeper within the sediment the dissociation of gas

  4. A molecular theory for optimal blue energy extraction by electrical double layer expansion.

    PubMed

    Kong, Xian; Gallegos, Alejandro; Lu, Diannan; Liu, Zheng; Wu, Jianzhong

    2015-10-01

    Electrical double layer expansion (CDLE) has been proposed as a promising alternative to reverse electrodialysis (RED) and pressure retarded osmosis (PRO) processes for extracting osmotic power generated by the salinity difference between freshwater and seawater. The performance of the CDLE process is sensitive to the configuration of porous electrodes and operation parameters for ion extraction and release cycles. In this work, we use a classical density functional theory (CDFT) to examine how the electrode pore size and charging/discharging potentials influence the thermodynamic efficiency of the CDLE cycle. The existence of an optimal charging potential that maximizes the energy output for a given pore configuration is predicted, which varies substantially with the pore size, especially when it is smaller than 2 nm. The thermodynamic efficiency is maximized when the electrode has a pore size about twice the ion diameter. PMID:26312731

  5. Cryogenic expansion machine

    DOEpatents

    Pallaver, Carl B.; Morgan, Michael W.

    1978-01-01

    A cryogenic expansion engine includes intake and exhaust poppet valves each controlled by a cam having adjustable dwell, the valve seats for the valves being threaded inserts in the valve block. Each cam includes a cam base and a ring-shaped cam insert disposed at an exterior corner of the cam base, the cam base and cam insert being generally circular but including an enlarged cam dwell, the circumferential configuration of the cam base and cam dwell being identical, the cam insert being rotatable with respect to the cam base. GI CONTRACTUAL ORIGIN OF THE INVENTION The invention described herein was made in the course of, or under, a contract with the UNITED STATES ENERGY RESEARCH AND DEVELOPMENT ADMINISTRATION.

  6. Facial skin pores: a multiethnic study

    PubMed Central

    Flament, Frederic; Francois, Ghislain; Qiu, Huixia; Ye, Chengda; Hanaya, Tomoo; Batisse, Dominique; Cointereau-Chardon, Suzy; Seixas, Mirela Donato Gianeti; Dal Belo, Susi Elaine; Bazin, Roland

    2015-01-01

    Skin pores (SP), as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc) that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage) on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 μm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm2) and determination of their respective sizes in mm2. Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage) that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1) were recorded in all studied subjects; 2) varied greatly with ethnicity; 3) plateaued with age in most cases; and 4) globally refected self-assessment by subjects, in particular those who self-declare having “enlarged pores” like Brazilian women. Inversely, Chinese women were clearly distinct from other ethnicities in having very low density and sizes. Analyzing the present results suggests that facial skin pore’s morphology as perceived by human eye less result from functional criteria of associated appendages such as sebaceous glands. To what extent skin pores may be viewed as additional criteria of a photo-altered skin is an issue to be further addressed. PMID:25733918

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  9. Real Time Pore Structure Evolution during Olivine Mineral Carbonation

    NASA Astrophysics Data System (ADS)

    Zhu, W.; Fusseis, F.; Lisabeth, H. P.; Xiao, X.

    2014-12-01

    Aqueous carbonation of ultramafic rocks has been proposed as a promising method for long-term, secure sequestration of carbon dioxide. While chemical kinetics data indicate that carbonation reaction in olivine is one of the fastest among the mg-bearing minerals, in practice, the factors that limit the extent and rate of carbonation in ultramafic rocks are fluid supply and flux. On the one hand, reaction products could produce passivating layer that prohibits further reactions. On the other hand, the increases in solid volume during carbonation could lead to cracking and create new fluid paths. Whether carbonation in ultramafic rocks is self-limiting or self-sustaining has been hotly debated. Experimental evidence of precipitation of reaction products during olivine carbonation was reported. To date, reaction-driven cracking has not been observed. In this paper, we present the first real-time pore structure evolution data using the x-ray synchrotron microtomography. Sodium bicarbonate (NaHCO3) solution was injected into porous olivine aggregates and in-situ pore structure change during olivine carbonation at a constant confining pressure (12 MPa) and a temperature of 200oC was captured at 30 min. interval for ~160 hours. Shortly after the experiment started, filling-in of the existing pores by precipitation of reaction products was visible. The size of the in-fills kept increasing as reactions continued. After ~48 hours, cracking around the in-fill materials became visible. After ~60 hours, these cracks started to show a clear polygonal pattern, similar to the crack patterns usually seen on the surface of drying mud. After ~72 hours, some of the cracks coalesced into large fractures that cut-through the olivine aggregates. New fractures continued to develop and at the end of the experiment, the sample was completely disintegrated by these fractures. We also conducted nanotomography experiments on a sub-volume of the reacted olivine aggregate. Orthogonal sets of

  10. Expansion of Interstitial Telomeric Sequences in Yeast.

    PubMed

    Aksenova, Anna Y; Han, Gil; Shishkin, Alexander A; Volkov, Kirill V; Mirkin, Sergei M

    2015-11-24

    Telomeric repeats located within chromosomes are called interstitial telomeric sequences (ITSs). They are polymorphic in length and are likely hotspots for initiation of chromosomal rearrangements that have been linked to human disease. Using our S. cerevisiae system to study repeat-mediated genome instability, we have previously shown that yeast telomeric (Ytel) repeats induce various gross chromosomal rearrangements (GCR) when their G-rich strands serve as the lagging strand template for replication (G orientation). Here, we show that interstitial Ytel repeats in the opposite C orientation prefer to expand rather than cause GCR. A tract of eight Ytel repeats expands at a rate of 4 × 10(-4) per replication, ranking them among the most expansion-prone DNA microsatellites. A candidate-based genetic analysis implicates both post-replication repair and homologous recombination pathways in the expansion process. We propose a model for Ytel repeat expansions and discuss its applications for genome instability and alternative telomere lengthening (ALT). PMID:26586439

  11. The Pathway of Membrane Fusion Catalyzed by Influenza Hemagglutinin: Restriction of Lipids, Hemifusion, and Lipidic Fusion Pore Formation

    PubMed Central

    Chernomordik, Leonid V.; Frolov, Vadim A.; Leikina, Eugenia; Bronk, Peter; Zimmerberg, Joshua

    1998-01-01

    The mechanism of bilayer unification in biological fusion is unclear. We reversibly arrested hemagglutinin (HA)-mediated cell–cell fusion right before fusion pore opening. A low-pH conformation of HA was required to form this intermediate and to ensure fusion beyond it. We present evidence indicating that outer monolayers of the fusing membranes were merged and continuous in this intermediate, but HA restricted lipid mixing. Depending on the surface density of HA and the membrane lipid composition, this restricted hemifusion intermediate either transformed into a fusion pore or expanded into an unrestricted hemifusion, without pores but with unrestricted lipid mixing. Our results suggest that restriction of lipid flux by a ring of activated HA is necessary for successful fusion, during which a lipidic fusion pore develops in a local and transient hemifusion diaphragm. PMID:9508770

  12. Pore Distribution and Water Uptake in a Cenosphere-Cement Paste Composite Material

    NASA Astrophysics Data System (ADS)

    Baronins, J.; Setina, J.; Sahmenko, G.; Lagzdina, S.; Shishkin, A.

    2015-11-01

    Alumina silicate cenospheres (CS) is a significant waste material from power plants that use a coal. Use CS as Portland cement replacement material gives opportunity to control physical and mechanical properties and makes a product lighter and more cost-effective. In the frame of this study, Portland cement paste samples were produced by adding CS in the concentration range from 0 to 40 volume %. Water uptake of hardened samples was checked and pore size distribution by using the mercury porosimetry was determined. In a cold climate where the temperature often falls below 0 °C, it is important to avoid the amount of micrometer sized pores in the final structure and to decrease water absorption capacity of material. In winter conditions, water fills such pores and causes additional stresses to their walls by expansion while freezing. It was found that generally water uptake capacity for cement paste samples decreased up to 20% by increasing the concentration of CS up to 40 volume %, at the same time, the volume of micrometer sized opened pores increases.

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

    PubMed Central

    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

    2014-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.04247.001 PMID:25457051

  14. Mediation Analysis

    PubMed Central

    MacKinnon, David P.; Fairchild, Amanda J.; Fritz, Matthew S.

    2010-01-01

    Mediating variables are prominent in psychological theory and research. A mediating variable transmits the effect of an independent variable on a dependent variable. Differences between mediating variables and confounders, moderators, and covariates are outlined. Statistical methods to assess mediation and modern comprehensive approaches are described. Future directions for mediation analysis are discussed. PMID:16968208

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

    PubMed Central

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

    2016-01-01

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

  16. Sequential protein unfolding through a carbon nanotube pore.

    PubMed

    Xu, Zhonghe; Zhang, Shuang; Weber, Jeffrey K; Luan, Binquan; Zhou, Ruhong; Li, Jingyuan

    2016-06-16

    An assortment of biological processes, like protein degradation and the transport of proteins across membranes, depend on protein unfolding events mediated by nanopore interfaces. In this work, we exploit fully atomistic simulations of an artificial, CNT-based nanopore to investigate the nature of ubiquitin unfolding. With one end of the protein subjected to an external force, we observe non-canonical unfolding behaviour as ubiquitin is pulled through the pore opening. Secondary structural elements are sequentially detached from the protein and threaded into the nanotube, interestingly, the remaining part maintains native-like characteristics. The constraints of the nanopore interface thus facilitate the formation of stable "unfoldon" motifs above the nanotube aperture that can exist in the absence of specific native contacts with the other secondary structure. Destruction of these unfoldons gives rise to distinct force peaks in our simulations, providing us with a sensitive probe for studying the kinetics of serial unfolding events. Our detailed analysis of nanopore-mediated protein unfolding events not only provides insight into how related processes might proceed in the cell, but also serves to deepen our understanding of structural arrangements which form the basis for protein conformational stability. PMID:26899409

  17. Pore size distribution and accessible pore size distribution in bituminous coals

    SciTech Connect

    Sakurovs, Richard; He, Lilin; Melnichenko, Yuri B; Radlinski, Andrzej Pawell; Blach, Tomasz P

    2012-01-01

    The porosity and pore size distribution of coals determine many of their properties, from gas release to their behavior on carbonization, and yet most methods of determining pore size distribution can only examine a restricted size range. Even then, only accessible pores can be investigated with these methods. Small-angle neutron scattering (SANS) and ultra small-angle neutron scattering (USANS) are increasingly used to characterize the size distribution of all of the pores non-destructively. Here we have used USANS/SANS to examine 24 well-characterized bituminous and subbituminous coals: three from the eastern US, two from Poland, one from New Zealand and the rest from the Sydney and Bowen Basins in Eastern Australia, and determined the relationships of the scattering intensity corresponding to different pore sizes with other coal properties. The range of pore radii examinable with these techniques is 2.5 nm to 7 {micro}m. We confirm that there is a wide range of pore sizes in coal. The pore size distribution was found to be strongly affected by both rank and type (expressed as either hydrogen or vitrinite content) in the size range 250 nm to 7 {micro}m and 5 to 10 nm, but weakly in intermediate regions. The results suggest that different mechanisms control coal porosity on different scales. Contrast-matching USANS and SANS were also used to determine the size distribution of the fraction of the pores in these coals that are inaccessible to deuterated methane, CD{sub 4}, at ambient temperature. In some coals most of the small ({approx} 10 nm) pores were found to be inaccessible to CD{sub 4} on the time scale of the measurement ({approx} 30 min - 16 h). This inaccessibility suggests that in these coals a considerable fraction of inherent methane may be trapped for extended periods of time, thus reducing the effectiveness of methane release from (or sorption by) these coals. Although the number of small pores was less in higher rank coals, the fraction of total

  18. Putative pore-loops of TMEM16/anoctamin channels affect channel density in cell membranes.

    PubMed

    Adomaviciene, Aiste; Smith, Keith J; Garnett, Hannah; Tammaro, Paolo

    2013-07-15

    The recently identified TMEM16/anoctamin protein family includes Ca(2+)-activated anion channels (TMEM16A, TMEM16B), a cation channel (TMEM16F) and proteins with unclear function. TMEM16 channels consist of eight putative transmembrane domains (TMs) with TM5-TM6 flanking a re-entrant loop thought to form the pore. In TMEM16A this region has also been suggested to contain residues involved in Ca(2+) binding. The role of the putative pore-loop of TMEM16 channels was investigated using a chimeric approach. Heterologous expression of either TMEM16A or TMEM16B resulted in whole-cell anion currents with very similar conduction properties but distinct kinetics and degrees of sensitivity to Ca(2+). Furthermore, whole-cell currents mediated by TMEM16A channels were ∼six times larger than TMEM16B-mediated currents. Replacement of the putative pore-loop of TMEM16A with that of TMEM16B (TMEM16A-B channels) reduced the currents by ∼six-fold, while the opposite modification (TMEM16B-A channels) produced a ∼six-fold increase in the currents. Unexpectedly, these changes were not secondary to variations in channel gating by Ca(2+) or voltage, nor were they due to changes in single-channel conductance. Instead, they depended on the number of functional channels present on the plasma membrane. Generation of additional, smaller chimeras within the putative pore-loop of TMEM16A and TMEM16B led to the identification of a region containing a non-canonical trafficking motif. Chimeras composed of the putative pore-loop of TMEM16F transplanted into the TMEM16A protein scaffold did not conduct anions or cations. These data suggest that the putative pore-loop does not form a complete, transferable pore domain. Furthermore, our data reveal an unexpected role for the putative pore-loop of TMEM16A and TMEM16B channels in the control of the whole-cell Ca(2+)-activated Cl(-) conductance. PMID:23613533

  19. Burial Ground Expansion Hydrogeologic Characterization

    SciTech Connect

    Gaughan , T.F.

    1999-02-26

    Sirrine Environmental Consultants provided technical oversight of the installation of eighteen groundwater monitoring wells and six exploratory borings around the location of the Burial Ground Expansion.

  20. Singularity Expansion Method

    NASA Astrophysics Data System (ADS)

    Riggs, Lloyd Stephen

    In this work the transient currents induced on an arbitrary system of thin linear scatterers by an electromagnetic plane wave are solved by using an electric field integral equation (EFIE) formulation. The transient analysis is carried out using the singularity expansion method (SEM). The general analysis developed here is useful for assessing the vulnerability of military aircraft to a nuclear generated electromagnetic pulse (EMP). It is also useful as a modal synthesis tool in the analysis and design of frequency selective surfaces (FSS). SEM parameters for a variety of thin cylindrical geometries have been computed. Specifically, SEM poles, modes, coupling coefficients, and transient currents are given for the two and three element planar array. Poles and modes for planar arrays with a larger number (as many as eight) of identical equally spaced elements are also considered. SEM pole-mode results are given for identical parallel elements with ends located at the vertices of a regular N-agon. Pole-mode patterns are found for symmetric (and slightly perturbed) single junction N-arm elements and for the five junction Jerusalem cross. The Jerusalem cross element has been used extensively in FSS.

  1. Signal Transduction to the Permeability Transition Pore

    PubMed Central

    Rasola, Andrea; Sciacovelli, Marco; Pantic, Boris; Bernardi, Paolo

    2010-01-01

    The permeability transition pore (PTP) is an inner mitochondrial membrane channel that has been thoroughly characterized functionally, yet remains an elusive molecular entity. The best characterized PTP-regulatory component, cyclophilin (CyP) D, is a matrix protein that favors pore opening. CyP inhibitors, CyPD null animals, and in situ PTP readouts have established the role of PTP as an effector mechanism of cell death, and the growing definition of PTP signaling mechanisms. This review briefly covers the functional features of the PTP and the role played by its dysregulation in disease pathogenesis. Recent progress on PTP modulation by kinase/phosphatase signal transduction is discussed, with specific emphasis on hexokinase and on the Akt-ERK-GSK3 axis, which might modulate the PTP through CyPD phosphorylation. PMID:20153328

  2. Mineral dissolution kinetics at the pore scale

    SciTech Connect

    Li, L.; Steefel, C.I.; Yang, L.

    2007-05-24

    Mineral dissolution rates in the field have been reported to be orders of magnitude slower than those measured in the laboratory, an unresolved discrepancy that severely limits our ability to develop scientifically defensible predictive or even interpretive models for many geochemical processes in the earth and environmental sciences. One suggestion links this discrepancy to the role of physical and chemical heterogeneities typically found in subsurface soils and aquifers in producing scale-dependent rates where concentration gradients develop. In this paper, we examine the possibility that scale-dependent mineral dissolution rates can develop even at the single pore and fracture scale, the smallest and most fundamental building block of porous media. To do so, we develop two models to analyze mineral dissolution kinetics at the single pore scale: (1) a Poiseuille Flow model that applies laboratory-measured dissolution kinetics at the pore or fracture wall and couples this to a rigorous treatment of both advective and diffusive transport, and (2) a Well-Mixed Reactor model that assumes complete mixing within the pore, while maintaining the same reactive surface area, average flow rate, and geometry as the Poiseuille Flow model. For a fracture, a 1D Plug Flow Reactor model is considered in addition to quantify the effects of longitudinal versus transverse mixing. The comparison of averaged dissolution rates under various conditions of flow, pore size, and fracture length from the three models is used as a means to quantify the extent to which concentration gradients at the single pore and fracture scale can develop and render rates scale-dependent. Three important minerals that dissolve at widely different rates, calcite, plagioclase, and iron hydroxide, are considered. The modeling indicates that rate discrepancies arise primarily where concentration gradients develop due to comparable rates of reaction and advective transport, and incomplete mixing via molecular

  3. Pores and Void in Asclepiades' Physical Theory.

    PubMed

    Leith, David

    2012-01-01

    This paper examines a fundamental, though relatively understudied, aspect of the physical theory of the physician Asclepiades of Bithynia, namely his doctrine of pores. My principal thesis is that this doctrine is dependent on a conception of void taken directly from Epicurean physics. The paper falls into two parts: the first half addresses the evidence for the presence of void in Asclepiades' theory, and concludes that his conception of void was basically that of Epicurus; the second half focuses on the precise nature of Asclepiadean pores, and seeks to show that they represent void interstices between the primary particles of matter which are the constituents of the human body, and are thus exactly analogous to the void interstices between atoms within solid objects in Epicurus' theory. PMID:22984299

  4. Pores and Void in Asclepiades’ Physical Theory

    PubMed Central

    Leith, David

    2012-01-01

    This paper examines a fundamental, though relatively understudied, aspect of the physical theory of the physician Asclepiades of Bithynia, namely his doctrine of pores. My principal thesis is that this doctrine is dependent on a conception of void taken directly from Epicurean physics. The paper falls into two parts: the first half addresses the evidence for the presence of void in Asclepiades’ theory, and concludes that his conception of void was basically that of Epicurus; the second half focuses on the precise nature of Asclepiadean pores, and seeks to show that they represent void interstices between the primary particles of matter which are the constituents of the human body, and are thus exactly analogous to the void interstices between atoms within solid objects in Epicurus’ theory. PMID:22984299

  5. Further characterization of Closed Pore Insulation (CPI)

    NASA Technical Reports Server (NTRS)

    Russak, M.; Feldman, C.

    1973-01-01

    The thermophysical and mechanical properties of closed pore insulation (CPI) were measured after exposure to 25 simulated reentry thermal cycles. In addition, mechanical properties were obtained at elevated temperatures before and after cycling. The properties of CPI were not compromised by the cycling. High temperature creep studies were done on three CPI compositions (4, 8, and 12 Wt% CoO additive). CPI-4 had the best creep resistance at temperatures up to 1363 K.

  6. Multistep Molecular Dynamics Simulations Identify the Highly Cooperative Activity of Melittin in Recognizing and Stabilizing Membrane Pores.

    PubMed

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-09-01

    The prototypical antimicrobial peptide, melittin, is well-known for its ability to induce pores in zwitterionic model lipid membranes. However, the mechanism by which melittin accomplishes this is not fully understood. We have conducted all-atom and coarse-grained molecular dynamics simulations which suggest that melittin employs a highly cooperative mechanism for the induction of both small and large membrane pores. The process by which this peptide induces membrane pores appears to be driven by its affinity to membrane defects via its N-terminus region. In our simulations, a membrane defect was deliberately created through either lipid flip-flop or the reorientation of one adsorbed melittin peptide. In a cooperative response, other melittin molecules also inserted their N-termini into the created defect, thus lowering the overall free energy. The insertion of these peptide molecules ultimately allowed the defect to develop into a small transmembrane pore, with an estimated diameter of ∼1.5 nm and a lifetime of the order of tens of milliseconds. In the presence of a finite membrane tension, we show that this small pore can act as a nucleation site for the stochastic rupture of the lipid bilayer, so as to create a much larger pore. We found that a threshold membrane tension of 25 mN/m was needed to create a ruptured pore. Furthermore, by actively accumulating at its edge, adsorbed peptides are able to cooperatively stabilize this larger pore. The defect-mediated pore formation mechanism revealed in this work may also apply to other amphipathic membrane-active peptides. PMID:26267389

  7. Pore destruction resulting from mechanical thermal expression

    SciTech Connect

    Clayton, S.A.; Wheeler, R.A.; Hoadley, A.F.A.

    2007-07-01

    Mechanical thermal expression (MTE) is a dewatering technology ideally suited for the dewatering of internally porous biomaterials. For such materials, the combined application of temperature and compressive force in the MTE process enhances the collapse of the porous structure, resulting in effective water removal. In this article, a comparison of the dewatering of titanium dioxide, which is an ideal incompressible, non-porous material, and lignite, which is a porous plant-based biomaterial, is presented. The comparison is based on the parameters critical to dewatering, namely the material compressibility and the permeability. With the aid of mercury porosimetry results, a detailed discussion of the pore destruction of lignite resulting from MTE processing is presented. It is illustrated that there is a well-defined relationship between the pore size distribution after MTE dewatering and the MTE temperature and pressure. The discussion is extended to an investigation of the effects of MTE processing conditions on the effective and noneffective porosity. The effective porosity is defined as the interconnected porosity, which contributes to flow through the compressed matrix, while the non-effective porosity is the remaining porosity, which does not contribute to flow. It is illustrated that there is a linear relationship in both the effective and non-effective porosity with the total porosity. The linear relationship is independent of the processing conditions. It is also shown that MTE processing collapses the effective and non-effective pores at roughly the same rate.

  8. Pore morphology study of silica aerogels

    SciTech Connect

    Hua, D.W.; Anderson, J.; Haereid, S.; Smith, D.M.

    1994-12-31

    Silica aerogels have numerous properties which suggest applications such as ultra high efficiency thermal insulation. These properties relate directly to the aerogel`s pore size distribution. The micro and meso pore size ranges can be investigated by normal small angle x-ray scattering and possibly, nitrogen adsorption. However, the measurement of larger pores (> 250 {angstrom}) is more difficult. Due to their limited mechanical strength, mercury porosimetry and nitrogen condensation can disrupt the gel structure and electron microscopy provides only limited large scale structure information. The use of small angle light scattering techniques seems to have promise, the only hurdle is that aerogels exhibit significant multiple scattering. This can be avoided if one observes the gels in the wet stage since the structure of the aerogel should be very similar to the wet gel (as the result of supercritical drying). Thus, if one can match the refractive index, the morphology can be probed. The combination of certain alcoholic solvents fit this index matching criteria. Preliminary results for the gel network (micron range) and primary particle structure (manometer) are reported by using small angle light scattering and ultra-small angle x-ray scattering. The effects on structure over the length scale range of <1 nm to >5 {mu}m under different conditions (precursors, pH, etc.) are presented. The change in structure of an aerogel during isostatic compaction to 228 MPa (to simulate drying from wetting solvents) are also discussed.

  9. CFTR: what's it like inside the pore?

    PubMed

    Liu, Xuehong; Smith, Stephen S; Dawson, David C

    2003-11-01

    The Cystic Fibrosis Conductance Regulator (CFTR) functions as a cAMP-activated, anion-selective channel, but the structural basis for anion permeation is not well understood. Here we summarize recent studies aimed at understanding how anions move through the CFTR channel, and the nature of the environment anions experience inside the pore. From these studies it is apparent that anion permeability selectivity and anion binding selectivity of the pore are consistent with a model based on a "dielectric tunnel." The selectivity pattern for halides and pseudohalides can be predicted if it is assumed that permeant anions partition between bulk water and a polarizable space that is characterized by an effective dielectric constant of about 19. Covalent labeling of engineered cysteines and pH titration of engineered cysteines and histidines lead to the conclusion that the CFTR anion conduction path includes a positively charged outer vestibule. A residue in transmembrane segment 6 (TM6) (R334) appears to reside in the outer vestibule of the CFTR pore where it creates a positive electrostatic potential that enhances anion conduction. PMID:14598388

  10. Biomimetic collagen scaffolds with anisotropic pore architecture.

    PubMed

    Davidenko, N; Gibb, T; Schuster, C; Best, S M; Campbell, J J; Watson, C J; Cameron, R E

    2012-02-01

    Sponge-like matrices with a specific three-dimensional structural design resembling the actual extracellular matrix of a particular tissue show significant potential for the regeneration and repair of a broad range of damaged anisotropic tissues. The manipulation of the structure of collagen scaffolds using a freeze-drying technique was explored in this work as an intrinsically biocompatible way of tailoring the inner architecture of the scaffold. The research focused on the influence of temperature gradients, imposed during the phase of crystallisation of collagen suspensions, upon the degree of anisotropy in the microstructures of the scaffolds produced. Moulding technology was employed to achieve differences in heat transfer rates during the freezing processes. For this purpose various moulds with different configurations were developed with a view to producing uniaxial and multi-directional temperature gradients across the sample during this process. Scanning electron microscopy analysis of different cross-sections (longitudinal and horizontal) of scaffolds revealed that highly aligned matrices with axially directed pore architectures were obtained where single unidirectional temperature gradients were induced. Altering the freezing conditions by the introduction of multiple temperature gradients allowed collagen scaffolds to be produced with complex pore orientations, and anisotropy in pore size and alignment. PMID:22005330

  11. Isotropic Negative Thermal Expansion Metamaterials.

    PubMed

    Wu, Lingling; Li, Bo; Zhou, Ji

    2016-07-13

    Negative thermal expansion materials are important and desirable in science and engineering applications. However, natural materials with isotropic negative thermal expansion are rare and usually unsatisfied in performance. Here, we propose a novel method to achieve two- and three-dimensional negative thermal expansion metamaterials via antichiral structures. The two-dimensional metamaterial is constructed with unit cells that combine bimaterial strips and antichiral structures, while the three-dimensional metamaterial is fabricated by a multimaterial 3D printing process. Both experimental and simulation results display isotropic negative thermal expansion property of the samples. The effective coefficient of negative thermal expansion of the proposed models is demonstrated to be dependent on the difference between the thermal expansion coefficient of the component materials, as well as on the circular node radius and the ligament length in the antichiral structures. The measured value of the linear negative thermal expansion coefficient of the three-dimensional sample is among the largest achieved in experiments to date. Our findings provide an easy and practical approach to obtaining materials with tunable negative thermal expansion on any scale. PMID:27333052

  12. Multiple pathways of commodity crop expansion in tropical forest landscapes

    NASA Astrophysics Data System (ADS)

    Meyfroidt, Patrick; Carlson, Kimberly M.; Fagan, Matthew E.; Gutiérrez-Vélez, Victor H.; Macedo, Marcia N.; Curran, Lisa M.; DeFries, Ruth S.; Dyer, George A.; Gibbs, Holly K.; Lambin, Eric F.; Morton, Douglas C.; Robiglio, Valentina

    2014-07-01

    Commodity crop expansion, for both global and domestic urban markets, follows multiple land change pathways entailing direct and indirect deforestation, and results in various social and environmental impacts. Here we compare six published case studies of rapid commodity crop expansion within forested tropical regions. Across cases, between 1.7% and 89.5% of new commodity cropland was sourced from forestlands. Four main factors controlled pathways of commodity crop expansion: (i) the availability of suitable forestland, which is determined by forest area, agroecological or accessibility constraints, and land use policies, (ii) economic and technical characteristics of agricultural systems, (iii) differences in constraints and strategies between small-scale and large-scale actors, and (iv) variable costs and benefits of forest clearing. When remaining forests were unsuitable for agriculture and/or policies restricted forest encroachment, a larger share of commodity crop expansion occurred by conversion of existing agricultural lands, and land use displacement was smaller. Expansion strategies of large-scale actors emerge from context-specific balances between the search for suitable lands; transaction costs or conflicts associated with expanding into forests or other state-owned lands versus smallholder lands; net benefits of forest clearing; and greater access to infrastructure in already-cleared lands. We propose five hypotheses to be tested in further studies: (i) land availability mediates expansion pathways and the likelihood that land use is displaced to distant, rather than to local places; (ii) use of already-cleared lands is favored when commodity crops require access to infrastructure; (iii) in proportion to total agricultural expansion, large-scale actors generate more clearing of mature forests than smallholders; (iv) property rights and land tenure security influence the actors participating in commodity crop expansion, the form of land use displacement

  13. INVESTIGATION INTO BIOFOULING PHENOMENA IN FINE PORE AERATION DEVICES

    EPA Science Inventory

    Microbiologically-based procedures were used to describe biofouling phenomena on fine pore aeration devices and to determine whether biofilm characteristics could be related to diffuser process performance parameters. ine pore diffusers were obtained from five municipal wastewate...

  14. INVESTIGATIONS INTO BIOFOULING PHENOMENA IN FINE PORE AERATION DEVICES

    EPA Science Inventory

    Microbiologically-based procedures were used to describe biofouling phenomena on fine pore aeration devices and to determine whether biofilm characteristics could be related to diffuser process performance parameters. Fine pore diffusers were obtained from five municipal wastewa...

  15. Impact of matric potential and pore size distribution on growth dynamics of filamentous and non-filamentous soil bacteria.

    PubMed

    Wolf, Alexandra B; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A

    2013-01-01

    The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities. PMID:24391805

  16. Impact of Matric Potential and Pore Size Distribution on Growth Dynamics of Filamentous and Non-Filamentous Soil Bacteria

    PubMed Central

    Wolf, Alexandra B.; Vos, Michiel; de Boer, Wietse; Kowalchuk, George A.

    2013-01-01

    The filamentous growth form is an important strategy for soil microbes to bridge air-filled pores in unsaturated soils. In particular, fungi perform better than bacteria in soils during drought, a property that has been ascribed to the hyphal growth form of fungi. However, it is unknown if, and to what extent, filamentous bacteria may also display similar advantages over non-filamentous bacteria in soils with low hydraulic connectivity. In addition to allowing for microbial interactions and competition across connected micro-sites, water films also facilitate the motility of non-filamentous bacteria. To examine these issues, we constructed and characterized a series of quartz sand microcosms differing in matric potential and pore size distribution and, consequently, in connection of micro-habitats via water films. Our sand microcosms were used to examine the individual and competitive responses of a filamentous bacterium (Streptomyces atratus) and a motile rod-shaped bacterium (Bacillus weihenstephanensis) to differences in pore sizes and matric potential. The Bacillus strain had an initial advantage in all sand microcosms, which could be attributed to its faster growth rate. At later stages of the incubation, Streptomyces became dominant in microcosms with low connectivity (coarse pores and dry conditions). These data, combined with information on bacterial motility (expansion potential) across a range of pore-size and moisture conditions, suggest that, like their much larger fungal counterparts, filamentous bacteria also use this growth form to facilitate growth and expansion under conditions of low hydraulic conductivity. The sand microcosm system developed and used in this study allowed for precise manipulation of hydraulic properties and pore size distribution, thereby providing a useful approach for future examinations of how these properties influence the composition, diversity and function of soil-borne microbial communities. PMID:24391805

  17. In situ TEM observation of electrochemical lithiation of sulfur confined within inner cylindrical pores of carbon nanotubes

    DOE PAGESBeta

    Kim, Hyea; Lee, Jung Tae; Magasinski, Alexandre; Zhao, Kejie; Liu, Yang; Yushin, Gleb

    2015-10-26

    Lithium insertion into sulfur confined within 200 nm cylindrical inner pores of individual carbon nanotubes (CNTs) was monitored in-situ in a transmission electron microscope (TEM). This electrochemical reaction was initiated at one end of the S-filled CNTs. The material expansion during lithiation was accommodated by the expansion into the remaining empty pore volume and no fracture of the CNT walls was detected. A sharp interface between the initial and lithiated S was observed. The reaction front was flat, oriented perpendicular to the confined S cylinder and propagated along the cylinder length. Lithiation of S in the proximity of conductive carbonmore » proceeded at the same rate as the one in the center of the pore, suggesting the presence of electron pathways at the Li2S/S interface. Density of states (DOS) calculations further confirmed this hypothesis. In-situ electron diffraction showed a direct phase transformation of S into nanocrystalline Li2S without detectable formation of any intermediates, such as polysulfides and LiS. These important insights may elucidate some of the reaction mechanisms and guide the improvements in the design of C-S nanocomposites for high specific energy Li-S batteries. As a result, the proposed use of conductive CNTs with tunable pore diameter as cylindrical reaction vessels for in-situ TEM studies of electrochemical reactions proved to be highly advantageous and may help to resolve the on-going problems in battery technology.« less

  18. Fusion Pore Size Limits 5-HT Release From Single Enterochromaffin Cell Vesicles.

    PubMed

    Raghupathi, Ravinarayan; Jessup, Claire F; Lumsden, Amanda L; Keating, Damien J

    2016-07-01

    Enterochromaffin cells are the major site of serotonin (5-HT) synthesis and secretion providing ∼95% of the body's total 5-HT. 5-HT can act as a neurotransmitter or hormone and has several important endocrine and paracrine roles. We have previously demonstrated that EC cells release small amounts of 5-HT per exocytosis event compared to other endocrine cells. We utilized a recently developed method to purify EC cells to demonstrate the mechanisms underlying 5-HT packaging and release. Using the fluorescent probe FFN511, we demonstrate that EC cells express VMAT and that VMAT plays a functional role in 5-HT loading into vesicles. Carbon fiber amperometry studies illustrate that the amount of 5-HT released per exocytosis event from EC cells is dependent on both VMAT and the H(+)-ATPase pump, as demonstrated with reserpine or bafilomycin, respectively. We also demonstrate that increasing the amount of 5-HT loaded into EC cell vesicles does not result in an increase in quantal release. As this indicates that fusion pore size may be a limiting factor involved, we compared pore diameter in EC and chromaffin cells by assessing the vesicle capture of different-sized fluorescent probes to measure the extent of fusion pore dilation. This identified that EC cells have a reduced fusion pore expansion that does not exceed 9 nm in diameter. These results demonstrate that the small amounts of 5-HT released per fusion event in EC cells can be explained by a smaller fusion pore that limits 5-HT release capacity from individual vesicles. PMID:26574734

  19. Resolving pore-space characteristics by rate-controlled porosimetry

    SciTech Connect

    Yuan, H.H.; Swanson, B.F.

    1989-03-01

    By monitoring the mercury capillary pressure in rate-controlled porosimetry (intrusion) experiments, new information regarding the pore space of a rock sample has been obtained. With this technique, called an apparatus for pore examination (APEX), it is now possible to resolve the pore space of a rock sample into two interconnected parts. One part identifies the individual pore systems (pore bodies), which are low-energy sumps or regions of low capillarity. The other part corresponds to the pore throats that interconnect with pore systems. New capillary-pressure curves have been obtained by partitioning the total capillary-pressure curve (normal capillary-pressure curve) into two subcurves: the subison capillary-pressure curve, which details the distribution of pore bodies, and the rison capillary-pressure curve, which details the distribution of pore throats. The authors present APEX data on Berea sandstone and San Andres dolomite that show the volume distribution of low-capillarity regions within the pore space of these rocks. These regions of low capillarity are the principal pore-space regions that trap the residual nonwetting phase upon imbibition of a strongly wetting fluid, as measured by toluene/air systems. The residual nonwetting-phase saturations as determined by the APEX method and by the toluene/air method are in excellent agreement. Thus, the detailed volume distribution of pore systems responsible for trapped nonwetting-phase saturation is determined from APEX measurements, which can have important implications for EOR.

  20. Emergence of a large pore subpopulation during electroporating pulses.

    PubMed

    Smith, Kyle C; Son, Reuben S; Gowrishankar, T R; Weaver, James C

    2014-12-01

    Electroporation increases ionic and molecular transport through cell membranes by creating transient aqueous pores. These pores cannot be directly observed experimentally, but cell system modeling with dynamic electroporation predicts pore populations that produce cellular responses consistent with experiments. We show a cell system model's response that illustrates the life cycle of a pore population in response to a widely used 1 kV/cm, 100 μs trapezoidal pulse. Rapid pore creation occurs early in the pulse, followed by the gradual emergence of a subpopulation of large pores reaching ~30 nm radius. After the pulse, pores rapidly contract to form a single thermally broadened distribution of small pores (~1 nm radius) that slowly decays. We also show the response of the same model to pulses of 100 ns to 1 ms duration, each with an applied field strength adjusted such that a total of 10,000±100 pores are created. As pulse duration is increased, the pore size distributions vary dramatically and a distinct subpopulation of large pores emerges for pulses of microsecond and longer duration. This subpopulation of transient large pores is relevant to understanding rapid transport of macromolecules into and out of cells during a pulse. PMID:24290730

  1. Structural and functional analysis of the pore-forming toxin NetB from Clostridium perfringens.

    PubMed

    Yan, Xu-Xia; Porter, Corrine J; Hardy, Simon P; Steer, David; Smith, A Ian; Quinsey, Noelene S; Hughes, Victoria; Cheung, Jackie K; Keyburn, Anthony L; Kaldhusdal, Magne; Moore, Robert J; Bannam, Trudi L; Whisstock, James C; Rood, Julian I

    2013-01-01

    Clostridium perfringens is an anaerobic bacterium that causes numerous important human and animal diseases, primarily as a result of its ability to produce many different protein toxins. In chickens, C. perfringens causes necrotic enteritis, a disease of economic importance to the worldwide poultry industry. The secreted pore-forming toxin NetB is a key virulence factor in the pathogenesis of avian necrotic enteritis and is similar to alpha-hemolysin, a β-barrel pore-forming toxin from Staphylococcus aureus. To address the molecular mechanisms underlying NetB-mediated tissue damage, we determined the crystal structure of the monomeric form of NetB to 1.8 Å. Structural comparisons with other members of the alpha-hemolysin family revealed significant differences in the conformation of the membrane binding domain. These data suggested that NetB may recognize different membrane receptors or use a different mechanism for membrane-protein interactions. Consistent with this idea, electrophysiological experiments with planar lipid bilayers revealed that NetB formed pores with much larger single-channel conductance than alpha-hemolysin. Channel conductance varied with phospholipid net charge. Furthermore, NetB differed in its ion selectivity, preferring cations over anions. Using hemolysis as a screen, we carried out a random-mutagenesis study that identified several residues that are critical for NetB-induced cell lysis. Mapping of these residues onto the crystal structure revealed that they were clustered in regions predicted to be required for oligomerization or membrane binding. Together these data provide an insight into the mechanism of NetB-mediated pore formation and will contribute to our understanding of the mode of action of this important toxin. IMPORTANCE Necrotic enteritis is an economically important disease of the worldwide poultry industry and is mediated by Clostridium perfringens strains that produce NetB, a β-pore-forming toxin. We carried out

  2. Climate-mediated cooperation promotes niche expansion in burying beetles

    PubMed Central

    Sun, Syuan-Jyun; Rubenstein, Dustin R; Chen, Bo-Fei; Chan, Shih-Fan; Liu, Jian-Nan; Liu, Mark; Hwang, Wenbe; Yang, Ping-Shih; Shen, Sheng-Feng

    2014-01-01

    The ability to form cooperative societies may explain why humans and social insects have come to dominate the earth. Here we examine the ecological consequences of cooperation by quantifying the fitness of cooperative (large groups) and non-cooperative (small groups) phenotypes in burying beetles (Nicrophorus nepalensis) along an elevational and temperature gradient. We experimentally created large and small groups along the gradient and manipulated interspecific competition with flies by heating carcasses. We show that cooperative groups performed as thermal generalists with similarly high breeding success at all temperatures and elevations, whereas non-cooperative groups performed as thermal specialists with higher breeding success only at intermediate temperatures and elevations. Studying the ecological consequences of cooperation may not only help us to understand why so many species of social insects have conquered the earth, but also to determine how climate change will affect the success of these and other social species, including our own. DOI: http://dx.doi.org/10.7554/eLife.02440.001 PMID:24842999

  3. Atom cooling by nonadiabatic expansion

    SciTech Connect

    Chen Xi; Muga, J. G.; Campo, A. del; Ruschhaupt, A.

    2009-12-15

    Motivated by the recent discovery that a reflecting wall moving with a square-root-in-time trajectory behaves as a universal stopper of classical particles regardless of their initial velocities, we compare linear-in-time and square-root-in-time expansions of a box to achieve efficient atom cooling. For the quantum single-atom wave functions studied the square-root-in-time expansion presents important advantages: asymptotically it leads to zero average energy whereas any linear-in-time (constant box-wall velocity) expansion leaves a nonzero residual energy, except in the limit of an infinitely slow expansion. For finite final times and box lengths we set a number of bounds and cooling principles which again confirm the superior performance of the square-root-in-time expansion, even more clearly for increasing excitation of the initial state. Breakdown of adiabaticity is generally fatal for cooling with the linear expansion but not so with the square-root-in-time expansion.

  4. Thermal Expansion of Polyurethane Foam

    NASA Technical Reports Server (NTRS)

    Lerch, Bradley A.; Sullivan, Roy M.

    2006-01-01

    Closed cell foams are often used for thermal insulation. In the case of the Space Shuttle, the External Tank uses several thermal protection systems to maintain the temperature of the cryogenic fuels. A few of these systems are polyurethane, closed cell foams. In an attempt to better understand the foam behavior on the tank, we are in the process of developing and improving thermal-mechanical models for the foams. These models will start at the microstructural level and progress to the overall structural behavior of the foams on the tank. One of the key properties for model characterization and verification is thermal expansion. Since the foam is not a material, but a structure, the modeling of the expansion is complex. It is also exacerbated by the anisoptropy of the material. During the spraying and foaming process, the cells become elongated in the rise direction and this imparts different properties in the rise direction than in the transverse directions. Our approach is to treat the foam as a two part structure consisting of the polymeric cell structure and the gas inside the cells. The polymeric skeleton has a thermal expansion of its own which is derived from the basic polymer chemistry. However, a major contributor to the thermal expansion is the volume change associated with the gas inside of the closed cells. As this gas expands it exerts pressure on the cell walls and changes the shape and size of the cells. The amount that this occurs depends on the elastic and viscoplastic properties of the polymer skeleton. The more compliant the polymeric skeleton, the more influence the gas pressure has on the expansion. An additional influence on the expansion process is that the polymeric skeleton begins to breakdown at elevated temperatures and releases additional gas species into the cell interiors, adding to the gas pressure. The fact that this is such a complex process makes thermal expansion ideal for testing the models. This report focuses on the thermal

  5. Pattern curvature to control pore shape and its ordering

    NASA Astrophysics Data System (ADS)

    Yu, Guiduk; Shin, Kyusoon

    2013-03-01

    Triangular pore in inverse-hexagonal packing was fabricated by anodizing Al with convex pattern in hexagonal packing. The convexly patterned Al was prepared via replication of the concave structure formed in self-assembled anodized aluminum oxide (AAO). Self-assembled AAO without pre-patterning produces hexagonal packing circular pores. Exploitation of the inversed structure was found to create well-defined triangular pores in inverse-hexagonal packing. Anisotropic pore feature was discussed to come from the alternating distance between the pits and the curvature of the pattern. Also, by controlling the topography of the convex pattern around pits, we investigated the effect of pattern topography on pore initiation.

  6. Energy conversion device with support member having pore channels

    DOEpatents

    Routkevitch, Dmitri [Longmont, CO; Wind, Rikard A [Johnstown, CO

    2014-01-07

    Energy devices such as energy conversion devices and energy storage devices and methods for the manufacture of such devices. The devices include a support member having an array of pore channels having a small average pore channel diameter and having a pore channel length. Material layers that may include energy conversion materials and conductive materials are coaxially disposed within the pore channels to form material rods having a relatively small cross-section and a relatively long length. By varying the structure of the materials in the pore channels, various energy devices can be fabricated, such as photovoltaic (PV) devices, radiation detectors, capacitors, batteries and the like.

  7. Pore-space alteration in source rock (shales) during hydrocarbons generation: X-ray microtomography and pore-scale modelling study

    NASA Astrophysics Data System (ADS)

    Korost, Dmitry; Gerke, Kirill; Akhmanov, Grigory; Vasilyev, Roman; Čapek, Pavel; Karsanina, Marina; Nadezhkin, Dmitry

    2013-04-01

    free and adsorbed HC and water; (3) 300-400˚? - initial stage of HC formation owing to high-temperature pyrolysis of the solid organic matter and discharge of the chemically bound water; (4) 400-470˚? - temperature interval fitting the most intense stage of HC formation; (5) 470-510˚? - final stage of HC formation. Maximum sample heating in the experiment was determined as temperature of the onset of active decomposition of carbonates, i.e., in essence, irreversible metamorphism of the rock. An additional experiment was accomplished to assess dependence of the thermal expansion and contraction of sample during experiments with the rock structure. After the first microtomographic measurement, the sample was placed into the pyrolyser furnace and heated to 470˚? in 10 min, which resulted in the cracks' network similar to step-by-step heating structure formation: i.e., rock with cracks along and perpendicular to bedding direction. To quantify pore space alteration at each stage we use cluster analysis, correlation functions, local porosity analysis and pore-size distributions. Permeability measurements using conventional laboratory techniques are not possible between stepwise heatings. We used pore-scale modeling approach to determine this property numerically based on the 3D pore space information obtained with microtomography. The results of our experiment confirmed the possibility of vertical migration of fluids in the initially impermeable source rocks. They also revealed that pore space of the finely dispersed organic-rich rock changes during its controlled heating for HC generation according to the following scenario: (a) pores in the initial rock are small and isolated; (b) after some heating, pores at first are bound with each other due to the propagation of fractures along bedding, resulting in the formation of isolated filtration intervals; (c) further heating provokes the formation of bedding-perpendicular fractures that connect the isolated filtration

  8. Reactive transport in porous media: pore-network model approach compared to pore-scale model.

    PubMed

    Varloteaux, Clément; Vu, Minh Tan; Békri, Samir; Adler, Pierre M

    2013-02-01

    Accurate determination of three macroscopic parameters governing reactive transport in porous media, namely, the apparent solute velocity, the dispersion, and the apparent reaction rate, is of key importance for predicting solute migration through reservoir aquifers. Two methods are proposed to calculate these parameters as functions of the Péclet and the Péclet-Dahmköhler numbers. In the first method called the pore-scale model (PSM), the porous medium is discretized by the level set method; the Stokes and convection-diffusion equations with reaction at the wall are solved by a finite-difference scheme. In the second method, called the pore-network model (PNM), the void space of the porous medium is represented by an idealized geometry of pore bodies joined by pore throats; the flow field is computed by solving Kirchhoff's laws and transport calculations are performed in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. Two synthetic geometries of porous media are addressed by using both numerical codes. The first geometry is constructed in order to validate the hypotheses implemented in PNM. PSM is also used for a better understanding of the various reaction patterns observed in the asymptotic regime. Despite the PNM approximations, a very good agreement between the models is obtained, which shows that PNM is an accurate description of reactive transport. PNM, which can address much larger pore volumes than PSM, is used to evaluate the influence of the concentration distribution on macroscopic properties of a large irregular network reconstructed from microtomography images. The role of the dimensionless numbers and of the location and size of the largest pore bodies is highlighted. PMID:23496613

  9. Displacement of soil pore water by trichloroethylene

    USGS Publications Warehouse

    Wershaw, R. L.; Aiken, G.R.; Imbrigiotta, T.E.; Goldberg, M.C.

    1994-01-01

    Dense nonaqueous phase liquids (DNAPLS) are important pollutants because of their widespread use as chemical and industrial solvents. An example of the pollution caused by the discharge of DNAPLs is found at the Picatinny Arsenal, New Jersey, where trichloroethylene (TCE) has been discharged directly into the unsaturated zone. This discharge has resulted in the formation of a plume of TCE-contaminated water in the aquifer downgradient of the discharge. A zone of dark-colored groundwater containing a high dissolved organic C content has been found near the point of discharge of the TCE. The colored-water plume extends from the point of discharge at least 30 m (100 feet) downgradient. Fulvic acids isolated from the colored-waters plume, from water from a background well that has not been affected by the discharge of chlorinated solvents, and from soil pore water collected in a lysimeter installed at an uncontaminated site upgradient of the study area have been compared. Nuclear magnetic resonance spectra of the fulvic acids from the colored waters and from the lysimeter are very similar, but are markedly different from the nuclear magnetic resonance spectrum of the fulvic acid from the background well. The three-dimensional fluorescence spectrum and the DOC fractionation profile of the colored groundwater and the soil pore water are very similar to each other, but quite different from those of the background water. It is proposed from these observations that this colored water is soil pore water that has been displaced by a separate DNAPL liquid phase downward to the saturated zone.

  10. 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

  11. Precipitation in pores: A geochemical frontier

    DOE PAGESBeta

    Stack, Andrew G.

    2015-07-29

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

  12. Soil Pore Characteristics, an Underappreciated Regulatory Factor in GHGs Emission and C Stabilization

    NASA Astrophysics Data System (ADS)

    Toosi, E. R.; Yu, J.; Doane, T. A.; Guber, A.; Rivers, M. L.; Marsh, T. L.; Ali, K.; Kravchenko, A. N.

    2015-12-01

    Enduring challenges in understanding soil organic matter (SOM) stability and emission of greenhouse gases (GHGs) from soil stem from complexities of soil processes, many of which occur at micro-scales. The goal of this study is to evaluate the interactive effects soil pore characteristics, soil moisture levels, inherent SOM levels and properties, and substrate quality, on GHGs emission, and accelerated decomposition of native SOM following addition of fresh substrate i.e. priming. Our core hypothesis is that soil pore characteristics play a major role as a mediator in (i) the decomposition of organic matter regardless of its source (i.e. litter vs. native SOM) or substrate quality, as well as in (ii) GHGs emissions. Samples with prevalence of small (<10 μm) vs. large (>30 μm) pores were prepared from soils with similar properties but under long-term contrasting management. The samples were incubated (110 d) at low and optimum soil moisture conditions after addition of high quality (13C-soybean) and low quality (13C-corn) substrate. Headspace gas was analyzed for 13C-CO2 and GHGs on a regularly basis (day 1, 3, 7, 14, 24, 36, 48, 60, 72, 90, and 110). Selected samples were scanned at the early stage of decomposition (7, 14, 24 d) at 2-6 μm resolutions using X-ray computed μ tomography in order to: (1) quantify soil pore characteristics; (2) visualize and quantify distribution of soil moisture within samples of different pore characteristics; and (3) to visualize and measure losses of decomposing plant residue. Initial findings indicate that, consistent with our hypotheses, pore characteristics influenced GHGs emission, and intensity and pattern of plant residue decomposition. The importance of pores was highly pronounced in presence of added plant residue where greater N2O emission occurred in samples with dominant large pores, in contrast to CO2. Further findings will be discussed upon completion of the study and analysis of the results.

  13. Extreme accumulation of nucleotides in simulated hydrothermal pore systems

    PubMed Central

    Baaske, Philipp; Weinert, Franz M.; Duhr, Stefan; Lemke, Kono H.; Russell, Michael J.; Braun, Dieter

    2007-01-01

    We simulate molecular transport in elongated hydrothermal pore systems influenced by a thermal gradient. We find extreme accumulation of molecules in a wide variety of plugged pores. The mechanism is able to provide highly concentrated single nucleotides, suitable for operations of an RNA world at the origin of life. It is driven solely by the thermal gradient across a pore. On the one hand, the fluid is shuttled by thermal convection along the pore, whereas on the other hand, the molecules drift across the pore, driven by thermodiffusion. As a result, millimeter-sized pores accumulate even single nucleotides more than 108-fold into micrometer-sized regions. The enhanced concentration of molecules is found in the bulk water near the closed bottom end of the pore. Because the accumulation depends exponentially on the pore length and temperature difference, it is considerably robust with respect to changes in the cleft geometry and the molecular dimensions. Whereas thin pores can concentrate only long polynucleotides, thicker pores accumulate short and long polynucleotides equally well and allow various molecular compositions. This setting also provides a temperature oscillation, shown previously to exponentially replicate DNA in the protein-assisted PCR. Our results indicate that, for life to evolve, complicated active membrane transport is not required for the initial steps. We find that interlinked mineral pores in a thermal gradient provide a compelling high-concentration starting point for the molecular evolution of life. PMID:17494767

  14. Pore space morphology analysis using maximal inscribed spheres

    NASA Astrophysics Data System (ADS)

    Silin, Dmitriy; Patzek, Tad

    2006-11-01

    A new robust algorithm analyzing the geometry and connectivity of the pore space of sedimentary rock is based on fundamental concepts of mathematical morphology. The algorithm distinguishes between the “pore bodies” and “pore throats,” and establishes their respective volumes and connectivity. The proposed algorithm also produces a stick-and-ball diagram of the rock pore space. The tests on a pack of equal spheres, for which the results are verifiable, confirm its stability. The impact of image resolution on the algorithm output is investigated on the images of computer-generated pore space. One of distinctive features of our approach is that no image thinning is applied. Instead, the information about the skeleton is stored through the maximal inscribed balls or spheres (MIS) associated with each voxel. These maximal balls retain information about the entire pore space. Comparison with the results obtained by a thinning procedure preserving some topological properties of the pore space shows that our method produces more realistic estimates of the number and shapes of pore bodies and pore throats, and the pore coordination numbers. The distribution of maximal inscribed spheres makes possible simulation of mercury injection and computation of the corresponding dimensionless capillary pressure curve. It turns out that the calculated capillary pressure curve is a robust descriptor of the pore space geometry and, in particular, can be used to determine the quality of computer-based rock reconstruction.

  15. Relaxation and short time dynamics of bulk liquids and fluids confined in spherical cavities and slit pores.

    PubMed

    Krishnan, S H; Ayappa, K G

    2005-12-15

    The density of states for bulk and confined fluids have been modeled using a recently proposed gamma distribution (Krishnan, S. H.; Ayappa, K. G. J. Chem. Phys. 2004, 121, 3197). The gamma distribution results in a closed form analytical expression for the velocity autocorrelation function and the relaxation time of the fluid. The two parameters of the gamma distribution are related analytically to the second and fourth frequency moments of the fluid using short time expansions. The predictions by the proposed gamma model are compared with the velocity autocorrelation functions obtained using the theory of instantaneous normal modes (INMs) and from molecular dynamics simulations. The model is applied to a bulk soft sphere liquid and fluids confined in a spherical cavity and slit-shaped pores. The gamma model is able to capture the resulting changes in relaxation time due to changes in density and temperature extremely well for both the bulk liquid and confined inhomogeneous fluid situations. In all cases, the predictions by the gamma model are superior to those obtained from the INM theory. In the case of the fluid confined in a slit pore, the loadings were obtained from a grand canonical Monte Carlo simulation where the pore is equilibrated with a bulk fluid. This is similar to a confinement situation in a surface force apparatus. The predicted relaxation times vs pore widths from the gamma model are seen to accurately capture the oscillations due to formation and disruption of layers within the slit pore. PMID:16375288

  16. Caterpillar regurgitant induces pore formation in plant membranes.

    PubMed

    Lühring, Hinrich; Nguyen, Van Dy; Schmidt, Lilian; Röse, Ursula S R

    2007-11-27

    Formation of channel-like pores in a plant membrane was induced within seconds after application of an aqueous solution containing regurgitant of the insect larvae Spodoptera littoralis. Gated pore currents recorded on the tonoplast of the Charophyte Chara corallina displayed conductances up to several hundred pS. A voltage-dependent gating reaction supports the assumption that pore-forming molecules have amphipathic properties. Regurgitant samples separated into masses smaller or larger than 3kDa were evaluated by patch-clamp and mass spectroscopy. Fractions containing peptides larger than 3kDa constituted pores of large conductances, peptides smaller than 3kDa constituted pores of small conductances. Peptide-free eluates did not constitute conducting pores, indicating that pore-forming components in regurgitant are membrane-spanning oligopeptides. PMID:17967419

  17. Range Expansion of Heterogeneous Populations

    NASA Astrophysics Data System (ADS)

    Reiter, Matthias; Rulands, Steffen; Frey, Erwin

    2014-04-01

    Risk spreading in bacterial populations is generally regarded as a strategy to maximize survival. Here, we study its role during range expansion of a genetically diverse population where growth and motility are two alternative traits. We find that during the initial expansion phase fast-growing cells do have a selective advantage. By contrast, asymptotically, generalists balancing motility and reproduction are evolutionarily most successful. These findings are rationalized by a set of coupled Fisher equations complemented by stochastic simulations.

  18. Warp drive with zero expansion

    NASA Astrophysics Data System (ADS)

    Natário, José

    2002-03-01

    It is commonly believed that Alcubierre's warp drive works by contracting space in front of the warp bubble and expanding the space behind it. We show that this contraction/expansion is but a marginal consequence of the choice made by Alcubierre and explicitly construct a similar spacetime where no contraction/expansion occurs. Global and optical properties of warp-drive spacetimes are also discussed.

  19. Interface engineering of synthetic pores: towards hypersensitive biosensors.

    PubMed

    Mora, Federico; Tran, Duy-Hien; Oudry, Natalie; Hopfgartner, Gerard; Jeannerat, Damien; Sakai, Naomi; Matile, Stefan

    2008-01-01

    Hydrophilic anchoring is introduced as a promising strategy to constructively control the various interactions of synthetic pore sensors with the surrounding biphasic environment. Artificial rigid-rod beta barrels are selected as classical synthetic multifunctional pores and random-coil tetralysines are attached as hydrophilic anchors. The synthesis of this advanced pore is accomplished in 32 steps from commercially available starting materials. With regard to pore activity as such, the key impact of hydrophilic anchoring is a change from a Hill coefficient n<1 to n=4. This change confirms successful suppression of the competing self-assembly with precipitation from the aqueous phase as the origin of the accomplished increase in pore activity. The hydrophilic anchors do not interfere with the blockage of the synthetic pore sensors by anionic analytes. In the case of stoichiometric binding of blockers (K(D)=EC(50) of the pore; EC(50)=concentration needed to observe 50 % pore activity), however, the increase in pore activity achieved by hydrophilic anchoring results in improved pore blockage under high dilution conditions. Controls confirm that this increase does not occur with analytes that do not exhibit stoichiometric binding (K(D)>EC(50)). These results not only reveal stoichiometric binding as the expected origin of the sensitivity limit of synthetic pore sensors, they also provide promising solutions for this problem. The combination of hydrophilic anchoring with targeted pore formation emerges as a particularly promising strategy to further reduce effective pore concentrations. The scope and limitations of this approach are exemplified with pertinent analyte pairs that are essential for the sensing of sucrose, lactose, acetate, and glutamate with synthetic pores in samples from the supermarket. PMID:18067110

  20. Mediation Analysis with Multiple Mediators

    PubMed Central

    VanderWeele, T.J.; Vansteelandt, S.

    2014-01-01

    Recent advances in the causal inference literature on mediation have extended traditional approaches to direct and indirect effects to settings that allow for interactions and non-linearities. In this paper, these approaches from causal inference are further extended to settings in which multiple mediators may be of interest. Two analytic approaches, one based on regression and one based on weighting are proposed to estimate the effect mediated through multiple mediators and the effects through other pathways. The approaches proposed here accommodate exposure-mediator interactions and, to a certain extent, mediator-mediator interactions as well. The methods handle binary or continuous mediators and binary, continuous or count outcomes. When the mediators affect one another, the strategy of trying to assess direct and indirect effects one mediator at a time will in general fail; the approach given in this paper can still be used. A characterization is moreover given as to when the sum of the mediated effects for multiple mediators considered separately will be equal to the mediated effect of all of the mediators considered jointly. The approach proposed in this paper is robust to unmeasured common causes of two or more mediators. PMID:25580377

  1. Size of diffusion pore of Alcaligenes faecalis.

    PubMed

    Ishii, J; Nakae, T

    1988-03-01

    The diffusion pore of the outer membrane of Alcaligenes faecalis was shown to be substantially smaller than the Escherichia coli porin pore. In experiments with intact cells, pentoses and hexoses penetrated into the NaCl-expanded periplasm, whereas saccharides of Mr greater than 342 did not. Cells treated with 0.5 M saccharides of Mr greater than 342 weighed 33 to 38% less than cells treated with isotonic solution, suggesting that these saccharides do not permeate through the outer membrane. The diffusion rates of various solutes through the liposome membranes reconstituted from the Mr-43,000 outer membrane protein showed the following characteristics. (i) The relative diffusion rates of pentoses, hexoses, and methylhexoses appeared to be about 1.0, 0.6, and negligibly small, respectively. (ii) The diffusion rate of glucose appeared to be about 1/10th that with the E. coli B porin. (iii) The diffusion rate of gluconic acid was five to seven times higher than that of glucose. (iv) The diffusion rates of beta-lactam antibiotics appeared to be 40 to less than 10% of those with the E. coli B porin. PMID:2835003

  2. Size of diffusion pore of Alcaligenes faecalis.

    PubMed Central

    Ishii, J; Nakae, T

    1988-01-01

    The diffusion pore of the outer membrane of Alcaligenes faecalis was shown to be substantially smaller than the Escherichia coli porin pore. In experiments with intact cells, pentoses and hexoses penetrated into the NaCl-expanded periplasm, whereas saccharides of Mr greater than 342 did not. Cells treated with 0.5 M saccharides of Mr greater than 342 weighed 33 to 38% less than cells treated with isotonic solution, suggesting that these saccharides do not permeate through the outer membrane. The diffusion rates of various solutes through the liposome membranes reconstituted from the Mr-43,000 outer membrane protein showed the following characteristics. (i) The relative diffusion rates of pentoses, hexoses, and methylhexoses appeared to be about 1.0, 0.6, and negligibly small, respectively. (ii) The diffusion rate of glucose appeared to be about 1/10th that with the E. coli B porin. (iii) The diffusion rate of gluconic acid was five to seven times higher than that of glucose. (iv) The diffusion rates of beta-lactam antibiotics appeared to be 40 to less than 10% of those with the E. coli B porin. Images PMID:2835003

  3. Bimodal mesoporous silica with bottleneck pores.

    PubMed

    Reber, M J; Brühwiler, D

    2015-11-01

    Bimodal mesoporous silica consisting of two sets of well-defined mesopores is synthesized by a partial pseudomorphic transformation of an ordered mesoporous starting material (SBA-15 type). The introduction of a second set of smaller mesopores (MCM-41 type) establishes a pore system with bottlenecks that restricts the access to the core of the bimodal mesoporous silica particles. The particle size and shape of the starting material are retained, but micropores present in the starting material disappear during the transformation, leading to a true bimodal mesoporous product. A varying degree of transformation allows the adjustment of the pore volume contribution of the two mesopore domains. Information on the accessibility of the mesopores is obtained by the adsorption of fluorescence-labeled poly(amidoamine) dendrimers and imaging by confocal laser scanning microscopy. This information is correlated with nitrogen sorption data to provide insights regarding the spatial distribution of the two mesopore domains. The bimodal mesoporous materials are excellent model systems for the investigation of cavitation effects in nitrogen desorption isotherms. PMID:26399172

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

    PubMed Central

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

    2014-01-01

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

  5. Mesoscale and microscale observations of biological growth in a silicon pore imaging element

    SciTech Connect

    Dupin, H.J.; McCarty, P.L.

    1999-04-15

    The factors contributing to biological clogging of filtration beds, recharge basins, and aquifers during in-situ bioremediation are yet poorly understood. Better physical understanding is needed of the processes affecting biological growth in aquifers, filtration beds, and recharge basins. Toward this end, a two-dimensional random width network pore model etched in a silicon wafer was developed to simulate microbial growth in porous media representative of fine sand. This Silicon Pore Imaging Element (SPIE) was seeded with a mixed culture and fed with 0.34 mM acetate under aerobic conditions and at fixed flow rate. Twelve filamentous colonies grew in a dense manner in the upgradient and lateral directions at low density in the downgradient direction. Heterogeneous colonization led to empty zones. Particle tracking suggested rerouting of flow due to biomass growth. Microscale time-lapse measured filamentous growth rates were in good agreement with measured mesoscale colony expansion rates. Rather than the microscale concept of biomass developing at the surface of soil grains, filamentous growth may be better represented as mesoscale colonies spanning over several pores and separated from each other by open flow channels. Biological clogging might be prevented if such flow channels could be kept open in some manner.

  6. Multi-ion pore behaviour in the CFTR chloride channel.

    PubMed

    Tabcharani, J A; Rommens, J M; Hou, Y X; Chang, X B; Tsui, L C; Riordan, J R; Hanrahan, J W

    1993-11-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a non-rectifying, low-conductance channel regulated by ATP and phosphorylation, which mediates apical chloride conductance in secretory epithelia and malfunctions in cystic fibrosis (CF). Mutations at Lys 335 and Arg 347 in the sixth predicted transmembrane helix of CFTR alter its halide selectivity in whole-cell studies and its single channel conductance, but the physical basis of these alterations is unknown and permeation in CFTR is poorly understood. Here we present evidence that wild-type CFTR can contain more than one anion simultaneously. The conductance of CFTR passes through a minimum when channels are bathed in mixtures of two permeant anions. This anomalous mole fraction effect can be abolished by replacing Arg 347 with an aspartate and can be toggled on or off by varying the pH after the same residue is replaced with a histidine. Thus the CFTR channel should provide a convenient model in which to study multi-ion pore behaviour and conduction. The loss of multiple occupancy may explain how naturally occurring CF mutations at this site cause disease. PMID:7694154

  7. Nanoscale Pore Imaging and Pore Scale Fluid Flow Modeling in Chalk

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy

    2004-08-19

    For many rocks of high economic interest such as chalk, diatomite, tight gas sands or coal, nanometer scale resolution is needed to resolve the 3D-pore structure, which controls the flow and trapping of fluids in the rocks. Such resolutions cannot be achieved with existing tomographic technologies. A new 3D imaging method, based on serial sectioning and using the Focused Ion Beam (FIB) technology has been developed. FIB allows for the milling of layers as thin as 10 nanometers by using accelerated Ga+ ions to sputter atoms from the sample surface. After each milling step, as a new surface is exposed, a 2D image of this surface is generated. Next, the 2D images are stacked to reconstruct the 3D pore or grain structure. Resolutions as high as 10 nm are achievable using such a technique. A new robust method of pore-scale fluid flow modeling has been developed and applied to sandstone and chalk samples. The method uses direct morphological analysis of the pore space to characterize the petrophysical properties of diverse formations. Not only petrophysical properties (porosity, permeability, relative permeability and capillary pressures) can be computed but also flow processes, such as those encountered in various IOR approaches, can be simulated. Petrophysical properties computed with the new method using the new FIB data will be presented. Present study is a part of the development of an Electronic Core Laboratory at LBNL/UCB.

  8. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    SciTech Connect

    Lin, Qingqing; Li, Huilin; Wang, Tong; London, Erwin

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakage assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.

  9. Decreasing transmembrane segment length greatly decreases perfringolysin O pore size

    DOE PAGESBeta

    Lin, Qingqing; Li, Huilin; Wang, Tong; London, Erwin

    2015-04-08

    Perfringolysin O (PFO) is a transmembrane (TM) β-barrel protein that inserts into mammalian cell membranes. Once inserted into membranes, PFO assembles into pore-forming oligomers containing 30–50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. In this study, we found that altering PFO TM segment length can alter the size of PFO pores. A PFO mutant with lengthened TM segments oligomerized to a similar extent as wild-type PFO, and exhibited pore-forming activity and a pore size very similar to wild-type PFO as measured by electron microscopy and a leakagemore » assay. In contrast, PFO with shortened TM segments exhibited a large reduction in pore-forming activity and pore size. This suggests that the interaction between TM segments can greatly affect the size of pores formed by TM β-barrel proteins. PFO may be a promising candidate for engineering pore size for various applications.« less

  10. Atomistic Simulations of Pore Formation and Closure in Lipid Bilayers

    PubMed Central

    Bennett, W. F. Drew; Sapay, Nicolas; Tieleman, D. Peter

    2014-01-01

    Cellular membranes separate distinct aqueous compartments, but can be breached by transient hydrophilic pores. A large energetic cost prevents pore formation, which is largely dependent on the composition and structure of the lipid bilayer. The softness of bilayers and the disordered structure of pores make their characterization difficult. We use molecular-dynamics simulations with atomistic detail to study the thermodynamics, kinetics, and mechanism of pore formation and closure in DLPC, DMPC, and DPPC bilayers, with pore formation free energies of 17, 45, and 78 kJ/mol, respectively. By using atomistic computer simulations, we are able to determine not only the free energy for pore formation, but also the enthalpy and entropy, which yields what is believed to be significant new insights in the molecular driving forces behind membrane defects. The free energy cost for pore formation is due to a large unfavorable entropic contribution and a favorable change in enthalpy. Changes in hydrogen bonding patterns occur, with increased lipid-water interactions, and fewer water-water hydrogen bonds, but the total number of overall hydrogen bonds is constant. Equilibrium pore formation is directly observed in the thin DLPC lipid bilayer. Multiple long timescale simulations of pore closure are used to predict pore lifetimes. Our results are important for biological applications, including the activity of antimicrobial peptides and a better understanding of membrane protein folding, and improve our understanding of the fundamental physicochemical nature of membranes. PMID:24411253

  11. Change of pore properties during carbonization of coking coal

    SciTech Connect

    Miura, S.; Silveston, P.L.

    1980-01-01

    Porosimetry, sorption and density measurements are reported on two caking bituminous coals. West Virginia Jewel No. 2 medium volatile and a Pennsylvania Pittsburgh seam high volatile C, for final carbonization temperatures between 400 and 1000/sup 0/C. Samples were not confined and heating rates of 3 and 8.2%/min were employed. The medium volatile samples exhibit pronounced maxima in pore volume, pore surface area and porosity between 600 and 800/sup 0/C. These temperatures are unexpectedly greater than those at which maximum particle dilation and maximum rate of devolatilization occur. An explanation for this observation is that closed pores are created during carbonization below 600/sup 0/C which are opened when carbonization is carried to higher temperatures. Shape of the pore volume curves suggest new pore initiation, pore growth and pore shrinkage are the dominant processes operating, although collapse of the ultra micro pore structure seems to occur above 800/sup 0/C. A pore development model employing simple expressions for the three dominant processes successfully predicts the pore volume and surface area changes. Apparent activation energies derived from the model indicate that the rates of these dominant steps are controled by basicaly physical, not chemical, changes.

  12. Electrokinetic induced solute dispersion in porous media; pore network modeling

    NASA Astrophysics Data System (ADS)

    Li, Shuai; Schotting, Ruud; Raoof, Amir

    2013-04-01

    Electrokinetic flow plays an important role in remediation process, separation technique, and chromatography. The solute dispersion is a key parameter to determine transport efficiency. In this study, we present the electrokinetic effects on solute dispersion in porous media at the pore scale, using a pore network model. The analytical solution of the electrokinetic coupling coefficient was obtained to quantity the fluid flow velocity in a cylinder capillary. The effect of electrical double layer on the electrokinetic coupling coefficient was investigated by applying different ionic concentration. By averaging the velocity over cross section within a single pore, the average flux was obtained. Applying such single pore relationships, in the thin electrical double layer limit, to each and every pore within the pore network, potential distribution and the induced fluid flow was calculated for the whole domain. The resulting pore velocities were used to simulate solute transport within the pore network. By averaging the results, we obtained the breakthrough curve (BTC) of the average concentration at the outlet of the pore network. Optimizing the solution of continuum scale advection-dispersion equation to such a BTC, solute dispersion coefficient was estimated. We have compared the dispersion caused by electrokinetic flow and pure pressure driven flow under different Peclet number values. In addition, the effect of microstructure and topological properties of porous media on fluid flow and solute dispersion is presented, mainly based on different pore coordination numbers.

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  14. A model for determining inaccessible pore volume in polymer flooding

    SciTech Connect

    Jensen, T.B. ); Satchwell, R.M. )

    1992-01-01

    Until now, only imprecise approximation of inaccessible pore volume have been employed in mathematical models of polymer flooding, causing these reservoir models to yield inaccurate results. This paper reports a new model to precisely describe inaccessible pore volume in polymer flow through porous media. The model can also be applied as a screening tool for determining candidate reservoirs for polymer flooding given a typical polymer, or it can be used to screen different polymer types once a candidate reservoir has been chosen. This new model is based on theoretical and actual pore throat entry and polymer molecule size distributions. Both pore throat and polymer size distributions are thoroughly reviewed. Inaccessible pore volume, in this model, is defined as the probability of randomly selected polymer molecules being larger than randomly selected pore throats, and is determined by statistically describing the polymer and pore throats as continuous distributions. Examples of the inaccessible pore volume model employing Uniform, Triangular, and Gamma distributions are included. Results obtained show an adequate match between experimental data and theoretical results. A nomograph for determining inaccessible pore volume in polymer flow through porous media based on pore throat and polymer molecule sizes is presented.

  15. Bovine Serum Albumin Adsorption in Mesoporous Titanium Dioxide: Pore Size and Pore Chemistry Effect.

    PubMed

    Liu, Chang; Guo, Yanhua; Hong, Qiliang; Rao, Chao; Zhang, Haijuan; Dong, Yihui; Huang, Liangliang; Lu, Xiaohua; Bao, Ningzhong

    2016-04-26

    Understanding the mechanism of protein adsorption and designing materials with high sensitivity, high specificity and fast response are critical to develop the next-generation biosensing and diagnostic platforms. Mesoporous materials with high surface area, tunable pores, and good thermal/hydrostatic stabilities are promising candidates in this field. Because of the excellent biocompatibility, titanium dioxide has received an increasing interest in the past decade for biomedical applications. In this work, we synthesized mesoporous titanium dioxide with controlled pore sizes (7.2-28.0 nm) and explored their application for bovine serum albumin (BSA) adsorption. Scanning electron microscopy (SEM), X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and nitrogen adsorption/desorption experiments were performed to characterize the mesoporous TiO2 samples before and after BSA adsorption. Isothermal microcalorimetry was applied to measure both the adsorption heat and conformation rearrangement heat of BSA in those mesopores. We also carried out thermogravimetry measurements to qualitatively estimate the concentration of hydroxyl groups, which plays an important role in stabilizing BSA in-pore adsorption. The adsorption stability was also examined by leaching experiments. The results showed that TiO2 mesopores can host BSA adsorption when their diameters are larger than the hydrodynamic size of BSA (∼9.5 nm). In larger mesopores studied, two BSA molecules were adsorbed in the same pores. In contrast to the general understanding that large mesopores demonstrate poor stabilities for protein adsorptions, the synthesized mesoporous TiO2 samples demonstrated good leaching stabilities for BSA adsorption. This is probably due to the combination of the mesoporous confinement and the in-pore hydroxyl groups. PMID:27048991

  16. Rock expansion caused by ultrasound

    NASA Astrophysics Data System (ADS)

    Hedberg, C.; Gray, A.

    2013-12-01

    It has during many years been reported that materials' elastic modulus decrease when exposed to influences like mechanical impacts, ultrasound, magnetic fields, electricity and even humidity. Non-perfect atomic structures like rocks, concrete, or damaged metals exhibit a larger effect. This softening has most often been recorded by wave resonance measurements. The motion towards equilibrium is slow - often taking hours or days, which is why the effect is called Slow Dynamics [1]. The question had been raised, if a material expansion also occurs. 'The most fundamental parameter to consider is the volume expansion predicted to occur when positive hole charge carriers become activated, causing a decrease of the electron density in the O2- sublattice of the rock-forming minerals. This decrease of electron density should affect essentially all physical parameters, including the volume.' [2]. A new type of configuration has measured expansion of a rock subjected to ultrasound. A PZT was used as a pressure sensor while the combined thickness of the rock sample and the PZT sensor was held fixed. The expansion increased the stress in both the rock and the PZT, which gave an out-put voltage from the PZT. Knowing its material properties then made it possible to calculate the rock expansion. The equivalent strain caused by the ultrasound was approximately 3 x 10-5. The temperature was monitored and accounted for during the tests and for the maximum expansion the increase was 0.7 C, which means the expansion is at least to some degree caused by heating of the material by the ultrasound. The fraction of bonds activated by ultrasound was estimated to be around 10-5. References: [1] Guyer, R.A., Johnson, P.A.: Nonlinear Mesoscopic Elasticity: The Complex Behaviour of Rocks, Soils, Concrete. Wiley-VCH 2009 [2] M.M. Freund, F.F. Freund, Manipulating the Toughness of Rocks through Electric Potentials, Final Report CIF 2011 Award NNX11AJ84A, NAS Ames 2012.

  17. Global functional analyses of cellular responses to pore-forming toxins.

    PubMed

    Kao, Cheng-Yuan; Los, Ferdinand C O; Huffman, Danielle L; Wachi, Shinichiro; Kloft, Nicole; Husmann, Matthias; Karabrahimi, Valbona; Schwartz, Jean-Louis; Bellier, Audrey; Ha, Christine; Sagong, Youn; Fan, Hui; Ghosh, Partho; Hsieh, Mindy; Hsu, Chih-Shen; Chen, Li; Aroian, Raffi V

    2011-03-01

    Here we present the first global functional analysis of cellular responses to pore-forming toxins (PFTs). PFTs are uniquely important bacterial virulence factors, comprising the single largest class of bacterial protein toxins and being important for the pathogenesis in humans of many Gram positive and Gram negative bacteria. Their mode of action is deceptively simple, poking holes in the plasma membrane of cells. The scattered studies to date of PFT-host cell interactions indicate a handful of genes are involved in cellular defenses to PFTs. How many genes are involved in cellular defenses against PFTs and how cellular defenses are coordinated are unknown. To address these questions, we performed the first genome-wide RNA interference (RNAi) screen for genes that, when knocked down, result in hypersensitivity to a PFT. This screen identifies 106 genes (∼0.5% of genome) in seven functional groups that protect Caenorhabditis elegans from PFT attack. Interactome analyses of these 106 genes suggest that two previously identified mitogen-activated protein kinase (MAPK) pathways, one (p38) studied in detail and the other (JNK) not, form a core PFT defense network. Additional microarray, real-time PCR, and functional studies reveal that the JNK MAPK pathway, but not the p38 MAPK pathway, is a key central regulator of PFT-induced transcriptional and functional responses. We find C. elegans activator protein 1 (AP-1; c-jun, c-fos) is a downstream target of the JNK-mediated PFT protection pathway, protects C. elegans against both small-pore and large-pore PFTs and protects human cells against a large-pore PFT. This in vivo RNAi genomic study of PFT responses proves that cellular commitment to PFT defenses is enormous, demonstrates the JNK MAPK pathway as a key regulator of transcriptionally-induced PFT defenses, and identifies AP-1 as the first cellular component broadly important for defense against large- and small-pore PFTs. PMID:21408619

  18. Silicon pore optics development for ATHENA

    NASA Astrophysics Data System (ADS)

    Collon, Maximilien J.; Vacanti, Giuseppe; Günther, Ramses; Yanson, Alex; Barrière, Nicolas; Landgraf, Boris; Vervest, Mark; Chatbi, Abdelhakim; Beijersbergen, Marco W.; Bavdaz, Marcos; Wille, Eric; Haneveld, Jeroen; Koelewijn, Arenda; Leenstra, Anne; Wijnperle, Maurice; van Baren, Coen; Müller, Peter; Krumrey, Michael; Burwitz, Vadim; Pareschi, Giovanni; Conconi, Paolo; Christensen, Finn E.

    2015-09-01

    The ATHENA mission, a European large (L) class X-ray observatory to be launched in 2028, will essentially consist of an X-ray lens and two focal plane instruments. The lens, based on a Wolter-I type double reflection grazing incidence angle design, will be very large (~ 3 m in diameter) to meet the science requirements of large effective area (1-2 m2 at a few keV) at a focal length of 12 m. To meet the high angular resolution (5 arc seconds) requirement the X-ray lens will also need to be very accurate. Silicon Pore Optics (SPO) technology has been invented to enable building such a lens and thus enabling the ATHENA mission. We will report in this paper on the latest status of the development, including details of X-ray test campaigns.

  19. Development of a closed pore insulation material

    NASA Technical Reports Server (NTRS)

    Tobin, A.; Feldman, C.; Russak, M.; Reichman, J.

    1973-01-01

    A closed pore ceramic foam insulation material (CPI) has been developed that offers possibilities for use as a reusable external heat shield for the NASA manned space shuttle. The outstanding characteristics of CPI are: (1) negligible water absorption due to a noninterconnecting network of cells; (2) high emittance at room and elevated temperature; (3) ability to survive at least 10 simulated reentry cycles to 1500 K using radiant heat lamps to simulate the reentry heat fluxes; (4) ability to survive, with no change in properties or appearance, at least 10 simulated plasma arc jet cycles to 1500 K (with the exception of some stress cracks induced either by the unduly severe nature of the initial arc splash heating pulse or by improper mechanical holding of the specimen in the test fixture); (5) strength (flexure); and (6) a low thermal conductivity throughout the temperature range of interest for the space shuttle.

  20. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1998-01-01

    A method for making a biocompatible polymer article using a uniform atomic oxygen treatment is disclosed. The sub-strate may be subsequently optionally grated with a compatibilizing compound. Compatibilizing compounds may include proteins, phosphorylcholine groups, platelet adhesion preventing polymers, albumin adhesion promoters, and the like. The compatibilized substrate may also have a living cell layer adhered thereto. The atomic oxygen is preferably produced by a flowing afterglow microwave discharge, wherein the substrate resides in a sidearm out of the plasma. Also, methods for culturing cells for various purposes using the various membranes are disclosed as well. Also disclosed are porous organic polymers having a distributed pore chemistry (DPC) comprising hydrophilic and hydrophobic region, and a method for making the DPC by exposing the polymer to atomic oxygen wherein the rate of hydrophilization is greater than the rate of mass loss.

  1. Distributed Pore Chemistry in Porous Organic Polymers

    NASA Technical Reports Server (NTRS)

    Koontz, Steven L. (Inventor)

    1999-01-01

    A method for making a biocompatible polymer article using a uniform atomic oxygen treatment is disclosed. The substrate may be subsequently optionally grated with a compatibilizing compound. Compatibilizing compounds may include proteins, phosphorylcholine groups, platelet adhesion preventing polymers, albumin adhesion promoters, and the like. The compatibilized substrate may also have a living cell layer adhered thereto. The atomic oxygen is preferably produced by a flowing afterglow microwave discharge. wherein the substrate resides in a sidearm out of the plasma. Also, methods for culturing cells for various purposes using the various membranes are disclosed as well. Also disclosed are porous organic polymers having a distributed pore chemistry (DPC) comprising hydrophilic and hydrophobic regions. and a method for making the DPC by exposing the polymer to atomic oxygen wherein the rate of hydrophilization is greater than the rate of mass loss.

  2. P2X7R large pore is partially blocked by pore forming proteins antagonists in astrocytes.

    PubMed

    Faria, Robson X; Reis, Ricardo A M; Ferreira, Leonardo G B; Cezar-de-Mello, Paula F T; Moraes, Milton O

    2016-06-01

    The ATP-gated P2X7R (P2X7R) is a channel, which is involved in events, such as inflammation, cell death, and pain. The most intriguing event concerning P2X7R functions is the phenomenon of pore dilation. Once P2X7R is activated, the permeability of the plasma membrane becomes higher, leading to the permeation of 1000 Da-weight solutes. The mechanisms involved in this process remain unclear. Nevertheless, this event is not exclusively through P2X7R, as other proteins may form large pores in the plasma membrane. Recent evidence concerning pore formation reveals putative P2X7R and other pores-associated protein complexes, revealing cross-interactive pharmacological and biophysical issues. In this work, we showed results that corroborated with cross-interactive aspects with P2X7R and pores in astrocytes. These cells expressed most of the pores, including P2X7R. We discovered that different pore types open with peculiar characteristics, as both anionic and cationic charged solutes permeate the plasma membrane, following P2X7R activation. Moreover, we showed that both synergic and additive relationships are found within P2X7, cationic, and anionic large pores. Therefore, our data suggest that other protein-related pores are assembled following the formation of P2X7R pore. PMID:26830892

  3. Morphological instability of whiskers, pores, and tubules

    NASA Astrophysics Data System (ADS)

    Kirill, Dimitri Jay

    1999-11-01

    A thin, stressed solid cylinder, a whisker, is subject to mass transport by curvature and elastic-stress-driven surface diffusion. The stability of the cylindrical surface is examined using linear stability theory. It is found that the applied stress leads to a greater range of unstable wavenumbers, and hence is destabilizing. The presence of elastic strains can excite non-axisymmetric modes, which, under certain conditions, are preferred and can give rise to helical surfaces. In addition, asymptotic formulas for growth rate in the limit of long and short wavelengths are found. A possible experiment is proposed which, if undertaken, should reveal the helical instability. The linear stability analysis is then extended to the case of cylindrical pore channels and hollow cylindrical tubules. In both cases, results similar to the whisker are found---increased applied stress leads to a greater range of unstable wavenumbers. For both the pore and tubule geometries, the dominant modes are axisymmetric for any value of applied stress; this contrasts with the solid whisker results. Since the tubule geometry consists of an inner and outer surface, there is a phase relationship between the two surface perturbations. The most dangerous eigenmode can exhibit either in-phase (sinuous) or 180° out-of-phase (varicose) perturbations, depending on the value of applied stress. Furthermore, there is a critical value of applied stress below which the most dangerous mode is varicose, and above which it is sinuous. Lastly, asymptotic formulas for growth rate are obtained in the limit of a thin-walled tubule. These results compare favorably to work done on stressed lamellar composites.

  4. The structure of a melittin-stabilized pore.

    PubMed

    Leveritt, John M; Pino-Angeles, Almudena; Lazaridis, Themis

    2015-05-19

    Melittin has been reported to form toroidal pores under certain conditions, but the atomic-resolution structure of these pores is unknown. A 9-μs all-atom molecular-dynamics simulation starting from a closely packed transmembrane melittin tetramer in DMPC shows formation of a toroidal pore after 1 μs. The pore remains stable with a roughly constant radius for the rest of the simulation. Surprisingly, one or two melittin monomers frequently transition between transmembrane and surface states. All four peptides are largely helical. A simulation in a DMPC/DMPG membrane did not lead to a stable pore, consistent with the experimentally observed lower activity of melittin on anionic membranes. The picture that emerges from this work is rather close to the classical toroidal pore, but more dynamic with respect to the configuration of the peptides. PMID:25992720

  5. Cylinder Expansion in Polypropylene Tubes

    NASA Astrophysics Data System (ADS)

    Pemberton, Steven; Tappan, Bryce; Manner, Virginia

    2015-06-01

    Cylinder Expansion has long been the benchmark test used to establish an equation of state for any detonable energetic material. However, some new explosives have properties that prevent the use of the traditional copper-walled test; two such issues are materials whose detonations proceed more slowly than the acoustic velocity in the copper liner, and materials with failure diameters large enough to render copper testing prohibitively expensive. Results are presented for experiments conducted using a stoichiometric mixture of ammonium perchlorate and dodecane, a slow-detonating explosive. In copper walls inconsistent expansion was observed due to acoustic precursor waves within the wall. Additional testing was performed in polyethylene and polypropylene tubes to determine whether sufficient expansion could be observed, and satisfactory results were achieved with polypropylene. (96TW-2015-0001) Membership Pending.

  6. Nonicosahedral pathways for capsid expansion

    NASA Astrophysics Data System (ADS)

    Cermelli, Paolo; Indelicato, Giuliana; Twarock, Reidun

    2013-09-01

    For a significant number of viruses a structural transition of the protein container that encapsulates the viral genome forms an important part of the life cycle and is a prerequisite for the particle becoming infectious. Despite many recent efforts the mechanism of this process is still not fully understood, and a complete characterization of the expansion pathways is still lacking. We present here a coarse-grained model that captures the essential features of the expansion process and allows us to investigate the conditions under which a viral capsid becomes unstable. Based on this model we demonstrate that the structural transitions in icosahedral viral capsids are likely to occur through a low-symmetry cascade of local expansion events spreading in a wavelike manner over the capsid surface.

  7. Pauli mechanism for universal expansion

    NASA Astrophysics Data System (ADS)

    Hayes, Robert

    2016-03-01

    By assuming the cosmological principle includes the Pauli exclusion principle (PEP) and that existence occurred post big bang within Planck time and length scales, a model for universal expansion can be argued. All Fermionic matter is forced by the PEP to make a quantum transition to minimally orthogonal states scaling with that predicted for a neutron star (NS). This predicts the minimum inflation time scale to be on the order of 1e-44 s. A coupling of primordial low mass neutrinos to have wavelengths comparable to or greater than the Hubble length is also postulated as a contributor to universal expansion. The model provides a mechanistic explanation for universal expansion using only physics from the standard model. This work supported in part under federal Grant NRC-HQ-84-14-G-0059.

  8. Thermal Expansion of Hafnium Carbide

    NASA Technical Reports Server (NTRS)

    Grisaffe, Salvatore J.

    1960-01-01

    Since hafnium carbide (HfC) has a melting point of 7029 deg. F, it may have many high-temperature applications. A literature search uncovered very little information about the properties of HfC, and so a program was initiated at the Lewis Research Center to determine some of the physical properties of this material. This note presents the results of the thermal expansion investigation. The thermal-expansion measurements were made with a Gaertner dilatation interferometer calibrated to an accuracy of +/- 1 deg. F. This device indicates expansion by the movement of fringes produced by the cancellation and reinforcement of fixed wave-length light rays which are reflected from the surfaces of two parallel quartz glass disks. The test specimens which separate these disks are three small cones, each approximately 0.20 in. high.

  9. An expansion for neutrino phenomenology

    NASA Astrophysics Data System (ADS)

    Grinstein, Benjamín; Trott, Michael

    2012-09-01

    We develop a formalism for constructing the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) matrix and neutrino masses using an expansion that originates when a sequence of heavy right handed neutrinos are integrated out, assuming a seesaw mechanism for the origin of neutrino masses. The expansion establishes relationships between the structure of the PMNS matrix and the mass differences of neutrinos, and allows symmetry implications for measured deviations from tri-bimaximal form to be studied systematically. Our approach does not depend on choosing the rotation between the weak and mass eigenstates of the charged lepton fields to be diagonal. We comment on using this expansion to examine the symmetry implications of the recent results from the Daya-Bay collaboration reporting the discovery of a non zero value for θ 13, indicating a deviation from tri-bimaximal form, with a significance of 5.2 σ.

  10. Tension-induced pore formation and leakage in adhering vesicles

    NASA Astrophysics Data System (ADS)

    Lenz, P.; Johnson, J. M.; Chan, Y.-H. M.; Boxer, S. G.

    2006-08-01

    The influence of inclusion-induced tension on pore formation is studied theoretically and experimentally. It is shown that fluorescently labeled lipids can enhance pore formation and induce leakage of adhering vesicles. These effects are more pronounced for smaller vesicles. The theoretical predictions are confirmed by experimental two-color fluorescent data. Finally, the influence of the pore formation dynamics on rupture processes of vesicles is analyzed yielding a new picture of the transition to bilayer disks.

  11. Fouling Study of Silicon Oxide Pores Exposed to Tap Water

    SciTech Connect

    Nilsson, J.; Bourcier, W.L.; Lee, J.R.I.; Letant, S.E.; /LLNL, Livermore

    2007-07-12

    We report on the fouling of Focused Ion Beam (FIB)-fabricated silicon oxide nanopores after exposure to tap water for two weeks. Pore clogging was monitored by Scanning Electron Microscopy (SEM) on both bare silicon oxide and chemically functionalized nanopores. While fouling occurred on hydrophilic silicon oxide pore walls, the hydrophobic nature of alkane chains prevented clogging on the chemically functionalized pore walls. These results have implications for nanopore sensing platform design.

  12. Preparation of mesoporous cadmium sulfide nanoparticles with moderate pore size

    SciTech Connect

    Han Zhaohui Zhu, Huaiyong; Shi, Jeffrey; Parkinson, Gordon; Lu, G.Q.

    2007-03-15

    The preparation of cadmium sulfide nanoparticles that have a moderate pore size is reported. This preparation method involves a hydrothermal process that produces a precursor mixture and a following acid treatment of the precursor to get the porous material. The majority of the particles have a pore size close to 20nm, which complements and fills in the gap between the existing cadmium sulfide materials, which usually have a pore size either less than 10nm or are well above 100nm.

  13. Expansion-based passive ranging

    NASA Technical Reports Server (NTRS)

    Barniv, Yair

    1993-01-01

    A new technique of passive ranging which is based on utilizing the image-plane expansion experienced by every object as its distance from the sensor decreases is described. This technique belongs in the feature/object-based family. The motion and shape of a small window, assumed to be fully contained inside the boundaries of some object, is approximated by an affine transformation. The parameters of the transformation matrix are derived by initially comparing successive images, and progressively increasing the image time separation so as to achieve much larger triangulation baseline than currently possible. Depth is directly derived from the expansion part of the transformation. To a first approximation, image-plane expansion is independent of image-plane location with respect to the focus of expansion (FOE) and of platform maneuvers. Thus, an expansion-based method has the potential of providing a reliable range in the difficult image area around the FOE. In areas far from the FOE the shift parameters of the affine transformation can provide more accurate depth information than the expansion alone, and can thus be used similarly to the way they were used in conjunction with the Inertial Navigation Unit (INU) and Kalman filtering. However, the performance of a shift-based algorithm, when the shifts are derived from the affine transformation, would be much improved compared to current algorithms because the shifts - as well as the other parameters - can be obtained between widely separated images. Thus, the main advantage of this new approach is that, allowing the tracked window to expand and rotate, in addition to moving laterally, enables one to correlate images over a very long time span which, in turn, translates into a large spatial baseline - resulting in a proportionately higher depth accuracy.

  14. Expansion-based passive ranging

    NASA Technical Reports Server (NTRS)

    Barniv, Yair

    1993-01-01

    This paper describes a new technique of passive ranging which is based on utilizing the image-plane expansion experienced by every object as its distance from the sensor decreases. This technique belongs in the feature/object-based family. The motion and shape of a small window, assumed to be fully contained inside the boundaries of some object, is approximated by an affine transformation. The parameters of the transformation matrix are derived by initially comparing successive images, and progressively increasing the image time separation so as to achieve much larger triangulation baseline than currently possible. Depth is directly derived from the expansion part of the transformation. To a first approximation, image-plane expansion is independent of image-plane location with respect to the focus of expansion (FOE) and of platform maneuvers. Thus, an expansion-based method has the potential of providing a reliable range in the difficult image area around the FOE. In areas far from the FOE the shift parameters of the affine transformation can provide more accurate depth information than the expansion alone, and can thus be used similarly to the way they have been used in conjunction with the Inertial Navigation Unit (INU) and Kalman filtering. However, the performance of a shift-based algorithm, when the shifts are derived from the affine transformation, would be much improved compared to current algorithms because the shifts--as well as the other parameters--can be obtained between widely separated images. Thus, the main advantage of this new approach is that, allowing the tracked window to expand and rotate, in addition to moving laterally, enables one to correlate images over a very long time span which, in turn, translates into a large spatial baseline resulting in a proportionately higher depth accuracy.

  15. Energy efficient perlite expansion process

    SciTech Connect

    Jenkins, K.L.

    1982-08-31

    A thermally efficient process for the expansion of perlite ore is described. The inlet port and burner of a perlite expansion chamber (Preferably a vertical expander) are enclosed such that no ambient air can enter the chamber. Air and fuel are metered to the burner with the amount of air being controlled such that the fuel/air premix contains at least enough air to start and maintain minimum combustion, but not enough to provide stoichiometric combustion. At a point immediately above the burner, additional air is metered into an insulated enclosure surrounding the expansion chamber where it is preheated by the heat passing through the chamber walls. This preheated additional air is then circulated back to the burner where it provides the remainder of the air needed for combustion, normally full combustion. Flow of the burner fuel/air premix and the preheated additional air is controlled so as to maintain a long luminous flame throughout a substantial portion of the expansion chamber and also to form a moving laminar layer of air on the inner surface of the expansion chamber. Preferably the burner is a delayed mixing gas burner which materially aids in the generation of the long luminous flame. The long luminous flame and the laminar layer of air at the chamber wall eliminate hot spots in the expansion chamber, result in relatively low and uniform temperature gradients across the chamber, significantly reduce the amount of fuel consumed per unit of perlite expanded, increase the yield of expanded perlite and prevent the formation of a layer of perlite sinter on the walls of the chamber.

  16. Pore-size-distribution of cationic polyacrylamide hydrogels. Progress report

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

    The pore size distribution of a AAm/MAPTAC (acrylamide copolymerized with (3-methacrylamidopropyl)trimethylammonium chloride) hydrogel was investigated using Kuga`s mixed-solute-exclusion method, taking into account the wall effect. A Brownian-motion model is also used. Results show the feasibility of determining pore-size distribution of porous materials using the mixed-solute-exclusion method in conjunction with solution of the Fredholm equation; good agreement was obtained with experiment, even for bimodal pore structures. However, different pore size distributions were calculated for the two different probe-solutes (Dextran and poly(ethylene glycol/oxide)). Future work is outlined. 32 figs, 25 refs.

  17. Pore-size-distribution of cationic polyacrylamide hydrogels

    SciTech Connect

    Kremer, M.; Prausnitz, J.M.

    1992-06-01

    The pore size distribution of a AAm/MAPTAC (acrylamide copolymerized with (3-methacrylamidopropyl)trimethylammonium chloride) hydrogel was investigated using Kuga's mixed-solute-exclusion method, taking into account the wall effect. A Brownian-motion model is also used. Results show the feasibility of determining pore-size distribution of porous materials using the mixed-solute-exclusion method in conjunction with solution of the Fredholm equation; good agreement was obtained with experiment, even for bimodal pore structures. However, different pore size distributions were calculated for the two different probe-solutes (Dextran and poly(ethylene glycol/oxide)). Future work is outlined. 32 figs, 25 refs.

  18. Ultrafast laser fabrication of submicrometer pores in borosilicate glass.

    PubMed

    An, Ran; Uram, Jeffrey D; Yusko, Erik C; Ke, Kevin; Mayer, Michael; Hunt, Alan J

    2008-05-15

    We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm. PMID:18483543

  19. Pore volume accessibility of particulate and monolithic stationary phases.

    PubMed

    Urban, Jiří

    2015-05-29

    A chromatographic characterization of pore volume accessibility for both particulate and monolithic stationary phases is presented. Size-exclusion calibration curves have been used to determine the pore volume fraction that is accessible for six alkylbenzenes and twelve polystyrene standards in tetrahydrofuran as the mobile phase. Accessible porosity has been then correlated with the size of the pores from which individual compounds are just excluded. I have determined pore volume accessibility of commercially available columns packed with fully and superficially porous particles, as well as with silica-based monolithic stationary phase. I also have investigated pore accessibility of polymer-based monolithic stationary phases. Suggested protocol is used to characterize pore formation at the early stage of the polymerization, to evaluate an extent of hypercrosslinking during modification of pore surface, and to characterize the pore accessibility of monolithic stationary phases hypercrosslinked after an early termination of polymerization reaction. Pore volume accessibility was also correlated to column efficiency of both particulate and monolithic stationary phases. PMID:25892635

  20. Extending membrane pore lifetime with AC fields: A modeling study

    NASA Astrophysics Data System (ADS)

    Garner, Allen L.; Bogdan Neculaes, V.

    2012-07-01

    AC (sinusoidal) fields with frequencies from kilohertz to gigahertz have been used for gene delivery. To understand the impact of AC fields on electroporation dynamics, we couple a nondimensionalized Smoluchowski equation to an exact representation of the cell membrane voltage obtained solving the Laplace equation. The slope of the pore energy function, dφ/dr, with respect to pore radius is critical in predicting pore dynamics in AC fields because it can vary from positive, inducing pore shrinkage, to negative, driving pore growth. Specifically, the net sign of the integral of dφ/dr over time determines whether the average pore size grows (negative), shrinks (positive), or oscillates (zero) indefinitely about a steady-state radius, rss. A simple analytic relationship predicting the amplitude of the membrane voltage necessary for this behavior agrees well with simulation for frequencies from 500 kHz to 5 MHz for rss < 10 nm. For larger pore size (rss > 10 nm), dφ/dr oscillates about a negative value, suggesting that a net creation of pores may be necessary to maintain a constant pore size. In both scenarios, the magnitude of rss depends only upon the amplitude of the membrane voltage and not directly upon the applied field frequency other than the relationship between the amplitudes of the applied field and membrane voltage.

  1. 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. PMID:22264795

  2. Relativistic effects on plasma expansion

    SciTech Connect

    Benkhelifa, El-Amine; Djebli, Mourad

    2014-07-15

    The expansion of electron-ion plasma is studied through a fully relativistic multi-fluids plasma model which includes thermal pressure, ambipolar electrostatic potential, and internal energy conversion. Numerical investigation, based on quasi-neutral assumption, is performed for three different regimes: nonrelativistic, weakly relativistic, and relativistic. Ions' front in weakly relativistic regime exhibits spiky structure associated with a break-down of quasi-neutrality at the expanding front. In the relativistic regime, ion velocity is found to reach a saturation limit which occurs at earlier stages of the expansion. This limit is enhanced by higher electron velocity.

  3. 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.

  4. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Expansion requests. 570... Continued Space Requirements 570.403 Expansion requests. (a) If the expansion space is in the general scope... justification under FAR 6.3. (b) If the expansion space needed is outside the general scope of the lease,...

  5. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  6. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  7. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  8. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  9. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Expansion requests. 570... Continued Space Requirements 570.403 Expansion requests. (a) If the expansion space is in the general scope... justification under FAR 6.3. (b) If the expansion space needed is outside the general scope of the lease,...

  10. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Expansion requests. 570... Continued Space Requirements 570.403 Expansion requests. (a) If the expansion space is in the general scope... justification under FAR 6.3. (b) If the expansion space needed is outside the general scope of the lease,...

  11. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Expansion requests. 570... Continued Space Requirements 570.403 Expansion requests. (a) If the expansion space is in the general scope... FAR 6.3. (b) If the expansion space needed is outside the general scope of the lease,...

  12. 18 CFR 154.309 - Incremental expansions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Incremental expansions... Changes § 154.309 Incremental expansions. (a) For every expansion for which incremental rates are charged... costs and revenues associated with the expansion, until the Commission authorizes the costs of...

  13. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false Expansion requests. 570... Continued Space Requirements 570.403 Expansion requests. (a) If the expansion space is in the general scope... justification under FAR 6.3. (b) If the expansion space needed is outside the general scope of the lease,...

  14. The Thermal Expansion Of Feldspars

    NASA Astrophysics Data System (ADS)

    Hovis, G. L.; Medford, A.; Conlon, M.

    2009-12-01

    Hovis and others (1) investigated the thermal expansion of natural and synthetic AlSi3 feldspars and demonstrated that the coefficient of thermal expansion (α) decreases significantly, and linearly, with increasing room-temperature volume (VRT). In all such feldspars, therefore, chemical expansion limits thermal expansion. The scope of this work now has been broadened to include plagioclase and Ba-K feldspar crystalline solutions. X-ray powder diffraction data have been collected between room temperature and 925 °C on six plagioclase specimens ranging in composition from anorthite to oligoclase. When combined with thermal expansion data for albite (2,3,4) a steep linear trend of α as a function of VRT emerges, reflecting how small changes in composition dramatically affect expansion behavior. The thermal expansion data for five synthetic Ba-K feldspars ranging in composition from 20 to 100 mole percent celsian, combined with data for pure K-feldspar (3,4), show α-VRT relationships similar in nature to the plagioclase series, but with a slope and intercept different from the latter. Taken as a group all Al2Si2 feldspars, including anorthite and celsian from the present study along with Sr- (5) and Pb-feldspar (6) from other workers, show very limited thermal expansion that, unlike AlSi3 feldspars, has little dependence on the divalent-ion (or M-) site occupant. This apparently is due to the necessitated alternation of Al and Si in the tetrahedral sites of these minerals (7), which in turn locks the tetrahedral framework and makes the M-site occupant nearly irrelevant to expansion behavior. Indeed, in feldspar series with coupled chemical substitution it is the change away from a 1:1 Al:Si ratio that gives feldspars greater freedom to expand. Overall, the relationships among α, chemical composition, and room-temperature volume provide useful predictive tools for estimating feldspar thermal expansion and give insight into the controls of expansion behavior in

  15. Pore morphologies of root induced biopores from single pore to network scale investigated by XRCT

    NASA Astrophysics Data System (ADS)

    Peth, Stephan; Wittig, Marlen C.; Uteau Puschmann, Daniel; Pagenkemper, Sebastian; Haas, Christoph; Holthusen, Dörthe; Horn, Rainer

    2015-04-01

    Biopores are assumed to be an important factor for nutrient acquisition by providing biologically highly active soil-root interfaces to re-colonizing roots and controlling oxygen and water flows at the pedon scale and within the rhizosphere through the formation of branching channel networks which potentially enhance microbial turnover processes. Characteristic differences in pore morphologies are to be expected depending on the genesis of biopores which, for example, can be earthworm-induced or root-induced or subsequently modified by one of the two. Our understanding of biophysical interactions between plants and soil can be significantly improved by quantifying 3D biopore architectures across scales ranging from single biopores to pedon scale pore networks and linking pore morphologies to microscale measurements of transport processes (e.g. oxygen diffusion). While a few studies in the past have investigated biopore networks on a larger scale yet little is known on the micro-morphology of root-induces biopores and their associated rhizosphere. Also little data is available on lateral transport of oxygen through the rhizosphere which will strongly influence microbial turnover processes and consequently control the release and uptake of nutrients. This paper highlights results gathered within a research unit on nutrient acquisition from the subsoil. Here we focus on X-ray microtomography (XRCT) studies ranging from large soil columns (70 cm length and 20 cm diameter) to individual biopores and its surrounding rhizosphere. Samples were collected from sites with different preceding crops (fescue, chicory, alfalfa) and various cropping durations (1-3 years). We will present an approach for quantitative image analysis combined with micro-sensor measurements of oxygen diffusion and spatial gradients of O2 partial pressures to relate pore structure with transport functions. Implications of various biopore architectures for the accessibility of nutrient resources in

  16. Investigating Hydrophilic Pores in Model Lipid Bilayers using Molecular Simulations: Correlating Bilayer Properties with Pore Formation Thermodynamics

    PubMed Central

    Hu, Yuan; Sinha, Sudipta Kumar

    2015-01-01

    Cell-penetrating and antimicrobial peptides show remarkable ability to translocate across physiological membranes. Along with factors such as electric potential induced-perturbations of membrane structure and surface tension effects, experiments invoke pore-like membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a non-trivial free energy cost, thus necessitating consideration of the factors associated with pore formation and attendant free energetics. Due to experimental and modeling challenges related to the long timescales of the translocation process, we use umbrella-sampling molecular dynamics simulations with a lipid-density based order parameter to investigate membrane pore-formation free energy employing Martini coarse-grained models. We investigate structure and thermodynamic features of the pore in 18 lipids spanning a range of head-groups, charge states, acyl chain lengths and saturation. We probe the dependence of pore-formation barriers on area per lipid, lipid bilayer thickness, membrane bending rigidities in three different lipid classes. The pore formation free energy in pure bilayers and peptide translocating scenarios are significantly coupled with bilayer thickness. Thicker bilayers require more reversible work to create pores. Pore formation free energy is higher in peptide-lipid systems relative to the peptide-free lipid systems due to penalties to maintain solvation of charged hydrophilic solutes within the membrane environment. PMID:25614183

  17. Mahler's Expansion and Boolean Functions

    NASA Astrophysics Data System (ADS)

    Michon, Jean-Francis; Valarcher, Pierre; YunÈs, Jean-Baptiste

    2007-03-01

    The substitution of X by X^2 in binomial polynomials generates sequences of integers by Mahler's expansion. We give some properties of these integers and a combinatorial interpretation with covers by projection. We also give applications to the classification of boolean functions. This sequence arose from our previous research on classification and complexity of Binary Decision Diagrams (BDD) associated with boolean functions.

  18. Educational Expansion and Economic Crisis.

    ERIC Educational Resources Information Center

    Klemm, Klaus

    1987-01-01

    Summarizes the expansion of education in the West Germany up to 1980. Examines the progress of the 1980s in view of unemployment and growing difficulties on entering a profession. Among the findings are a decline in enrollment of 20-24 year olds and a growth in opportunities for the children of immigrants. (Author/GEA)

  19. An automated gas expansion system

    SciTech Connect

    Abercrombie, K.

    1993-01-01

    The Metrology Laboratory at the Rocky Flats Plant has constructed a new Vacuum Gauge Calibration System based on gas expansion. The system is used to calibrate vacuum pressure gauges between 1 mTorr and 1000 mTorr. The paper discusses an overview of the system including layout, software, testing and performance.

  20. An automated gas expansion system

    SciTech Connect

    Abercrombie, K.

    1993-05-01

    The Metrology Laboratory at the Rocky Flats Plant has constructed a new Vacuum Gauge Calibration System based on gas expansion. The system is used to calibrate vacuum pressure gauges between 1 mTorr and 1000 mTorr. The paper discusses an overview of the system including layout, software, testing and performance.

  1. Westward Expansion: The Oregon Trail.

    ERIC Educational Resources Information Center

    Salisbury, James F.

    This 8-week interdisciplinary unit for fourth- and fifth-grade students helps children address the U.S. westward expansion in the 1840's using the interactive software program, The Oregon Trail. The unit provides connections to literature, geography, computer/mathematics skills, language arts, and research skills. The work is done in cooperative…

  2. Clamshell Thermal-Expansion Bellows

    NASA Technical Reports Server (NTRS)

    Fesmire, J.; Moore, W. I.; Dipasquale, S. D.

    1993-01-01

    Improved bellows serves as thermal-expansion joint in vacuum-jacketed cyrogenic piping system. Made of Hastelloy C-22 and fabricated in field by welding two clam-shell-like half bellows. No protective paint or maintenance needed. Design modified to fit most thin-wall bellows.

  3. Process of inducing pores in membranes by melittin

    PubMed Central

    Lee, Ming-Tao; Sun, Tzu-Lin; Hung, Wei-Chin; Huang, Huey W.

    2013-01-01

    Melittin is a prototype of the ubiquitous antimicrobial peptides that induce pores in membranes. It is commonly used as a molecular device for membrane permeabilization. Even at concentrations in the nanomolar range, melittin can induce transient pores that allow transmembrane conduction of atomic ions but not leakage of glucose or larger molecules. At micromolar concentrations, melittin induces stable pores allowing transmembrane leakage of molecules up to tens of kilodaltons, corresponding to its antimicrobial activities. Despite extensive studies, aspects of the molecular mechanism for pore formation remain unclear. To clarify the mechanism, one must know the states of the melittin-bound membrane before and after the process. By correlating experiments using giant unilamellar vesicles with those of peptide-lipid multilayers, we found that melittin bound on the vesicle translocated and redistributed to both sides of the membrane before the formation of stable pores. Furthermore, stable pores are formed only above a critical peptide-to-lipid ratio. The initial states for transient and stable pores are different, which implies different mechanisms at low and high peptide concentrations. To determine the lipidic structure of the pore, the pores in peptide–lipid multilayers were induced to form a lattice and examined by anomalous X-ray diffraction. The electron density distribution of lipid labels shows that the pore is formed by merging of two interfaces through a hole. The molecular property of melittin is such that it adsorbs strongly to the bilayer interface. Pore formation can be viewed as the bilayer adopting a lipid configuration to accommodate its excessive interfacial area. PMID:23940362

  4. Effective Expansion: Balance between Shrinkage and Hygroscopic Expansion.

    PubMed

    Suiter, E A; Watson, L E; Tantbirojn, D; Lou, J S B; Versluis, A

    2016-05-01

    The purpose of this study was to investigate the relationship between hygroscopic expansion and polymerization shrinkage for compensation of polymerization shrinkage stresses in a restored tooth. One resin-modified glass-ionomer (RMGI) (Ketac Nano, 3M ESPE), 2 compomers (Dyract, Dentsply; Compoglass, Ivoclar), and a universal resin-based composite (Esthet•X HD, Dentsply) were tested. Volumetric change after polymerization ("total shrinkage") and during 4 wk of water storage at 37°C was measured using an optical method (n= 10). Post-gel shrinkage was measured during polymerization using a strain gauge method (n= 10). Extracted human molars with large mesio-occluso-distal slot preparations were restored with the tested restorative materials. Tooth surfaces at baseline (preparation), after restoration, and during 4 wk of 37°C water storage were scanned with an optical scanner to determine cuspal flexure (n= 8). Occlusal interface integrity was measured using dye penetration. Data were analyzed using analysis of variance and post hoc tests (significance level 0.05). All tested materials shrunk after polymerization. RMGI had the highest total shrinkage (4.65%) but lowest post-gel shrinkage (0.35%). Shrinkage values dropped significantly during storage in water but had not completely compensated polymerization shrinkage after 4 wk. All restored teeth initially exhibited inward (negative) cuspal flexure due to polymerization shrinkage. Cuspal flexure with the RMGI restoration was significantly less (-6.4 µm) than with the other materials (-12.1 to -14.1 µm). After 1 d, cuspal flexure reversed to +5.0 µm cuspal expansion with the RMGI and increased to +9.3 µm at 4 wk. After 4 wk, hygroscopic expansion compensated cuspal flexure in a compomer (Compoglass) and reduced flexure with Dyract and resin-based composite. Marginal integrity (93.7% intact restoration wall) was best for the Compoglass restorations and lowest (73.1%) for the RMGI restorations. Hygroscopic

  5. The Impact of Medicaid Expansion on Oral Health Equity for Older Adults: A Systems Perspective

    PubMed Central

    Metcalf, Sara S.; Birenz, Shirley S.; Kunzel, Carol; Wang, Hua; Schrimshaw, Eric W.; Marshall, Stephen E.; Northridge, Mary E.

    2015-01-01

    This paper uses a collaborative, interdisciplinary systems science inquiry to explore implications of Medicaid expansion on achieving oral health equity for older adults. Through an iterative modeling process oriented toward the experiences of both patients and oral health care providers, complex feedback mechanisms for promoting oral health equity are articulated that acknowledge the potential for stigma as well as disparities in oral health care accessibility. Multiple factors mediate the impact of Medicaid expansion on oral health equity. PMID:26457047

  6. Roles of Anthrax Toxin Receptor 2 in Anthrax Toxin Membrane Insertion and Pore Formation

    PubMed Central

    Sun, Jianjun; Jacquez, Pedro

    2016-01-01

    Interaction between bacterial toxins and cellular surface receptors is an important component of the host-pathogen interaction. Anthrax toxin protective antigen (PA) binds to the cell surface receptor, enters the cell through receptor-mediated endocytosis, and forms a pore on the endosomal membrane that translocates toxin enzymes into the cytosol of the host cell. As the major receptor for anthrax toxin in vivo, anthrax toxin receptor 2 (ANTXR2) plays an essential role in anthrax toxin action by providing the toxin with a high-affinity binding anchor on the cell membrane and a path of entry into the host cell. ANTXR2 also acts as a molecular clamp by shifting the pH threshold of PA pore formation to a more acidic pH range, which prevents premature pore formation at neutral pH before the toxin reaches the designated intracellular location. Most recent studies have suggested that the disulfide bond in the immunoglobulin (Ig)-like domain of ANTXR2 plays an essential role in anthrax toxin action. Here we will review the roles of ANTXR2 in anthrax toxin action, with an emphasis on newly updated knowledge. PMID:26805886

  7. Roles of Anthrax Toxin Receptor 2 in Anthrax Toxin Membrane Insertion and Pore Formation.

    PubMed

    Sun, Jianjun; Jacquez, Pedro

    2016-02-01

    Interaction between bacterial toxins and cellular surface receptors is an important component of the host-pathogen interaction. Anthrax toxin protective antigen (PA) binds to the cell surface receptor, enters the cell through receptor-mediated endocytosis, and forms a pore on the endosomal membrane that translocates toxin enzymes into the cytosol of the host cell. As the major receptor for anthrax toxin in vivo, anthrax toxin receptor 2 (ANTXR2) plays an essential role in anthrax toxin action by providing the toxin with a high-affinity binding anchor on the cell membrane and a path of entry into the host cell. ANTXR2 also acts as a molecular clamp by shifting the pH threshold of PA pore formation to a more acidic pH range, which prevents premature pore formation at neutral pH before the toxin reaches the designated intracellular location. Most recent studies have suggested that the disulfide bond in the immunoglobulin (Ig)-like domain of ANTXR2 plays an essential role in anthrax toxin action. Here we will review the roles of ANTXR2 in anthrax toxin action, with an emphasis on newly updated knowledge. PMID:26805886

  8. Development of Layered Sediment Structure and its Effects on Pore Water Transport and Hyporheic Exchange

    SciTech Connect

    Packman, Aaron I.; Marion, Andrea; Zaramella, Mattia; Chen, Cheng; Gaillard, Jean-François; Keane, Denis T.

    2008-04-15

    Hyporheic exchange is known to provide an important control on nutrient and contaminant fluxes across the stream-subsurface interface. Similar processes also mediate interfacial transport in other permeable sediments. Recent research has focused on understanding the mechanics of these exchange processes and improving estimation of exchange rates in natural systems. While the structure of sediment beds obviously influences pore water flow rates and patterns, little is known about the interplay of typical sedimentary structures, hyporheic exchange, and other transport processes in fluvial/alluvial sediments. Here we discuss several processes that contribute to local-scale sediment heterogeneity and present results that illustrate the interaction of overlying flow conditions, the development of sediment structure, pore water transport, and stream-subsurface exchange. Layered structures are shown to develop at several scales within sediment beds. Surface sampling is used to analyze the development of an armor layer in a sand-and-gravel bed, while innovative synchrotron-based X-ray microtomography is used to observe patterns of grain sorting within sand bedforms. We show that layered bed structures involving coarsening of the bed surface increase interfacial solute flux but produce an effective anisotropy that favors horizontal pore water transport while limiting vertical penetration.

  9. Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel

    PubMed Central

    Habermacher, Chloé; Martz, Adeline; Calimet, Nicolas; Lemoine, Damien; Peverini, Laurie; Specht, Alexandre; Cecchini, Marco; Grutter, Thomas

    2016-01-01

    P2X receptors function by opening a transmembrane pore in response to extracellular ATP. Recent crystal structures solved in apo and ATP-bound states revealed molecular motions of the extracellular domain following agonist binding. However, the mechanism of pore opening still remains controversial. Here we use photo-switchable cross-linkers as ‘molecular tweezers’ to monitor a series of inter-residue distances in the transmembrane domain of the P2X2 receptor during activation. These experimentally based structural constraints combined with computational studies provide high-resolution models of the channel in the open and closed states. We show that the extent of the outer pore expansion is significantly reduced compared to the ATP-bound structure. Our data further reveal that the inner and outer ends of adjacent pore-lining helices come closer during opening, likely through a hinge-bending motion. These results provide new insight into the gating mechanism of P2X receptors and establish a versatile strategy applicable to other membrane proteins. DOI: http://dx.doi.org/10.7554/eLife.11050.001 PMID:26808983

  10. Observations of pore-scale growth patterns of carbon dioxide hydrate using X-ray computed microtomography

    NASA Astrophysics Data System (ADS)

    Ta, Xuan Hien; Yun, Tae Sup; Muhunthan, Balasingam; Kwon, Tae-Hyuk

    2015-03-01

    Natural and artificial gas hydrates with internal pores of nano to centimeters and weak grain-cementation have been widely reported, while the detailed formation process of grain-cementing hydrates remains poorly identified. Pore-scale morphology of carbon dioxide (CO2) hydrate formed in a partially brine-saturated porous medium was investigated via X-ray computed microtomography (X-ray CMT). Emphasis is placed on the pore-scale growth patterns of gas hydrate, including the growth of dendritic hydrate crystals on preformed hydrate and water-wetted grains, porous nature of the hydrate phase, volume expansion of more than 200% during the water-to-hydrate phase transformation, preference of unfrozen water wetting hydrophilic minerals, and the relevance to a weak cementation effect on macroscale physical properties. The presented pore-scale morphology and growth patterns of gas hydrate are expected in natural sediment settings where free gas is available for hydrate formation, such as active gas vents, gas seeps, mud volcanoes, permafrost gas hydrate provinces, and CO2 injected formation for the sake of geologic carbon storage; and in laboratory hydrate samples synthesized from partially brine-saturated sediments or formed from water-gas interfaces.

  11. Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel.

    PubMed

    Habermacher, Chloé; Martz, Adeline; Calimet, Nicolas; Lemoine, Damien; Peverini, Laurie; Specht, Alexandre; Cecchini, Marco; Grutter, Thomas

    2016-01-01

    P2X receptors function by opening a transmembrane pore in response to extracellular ATP. Recent crystal structures solved in apo and ATP-bound states revealed molecular motions of the extracellular domain following agonist binding. However, the mechanism of pore opening still remains controversial. Here we use photo-switchable cross-linkers as 'molecular tweezers' to monitor a series of inter-residue distances in the transmembrane domain of the P2X2 receptor during activation. These experimentally based structural constraints combined with computational studies provide high-resolution models of the channel in the open and closed states. We show that the extent of the outer pore expansion is significantly reduced compared to the ATP-bound structure. Our data further reveal that the inner and outer ends of adjacent pore-lining helices come closer during opening, likely through a hinge-bending motion. These results provide new insight into the gating mechanism of P2X receptors and establish a versatile strategy applicable to other membrane proteins. PMID:26808983

  12. MEASUREMENT AND CONTROL OF FOULING IN FINE PORE DIFFUSER SYSTEMS

    EPA Science Inventory

    The purpose of the study was two-fold: First, to define the efficiency of various methods of cleaning fine pore diffusers and, second, to develop a methodology that could be used to evaluate the efficiency of the cleaning techniques. Dirty fine pore domes from the North Texas Mu...

  13. FINE PORE DIFFUSER FOULING: THE LOS ANGELES STUDIES

    EPA Science Inventory

    This report describes five fine pore diffuser evaluations conducted at three different wastewater treatment plants located in the greater Los Angeles area. he overall goal of the study was to evaluate the performance of fine pore diffusers using selected cleaning methods for exte...

  14. Secondary pores in carbonate reservoirs on Arabian Peninsula

    SciTech Connect

    Nurmi, R.; Waterhouse, M.; Watfa, M.

    1987-05-01

    Nearly all of the giant carbonate reservoirs on the Arabian Peninsula have both primary and secondary pore systems. There are, however, significant stratigraphic and geographic variations of origin, volume, and reservoir importance of secondary pores. The Permian Khuff reservoir zones generally has more secondary porosity than any younger, or shallower, reservoir formations. Highly permeable idiotopic (sucrosic) dolomites are commonly developed in zones which originally contained primary pores. The zones with the highest porosity often contain secondary pores, with calcite-free oomoldic dolomites having higher permeability than oomoldic limestones. Fractures resulting from halokinetics and/or salt dissolution are generally the most important secondary pores in Khuff reservoirs. The prolific Jurassic Arab reservoir zones, generally have lesser amounts of secondary pores than Khuff reservoirs, but a variety of secondary pores are present. Commonly the Arab C zone contains the greatest volume of secondary pores, generally of a moldic (grain and/or skeletal) nature. Secondary porosity associated with dolomitization is regionally more common in the eastern Gulf. Cretaceous (rudist) reefal and chalk reservoirs often contain zones of secondary porosity with enhanced permeability resulting from the leaching of aragonitic and high-magnesium calcite skeletal material. Secondary porosity is present in the western gulf in both the Minagish grainstones and dolomitized Shuaiba Formation, whereas the grainstones of the eastern gulf have little secondary porosity. Large fracture systems are present everywhere in low-permeability chalks and wackestones. An unusually high degree of porosity heterogeneity appears to be ubiquitous in Cretaceous sequences.

  15. FINE PORE DIFFUSER FOULING: THE LOS ANGELES STUDIES

    EPA Science Inventory

    This report describes five fine pore diffuser evaluations conducted at three different wastewater treatment plants located in the greater Los Angeles area. The overall goal of the study was to evaluate the performance of fine pore diffusers using selected cleaning methods for ex...

  16. MEASUREMENT AND CONTROL OF FOULING IN FINE PORE DIFFUSER SYSTEMS

    EPA Science Inventory

    The purpose of the study was two-fold: irst, to define the efficiency of various methods of cleaning fine pore diffusers and, second, to develop a methodology that could be used to evaluate the efficiency of the cleaning techniques. irty fine pore domes from the North Texas Munic...

  17. Partitioning of habitable pore space in earthworm burrows.

    PubMed

    Gorres, Josef H; Amador, Jose A

    2010-03-01

    Earthworms affect macro-pore structure of soils. However, some studies suggest that earthworm burrow walls and casts themselves differ greatly in structure from surrounding soils, potentially creating habitat for microbivorours nematodes which accelerate the decomposition and C and N mineralization. In this study aggregates were sampled from the burrow walls of the anecic earthworm Lumbricus terrestris and bulk soil (not altered by earthworms) from mesocosm incubated in the lab for 0, 1, 3, 5 and 16 weeks. Pore volumes and pore sizes were measured in triplicate with Mercury Intrusion Porosimetry (MIP). This method is well suited to establish pore size structure in the context of habitat, because it measures the stepwise intrusion of mercury from the outside of the aggregate into ever smaller pores. The progress of mercury into the aggregate interior thus resembles potential paths of a nematode into accessible habitable pore spaces residing in an aggregate. Total specific pore volume, V(s), varied between 0.13 and 0.18 mL/g and increased from 3 to 16 weeks in both burrow and bulk soil. Differences between total V(s) of bulk and burrow samples were not significant on any sampling date. However, differences were significant for pore size fractions at the scale of nematode body diameter. PMID:22736839

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

    PubMed

    Dasso, Mary; Fontoura, Beatriz M A

    2016-09-01

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

  19. Influence of Pore Size on Fracture Strength of Porous Ceramics

    NASA Astrophysics Data System (ADS)

    Yoshida, Keigo; Tsukidate, Hironori; Murakami, Akira; Miyata, Hiroshi

    Porous ceramics possess the excellent penetration and adiabatic characteristics, etc., and are used as heatproof filter materials for environmental equipments, etc. Moreover, porous ceramics controlled with porosity and pore size in the wide range have been actively developed. However, how the strength characteristics of porous ceramics are influenced by porosity and pore size of the material are not understood still enough. In this research, the evaluation tests on fracture strength, fracture energy and fracture toughness of porous alumina ceramics which porosity are almost equal, while pore sizes are different mutually were performed, and the relation between the pore size and the fracture strength was studied. The tests results show that the dispersion of fracture strength data is few though fracture strength of porous ceramics is lower than that of high-density ceramics. The relation based on linear fracture mechanics between the defect size and the fracture strength is valid when the one that a pore accompanies with the peculiar defect of the material was regarded as a defect size. In addition, fracture energy increases with the increase of pore size, and this seems based on a crooked propagation path of a crack. Finally, the process zone fracture model with considering the effect of the pore and grain size of the material is proposed. According to this model, for all pore size and crack length, it was shown that the fracture strengths of cracked specimens are evaluated.

  20. Porous Boron Nitride with Tunable Pore Size.

    PubMed

    Dai, Jun; Wu, Xiaojun; Yang, Jinlong; Zeng, Xiao Cheng

    2014-01-16

    On the basis of a global structural search and first-principles calculations, we predict two types of porous boron-nitride (BN) networks that can be built up with zigzag BN nanoribbons (BNNRs). The BNNRs are either directly connected with puckered B (N) atoms at the edge (type I) or connected with sp(3)-bonded BN chains (type II). Besides mechanical stability, these materials are predicted to be thermally stable at 1000 K. The porous BN materials entail large surface areas, ranging from 2800 to 4800 m(2)/g. In particular, type-II BN material with relatively large pores is highly favorable for hydrogen storage because the computed hydrogen adsorption energy (-0.18 eV) is very close to the optimal adsorption energy (-0.15 eV) suggested for reversible hydrogen storage at room temperature. Moreover, the type-II materials are semiconductors with width-dependent direct bandgaps, rendering the type-II BN materials promising not only for hydrogen storage but also for optoelectronic and photonic applications. PMID:26270717

  1. Two interacting particles in a spherical pore

    NASA Astrophysics Data System (ADS)

    Urrutia, Ignacio; Castelletti, Gabriela

    2011-02-01

    In this work we analytically evaluate, for the first time, the exact canonical partition function for two interacting spherical particles into a spherical pore. The interaction with the spherical substrate and between particles is described by an attractive square-well and a square-shoulder potential. In addition, we obtain exact expressions for both the one particle and an averaged two particle density distribution. We develop a thermodynamic approach to few-body systems by introducing a method based on thermodynamic measures [I. Urrutia, J. Chem. Phys. 134, 104503 (2010)] for nonhard interaction potentials. This analysis enables us to obtain expressions for the pressure, the surface tension, and the equivalent magnitudes for the total and Gaussian curvatures. As a by-product, we solve systems composed of two particles outside a fixed spherical obstacle. We study the low density limit for a many-body system confined to a spherical cavity and a many-body system surrounding a spherical obstacle. From this analysis we derive the exact first order dependence of the surface tension and Tolman length. Our findings show that the Tolman length goes to zero in the case of a purely hard wall spherical substrate, but contains a zero order term in density for square-well and square-shoulder wall-fluid potentials. This suggests that any nonhard wall-fluid potential should produce a non-null zero order term in the Tolman length.

  2. Improving the ruggedness of silicon pore optics

    NASA Astrophysics Data System (ADS)

    Ackermann, Marcelo D.; Collon, Maximilien J.; Günther, Ramses; Partapsing, Rakesh; Bavdaz, Marcos; Wallace, Kotska; Wille, Eric; van Baren, Coen; Kampf, Dirk; Erhard, Markus

    2010-07-01

    In this paper we present the latest developments on the ruggedisation of the Silicon Pore Optics (SPO) mirror modules. SPO is one of the candidate technologies for producing the X-ray optics for the future space based Xray telescope, the International X-ray Observatory (IXO). To produce SPO mirror modules, Si mirrors are first bonded together using direct Si bonding to form a stack. These stacks are the glued into brackets, which then connect to the supporting optical bench by invar pins. The combination of brackets and invar pins now forms a full isostatic mount, and is rugged enough to allow the mirror module to survive the high loads of a launch. The mounting system furthermore allows for a certain level of manufacturing tolerances for the support structure, and ensures interchangeability of the mirror modules within one single ring of the optical bench. To prove this, a test interface has been designed and manufactured, on which a single, full fledged mirror module will be mounted to be exposed to environmental tests.

  3. Silicon pore optics developments and status

    NASA Astrophysics Data System (ADS)

    Bavdaz, Marcos; Wille, Eric; Wallace, Kotska; Shortt, Brian; Collon, Maximilien; Ackermann, Marcelo; Olde Riekerink, Mark; Haneveld, Jeroen; van Baren, Coen; Erhard, Markus; Christensen, Finn; Krumrey, Michael; Burwitz, Vadim

    2012-09-01

    Silicon Pore Optics (SPO) is a lightweight high performance X-ray optics technology being developed in Europe, driven by applications in observatory class high energy astrophysics missions. An example of such application is the former ESA science mission candidate ATHENA (Advanced Telescope for High Energy Astrophysics), which uses the SPO technology for its two telescopes, in order to provide an effective area exceeding 1 m2 at 1 keV, and 0.5 m2 at 6 keV, featuring an angular resolution of 10” or better [1 to 24]. This paper reports on the development activities led by ESA, and the status of the SPO technology. The technology development programme has succeeded in maturing the SPO further and achieving important milestones, in each of the main activity streams: environmental compatibility, industrial production and optical performance. In order to accurately characterise the increasing performance of this innovative optical technology, the associated X-ray test facilities and beam-lines have been refined and upgraded.

  4. Physical modelling of the nuclear pore complex

    PubMed Central

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

    2013-01-01

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

  5. Bacterial pore-forming proteins as anthelmintics

    PubMed Central

    2013-01-01

    Crystal (Cry) proteins are made by the Gram-positive bacterium Bacillus thuringiensis (Bt). Cry proteins are pore-forming proteins and are the most widely used biological insecticides in the world. Our laboratory found some Cry proteins are highly effective against a broad range of nematodes (roundworms). Here, we discuss our results of Cry protein activity against intestinal roundworms. Both Cry5B and Cry21A have therapeutic activities against infections of the roundworm Heligmosomoides polygyrus bakeri in mice. Cry5B also shows highly therapeutic activity against Ancylostoma ceylanicum infection in hamsters. A. ceylanicum is a minor hookworm parasite of humans, and it is closely related to the more prevalent Ancylostoma duodenale. In addition, Cry proteins show excellent combinatorial therapeutic properties with nicotinic acetylcholine receptor (nAChR) agonists, one of the two classes of compounds approved by the World Health Organization for the treatment for intestinal roundworms in humans. Given their non-toxicity to humans and their broad spectrum of nematicidal action, Cry proteins show great potential as next-generation anthelmintics. PMID:22562659

  6. THERMODYNAMIC AND MASS BALANCE ANALYSIS OF EXPANSIVE PHASE PRECIPITATION IN SALTSTONE

    SciTech Connect

    Denham, M

    2008-05-06

    This report assesses the potential for future precipitation of expansive phases that could cause fracturing in saltstone. It examines the equilibrium case using The Geochemist's Workbench{reg_sign} reaction path model. The scenarios simulated examine the effects of different possible infiltrating fluids, different saltstone formulations, and different amounts of minerals available for reaction. Mineralogy of the vault cement and saltstone were estimated using reported chemical compositions of each. The infiltrating fluid was assumed to be either rainwater equilibrated with vault cement or rainwater itself. The simulations assumed that minerals were homogeneously distributed in saltstone and that each pore volume of infiltration reached equilibrium with the mineral assemblage. Fracturing that initiates in pores by expansive phase precipitation is unlikely to occur in saltstone because the maximum amount of porosity filled is 34%. If less than 100% of the saltstone minerals are available for reaction, less porosity will be lost to expansive phases. Likewise, the formulation of saltstone used will affect the amount of porosity filled by expansive phases.

  7. THERMODYNAMIC AND MASS BALANCE ANALYSIS OF EXPANSIVE PHASE PRECIPITATION IN SALTSTONE

    SciTech Connect

    Fletcher, D

    2008-05-01

    This report assesses the potential for future precipitation of expansive phases that could cause fracturing in saltstone. It examines the equilibrium case using The Geochemist's Workbench{reg_sign} reaction path model. The scenarios simulated examine the effects of different possible infiltrating fluids, different saltstone formulations, and different amounts of minerals available for reaction. Mineralogy of the vault cement and saltstone were estimated using reported chemical compositions of each. The infiltrating fluid was assumed to be either rainwater equilibrated with vault cement or rainwater itself. The simulations assumed that minerals were homogeneously distributed in saltstone and that each pore volume of infiltration reached equilibrium with the mineral assemblage. Fracturing that initiates in pores by expansive phase precipitation is unlikely to occur in saltstone because the maximum amount of porosity filled is 34%. If less than 100% of the saltstone minerals are available for reaction, less porosity will be lost to expansive phases. Likewise, the formulation of saltstone used will affect the amount of porosity filled by expansive phases.

  8. Expansion of the fusion stalk and its implication for biological membrane fusion

    PubMed Central

    Risselada, Herre Jelger; Bubnis, Gregory; Grubmüller, Helmut

    2014-01-01

    Over the past 20 years, it has been widely accepted that membrane fusion proceeds via a hemifusion step before opening of the productive fusion pore. An initial hourglass-shaped lipid structure, the fusion stalk, is formed between the adjacent membrane leaflets (cis leaflets). It remains controversial if and how fusion proteins drive the subsequent transition (expansion) of the stalk into a fusion pore. Here, we propose a comprehensive and consistent thermodynamic understanding in terms of the underlying free-energy landscape of stalk expansion. We illustrate how the underlying free energy landscape of stalk expansion and the concomitant pathway is altered by subtle differences in membrane environment, such as leaflet composition, asymmetry, and flexibility. Nonleaky stalk expansion (stalk widening) requires the formation of a critical trans-leaflet contact. The fusion machinery can mechanically enforce trans-leaflet contact formation either by directly enforcing the trans-leaflets in close proximity, or by (electrostatically) condensing the area of the cis leaflets. The rate of these fast fusion reactions may not be primarily limited by the energetics but by the forces that the fusion proteins are able to exert. PMID:25024174

  9. Relationship between the Averaged Deposition Rate Coefficients for Colloids in a Single Pore and Various Pore-scale Parameters

    NASA Astrophysics Data System (ADS)

    Narayanan, S.; Mohan Kumar, M.; Hassanizadeh, S. M.; Raoof, A.

    2014-12-01

    The colloid deposition behavior observed at the Darcy scale represents an average of the processes occurring at the pore scale. Hence, a better understanding of the processes occurring at the Darcy scale can be obtained by studying colloid transport at the pore-scale and then upscaling the results. In this study, we have developed a mathematical model to simulate the transport of colloids in a cylindrical pore by considering various processes such as advection, diffusion, colloid-soil surface interactions and hydrodynamic wall effects. The pore space is divided into three different regions, namely, the bulk, diffusion and potential regions, based on the dominant processes acting in each of these regions. In the bulk region, colloid transport is governed by advection and diffusion; whereas in the diffusion region, colloid mobility due to diffusion is retarded by hydrodynamic wall effects. Colloid-solid interaction forces dominate the transport in the potential region where colloid deposition occurs and are calculated using DLVO theory. The expressions for mass transfer rate coefficients between the diffusion and potential regions have been derived for different DLVO energy profiles. These are incorporated in the pore-scale equations in the form of a boundary condition at the diffusion-potential region interface. The model results are used to obtain the colloid breakthrough curve at the end of a long pore, and then it is fitted with 1D advection-dispersion-adsorption model so as to determine the averaged attachment and detachment rate coefficients at the scale of a single pore. A sensitivity analysis of the model to six pore-scale parameters (colloid and wall surface potentials, solution ionic strength, average pore-water velocity, colloid radius, and pore radius) is carried out so as to find the relation between the averaged deposition rate coefficients at pore scale vs the pore-scale parameters. We found an hyper exponential relation between the colloid attachment

  10. Two-Pore Channels: Lessons from Mutant Mouse Models

    PubMed Central

    Ruas, Margarida; Galione, Antony; Parrington, John

    2016-01-01

    Recent interest in two-pore channels (TPCs) has resulted in a variety of studies dealing with the functional role and mechanism of action of these endo-lysosomal proteins in diverse physiological processes. With the availability of mouse lines harbouring mutant alleles for Tpcnl and/or Tpcn2 genes, several studies have made use of them to validate, consolidate and discover new roles for these channels not only at the cellular level but, importantly, also at the level of the whole organism. The different mutant mouse lines that have been used were derived from distinct genetic manipulation strategies, with the aim of knocking out expression of TPC proteins. However, the expression of different residual TPC sequences predicted to occur in these mutant mouse lines, together with the varied degree to which the effects on Tpcn expression have been studied, makes it important to assess the true knockout status of some of the lines. In this review we summarize these Tpcn mutant mouse lines with regard to their predicted effect on Tpcn expression and the extent to which they have been characterized. Additionally, we discuss how results derived from studies using these Tpcn mutant mouse lines have consolidated previously proposed roles for TPCs, such as mediators of NAADP signalling, endo-lysosomal functions, and pancreatic β cell physiology. We will also review how they have been instrumental in the assignment of new physiological roles for these cation channels in processes such as membrane electrical excitability, neoangiogenesis, viral infection and brown adipose tissue and heart function, revealing, in some cases, a specific contribution of a particular TPC isoform. PMID:27330869

  11. Influence of pore structure on compressive strength of cement mortar.

    PubMed

    Zhao, Haitao; Xiao, Qi; Huang, Donghui; Zhang, Shiping

    2014-01-01

    This paper describes an experimental investigation into the pore structure of cement mortar using mercury porosimeter. Ordinary Portland cement, manufactured sand, and natural sand were used. The porosity of the manufactured sand mortar is higher than that of natural sand at the same mix proportion; on the contrary, the probable pore size and threshold radius of manufactured sand mortar are finer. Besides, the probable pore size and threshold radius increased with increasing water to cement ratio and sand to cement ratio. In addition, the existing models of pore size distribution of cement-based materials have been reviewed and compared with test results in this paper. Finally, the extended Bhattacharjee model was built to examine the relationship between compressive strength and pore structure. PMID:24757414

  12. Respiratory Pores on Ostrich Struthio camelus (Aves: Struthionidae) Eggshells.

    PubMed

    Koyama, T; Tennyson, A J D

    2016-01-01

    Respiratory pores are essential for the survival of the embryo within the eggshell. Distribution patterns of such pores on ostrich (Struthio camelus) eggshells show remarkable variations in bird group. Eggshells preserved in the museum of New Zealand have long, superficial, winding grooves and ridges, with pores distributed densely in the bottom of grooves. Both the grooves and ridges that separate them are twisted. By contrast, the surfaces of eggs from farmed ostriches are mostly smooth, with only occasional, short grooves, and respiratory pores distributed more evenly. The cause of ridging and grooving of the surface of eggs from wild birds is unclear but may be due to the need for stronger shells and effects of environmental stresses. It appears that the arrangement of respiratory pores on ostrich eggshells seems to be changeable by surrounding stresses. PMID:27526124

  13. Pore size engineering applied to starved electrochemical cells and batteries

    NASA Technical Reports Server (NTRS)

    Abbey, K. M.; Thaller, L. H.

    1982-01-01

    To maximize performance in starved, multiplate cells, the cell design should rely on techniques which widen the volume tolerance characteristics. These involve engineering capillary pressure differences between the components of an electrochemical cell and using these forces to promote redistribution of electrolyte to the desired optimum values. This can be implemented in practice by prescribing pore size distributions for porous back-up plates, reservoirs, and electrodes. In addition, electrolyte volume management can be controlled by incorporating different pore size distributions into the separator. In a nickel/hydrogen cell, the separator must contain pores similar in size to the small pores of both the nickel and hydrogen electrodes in order to maintain an optimum conductive path for the electrolyte. The pore size distributions of all components should overlap in such a way as to prevent drying of the separator and/or flooding of the hydrogen electrode.

  14. Voltage Dependent Charge Storage Modes and Capacity in Subnanometer Pores

    SciTech Connect

    Qiao, Rui; Meunier, V.; Huang, Jingsong; Wu, Peng; Sumpter, Bobby G

    2012-01-01

    Using molecular dynamics simulations, we show that charge storage in subnanometer pores follows a distinct voltage-dependent behavior. Specifically, at lower voltages, charge storage is achieved by swapping co-ions in the pore with counterions in the bulk electrolyte. As voltage increases, further charge storage is due mainly to the removal of co-ions from the pore, leading to a capacitance increase. The capacitance eventually reaches a maximum when all co-ions are expelled from the pore. At even higher electrode voltages, additional charge storage is realized by counterion insertion into the pore, accompanied by a reduction of capacitance. The molecular mechanisms of these observations are elucidated and provide useful insight for optimizing energy storage based on supercapacitors.

  15. Surface and pore properties of ANL and PETC coals

    SciTech Connect

    Bartholomew, C.H.; White, W.E.; Thornock, D.; Wells, W.F.; Hecker, W.C.; Smoot, L.D.; Smith, D.M.; Williams, F.L.

    1988-01-01

    Surface areas, pore volumes, pore size distribution, and solid densities were measured for three ANL coals (Pittsburgh No. 8, Wyodak, and Beulah Zap Lignite), two PETC coals (Lower Wilcox, and Dietz) and a Utah Scofield coal and for chars derived from these coals. Surface areas were measured using nitrogen and carbon dioxide adsorptions; pore volumes were determined using nitrogen adsorption, mercury porosimetry, and NMR spin-lattice relaxation measurements of samples saturated with water. Solid densities were obtained using helium displacement. The results indicate that chars have larger surface areas and pores relative to coals; large fractions of the internal surfaces of coals are not penetrated by nitrogen molecules but are penetrated by carbon dioxide suggesting that the pores are mostly smaller than 1 nm.

  16. Cation-halide transport through peptide pores containing aminopicolinic acid.

    PubMed

    Basak, Debajyoti; Sridhar, Sucheta; Bera, Amal K; Madhavan, Nandita

    2016-05-18

    Synthetic pores that selectively transport ions of biological significance through membranes could be potentially used in medical diagnostics or therapeutics. Herein, we report cation-selective octapeptide pores derived from alanine and aminopicolinic acid. The ion transport mechanism through the pores has been established to be a cation-chloride symport. The cation-chloride co-transport is biologically essential for the efficient functioning of the central nervous system and has been implicated in diseases such as epilepsy. The pores formed in synthetic lipid bilayers do not exhibit any closing events. The ease of synthesis as well as infinite lifetimes of these pores provides scope for modifying their transport behaviour to develop sensors. PMID:27137995

  17. Electroosmotic Flow Rectification in Pyramidal-Pore Mica Membranes

    SciTech Connect

    Jin, P.; Mukaibo, H.; Horne, L.; Bishop, G.; Martin, C. R.

    2010-02-01

    We demonstrate here a new electrokinetic phenomenon, Electroosmotic flow (EOF) rectification, in synthetic membranes containing asymmetric pores. Mica membranes with pyramidally shaped pores prepared by the track-etch method were used. EOF was driven through these membranes by using an electrode in solutions on either side to pass a constant ionic current through the pores. The velocity of EOF depends on the polarity of the current. A high EOF velocity is obtained when the polarity is such that EOF is driven from the larger base opening to the smaller tip opening of the pore. A smaller EOF velocity is obtained when the polarity is reversed such that EOF goes from tip to base. We show that this rectified EOF phenomenon is the result of ion current-rectification observed in such asymmetric-pore membranes.

  18. Thermal expansion of plagioclase feldspars

    NASA Astrophysics Data System (ADS)

    Tribaudino, M.; Angel, R. J.; Cámara, F.; Nestola, F.; Pasqual, D.; Margiolaki, I.

    2010-12-01

    The volume thermal expansion coefficient and the anisotropy of thermal expansion were determined for nine natural feldspars with compositions, in terms of albite (NaAlSi3O8, Ab) and anorthite (CaAl2Si2O8, An), of Ab100, An27Ab73, An35Ab65, An46Ab54, An60Ab40, An78Ab22, An89Ab11, An96Ab4 and An100 by high resolution powder diffraction with a synchrotron radiation source. Unit-cell parameters were determined from 124 powder patterns of each sample, collected over the temperature range 298-935 K. The volume thermal expansion coefficient of the samples determined by a linear fit of V/ V 0 = α( T - T 0) varies with composition ( X An in mol %) as: αV = 2.90left( 4 right) × 10^{ - 5} - 3.0left( 2 right) × 10^{ - 7} *X_{text{An}} + 1.8left( 2 right) × 10^{ - 9} *X_{text{An}}2 Two empirical models for the non-linear behaviour of volume with temperature give a better fit to the experimental data. The change with composition in the a° parameter of the non-linear Holland-Powell model V/ V 0 = 1 + a°( T - T 0) + 20a° (√ T - √ T 0) is: a^circ = 4.96left( 5 right) × 10^{ - 5} - 4.7left( 2 right) × 10^{ - 7} *X_{text{An}} + 2.2left( 2 right) × 10^{ - 9} *X_{text{An}}2 For the Berman model, V/ V 0 = a 1( T - T 0) + a 2*( T- T 0)2, the parameters change with composition as: begin{aligned}& a1 = 2.44left( {15} right) × 10^{ - 5} - 3.1left( 6 right) × 10^{ - 7} *X_{text{An}}\\& quad + 1.8left( 5 right) × 10^{ - 9} *X_{text{An}}2 \\& a2 = 9left( 1 right) × 10^{ - 9} - 4left( 2 right) × 10^{ - 11} *X_{text{An}} \\ The thermal expansion of all plagioclases is very anisotropic, with more than 70% of the volume expansion being accommodated by a direction fairly close to the (100) plane normal, whereas perpendicular directions exhibit smaller, and in some cases slightly negative or zero, thermal expansion.

  19. Biophysics, pathophysiology, and pharmacology of ion channel gating pores

    PubMed Central

    Moreau, Adrien; Gosselin-Badaroudine, Pascal; Chahine, Mohamed

    2014-01-01

    Voltage sensor domains (VSDs) are a feature of voltage gated ion channels (VGICs) and voltage sensitive proteins. They are composed of four transmembrane (TM) segments (S1–S4). Currents leaking through VSDs are called omega or gating pore currents. Gating pores are caused by mutations of the highly conserved positively charged amino acids in the S4 segment that disrupt interactions between the S4 segment and the gating charge transfer center (GCTC). The GCTC separates the intracellular and extracellular water crevices. The disruption of S4–GCTC interactions allows these crevices to communicate and create a fast activating and non-inactivating alternative cation-selective permeation pathway of low conductance, or a gating pore. Gating pore currents have recently been shown to cause periodic paralysis phenotypes. There is also increasing evidence that gating pores are linked to several other familial diseases. For example, gating pores in Nav1.5 and Kv7.2 channels may underlie mixed arrhythmias associated with dilated cardiomyopathy (DCM) phenotypes and peripheral nerve hyperexcitability (PNH), respectively. There is little evidence for the existence of gating pore blockers. Moreover, it is known that a number of toxins bind to the VSD of a specific domain of Na+ channels. These toxins may thus modulate gating pore currents. This focus on the VSD motif opens up a new area of research centered on developing molecules to treat a number of cell excitability disorders such as epilepsy, cardiac arrhythmias, and pain. The purpose of the present review is to summarize existing knowledge of the pathophysiology, biophysics, and pharmacology of gating pore currents and to serve as a guide for future studies aimed at improving our understanding of gating pores and their pathophysiological roles. PMID:24772081

  20. X-ray CT analysis of pore structure in sand

    NASA Astrophysics Data System (ADS)

    Mukunoki, Toshifumi; Miyata, Yoshihisa; Mikami, Kazuaki; Shiota, Erika

    2016-06-01

    The development of microfocused X-ray computed tomography (CT) devices enables digital imaging analysis at the pore scale. The applications of these devices are diverse in soil mechanics, geotechnical and geoenvironmental engineering, petroleum engineering, and agricultural engineering. In particular, the imaging of the pore space in porous media has contributed to numerical simulations for single-phase and multiphase flows or contaminant transport through the pore structure as three-dimensional image data. These obtained results are affected by the pore diameter; therefore, it is necessary to verify the image preprocessing for the image analysis and to validate the pore diameters obtained from the CT image data. Moreover, it is meaningful to produce the physical parameters in a representative element volume (REV) and significant to define the dimension of the REV. This paper describes the underlying method of image processing and analysis and discusses the physical properties of Toyoura sand for the verification of the image analysis based on the definition of the REV. On the basis of the obtained verification results, a pore-diameter analysis can be conducted and validated by a comparison with the experimental work and image analysis. The pore diameter is deduced from Young-Laplace's law and a water retention test for the drainage process. The results from previous study and perforated-pore diameter originally proposed in this study, called the voxel-percolation method (VPM), are compared in this paper. In addition, the limitations of the REV, the definition of the pore diameter, and the effectiveness of the VPM for an assessment of the pore diameter are discussed.

  1. Transport properties of single-file pores with two conformational states.

    PubMed Central

    Hernández, J A; Fischbarg, J

    1994-01-01

    Complex facilitative membrane transporters of specific ligands may operate via inner channels subject to conformational transitions. To describe some properties of these systems, we introduce here a kinetic model of coupled transport of two species, L and w, through a two-conformational pore. The basic assumptions of the model are: a) single-file of, at most, n molecules inside the channel; b) each pore state is open to one of the compartments only; c) there is at most only one vacancy per pore; d) inside the channel, a molecule of L occupies the same positions as a molecule of w; and e) there is at most only one molecule of L per pore. We develop a general representation of the kinetic diagram of the model that is formally similar to the one used to describe one-vacancy transport through a one-conformational single-file pore. In many cases of biological importance, L could be a hydrophilic (ionic or nonionic) ligand and w could be water. The model also finds application to describe solute (w) transport under saturation conditions. In this latter case, L would be another solute, or a tracer of w. We derive steady-state expressions for the fluxes of L and w, and for the permeability coefficients. The main results obtained from the analysis of the model are the following. 1) Under the condition of equilibrium of w, the expression derived for the flux of L is formally indistinguishable from the one obtainable from a standard four-state model of ligand transport mediated by a two-conformational transporter. 2) When L is a tracer of w, we can derive an expression for the ratio between the main isotope and tracer permeability coefficients (Pw/Pd). We find that the near-equilibrium permeability ratio satisfies (n - 1) < or = (Pw/Pd)eq < or = n, a result previously derived for the one-conformational, single-file pore for the case that n > or = 2. 3) The kinetic model studied here represents a generalization of the carrier concept. In fact, for the case that n = 1

  2. MRI and PGSE NMR Studies of Long-range, Pore-pore Interaction Effects in Gas Adsorption

    NASA Astrophysics Data System (ADS)

    Hitchcock, Iain; Rigby, Sean; Chudek, John; Holt, Liz; Lowe, John

    2011-03-01

    In this work MRI and PGSE NMR have been used to directly study the advanced condensation effect during water adsorption in a macroscopically heterogeneous sol-gel silica pellet. It has been found that capillary condensation will occur at unexpectedly lower pressures in regions of much larger pores that lie in close proximity to smaller pores.

  3. Dissociation of membrane binding and lytic activities of the lymphocyte pore-forming protein (perforin).

    PubMed

    Young, J D; Damiano, A; DiNome, M A; Leong, L G; Cohn, Z A

    1987-05-01

    Granules isolated from CTL and NK cells contain a cytolytic pore-forming protein (PFP/perforin). At low temperatures (on ice), PFP binds to erythrocyte membranes without producing hemolysis. Hemolysis occurs when the PFP-bound erythrocytes are warmed up to 37 degrees C, which defines a temperature-dependent, lytic (pore-formation) step distinct from the membrane-binding event. Ca2+ and neutral pH are required for both membrane binding and pore formation by PFP. Serum, LDL, HDL, and heparin inhibit the hemolytic activity of PFP by blocking its binding to lipid membranes. Lysis by PFP that has bound to erythrocyte membranes is no longer susceptible to the effect of these inhibitors. The hemolytic activities associated with intact granules and solubilized PFP show different requirements for Ca2+ and pH, indicating that cytolysis produced by isolated granules may involve an additional step, possibly fusion of granules with membranes. It is suggested that three distinct Ca2+- and pH-dependent events may be involved during cell killing by CTL and NK cells: fusion of cytoplasmic granules of effector cells with their plasma membrane, releasing PFP from cells; binding of the released PFP to target membranes; and insertion of monomers and the subsequent formation of lytic pores in the target membrane. The serum-mediated inhibition of membrane binding by PFP could prevent the accidental injury of bystander cells by cell-released PFP, but would allow cytolysis to proceed to completion once PFP has bound to the target membrane. PMID:3494808

  4. Specialized Mediation.

    ERIC Educational Resources Information Center

    Hammond, Carol; And Others

    1992-01-01

    Six articles discuss librarians as mediators in special circumstances. Highlights include the reference librarian and the information paraprofessional; effective reference mediation for nontraditional public library users, including mentally impaired patrons and illiterate adults; the academic librarian's role in the education process; and…

  5. Multipole expansions and intense fields

    NASA Astrophysics Data System (ADS)

    Reiss, Howard R.

    1984-02-01

    In the context of two-body bound-state systems subjected to a plane-wave electromagnetic field, it is shown that high field intensity introduces a distinction between long-wavelength approximation and electric dipole approximation. This distinction is gauge dependent, since it is absent in Coulomb gauge, whereas in "completed" gauges of Göppert-Mayer type the presence of high field intensity makes electric quadrupole and magnetic dipole terms of importance equal to electric dipole at long wavelengths. Another consequence of high field intensity is that multipole expansions lose their utility in view of the equivalent importance of a number of low-order multipole terms and the appearance of large-magnitude terms which defy multipole categorization. This loss of the multipole expansion is gauge independent. Also gauge independent is another related consequence of high field intensity, which is the intimate coupling of center-of-mass and relative coordinate motions in a two-body system.

  6. Class of discrete Gabor expansion

    NASA Astrophysics Data System (ADS)

    Li, Shidong; Healy, Dennis M., Jr.

    1994-03-01

    We present a new approach to studying a discrete Gabor expansion (DGE). We show that, in general, DGE is not the usual biorthogonal decomposition, but belongs to a larger and looser decomposition scheme which we call pseudo frame decomposition. It includes the DGE scheme proposed as a special case. The standard dual frame decomposition is also a special case. We derive algorithms using techniques for Gabor sequences to compute 'biorthogonal' sequences through proper matrix representation. Our algorithms involve solutions to a linear system to obtain the 'biorthogonal' windows. This approach provides a much broader mathematical view of the DGE, and therefore, establishes a wider mathematical foundation towards the theory of DGE. The general algorithm derived also provides a whole class of discrete Gabor expansions, among which 'good' ones can be generated. Simulation results are also provided.

  7. Resolving single membrane fusion events on planar pore-spanning membranes

    PubMed Central

    Schwenen, Lando L. G.; Hubrich, Raphael; Milovanovic, Dragomir; Geil, Burkhard; Yang, Jian; Kros, Alexander; Jahn, Reinhard; Steinem, Claudia

    2015-01-01

    Even though a number of different in vitro fusion assays have been developed to analyze protein mediated fusion, they still only partially capture the essential features of the in vivo situation. Here we established an in vitro fusion assay that mimics the fluidity and planar geometry of the cellular plasma membrane to be able to monitor fusion of single protein-containing vesicles. As a proof of concept, planar pore-spanning membranes harboring SNARE-proteins were generated on highly ordered functionalized 1.2 μm-sized pore arrays in Si3N4. Full mobility of the membrane components was demonstrated by fluorescence correlation spectroscopy. Fusion was analyzed by two color confocal laser scanning fluorescence microscopy in a time resolved manner allowing to readily distinguish between vesicle docking, intermediate states such as hemifusion and full fusion. The importance of the membrane geometry on the fusion process was highlighted by comparing SNARE-mediated fusion with that of a minimal SNARE fusion mimetic. PMID:26165860

  8. Polygons and the Lace Expansion

    NASA Astrophysics Data System (ADS)

    Clisby, Nathan; Slade, Gordon

    The lace expansion was introduced by Brydges and Spencer in 1985 [7] to analyse weakly self-avoiding walks in dimensions d > 4. Subsequently it has been generalised and greatly extended, so that it now applies to a variety of problems of interest in probability theory, statistical physics, and combinatorics, including the strictly self-avoiding walk, lattice trees, lattice animals, percolation, oriented percolation, the contact process, random graphs, and the Ising model. A recent survey is [42].

  9. Pore Scale Dynamics of Microemulsion Formation.

    PubMed

    Unsal, Evren; Broens, Marc; Armstrong, Ryan T

    2016-07-19

    consequences on the pore scale mixing behavior and resulting microemulsion properties. PMID:27336294

  10. [Familiy mediation within the counselling system].

    PubMed

    Bastine, Reiner; Römer-Wolf, Birgit; Decker, Frauke; Haid-Loh, Achim; Mayer, Stefan; Normann, Katrin

    2006-01-01

    Family mediation has been established as a method of resolving family conflicts within the counselling system. Unfortunately there existed only rare information about the real presence and efficacy of family mediation services within this system. 726 counselling centres from all over the country participated at the present study, which was outlined to evaluate their supply of family mediation and the use of it. The results show that nearly one third of the centres are offering family mediation as a regular service to their clients, and that mediative skills are quite frequently used by the counselling professionals. Centres, which offer a regular service of mediation, have an obviously higher percentage of honorary staff, indicating that this service might have a more fragile status. Each centre, which conducted mediation, had an average mediation caseload of 32 in 2003, which means a percentage of 7 percent of all counselling cases treated in this year. These mediations needed an average treatment of 7 hours. Most frequent cases in mediation are separated married or separated non-married parents with 2 children. In most cases, family mediation was used to regulate conflicts in separation, divorce or post divorce, mainly concerned with issues of child custody. In contrast to the researchers' expectations, children were introduced at the mediation process only rarely. The need for mediation in the local population was rated much higher than the factual demand for and the factual supply of mediation. Based on the outcomes of the study, some recommendations are made: for the improvement of the supply of family mediation, for the expansion of the issues to which mediation is offered, and for strengthening the approaches to include children into the mediation process. PMID:17152893

  11. Femtosecond dynamics of cluster expansion

    NASA Astrophysics Data System (ADS)

    Gao, Xiaohui; Wang, Xiaoming; Shim, Bonggu; Arefiev, Alexey; Tushentsov, Mikhail; Breizman, Boris; Downer, Mike

    2010-03-01

    Noble gas clusters irradiated by intense ultrafast laser expand quickly and become typical plasma in picosecond time scale. During the expansion, the clustered plasma demonstrates unique optical properties such as strong absorption and positive contribution to the refractive index. Here we studied cluster expansion dynamics by fs-time-resolved refractive index and absorption measurements in cluster gas jets after ionization and heating by an intense pump pulse. The refractive index measured by frequency domain interferometry (FDI) shows the transient positive peak of refractive index due to clustered plasma. By separating it from the negative contribution of the monomer plasma, we are able to determine the cluster fraction. The absorption measured by a delayed probe shows the contribution from clusters of various sizes. The plasma resonances in the cluster explain the enhancement of the absorption in our isothermal expanding cluster model. The cluster size distribution can be determined. A complete understanding of the femtosecond dynamics of cluster expansion is essential in the accurate interpretation and control of laser-cluster experiments such as phase-matched harmonic generation in cluster medium.

  12. Clinical grade expansion of MSCs.

    PubMed

    Capelli, C; Pedrini, O; Valgardsdottir, R; Da Roit, F; Golay, J; Introna, M

    2015-12-01

    Producing advanced therapy medicinal products (ATMP) according to Good Manufacturing Practice (GMP) guidelines represents a global challenge for the expansion of cells intended for human use. Mesenchymal stromal cells (MSCs) from different sources are one of the most actively developed cell type for a variety of clinical applications in cellular therapy. Complying with GMP means defining accurately both the production process and the release criteria required for a final safe product. We have here reported our manufacturing experience on 103 consecutive clinical-grade in vitro expansions of both bone marrow-derived and umbilical cord-derived mesenchymal stromal cells together with description of methods and reagents utilized in our Cell Factory. The same animal- and serum-free medium, additioned with human platelet lysate, has been used for all the expansions performed. This is the largest experience published so far with this alternative and clinical-grade reagent (compared to the traditional fetal bovine serum) and shows the feasibility and the reproducibility of the method. Indeed, we have been able to produce a sufficient number of MSCs to treat 57 patients so far, enrolled in 7 different experimental phase I/II protocols. PMID:26092523

  13. Pore size and pore throat types in a heterogeneous dolostone reservoir, Devonian Grosmont formation, western Canada sedimentary basin

    SciTech Connect

    Luo, P.; Machel, H. G.

    1995-11-01

    The Devonian Grosmont Formation in northeastern Alberta, Canada, is a giant heavy-oil reservoir. The main reservoir rocks are dolomitized and karstified platform and ramp carbonates, and the best reservoir facies occur in the upper Grosmont (UGM) units 3 and 2. In these units, reservoir properties are highly heterogeneous. Hand specimen, thin section, UV, and SEM petrography, as well as grading scales, mercury capillary pressure curve analysis, and statistics, have been used to characterize reservoir heterogeneity. Our investigation led to a new pore size classification for carbonate reservoirs; this new classification has four pore sizes: microporosity (pore diameters <1 {mu}m), mesoporosity (pore diameters 1-1000 {mu}m), macroporosity (pore diameters 1-256 mm), and megaporosity (pore diameters >256 mm). A combination of microscopic observations and capillary pressure curve characteristics led to the recognition of four pore throat texture types on the microporosity scale, and to five types on the mesoporosity scale. Microporosity pore types include (1) intracrystal dissolution porosity, (2) pervasive intercrystal and intracrystal dissolution porosity, (3) intergranular and/or intercrystal porosity in grainstones, and (4) primary or solution microporosity in mud matrix (only in limestones). Mesoporosity pore types include (1) intercrystal porosity, (2) solution-enhanced intercrystal porosity, (3) oversized porosity, (4) intragranular solution porosity, and (5) intergranular solution porosity. Some of these types are homogeneous (e.g., non-fabric selective dissolution porosity and intercrystal primary porosity), whereas others are heterogeneous. Generally, hydrocarbon recovery efficiency is good in the homogeneous pore throat types, but poor in the heterogeneous types.

  14. 78 FR 36165 - Reorganization/Expansion of Foreign-Trade Zone 104; (Expansion of Service Area and Expansion of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-17

    ... Federal Register (77 FR 43047, 07/23/12) and the application has been processed pursuant to the FTZ Act... Foreign-Trade Zones Board Reorganization/Expansion of Foreign-Trade Zone 104; (Expansion of Service Area and Expansion of Zone); Under Alternative Site Framework, Savannah, Georgia Pursuant to its...

  15. The Type III Secretion Translocation Pore Senses Host Cell Contact

    PubMed Central

    Armentrout, Erin I.; Rietsch, Arne

    2016-01-01

    Type III secretion systems (T3SS) are nano-syringes used by a wide range of Gram-negative pathogens to promote infection by directly injecting effector proteins into targeted host cells. Translocation of effectors is triggered by host-cell contact and requires assembly of a pore in the host-cell plasma membrane, which consists of two translocator proteins. Our understanding of the translocation pore, how it is assembled in the host cell membrane and its precise role in effector translocation, is extremely limited. Here we use a genetic technique to identify protein-protein contacts between pore-forming translocator proteins, as well as the T3SS needle-tip, that are critical for translocon function. The data help establish the orientation of the translocator proteins in the host cell membrane. Analysis of translocon function in mutants that break these contacts demonstrates that an interaction between the pore-forming translocator PopD and the needle-tip is required for sensing host cell contact. Moreover, tethering PopD at a dimer interface also specifically prevents host-cell sensing, arguing that the translocation pore is actively involved in detecting host cell contact. The work presented here therefore establishes a signal transduction pathway for sensing host cell contact that is initiated by a conformational change in the translocation pore, and is subsequently transmitted to the base of the apparatus via a specific contact between the pore and the T3SS needle-tip. PMID:27022930

  16. Hetero-oligomeric MspA pores in Mycobacterium smegmatis.

    PubMed

    Pavlenok, Mikhail; Niederweis, Michael

    2016-04-01

    The porin MspA of Mycobacterium smegmatis is a biological nanopore used for DNA sequencing. The octameric MspA pore can be isolated from M. smegmatis in milligram quantities, is extremely stable against denaturation and rapidly inserts into lipid membranes. Here, we show that MspA pores composed of different Msp subunits are formed in M. smegmatis and that hetero-oligomers of different Msp monomers increase the heterogeneity of MspA pores designed for DNA sequencing. To improve the quality of preparations of mutant MspA proteins, all four msp genes were deleted from the M. smegmatis genome after insertion of an inducible porin gene from M. tuberculosis. In the msp quadruple mutant M. smegmatis ML712 no Msp porins were detected and mutant MspA proteins were produced at wild-type levels. Lipid bilayer experiments demonstrated that MspA pores isolated from ML712 formed functional channels and had a narrower conductance distribution than pores purified from M. smegmatis with background msp expression. Thus, the M. smegmatis msp quadruple mutant improves the homogeneity of MspA pores designed for DNA sequencing and might also facilitate the identification and functional characterization of other mycobacterial pore proteins. PMID:26912121

  17. The dielectric properties of water within model transbilayer pores.

    PubMed Central

    Sansom, M S; Smith, G R; Adcock, C; Biggin, P C

    1997-01-01

    Ion channels contain extended columns of water molecules within their transbilayer pores. The dynamic properties of such intrapore water have been shown to differ from those of water in its bulk state. In previous molecular dynamics simulations of two classes of model pore (parallel bundles of Ala20 alpha-helices and antiparallel barrels of Ala10 beta-strands), a substantially reduced translational and rotational mobility of waters was observed within the pore relative to bulk water. Molecular dynamics simulations in the presence of a transpore electrostatic field (i.e., a voltage drop along the pore axis) have been used to estimate the resultant polarization (due to reorientation) of the intrapore water, and hence to determine the local dielectric behavior within the pore. It is shown that the local dielectric constant of water within a pore is reduced for models formed by parallel alpha-helix bundles, but not by those formed by beta-barrels. This result is discussed in the context of electrostatics calculations of ion permeation through channels, and the effect of the local dielectric of water within a helix bundle pore is illustrated with a simple Poisson-Boltzmann calculation. Images FIGURE 1 PMID:9370434

  18. Pore formation by actinoporins, cytolysins from sea anemones.

    PubMed

    Rojko, Nejc; Dalla Serra, Mauro; Maček, Peter; Anderluh, Gregor

    2016-03-01

    Actinoporins (APs) from sea anemones are ~20kDa pore forming toxins with a β-sandwich structure flanked by two α-helices. The molecular mechanism of APs pore formation is composed of several well-defined steps. APs bind to membrane by interfacial binding site composed of several aromatic amino acid residues that allow binding to phosphatidylcholine and specific recognition of sphingomyelin. Subsequently, the N-terminal α-helix from the β-sandwich has to be inserted into the lipid/water interphase in order to form a functional pore. Functional studies and single molecule imaging revealed that only several monomers, 3-4, oligomerise to form a functional pore. In this model the α-helices and surrounding lipid molecules build toroidal pore. In agreement, AP pores are transient and electrically heterogeneous. On the contrary, crystallized oligomers of actinoporin fragaceatoxin C were found to be composed of eight monomers with no lipids present between the adjacent α-helices. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Maur Dalla Serra and Franco Gambale. PMID:26351738

  19. EFFECT OF PORE SIZE ON TRAPPING ZINC VAPORS

    SciTech Connect

    Korinko, P.

    2010-12-17

    A series of experiments were conducted to determine the effect of pore size on pumping efficiency and zinc vapor trapping efficiency. A simple pumping efficiency test was conducted for all five pore diameters where it was observed that evacuation times were adversely affected by reducing the pore size below 5 {micro}m. Common test conditions for the zinc trapping efficiency experiments were used. These conditions resulted in some variability, to ascribe different efficiencies to the filter media. However, the data suggest that there is no significant difference in trapping efficiency for filter media with pores from 0.2 to 20 {micro}m with a thickness of 0.065-inch. Consequently, the 20 {micro}m pore filter media that is currently used at SRS is a suitable filter material for to utilize for future extractions. There is evidence that smaller pore filter will adversely affect the pumping times for the TEF and little evidence to suggest that a smaller pore diameters have significant impact on the trapping efficiency.

  20. Assembly and stability of nisin-lipid II pores.

    PubMed

    Hasper, Hester Emilie; de Kruijff, Ben; Breukink, Eefjan

    2004-09-14

    The peptide antibiotic nisin was the first reported example of an antibiotic that kills bacteria via targeted pore formation. The specific target of nisin is Lipid II, an essential intermediate in the bacterial cell-wall synthesis. High-affinity binding of the antibiotic to Lipid II is followed by rapid permeabilization of the membrane. Here, we investigated the assembly and stability of nisin-Lipid II pore complexes by means of pyrene fluorescence and circular dichroism. We demonstrated that nisin uses all available Lipid II molecules in the membrane to form pore complexes. The pore complexes have a uniform structure and consist of 8 nisin and 4 Lipid II molecules. Moreover, the pores displayed a remarkable stability, because they were able to resist the solubilization of the membrane environment by mild detergents. Similar experiments with [N20P/M21P]nisin showed that the hinge region is essential for the assembly into stable pore complexes. The new insights were used to propose a refined model for nisin pore formation. PMID:15350143

  1. Morphological Characterization of the Polyflux 210H Hemodialysis Filter Pores

    PubMed Central

    Hedayat, A.; Szpunar, J.; Kumar, N. A. P. Kiran; Peace, R.; Elmoselhi, H.; Shoker, A.

    2012-01-01

    Background. Morphological characterization of hemodialysis membranes is necessary to improve pore design. Aim. To delineate membrane pore structure of a high flux filter, Polyflux 210H. Methods. We used a Joel JSM-6010LV scanning electron microscope (SEM) and a SU6600 Hitachi field emission scanning electron microscope (FESEM) to characterize the pore and fiber morphology. The maximal diameters of selected uremic toxins were calculated using the macromolecular modeling Crystallographic Object-Oriented Toolkit (COOT) software. Results. The mean pore densities on the outermost and innermost surfaces of the membrane were 36.81% and 5.45%, respectively. The membrane exhibited a tortuous structure with poor connection between the inner and outer pores. The aperture's width in the inner surface ranged between 34 and 45 nm, which is 8.76–11.60 times larger than the estimated maximum diameter of β2-microglobulin (3.88 nm). Conclusion. The results suggest that the diameter size of inner pore apertures is not a limiting factor to middle molecules clearance, the extremely diminished density is. Increasing inner pore density and improving channel structure are strategies to improve clearance of middle molecules. PMID:23209902

  2. Impact of Casing Expansion on the Mechanical and Petro-Physical Properties of Wellbore Cements

    NASA Astrophysics Data System (ADS)

    Oyibo, A. E.

    2014-12-01

    The main objective of this research is to investigate the applicability of expandable casing technology as a remediation technique for leaky wells resulting in gas migration problems. Micro annulus is usually created at the cement-formation/cement-casing interface or within the cement matrix either due to poor primary cementing or as a result of activities such as temperature and pressure variation or fracturing operations. Recent reports on gas migration in hydraulically fractured wellbores, has raised concerns on the contamination of fresh water aquifers resulting from fluid migration though this flow path. A unique bench-scale physical model which utilizes expandable tubulars in the remediation of micro annular gas flow has been used to simulate expansion of a previously-cemented casing under field-like conditions. Three different designs of cement slurry: regular 16.4 lb. /gal, 16.4 lb. /gal base slurry foamed to 13 lb. /gal and 16.4 lb. /gal cement slurry with 10% salt concentration. Gas flow path (microannulus) was artificially created at the pipe-cement interface by rotating the inner pipe in a pipe inside pipe assembly with cement in the annulus within the first few hours of hydration to create debonding at the cement-casing interface. Nitrogen gas flow-through experiments were performed before and after the expansion to confirm the sealing of the microannulus. The results obtained confirmed the effectiveness of this technique in the complete closure of gas leakage path, providing seal-tight cement-formation interface free of microannulus. The manipulation of the cement sheath during the casing expansion resulted in improved porosity, permeability and the strength of the cement sheath. SEM micrographs revealed decrease in pore size and fracturing of unhydrated cement grains within the cement matrix. This technology has great potential to become one of the leading cement remediation techniques for leaks behind the casing if implemented. Keywords: Wellbore

  3. Connecting Wastewater Injection and Seismicity through Pore Pressure

    NASA Astrophysics Data System (ADS)

    Ge, S.; Weingarten, M.; Person, M. A.; Bekins, B. A.

    2014-12-01

    Increased seismicity in recent years in some geologically quiescent regions in the US has been linked to wastewater injection associated with oil and gas production. While seismicity in some cases appears to be well correlated with injection activities, in many other injection locations no seismicity has been reported. How pore pressures generated from injection propagate spatially and evolve temporally is likely a key control in inducing earthquakes, providing a physical linkage between injection activity and seismicity occurrence. Yet, the linkage remains controversial and inconclusive, in spite of the basic physics of pore pressure propagation being well established. This study aims at better understanding the physical processes of pore pressure propagation around injection sites and identifying factors that are most likely contributors to induced seismicity. Numerical modeling suggests that pore pressure increases in the Jones seismicity swarm northeast of Oklahoma City were primarily from several high rate injection wells. Preliminary analysis on injection and seismicity data from Greeley, Colorado also points to a potential pore pressure link between high injection rates and seismicity. Modeling of pore pressures in the Lake County, Ohio, illustrates that permeable faults in the crystalline basement could facilitate pore pressure propagation from injection in the basal aquifer and host earthquakes, which could explain the earthquakes that occurred in the mid-1980s. In many of the above examples, wastewater injection in basal aquifers promoted downward propagation of pore pressures into the crystalline basement. In connecting injection and seismicity through pore pressure propagation, high rate injection wells and permeable basement faults are merging as important players contributing to induced seismicity. It is the intention of this study that findings like these would provide a scientific basis to inform future regulations and policies on wastewater

  4. Chemical recombination in an expansion tube

    NASA Technical Reports Server (NTRS)

    Bakos, Robert J.; Morgan, Richard G.

    1994-01-01

    The note describes the theoretical basis of chemical recombination in an expansion tube which simulates energy, Reynolds number, and stream chemistry at near-orbital velocities. Expansion tubes can satisfy ground-based hypersonic propulsion and aerothermal testing requirements.

  5. A Power Series Expansion and Its Applications

    ERIC Educational Resources Information Center

    Chen, Hongwei

    2006-01-01

    Using the power series solution of a differential equation and the computation of a parametric integral, two elementary proofs are given for the power series expansion of (arcsin x)[squared], as well as some applications of this expansion.

  6. Nonlinear effects on composite laminate thermal expansion

    NASA Technical Reports Server (NTRS)

    Hashin, Z.; Rosen, B. W.; Pipes, R. B.

    1979-01-01

    Analyses of Graphite/Polyimide laminates shown that the thermomechanical strains cannot be separated into mechanical strain and free thermal expansion strain. Elastic properties and thermal expansion coefficients of unidirectional Graphite/Polyimide specimens were measured as a function of temperature to provide inputs for the analysis. The + or - 45 degrees symmetric Graphite/Polyimide laminates were tested to obtain free thermal expansion coefficients and thermal expansion coefficients under various uniaxial loads. The experimental results demonstrated the effects predicted by the analysis, namely dependence of thermal expansion coefficients on load, and anisotropy of thermal expansion under load. The significance of time dependence on thermal expansion was demonstrated by comparison of measured laminate free expansion coefficients with and without 15 day delay at intermediate temperature.

  7. Managing Free-energy Barriers in Nuclear Pore Transport

    PubMed Central

    Nielsen, Brian; Jeppesen, Claus

    2006-01-01

    The Nuclear Pore Complexes (NPC) facilitate highly selective gateways for transport of macromolecules across the Nuclear Envelope (NE). Based on the current accumulated knowledge of the architecture of NPC we have established a minimal physical model of the pore and the transport mechanism. The barrier properties of the NPC model are analyzed by the recently established Wang–Landau Monte Carlo computer simulation technique and the transport properties are extracted by employing Kramers’ theory of reaction rates. We show that our physical model can account for a range of characteristics observed for nuclear pore transport. PMID:19669451

  8. Metal oxide porous ceramic membranes with small pore sizes

    DOEpatents

    Anderson, Marc A.; Xu, Qunyin

    1991-01-01

    A method is disclosed for the production of metal oxide ceramic membranes of very small pore size. The process is particularly useful in the creation of titanium and other transition metal oxide membranes. The method utilizes a sol-gel process in which the rate of particle formation is controlled by substituting a relatively large alcohol in the metal alkoxide and by limiting the available water. Stable, transparent metal oxide ceramic membranes are created having a narrow distribution of pore size, with the pore diameter being manipulable in the range of 5 to 40 Angstroms.

  9. Metal oxide porous ceramic membranes with small pore sizes

    DOEpatents

    Anderson, Marc A.; Xu, Qunyin

    1992-01-01

    A method is disclosed for the production of metal oxide ceramic membranes of very small pore size. The process is particularly useful in the creation of titanium and other transition metal oxide membranes. The method utilizes a sol-gel process in which the rate of particle formation is controlled by substituting a relatively large alcohol in the metal alkoxide and by limiting the available water. Stable, transparent metal oxide ceramic membranes are created having a narrow distribution of pore size, with the pore diameter being manipulable in the range of 5 to 40 Angstroms.

  10. The effect of pore water pressure on debris flow dynamics

    NASA Astrophysics Data System (ADS)

    Okura, Y.; Parker, G.; Marr, J. G.; Yu, B.; Ochiai, H.

    2003-12-01

    Pore-water likely plays an important role to reduce shear force in debris flow. In experiments, we observed pore-water pressure during flow to clarify the relationship between the flow speed and pore water pressure which would be affected by flow depth and particle size distribution. Soil materials were prepared with mixing materials of sand, silt and clay. Pore-water pressure on the flume bed, flow depth, velocity and run out distance was observed, and the following results were quantitatively obtained in this series of experiments. 1. A positive relation was observed between strain rate and pore-water pressure ratio in the flow. The strain rate and pressure ratio were dimensionless parameters of the ratios of surface velocity to flow depth and pore-water pressure head to flow depth, respectively. This relationship indicated that shear resistance decreased as the pressure potential leading to acceleration of flow velocity increased. 2. A positive relation was also observed between flow depth and pore-water pressure ratio. This indicated that the pore pressure diffusion became increasingly obstructed as the flow depth increased. 3. The pore-water pressure ratio tended to increase with the uniformity coefficient of debris flow materials. The reason for this might have been that smaller particles suspended in the flow increased pore-water pressure, and the wider range of particle distribution effectively prevented pore-water pressure diffusion. 4. There was an apparently negative correlation between the equivalent coefficient of frictions and the pressure ratios. Equivalent friction is apparent friction during flow. The most likely reason for this is that shear resistance would decrease and run out distance increase as the pressure ratio increased. These results indicated that the effect of pore water fluctuations should be one of the most important factors affecting the shear resistance in debris flows. This work was supported by the National Science Foundation

  11. Gaseous Diffusion and Pore Structure in Nuclear Graphites.

    NASA Astrophysics Data System (ADS)

    Mays, Timothy John

    Available from UMI in association with The British Library. With the incentive of providing more information for oxidation and safety studies of graphite components in thermal nuclear reactors, a new method has been developed to determine the gas transport pore structure in nuclear graphites. It involves an analysis of the dependence on pressure of the isobaric, isothermal (room temperature) diffusivity ratios of components in a binary gas mixture flowing through annular graphite samples. A Wicke-Kallenbach apparatus was specially built to measure He-Ar diffusivity ratios at pressures below 100 Torr. The new apparatus incorporates capacitance manometers and servovalves for pressure measurement and control, hot wire meters for flow rate measurements, and a mass spectrometer for gas analysis. As pressure decreased, the diffusivity ratios were observed to decrease non-linearly, indicating that the mechanism of flow in the materials was in the transition region between molecular and Knudsen diffusion. A mathematical model was derived to relate the pressure dependence of the transition diffusivity ratio to gas transport pore structure, and a statistical analysis based on Tikhonov regularisation was developed which gave a good fit of the model to the data, and optimal estimates of the number of model capillary pores, and the distribution of pore sizes. In comparison, the established methods of molecular diffusion and permeation (flow of pure gases) only give mean data on the pore size distribution. Pore structure data from the new method accurately predicted CO_2-Ar molecular diffusivity ratios, but overestimated N_2 permeability coefficients, due, it was assumed, to differences between diffusion and permeation pore structure. The cumulative volume distributions for transport pores from the transition diffusion data were similar in shape to those for open pores from mercury porosimetry, but shifted towards higher pore radii, indicating that diffusion is not so influenced

  12. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    DOEpatents

    Sachtler, Wolfgang M. H.; Huang, Yin-Yan

    1998-01-01

    Methods for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physisorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics.

  13. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    DOEpatents

    Sachtler, W.M.H.; Huang, Y.Y.

    1998-07-28

    Methods are disclosed for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physical sorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics. 17 figs.

  14. Diffusion Pore Imaging by Hyperpolarized Xenon-129 Nuclear Magnetic Resonance

    NASA Astrophysics Data System (ADS)

    Kuder, Tristan Anselm; Bachert, Peter; Windschuh, Johannes; Laun, Frederik Bernd

    2013-07-01

    While NMR diffusion measurements are widely used to derive parameters indirectly related to the microstructure of biological tissues and porous media, direct imaging of pore shapes would be of high interest. Here we demonstrate experimentally that complexly shaped closed pores can be imaged by diffusion acquisitions. Collecting the signal from the whole sample eliminates the problem of vanishing signal at increasing resolution of conventional NMR imaging. This approach may be used to noninvasively obtain structural information inaccessible so far such as pore or cell shapes, cell density, or axon integrity.

  15. Topology of a percolating soil pore network

    NASA Astrophysics Data System (ADS)

    Capa-Morocho, M.; Ruiz-Ramos, M.; Hapca, S. M.; Houston, A.; Tarquis, A. M.

    2012-04-01

    A connectivity function defined by the 3D-Euler number, is a topological indicator and can be related to hydraulic properties (Vogel and Roth, 2001). This study aims to develop connectivity Euler indexes as indicators of the ability of soils for fluid percolation. The starting point was a 3D grey image acquired by X-ray computed tomography of a soil at bulk density of 1.2 mg cm-3. This image was used in the simulation of 40000 particles following a directed random walk algorithms with 7 binarization thresholds. These data consisted of 7 files containing the simulated end points of the 40000 random walks, obtained in Ruiz-Ramos et al. (2010). MATLAB software was used for computing the frequency matrix of the number of particles arriving at every end point of the random walks and their 3D representation. In a former work (Capa et al., 2011) a criteria for choosing the optimal threshold of grey value was identified: Final positions were divided in two subgroups, cg1 (positions with frequency of the number of particles received greater than the median) and cg2 (frequency lower or equal to median). Images with maximum difference between the Z coordinate of the center of gravity of both subgroups were selected as those with optimal threshold that reflects the major internal differences in soil structure that are relevant to percolation. According to this criterion, the optimal threshold for the soil with density 1.2 mg cm-3 was 24.Thresholds above and below the optimal (23 and 25) were also considered to confirm this selection; therefore the analysis were conducted for three files (1 image with 3 grey threshold values, which have different porosity). Additionally, three random matrix simulations with the same porosity than the selected binaries images were used to test the existence of pore connectivity as a consequence of a non-random soil structure. Therefore, 6 matrix were considered (three structured and three random) for this study. Random matrix presented a normal

  16. Intumescence and pore structure of alkali-activated volcanic glasses upon exposure to high temperatures

    NASA Astrophysics Data System (ADS)

    Erdogan, S. T.

    2015-12-01

    Structures formed with ground perlite, a natural volcanic glass, activated with NaOH solutions, are shown to possess the ability to expand up to ~225 % of their original volumes upon exposure to temperatures in the 200-600 °C range. Porous solid with 3-7 MPa compressive strength and ˜450 kg/m3 or higher density are obtained. The observed expansion is believed to occur due to a loss of silanol condensation water, as vapor and is accompanied by an up to ~20 % loss in mass. A drop in pH to near-neutral values supports this idea. The size and total amount of pores in the final solid are controlled by concentration of the NaOH solution and thermal processing conditions. The pores formed are observed to be ~1-10 μm to mm-sized. The ability of perlite-based solids to intumesce over specific temperature ranges could be beneficial in applications where absorption of thermal energy is necessary, such as passive fire protection.

  17. Reducing Thermal Expansivity of Composite Panels

    NASA Technical Reports Server (NTRS)

    Smith, D. D.

    1985-01-01

    Coefficient of thermal expansion of laminated graphite/epoxy composite panels altered after panels cured by postcuring heat treatment. Postcure decreases coefficient of thermal expansion by increasing crosslinking between molecules. Treatment makes it possible to reprocess costly panels for requisite thermal expansivity instead of discarding them.

  18. 32 CFR 169a.11 - Expansions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 1 2012-07-01 2012-07-01 false Expansions. 169a.11 Section 169a.11 National... PROGRAM PROCEDURES Procedures § 169a.11 Expansions. In cases where expansion of an in-house commercial activity is anticipated, a review of the entire commercial activity, including the proposed...

  19. 32 CFR 169a.11 - Expansions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 1 2013-07-01 2013-07-01 false Expansions. 169a.11 Section 169a.11 National... PROGRAM PROCEDURES Procedures § 169a.11 Expansions. In cases where expansion of an in-house commercial activity is anticipated, a review of the entire commercial activity, including the proposed...

  20. 32 CFR 169a.11 - Expansions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 1 2014-07-01 2014-07-01 false Expansions. 169a.11 Section 169a.11 National... PROGRAM PROCEDURES Procedures § 169a.11 Expansions. In cases where expansion of an in-house commercial activity is anticipated, a review of the entire commercial activity, including the proposed...

  1. 32 CFR 169a.11 - Expansions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 1 2010-07-01 2010-07-01 false Expansions. 169a.11 Section 169a.11 National... PROGRAM PROCEDURES Procedures § 169a.11 Expansions. In cases where expansion of an in-house commercial activity is anticipated, a review of the entire commercial activity, including the proposed...

  2. 32 CFR 169a.11 - Expansions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 32 National Defense 1 2011-07-01 2011-07-01 false Expansions. 169a.11 Section 169a.11 National... PROGRAM PROCEDURES Procedures § 169a.11 Expansions. In cases where expansion of an in-house commercial activity is anticipated, a review of the entire commercial activity, including the proposed...

  3. Space nuclear system expansion joints

    NASA Technical Reports Server (NTRS)

    Whitaker, W. D.; Shimazki, T. T.

    1973-01-01

    The engineering, design, and fabrication status of the expansion joint unit (EJU) to be employed in the NaK primary coolant piping loop of the 5-kwe Reactor thermoelectric system are described. Four EJU's are needed in the NaK primary coolant piping loop. The four EJU's which will be identical, utilize bellows as the flexing member, are hermetically sealed, and provide double containment. The bellows are of a nested-formed design, and are to be constructed of 1-ply thickness of 0.010-in. Inconel 718. The EJU's provide a minimum piping load margin of safety of +0.22.

  4. Calculation of Turbulent Expansion Processes

    NASA Technical Reports Server (NTRS)

    Tollmien, Walter

    1945-01-01

    On the basis of certain formulas recently established by L. Prandtl for the turbulent interchange of momentum in stationary flows, various cases of "free turbulence" - that is, of flows without boundary walls - are treated in the present report. Prandtl puts the apparent shearing stress introduced by the turbulent momentum interchange. This present report deals first with the mixing of an air stream of uniform velocity with the adjacent still air, than with the expansion or diffusion of an air jet in the surrounding air space.

  5. Formation of an ink-bottle-like pore structure in SBA-15 by MOCVD.

    PubMed

    Zhang, Ying; Lam, Frank Leung-Yuk; Hu, Xijun; Yan, Zifeng

    2008-11-01

    Metallorganic chemical vapor deposition is used as a simple pore-modifying method to fine tune the pore-opening size of SBA-15 materials without significant loss in pore volume and surface area. PMID:18956045

  6. Ion transport and dehydration in sub-nanoscale pores

    NASA Astrophysics Data System (ADS)

    Sahu, Subin; di Ventra, Massimiliano; Zwolak, Michael

    Ions in solution develop tightly bound layers of water - hydration layers - which stabilize disassociation and enable ionic currents to flow. Sub-nanometer pores in a membrane enable ions to pass provided that they shed their hydration shell. This process has an associated large energy penalty that is predicted to give rise to ''quantized'' steps in the ionic conductance. Using all-atom molecular dynamics simulation, we demonstrate that the ionic current begins to show nonlinear behavior as the radius of the pore is reduced to the sub-nanometer scale. This nonlinear behavior is seen as a sharp rise in the pore resistance and excess noise in the current. Our work sheds light on basic mechanism of ion transport through sub-nanoscale pores. S. Sahu acknowledges support by UMD/CNST Cooperative Research Agreement, Award 70NANB10H193 through University of Maryland.

  7. Hydrochromic conjugated polymers for human sweat pore mapping

    NASA Astrophysics Data System (ADS)

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-Hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-01

    Hydrochromic materials have been actively investigated in the context of humidity sensing and measuring water contents in organic solvents. Here we report a sensor system that undergoes a brilliant blue-to-red colour transition as well as ‘Turn-On’ fluorescence upon exposure to water. Introduction of a hygroscopic element into a supramolecularly assembled polydiacetylene results in a hydrochromic conjugated polymer that is rapidly responsive (<20 μs), spin-coatable and inkjet-compatible. Importantly, the hydrochromic sensor is found to be suitable for mapping human sweat pores. The exceedingly small quantities (sub-nanolitre) of water secreted from sweat pores are sufficient to promote an instantaneous colorimetric transition of the polymer. As a result, the sensor can be used to construct a precise map of active sweat pores on fingertips. The sensor technology, developed in this study, has the potential of serving as new method for fingerprint analysis and for the clinical diagnosis of malfunctioning sweat pores.

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

    PubMed

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

    2014-03-28

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

  9. Porosity, pore size distribution and in situ strength of concrete

    SciTech Connect

    Kumar, Rakesh; Bhattacharjee, B

    2003-01-01

    In this study, in situ strength of concrete was determined through compression test of cores drilled out from laboratory cast beams. The apparent porosity and pore size distribution of the same concrete were determined through mercury intrusion porosimetry, performed on small-drilled cores. The normal-strength concrete mixes used in the experimental investigation were designed to exhibit a wide variation in their strengths. To ensure further variation in porosity, pore size distribution and strength, two modes of compaction, two varieties of coarse aggregates, different levels of age, curing period and exposure condition of concrete were also introduced in experimental scheme. With the data so generated, an appraisal of the most frequently referred relationships involving strength, porosity and pore size of cement-based materials was carried out. Finally, a new empirical model relating the in situ strength of concrete with porosity, pore size characteristics, cement content, aggregate type, exposure conditions, etc., is presented.

  10. Pore-scale simulation of laminar flow through porous media

    NASA Astrophysics Data System (ADS)

    Piller, M.; Casagrande, D.; Schena, G.; Santini, M.

    2014-04-01

    The experimental investigation of flow through porous media is inherently difficult due to the lack of optical access. The recent developments in the fields of X-ray micro-tomography (micro-CT hereafter), digital sample reconstruction by image-processing techniques and fluid-dynamics simulation, together with the increasing power of super-computers, allow to carry out pore-scale simulations through digitally-reconstructed porous samples. The scientific relevance of pore-scale simulations lies in the possibility of upscaling the pore-level data, yielding volume-averaged quantities useful for practical purposes. One of the best-known examples of upscaling is the calculation of absolute and relative permeability of reservoir rocks. This contribution presents a complete work-flow for setting up pore-scale simulations, starting from the micro-CT of a (in general small) porous sample. Relevant applications are discussed in order to reveal the potential of the proposed methodology.

  11. Membrane pore formation at protein-lipid interfaces.

    PubMed

    Gilbert, Robert J C; Dalla Serra, Mauro; Froelich, Christopher J; Wallace, Mark I; Anderluh, Gregor

    2014-11-01

    Pore-forming proteins (PFPs) interact with lipid bilayers to compromise membrane integrity. Many PFPs function by inserting a ring of oligomerized subunits into the bilayer to form a protein-lined hydrophilic channel. However, mounting evidence suggests that PFPs can also generate 'proteolipidic' pores by contributing to the fusion of inner and outer bilayer leaflets to form a toroidal structure. We discuss here toroidal pore formation by peptides including melittin, protegrin, and Alzheimer's Aβ1-41, as well as by PFPs from several evolutionarily unrelated families: the colicin/Bcl-2 grouping including the pro-apoptotic protein Bax, actinoporins derived from sea anemones, and the membrane attack complex-perforin/cholesterol dependent cytolysin (MACPF/CDC) set of proteins. We also explore how the structure and biological role of toroidal pores might be investigated further. PMID:25440714

  12. Pores with longitudinal irregularities distinguish objects by shape.

    PubMed

    Qiu, Yinghua; Hinkle, Preston; Yang, Crystal; Bakker, Henriette E; Schiel, Matthew; Wang, Hong; Melnikov, Dmitriy; Gracheva, Maria; Toimil-Molares, Maria Eugenia; Imhof, Arnout; Siwy, Zuzanna S

    2015-04-28

    The resistive-pulse technique has been used to detect and size objects which pass through a single pore. The amplitude of the ion current change observed when a particle is in the pore is correlated with the particle volume. Up to date, however, the resistive-pulse approach has not been able to distinguish between objects of similar volume but different shapes. In this manuscript, we propose using pores with longitudinal irregularities as a sensitive tool capable of distinguishing spherical and rod-shaped particles with different lengths. The ion current modulations within resulting resistive pulses carry information on the length of passing objects. The performed experiments also indicate the rods rotate while translocating, and displace an effective volume that is larger than their geometrical volume, and which also depends on the pore diameter. PMID:25787224

  13. Applications of biological pores in nanomedicine, sensing, and nanoelectronics

    PubMed Central

    Majd, Sheereen; Yusko, Erik C; Billeh, Yazan N; Macrae, Michael X; Yang, Jerry; Mayer, Michael

    2011-01-01

    Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated – often regulated – functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics. PMID:20561776

  14. Exocytotic fusion pores are composed of both lipids and proteins

    PubMed Central

    Bao, Huan; Goldschen-Ohm, Marcel; Jeggle, Pia; Chanda, Baron; Edwardson, J Michael; Chapman, Edwin R

    2016-01-01

    During exocytosis, fusion pores form the first aqueous connection that allows escape of neurotransmitters and hormones from secretory vesicles. Although it is well established that SNARE proteins catalyze fusion, the structure and composition of fusion pores remain unknown. Here, we exploited the rigid framework and defined size of nanodiscs to interrogate the properties of reconstituted fusion pores, using the neurotransmitter glutamate as a content-mixing marker. Efficient Ca2+-stimulated bilayer fusion, and glutamate release, occurred with approximately two molecules of mouse synaptobrevin 2 reconstituted into ~6-nm nanodiscs. The transmembrane domains of SNARE proteins assumed distinct roles in lipid mixing versus content release and were exposed to polar solvent during fusion. Additionally, tryptophan substitutions at specific positions in these transmembrane domains decreased glutamate flux. Together, these findings indicate that the fusion pore is a hybrid structure composed of both lipids and proteins. PMID:26656855

  15. PORE-SCALE MODELING OF BIOLOGICAL CLOGGING DUE TO AGGREGATE EXPANSION: A MATERIAL MECHANICS APPROACH. (R828772)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  16. Upscaling of Bio-mediated Soil Improvement

    SciTech Connect

    J. T. DeJong; B. C. Martinez; B. M. Mortensen; D. C. Nelson; J. T. Waller; M. H. Weil; T. R. Ginn; T. Weathers; T. Barkouki; Y. Fujita; G. Redden; C. Hunt; D. Major; B. Tunyu

    2009-10-01

    As demand for soil improvement continues to increase, new, sustainable, and innocuous methods are needed to alter the mechanical properties of soils. Recent research has demonstrated the potential of bio-mediated soil improvement for geotechnical applications (DeJong et al. 2006, Whiffin et al. 2007). Upscaling the bio-mediated treatment process for in situ implementation presents a number of challenges to be addressed, including soil and pore fluid interactions, bioaugmentation versus biostimulation of microbial communities, controlled distribution of mediated calcite precipitation, and permanence of the cementation. Current studies are utilizing large-scale laboratory experiments, non-destructive geophysical measurements, and modeling, to develop an optimized and predictable bio-mediated treatment method.

  17. Validity of the field line resonance expansion

    NASA Technical Reports Server (NTRS)

    Hansen, P. J.; Goertz, C. K.

    1992-01-01

    The field line resonance expansion is studied with a magnetohydrodynamic (MHD) model applicable to earth's magnetotail. Using a Frobenius series solution, this expansion is found to be inconsistent. The inconsistency is seen by evaluating the terms in the model equations that the expansion neglects as small. Their effect is to provide a solution more singular than that determined by the expansion procedure. A tentative alternative expansion procedure, retaining these neglected terms approximately, yields a nonsingular solution, suggesting that resonant mode conversion rather than field line resonance is the appropriate phenomenon.

  18. Dynamic pore-pressure fluctuations in rapidly shearing granular materials

    USGS Publications Warehouse

    Iverson, R.M.; LaHusen, R.G.

    1989-01-01

    Results from two types of experiments show that intergranular pore pressures fluctuated dynamically during rapid, steady shear deformation of water-saturated granular materials. During some fluctuations, the pore water locally supported all normal and shear stresses, while grain-contact stresses transiently fell to zero. Fluctuations also propagated outward from the shear zone; this process modifies grain-contact stresses in adjacent areas and potentially instigates shear-zone growth.

  19. Pore structure characterization of catalyst supports via low field NMR

    SciTech Connect

    Smith, D.M.; Glaves, C.L.; Gallegos, D.P.; Brinker, C.J.

    1988-01-01

    In this paper, the application of low-field NMR to both surface area and pore structure analysis of catalyst supports will be presented. Low-field (20 MHz) spin-lattice relaxation (T/sub 1/) experiments are performed on fluids contained in alumina and silica catalyst supports. Pore size distributions (PSD) calculated from these NMR experiments are compared to those obtained from mercury porosimetry and nitrogen condensation. 18 refs., 4 figs., 2 tabs.

  20. Comparative squamation of the lateral line canal pores in sharks.

    PubMed

    McKenzie, R W; Motta, P J; Rohr, J R

    2014-05-01

    The current study collected the first quantitative data on lateral line pore squamation patterns in sharks and assessed whether divergent squamation patterns are similar to experimental models that cause reduction in boundary layer turbulence. In addition, the hypothesis that divergent orientation angles are exclusively found in fast-swimming shark species was tested. The posterior lateral line and supraorbital lateral line pore squamation of the fast-swimming pelagic shortfin mako shark Isurus oxyrinchus and the slow-swimming epi-benthic spiny dogfish shark Squalus acanthias was examined. Pore scale morphology and pore coverage were qualitatively analysed and compared. In addition, pore squamation orientation patterns were quantified for four regions along the posterior lateral line and compared for both species. Isurus oxyrinchus possessed consistent pore scale coverage among sampled regions and had a divergent squamation pattern with multiple scale rows directed dorsally and ventrally away from the anterior margin of the pore with an average divergent angle of 13° for the first row of scales. Squalus acanthias possessed variable amounts of scale coverage among the sampled regions and had a divergent squamation pattern with multiple scale rows directed ventrally away from the anterior margin of the pore with an average angle of 19° for the first row of scales. Overall, the squamation pattern measured in I. oxyrinchus fell within the parameters used in the fluid flow analysis, which suggests that this pattern may reduce boundary layer turbulence and affect lateral line sensitivity. The exclusively ventral oriented scale pattern seen in S. acanthias possessed a high degree of divergence but the pattern did not match that of the fluid flow models. Given current knowledge, it is unclear how this would affect boundary layer flow. By studying the relationship between squamation patterns and the lateral line, new insights are provided into sensory biology that warrant

  1. Phase-Field Modeling of Lipid Vesicles With Pores

    NASA Astrophysics Data System (ADS)

    Seifi, Saman; Salac, David

    2013-11-01

    The formation and annihilation of pores in a lipid vesicle membrane is critical to a number of biotechnologies, such as drug delivery. Previous models of vesicle behavior have ignored the influence of topological changes in the vesicle membrane. Here the entire Helfrich model of a vesicle membrane is considered. Topological changes in the vesicle membrane, such as the formation of a pore, are captured through the use of an embedded phase-field model. The numerical method and sample results will be presented.

  2. Interactions between bedforms, turbulence and pore flow

    NASA Astrophysics Data System (ADS)

    Blois, G.; Best, J.; Sambrook Smith, G.; Hardy, R. J.; Lead, J.

    2010-12-01

    A widespread occurrence of flow-form interaction in rivers is represented by subaqueous bedforms such as dunes. Many models have been proposed to explain how bedform generation and evolution are driven by turbulent flow structures that control the incipient motion of cohesionless sediments and later bedform development. However, most of these models have assumed such bedforms to be migrating over an impermeable bed, and that any surface-subsurface flow interaction is negligible. However, for some gravel-bed rivers the porosity can be high, up to 43%, which may result in significant flow both through the permeable bed (hyporheic flow) and across the surface-subsurface interface. The mass and momentum exchange occurring at the interface may have a strong impact on the structure of turbulent flow in the near-bed region. In the case of a dune, its topography induces a local pressure gradient that enhances flow across the interface. This results in a flow structure that may be radically different from that commonly proposed by past work. This paper presents results from a simplified laboratory model akin to a fine-grained bedform generated on top of a coarser sediment bed. Particle imaging velocimetry (PIV) measurements were conducted in order to characterise flow both over and underneath an idealised 2-dimensional dune (0.41 m long, 0.056 m high and having a leeside angle of 27°) overlaying a packed bed of uniform size spheres (D = 0.04 m diameter). Experiments were conducted in free surface flow conditions (Froude number = 0.1; Reynolds number = 25,000) for one bedform height: flow depth ratio (0.31). The flow above the dune was measured using a standard PIV technique while a novel endoscopic PIV (EPIV) system allowed collection of flow data within the pore spaces beneath the dune. The results show that topographically-induced subsurface flow significantly modifies the structure of flow in the leeside of the dune, resulting in a flow field that is radically different

  3. Pore size and the lab-field reaction rate riddle

    NASA Astrophysics Data System (ADS)

    Emmanuel, S.; Ague, J. J.; Walderhaug, O.

    2009-12-01

    Pore size is usually thought to influence the rate of crystal growth during diagenesis and metamorphism by controlling the ratio of surface area to fluid volume. However, theory suggests that in micron-scale to nanometer-scale pores, interfacial energy effects can also become important. We used mercury porosimetry to investigate the pore-size distributions in naturally cemented sandstone adjacent to stylolites and found that quartz precipitation was inhibited in pores smaller than 10 microns in diameter. We demonstrate that standard kinetic models cannot reproduce the observed pore-size patterns in mineralized samples; by contrast, excellent fits with the data are obtained when interfacial energy effects are taken into account. Moreover, as such micron-scale pores comprise the overwhelming majority of surface area in the sandstone, average reaction rates for the rock are significantly reduced. Reaction rates in geological media determined in field studies can be orders of magnitude lower than those measured in laboratory experiments, and we propose that reduced reaction rates in rocks with micron-scale porosity could account for the apparent paradox.

  4. Smooth DNA transport through a narrowed pore geometry.

    PubMed

    Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

    2014-11-18

    Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35-20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics. PMID:25418307

  5. Membrane pore formation in atomistic and coarse-grained simulations.

    PubMed

    Kirsch, Sonja A; Böckmann, Rainer A

    2016-10-01

    Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. PMID:26748016

  6. Melting transition of Lennard-Jones fluid in cylindrical pores

    SciTech Connect

    Das, Chandan K.; Singh, Jayant K.

    2014-05-28

    Three-stage pseudo-supercritical transformation path and multiple-histogram reweighting technique are employed for the determination of solid-liquid coexistence of the Lennard-Jones (12-6) fluid, in a structureless cylindrical pore of radius, R, ranging from 4 to 20 molecular diameters. The Gibbs free energy difference is evaluated using thermodynamic integration method by connecting solid and liquid phases under confinement via one or more intermediate states without any first order phase transition among them. The thermodynamic melting temperature, T{sub m}, is found to oscillate for pore size, R < 8, which is in agreement with the behavior observed for the melting temperature in slit pores. However, T{sub m} for almost all pore sizes is less than the bulk case, which is contrary to the behavior seen for the slit pore. The oscillation in T{sub m} decays at around pore radius R = 8, and beyond that shift in the melting temperature with respect to the bulk case is in line with the prediction of the Gibbs-Thomson equation.

  7. Smooth DNA Transport through a Narrowed Pore Geometry

    PubMed Central

    Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni

    2014-01-01

    Voltage-driven transport of double-stranded DNA through nanoscale pores holds much potential for applications in quantitative molecular biology and biotechnology, yet the microscopic details of translocation have proven to be challenging to decipher. Earlier experiments showed strong dependence of transport kinetics on pore size: fast regular transport in large pores (> 5 nm diameter), and slower yet heterogeneous transport time distributions in sub-5 nm pores, which imply a large positional uncertainty of the DNA in the pore as a function of the translocation time. In this work, we show that this anomalous transport is a result of DNA self-interaction, a phenomenon that is strictly pore-diameter dependent. We identify a regime in which DNA transport is regular, producing narrow and well-behaved dwell-time distributions that fit a simple drift-diffusion theory. Furthermore, a systematic study of the dependence of dwell time on DNA length reveals a single power-law scaling of 1.37 in the range of 35–20,000 bp. We highlight the resolution of our nanopore device by discriminating via single pulses 100 and 500 bp fragments in a mixture with >98% accuracy. When coupled to an appropriate sequence labeling method, our observation of smooth DNA translocation can pave the way for high-resolution DNA mapping and sizing applications in genomics. PMID:25418307

  8. Transport pathways within percolating pore space networks of granular materials

    NASA Astrophysics Data System (ADS)

    Vo, Kevin; Walker, David M.; Tordesillas, Antoinette

    2013-06-01

    Granular media can be regarded as a mixture of two components: grains and the material filling the voids or pores between the grains. Pore properties give rise to a range of applications such as modelling ground water flow, carbon capture and sequestration. The grains within a dense granular material respond to deformation (e.g., shearing or compression) by rearranging to create local zones of compression and zones of dilatation (i.e., regions of high pore space). Descriptions of the deformation are typically focused on analysis of the solid skeleton via topology of physical contact networks of grains but an alternative perspective is to consider network representations of the evolving anisotropic pore space. We demonstrate how to construct pore space networks that express the local size of voids about a grain through network edge weights. We investigate sectors of the loading history when a percolating giant component of the pore space network exists. At these states the grains are in a configuration more prone to the efficient transport of material (e.g., fluid flow, mineral/gas deposits). These pathways can be found through examination of the weighted shortest paths percolating the boundaries of the material. In particular, network weights biased towards large void space results in efficient percolating pathways traversing the shear band in the direction of principal stress within a 2D granular assembly subject to high strains.

  9. Local membrane mechanics of pore-spanning bilayers.

    PubMed

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

    2009-05-27

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

  10. Pore growth in U-Mo/Al dispersion fuel

    NASA Astrophysics Data System (ADS)

    Kim, Yeon Soo; Jeong, G. Y.; Sohn, D.-S.; Jamison, L. M.

    2016-09-01

    U-Mo/Al dispersion fuel is currently under development in the DOE's Material Management and Minimization program to convert HEU-fueled research reactors to LEU-fueled reactors. In some demanding conditions in high-power and high-performance reactors, large pores form in the interaction layers between the U-Mo fuel particles and the Al matrix, which pose a potential to cause fuel failure. In this study, comprehension of the formation and growth of these pores was explored. As a product, a model to predict pore growth and porosity increase was developed. The model includes three major topics: fission gas release from the U-Mo and the IL to the pores, stress evolution in the fuel meat, and the effect of amorphous IL growth. Well-characterized in-pile data from reduced-size plates were used to fit the model parameters. A data set from full-sized plates, independent and distinctively different from those used to fit the model parameters, was used to examine the accuracy of the model. The model showed fair agreement with the measured data. The model suggested that the growth of the IL has a critical effect on pore growth, as both its material properties and energetics are favorable to pore formation. Therefore, one area of the current effort, focused on suppressing IL growth, appears to be on the right track to improve the performance of this fuel.

  11. Pore Scale Analysis of Oil Shale/Sands Pyrolysis

    SciTech Connect

    Lin, Chen-Luh; Miller, Jan

    2011-03-01

    There are important questions concerning the quality and volume of pore space that is created when oil shale is pyrolyzed for the purpose of producing shale oil. In this report, 1.9 cm diameter cores of Mahogany oil shale were pyrolyzed at different temperatures and heating rates. Detailed 3D imaging of core samples was done using multiscale X-ray computed tomography (CT) before and after pyrolysis to establish the pore structure. The pore structure of the unreacted material was not clear. Selected images of a core pyrolyzed at 400oC were obtained at voxel resolutions from 39 microns (Οm) to 60 nanometers (nm). Some of the pore space created during pyrolysis was clearly visible at these resolutions and it was possible to distinguish between the reaction products and the host shale rock. The pore structure deduced from the images was used in Lattice Boltzmann simulations to calculate the permeability in the pore space. The permeabilities of the pyrolyzed samples of the silicate-rich zone were on the order of millidarcies, while the permeabilities of the kerogen-rich zone after pyrolysis were very anisotropic and about four orders of magnitude higher.

  12. Regulation of landslide motion by dilatancy and pore pressure feedback

    USGS Publications Warehouse

    Iverson, R.M.

    2005-01-01

    A new mathematical model clarifies how diverse styles and rates of landslide motion can result from regulation of Coulomb friction by dilation or contraction of water-saturated basal shear zones. Normalization of the model equations shows that feedback due to coupling between landslide motion, shear zone volume change, and pore pressure change depends on a single dimensionless parameter ??, which, in turn, depends on the dilatancy angle ?? and the intrinsic timescales for pore pressure generation and dissipation. If shear zone soil contracts during slope failure, then ?? 0, and negative feedback permits slow, steady landslide motion to occur while positive pore pressure is supplied by rain infiltration. Steady state slip velocities v0 obey v0 = -(K/??) p*e, where K is the hydraulic conductivity and p*e is the normalized (dimensionless) negative pore pressure generated by dilation. If rain infiltration and attendant pore pressure growth continue unabated, however, their influence ultimately overwhelms the stabilizing influence of negative p*e. Then, unbounded landslide acceleration occurs, accentuated by an instability that develops if ?? diminishes as landslide motion proceeds. Nonetheless, numerical solutions of the model equations show that slow, nearly steady motion of a clay-rich landslide may persist for many months as a result of negative pore pressure feedback that regulates basal Coulomb friction. Similarly stabilized motion is less likely to occur in sand-rich landslides that are characterized by weaker negative feedback.

  13. Determinants of pore folding in potassium channel biogenesis

    PubMed Central

    Delaney, Erin; Khanna, Pooja; Tu, LiWei; Robinson, John M.; Deutsch, Carol

    2014-01-01

    Many ion channels, both selective and nonselective, have reentrant pore loops that contribute to the architecture of the permeation pathway. It is a fundamental feature of these diverse channels, regardless of whether they are gated by changes of membrane potential or by neurotransmitters, and is critical to function of the channel. Misfolding of the pore loop leads to loss of trafficking and expression of these channels on the cell surface. Mature tetrameric potassium channels contain an α-helix within the pore loop. We systematically mutated the “pore helix” residues of the channel Kv1.3 and assessed the ability of the monomer to fold into a tertiary reentrant loop. Our results show that pore loop residues form a canonical α-helix in the monomer early in biogenesis and that disruption of tertiary folding is caused by hydrophilic substitutions only along one face of this α-helix. These results provide insight into the determinants of the reentrant pore conformation, which is essential for ion channel function. PMID:24616516

  14. Do conservative solutes migrate at average pore-water velocity?

    PubMed

    Rovey, Charles W; Niemann, William L

    2005-01-01

    According to common understanding, the advective velocity of a conservative solute equals the average linear pore-water velocity. Yet direct monitoring indicates that the two velocities may be different in heterogeneous media. For example, at the Camp Dodge, Iowa, site the advective velocity of discrete Cl- plumes was less than one tenth of the average pore-water velocity calculated from Darcy's law using the measured hydraulic gradient, effective porosity, and hydraulic conductivity (K) from large-scale three-dimensional (3D) techniques, e.g., pumping tests. Possibly, this difference reflects the influence of different pore systems, if the K relevant to transient solute flux is influenced more by lower-K heterogeneity than a steady or quasi-steady water flux. To test this idea, tracer tests were conducted under controlled laboratory conditions. Under one-dimensional flow conditions, the advective velocity of discrete conservative solutes equaled the average pore-water velocity determined from volumetric flow rates and Darcy's law. In a larger 3D flow system, however, the same solutes migrated at approximately 65% of the average pore-water velocity. These results, coupled with direct observation of dye tracers and their velocities as they migrated through both homogeneous and heterogeneous sections of the same model, demonstrate that heterogeneity can slow the advective velocity of discrete solute plumes relative to the average pore-water velocity within heterogeneous 3D flow sytems. PMID:15726924

  15. Pore opening dynamics in the exocytosis of serotonin

    NASA Astrophysics Data System (ADS)

    Ramirez-Santiago, Guillermo; Cercos, Montserrat G.; Martinez-Valencia, Alejandro; Salinas Hernandez, Israel; Rodríguez-Sosa, Leonardo; de-Miguel, Francisco F.

    2015-03-01

    The current view of the exocytosis of transmitter molecules is that it starts with the formation of a fusion pore that connects the intravesicular and the extracellular spaces, and is completed by the release of the rest of the transmitter contained in the vesicle upon the full fusion and collapse of the vesicle with the plasma membrane. However, under certain circumstances, a rapid closure of the pore before the full vesicle fusion produces only a partial release of the transmitter. Here we show that whole release of the transmitter occurs through fusion pores that remain opened for tens of milliseconds without vesicle collapse. This was demonstrated through amperometric measurements of serotonin release from electrodense vesicles in the axon of leech Retzius neurons and mathematical modelling. By modeling transmitter release with a diffusion equation subjected to boundary conditions that are defined by the experiment, we showed that those pores with a fast half rise time constant remained opened and allowed the full quantum release without vesicle collapse, whereas pores with a slow rise time constant closed rapidly, thus producing partial release. We conclude that a full transmitter release may occur through the fusion pore in the absence of vesicle collapse. This work was founded by a DGAPA-UNAM grants IN200914 and IN118410 CONACYT GRANT 130031, and CONACyT doctoral fellowships.

  16. Atomic structure of anthrax PA pore elucidates toxin translocation

    PubMed Central

    Jiang, Jiansen; Pentelute, Bradley L.; Collier, R. John; Zhou, Z. Hong

    2015-01-01

    Summary Anthrax toxin, comprising protective antigen (PA), lethal factor (LF) and edema factor (EF), is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in human and animals. PA forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes LF and EF into the cytosol of target cells1. PA is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. Based on biochemical and electrophysiological results, researchers have proposed that a Φ-clamp composed of Phe427 residues of PA catalyzes protein translocation via a charge-state dependent Brownian ratchet2–9. Although atomic structures of PA prepores are available10–14, how PA senses low pH, converts to active pore and translocates LF and EF are not well defined without an atomic model of the PA pore. Here, by cryo electron microscopy (cryoEM) with direct electron counting, we have determined the PA pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low-pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  17. On the Minimum Energy Path to Membrane Pore Formation

    NASA Astrophysics Data System (ADS)

    Ting, Christina; Wang, Zhen-Gang

    2011-03-01

    Several experimental methods have been developed to study the mechanical response of vesicles under an applied tension. Of particular note are the micropipette aspiration techniques and the use of a viscous solution to extend the lifetime of pores. MD simulations have also been used to study the energetic and structural properties of these transient pores on a molecular level. However, they often require extremely high tensions beyond the regime where pore formation is a thermally-activated event. We approach the nucleation problem by combining the string method with dynamic self-consistent field (DSCF) theory to obtain the full minimum energy path (MEP) to pore formation for a range of surface tensions γ . We compare our results with classical nucleation theory (CNT). Near the coexistence (γ --> 0) the rim of the pore is well-defined and the line tension is well approximated by the macroscopic definition given by CNT. However, when the free energy barrier is within ~ 10 kT , the transition state is somewhere between a stalk-like structure and a thinned membrane leading to a hole that is partially exposed to solvents. These molecular rearrangements involved in the formation of a pore are not captured by CNT.

  18. Properties of Aqueous Electrolytes within Narrow Slit-Shaped Pores

    NASA Astrophysics Data System (ADS)

    Ho, Tuan A.; Argyris, Dimitrios; Striolo, Alberto

    2011-03-01

    We report equilibrium molecular dynamics simulation results for structural and dynamic properties of aqueous electrolyte solutions confined within narrow pores. The slit-shaped pores are carved from cristobalite silica, corundum alumina, magnesium oxide, and other materials. The pore width is in the range 0.8 -- 2.0 nm. The aqueous solutions contain NaCl, CsCl, CaCl 2 , and SrCl 2 electrolytes at 1M concentration or larger. Equilibrium simulations are performed at ambient conditions within the NVT ensemble. The data suggest the formation of layered structures, which are consistent with results obtained for thin films of solution supported on free-standing surfaces. However, confinement enhances the differences in transport properties observed between those ions that are near the solid and those at the pore center. Because the self-diffusion coefficient is faster as the distance from the solid increases, the ions that are at the pore center diffuse more quickly through the pore than those adsorbed closer to the wall. Thus our results could be used to design membranes to separate, e.g., aqueous NaCl from CsCl solutions. Research supported by the Department of Energy and, in part, by the National Science Foundation.

  19. Mangrove pore water exchange across a latitudinal gradient

    NASA Astrophysics Data System (ADS)

    Tait, Douglas R.; Maher, Damien T.; Macklin, Paul A.; Santos, Isaac R.

    2016-04-01

    We combined observations of the natural tracer radon (222Rn) with hydrodynamic models across a broad latitudinal gradient covering several climate zones to estimate pore water exchange rates in mangroves. Pore water exchange ranged from 2.1 to 35.5 cm d-1 from temperate to tropical regions and averaged 16.3 ± 5.1 cm d-1. If upscaled to the global weighted mangrove area, pore water exchange in mangroves would recirculate the entire volume of water overlying the continental shelf in less than 153 years. Although pore water exchange (recirculated seawater) and river discharge represent different pathways for water entering the coastal ocean, the estimated global mangrove pore water exchange would be equal to approximately one third of annual global river discharge to the ocean (3.84 × 1013 m3 yr-1). Because biogeochemical processes in mangroves are largely dependent on pore water exchange, these large exchange rates have major implications for coastal nutrient, carbon, and greenhouse gas cycling in tropical marine systems.

  20. Pore scale definition and computation from tomography data

    NASA Astrophysics Data System (ADS)

    Dupuy, P. M.; Austin, P.; Delaney, G. W.; Schwarz, M. P.

    2011-10-01

    During recent years characterisation capabilities of porous media have been transformed by advances in computation and visualisation technologies. It is now possible to obtain detailed topological and hydrodynamic information of porous media by combining tomographic and computational fluid dynamic studies. Despite the existence of these new capabilities, the characterisation process itself is based on the same antiquated experimental macroscopic concepts. We are interested in an up-scaling process where we can keep key information for every pore size present in the media in order to feed multi-scale transport models. Hydrometallurgical, environmental, food, pharmaceutical and chemical engineering are industries with process outcomes based on homogeneous and heterogeneous reactions and therefore sensitive to the reaction and transport processes happening at different pore scales. The present work addresses a key step in the information up-scaling process, i.e. a pore identification algorithm similar to alternating sequential filters. In a preliminary study, topological and hydrodynamic variables are correlated with the pore size. Micrometre and millimetre resolution tomographies are used to characterise the pore size distribution of a packed column and different rocks. Finally, we compute the inter-pore-scale redistribution function which is a measure of the heterogeneity of the media and magnitude needed in multi-scale modelling.

  1. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases.

    PubMed

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K G; Wiegand, Simone

    2016-04-19

    Formamide is one of the important compounds from which prebiotic molecules can be synthesized, provided that its concentration is sufficiently high. For nucleotides and short DNA strands, it has been shown that a high degree of accumulation in hydrothermal pores occurs, so that temperature gradients might play a role in the origin of life [Baaske P, et al. (2007)Proc Natl Acad Sci USA104(22):9346-9351]. We show that the same combination of thermophoresis and convection in hydrothermal pores leads to accumulation of formamide up to concentrations where nucleobases are formed. The thermophoretic properties of aqueous formamide solutions are studied by means of Infrared Thermal Diffusion Forced Rayleigh Scattering. These data are used in numerical finite element calculations in hydrothermal pores for various initial concentrations, ambient temperatures, and pore sizes. The high degree of formamide accumulation is due to an unusual temperature and concentration dependence of the thermophoretic behavior of formamide. The accumulation fold in part of the pores increases strongly with increasing aspect ratio of the pores, and saturates to highly concentrated aqueous formamide solutions of ∼85 wt% at large aspect ratios. Time-dependent studies show that these high concentrations are reached after 45-90 d, starting with an initial formamide weight fraction of[Formula: see text]wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

  2. Atomic structure of anthrax protective antigen pore elucidates toxin translocation.

    PubMed

    Jiang, Jiansen; Pentelute, Bradley L; Collier, R John; Zhou, Z Hong

    2015-05-28

    Anthrax toxin, comprising protective antigen, lethal factor, and oedema factor, is the major virulence factor of Bacillus anthracis, an agent that causes high mortality in humans and animals. Protective antigen forms oligomeric prepores that undergo conversion to membrane-spanning pores by endosomal acidification, and these pores translocate the enzymes lethal factor and oedema factor into the cytosol of target cells. Protective antigen is not only a vaccine component and therapeutic target for anthrax infections but also an excellent model system for understanding the mechanism of protein translocation. On the basis of biochemical and electrophysiological results, researchers have proposed that a phi (Φ)-clamp composed of phenylalanine (Phe)427 residues of protective antigen catalyses protein translocation via a charge-state-dependent Brownian ratchet. Although atomic structures of protective antigen prepores are available, how protective antigen senses low pH, converts to active pore, and translocates lethal factor and oedema factor are not well defined without an atomic model of its pore. Here, by cryo-electron microscopy with direct electron counting, we determine the protective antigen pore structure at 2.9-Å resolution. The structure reveals the long-sought-after catalytic Φ-clamp and the membrane-spanning translocation channel, and supports the Brownian ratchet model for protein translocation. Comparisons of four structures reveal conformational changes in prepore to pore conversion that support a multi-step mechanism by which low pH is sensed and the membrane-spanning channel is formed. PMID:25778700

  3. Impact of pore fluid composition changes on soil filter clogging

    SciTech Connect

    Reddi, L.N.; Bonala, M.V.S.

    1997-12-31

    Current design criteria for soil filters in geotechnical engineering are based on mechanical principles of straining alone without any physico-chemical considerations. Transport and deposition of colloid-size particles in the subsurface are influenced by pore fluid composition. It is essential to design filters in contaminated environment, such as those for leachate collection systems, with due considerations of the pore fluid composition. In this paper, the impact of changes in pore fluid composition on sod filter clogging is assessed with the help of a mathematical model. The role of pore fluid composition in soil filter clogging is studied by evaluating its effect on the erodibility of base soils, size of the migrating particles, and on the likelihood of particle deposition. The results suggest that pore fluid composition influences the deposition to the extent it can cause significant changes in pore clogging. In the cases where particles are generated from base soils, filter clogging increased at low salt concentrations but was limited by reduced erodibilities at high salt concentrations.

  4. Imagination as expansion of experience.

    PubMed

    Zittoun, Tania; Cerchia, Frédéric

    2013-09-01

    This paper proposes a developmental view on imagination: from this perspective, imagination can be seen as triggered by some disrupting event, which generates a disjunction from the person's unfolding experience of the "real" world, and as unfolding as a loop, which eventually comes back to the actual experience. Examining recent and classical theorization of imagination in psychology, the paper opposes a deficitary view of imagination to an expansive notion of imagination. The paper explores Piaget, Vygotsky, Harris and Pelaprat & Cole consider: 1) What does provoke a "rupture" or disjunction? 2) What are the psychological processes involved in the imaginary loop? 3) What nourishes such processes? 4) What are the consequences of such imaginary loop, or what does it enable doing? The paper proposes to adopt an expansive view of imagination, as Vygotsky proposed-a perspective that has been under-explored empirically since his seminal work. To stimulate such sociocultural psychology of imagination, two empirical examples are provided, one showing how children make sense of metaphor in an experimental setting, the other showing a young person using a novel met at school as symbolic resource. PMID:23625542

  5. Mechanoinduction of lymph vessel expansion

    PubMed Central

    Planas-Paz, Lara; Strilić, Boris; Goedecke, Axel; Breier, Georg; Fässler, Reinhard; Lammert, Eckhard

    2012-01-01

    In the mammalian embryo, few mechanical signals have been identified to influence organ development and function. Here, we report that an increase in the volume of interstitial or extracellular fluid mechanically induces growth of an organ system, that is, the lymphatic vasculature. We first demonstrate that lymph vessel expansion in the developing mouse embryo correlates with a peak in interstitial fluid pressure and lymphatic endothelial cell (LEC) elongation. In ‘loss-of-fluid' experiments, we then show that aspiration of interstitial fluid reduces the length of LECs, decreases tyrosine phosphorylation of vascular endothelial growth factor receptor-3 (VEGFR3), and inhibits LEC proliferation. Conversely, in ‘gain-of-fluid' experiments, increasing the amount of interstitial fluid elongates the LECs, and increases both VEGFR3 phosphorylation and LEC proliferation. Finally, we provide genetic evidence that β1 integrins are required for the proliferative response of LECs to both fluid accumulation and cell stretching and, therefore, are necessary for lymphatic vessel expansion and fluid drainage. Thus, we propose a new and physiologically relevant mode of VEGFR3 activation, which is based on mechanotransduction and is essential for normal development and fluid homeostasis in a mammalian embryo. PMID:22157817

  6. High thermal expansion, sealing glass

    DOEpatents

    Brow, R.K.; Kovacic, L.

    1993-11-16

    A glass composition is described for hermetically sealing to high thermal expansion materials such as aluminum alloys, stainless steels, copper, and copper/beryllium alloys, which includes between about 10 and about 25 mole percent Na[sub 2]O, between about 10 and about 25 mole percent K[sub 2]O, between about 5 and about 15 mole percent Al[sub 2]O[sub 3], between about 35 and about 50 mole percent P[sub 2]O[sub 5] and between about 5 and about 15 mole percent of one of PbO, BaO, and mixtures thereof. The composition, which may also include between 0 and about 5 mole percent Fe[sub 2]O[sub 3] and between 0 and about 10 mole percent B[sub 2]O[sub 3], has a thermal expansion coefficient in a range of between about 160 and 210[times]10[sup [minus]7]/C and a dissolution rate in a range of between about 2[times]10[sup [minus]7] and 2[times]10[sup [minus]9]g/cm[sup 2]-min. This composition is suitable to hermetically seal to metallic electrical components which will be subjected to humid environments over an extended period of time.

  7. Gyrification from constrained cortical expansion

    PubMed Central

    Tallinen, Tuomas; Chung, Jun Young; Biggins, John S.; Mahadevan, L.

    2014-01-01

    The exterior of the mammalian brain—the cerebral cortex—has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highly convoluted. Furthermore, this dependence on two simple geometric parameters that characterize the brain also allows us to qualitatively explain how variations in these parameters lead to anatomical anomalies in such situations as polymicrogyria, pachygyria, and lissencephalia. PMID:25136099

  8. High thermal expansion, sealing glass

    DOEpatents

    Brow, Richard K.; Kovacic, Larry

    1993-01-01

    A glass composition for hermetically sealing to high thermal expansion materials such as aluminum alloys, stainless steels, copper, and copper/beryllium alloys, which includes between about 10 and about 25 mole percent Na.sub.2 O, between about 10 and about 25 mole percent K.sub.2 O, between about 5 and about 15 mole percent Al.sub.2 O.sub.3, between about 35 and about 50 mole percent P.sub.2 O.sub.5 and between about 5 and about 15 mole percent of one of PbO, BaO, and mixtures thereof. The composition, which may also include between 0 and about 5 mole percent Fe.sub.2 O.sub.3 and between 0 and about 10 mole percent B.sub.2 O.sub.3, has a thermal expansion coefficient in a range of between about 160 and 210.times.10-7/.degree.C. and a dissolution rate in a range of between about 2.times.10.sup.- 7 and 2.times.10.sup.-9 g/cm.sup.2 -min. This composition is suitable to hermetically seal to metallic electrical components which will be subjected to humid environments over an extended period of time.

  9. Expansion techniques for collisionless stellar dynamical simulations

    NASA Astrophysics Data System (ADS)

    Meiron, Yohai

    2016-02-01

    We present ETICS, a collisionless N-body code based on two kinds of series expansions of the Poisson equation, implemented for graphics processing units (GPUs). The code is publicly available and can be used as a standalone program or as a library (an AMUSE plugin is included). One of the two expansion methods available is the self-consistent field (SCF) method, which is a Fourier-like expansion of the density field in some basis set; the other is the multipole expansion (MEX) method, which is a Taylor-like expansion of the Green's function. MEX, which has been advocated in the past, has not gained as much popularity as SCF. Both are particle-field methods and optimized for collisionless galactic dynamics, but while SCF is a ``pure'' expansion, MEX is an expansion in just the angular part; thus, MEX is capable of capturing radial structure easily, while SCF needs a large number of radial terms.

  10. Pore dimensions and the role of occupancy in unitary conductance of Shaker K channels.

    PubMed

    Díaz-Franulic, Ignacio; Sepúlveda, Romina V; Navarro-Quezada, Nieves; González-Nilo, Fernando; Naranjo, David

    2015-08-01

    K channels mediate the selective passage of K(+) across the plasma membrane by means of intimate interactions with ions at the pore selectivity filter located near the external face. Despite high conservation of the selectivity filter, the K(+) transport properties of different K channels vary widely, with the unitary conductance spanning a range of over two orders of magnitude. Mutation of Pro475, a residue located at the cytoplasmic entrance of the pore of the small-intermediate conductance K channel Shaker (Pro475Asp (P475D) or Pro475Gln (P475Q)), increases Shaker's reported ∼ 20-pS conductance by approximately six- and approximately threefold, respectively, without any detectable effect on its selectivity. These findings suggest that the structural determinants underlying the diversity of K channel conductance are distinct from the selectivity filter, making P475D and P475Q excellent probes to identify key determinants of the K channel unitary conductance. By measuring diffusion-limited unitary outward currents after unilateral addition of 2 M sucrose to the internal solution to increase its viscosity, we estimated a pore internal radius of capture of ∼ 0.82 Å for all three Shaker variants (wild type, P475D, and P475Q). This estimate is consistent with the internal entrance of the Kv1.2/2.1 structure if the effective radius of hydrated K(+) is set to ∼ 4 Å. Unilateral exposure to sucrose allowed us to estimate the internal and external access resistances together with that of the inner pore. We determined that Shaker resistance resides mainly in the inner cavity, whereas only ∼ 8% resides in the selectivity filter. To reduce the inner resistance, we introduced additional aspartate residues into the internal vestibule to favor ion occupancy. No aspartate addition raised the maximum unitary conductance, measured at saturating [K(+)], beyond that of P475D, suggesting an ∼ 200-pS conductance ceiling for Shaker. This value is approximately one third of

  11. Pore dimensions and the role of occupancy in unitary conductance of Shaker K channels

    PubMed Central

    Díaz-Franulic, Ignacio; Sepúlveda, Romina V.; Navarro-Quezada, Nieves; González-Nilo, Fernando

    2015-01-01

    K channels mediate the selective passage of K+ across the plasma membrane by means of intimate interactions with ions at the pore selectivity filter located near the external face. Despite high conservation of the selectivity filter, the K+ transport properties of different K channels vary widely, with the unitary conductance spanning a range of over two orders of magnitude. Mutation of Pro475, a residue located at the cytoplasmic entrance of the pore of the small-intermediate conductance K channel Shaker (Pro475Asp (P475D) or Pro475Gln (P475Q)), increases Shaker’s reported ∼20-pS conductance by approximately six- and approximately threefold, respectively, without any detectable effect on its selectivity. These findings suggest that the structural determinants underlying the diversity of K channel conductance are distinct from the selectivity filter, making P475D and P475Q excellent probes to identify key determinants of the K channel unitary conductance. By measuring diffusion-limited unitary outward currents after unilateral addition of 2 M sucrose to the internal solution to increase its viscosity, we estimated a pore internal radius of capture of ∼0.82 Å for all three Shaker variants (wild type, P475D, and P475Q). This estimate is consistent with the internal entrance of the Kv1.2/2.1 structure if the effective radius of hydrated K+ is set to ∼4 Å. Unilateral exposure to sucrose allowed us to estimate the internal and external access resistances together with that of the inner pore. We determined that Shaker resistance resides mainly in the inner cavity, whereas only ∼8% resides in the selectivity filter. To reduce the inner resistance, we introduced additional aspartate residues into the internal vestibule to favor ion occupancy. No aspartate addition raised the maximum unitary conductance, measured at saturating [K+], beyond that of P475D, suggesting an ∼200-pS conductance ceiling for Shaker. This value is approximately one third of the maximum

  12. Carbon turnover in pore spaces - CIPS model approach

    NASA Astrophysics Data System (ADS)

    Kuka, Katrin

    2010-05-01

    The CIPS (Carbon turnover In Pore Spaces) model has been developed to overcome the constraints of conceptual pools and to get a better insight into the nature of carbon stabilization in soil (KUKA, 2007). This pure carbon turnover model was implemented in CANDY (CArbon and Nitrogen Dynamics) model system (Franko, 1995). The CIPS model did overcome the empirical pools taking into account soil structure effects. It is based on quality driven primary stabilisation mechanism (recalcitrance of SOM) and process driven secondary stabilisation mechanism (place of turnover) of SOM in soil. In addition to the division of SOM in the qualitative pools on the basis of chemical measurability, a dependence of the turnover conditions from the location of SOM in pore space is implemented taking into account different turnover conditions in the particular pore space and the accessibility for microbial biomass. The main assumption of the CIPS model is that the biological activity is not evenly distributed through the whole pore space. The pore space classes - micro, meso and macro pores - used in the model are marked by wilting point, field capacity and pore volume as a first approach. Because of the poor aeration in the micro pores they show very low biological activity leading to a strong protection of the carbon localized in this pore space. The biological active time (BAT) concept of the CANDY model was adapted to the CIPS model in order to calculate the distribution of biological activity for each pore space class. The reduction functions of the turnover active time concept of CANDY model, related to soil temperature, soil moisture, soil texture, relative air volume and distance to the soil surface are multiplied by the step width of calendar time producing the transformed time step as total BAT (BATtot). The calculated BATtot corresponds to the time that would be required under optimal conditions in the laboratory to perform the same turnover result as under the given

  13. Quantification of subsurface pore pressure through IODP drilling

    NASA Astrophysics Data System (ADS)

    Saffer, D. M.; Flemings, P. B.

    2010-12-01

    It is critical to understand the magnitude and distribution of subsurface pore fluid pressure: it controls effective stress and thus mechanical strength, slope stability, and sediment compaction. Elevated pore pressures also drive fluid flows that serve as agents of mass, solute, and heat fluxes. The Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) have provided important avenues to quantify pore pressure in a range of geologic and tectonic settings. These approaches include 1) analysis of continuous downhole logs and shipboard physical properties data to infer compaction state and in situ pressure and stress, 2) laboratory consolidation testing of core samples collected by drilling, 3) direct downhole measurements using pore pressure probes, 3) pore pressure and stress measurements using downhole tools that can be deployed in wide diameter pipe recently acquired for riser drilling, and 4) long-term monitoring of formation pore pressure in sealed boreholes within hydraulically isolated intervals. Here, we summarize key advances in quantification of subsurface pore pressure rooted in scientific drilling, highlighting with examples from subduction zones, the Gulf of Mexico, and the New Jersey continental shelf. At the Nankai, Costa Rican, and Barbados subduction zones, consolidation testing of cores samples, combined with analysis of physical properties data, indicates that even within a few km landward of the trench, pore pressures in and below plate boundary décollement zones reach a significant fraction of the lithostatic load (λ*=0.25-0.91). These results document a viable and quantifiable mechanism to explain the mechanical weakness of subduction décollements, and are corroborated by a small number of direct measurements in sealed boreholes and by inferences from seismic reflection data. Recent downhole measurements conducted during riser drilling using the modular formation dynamics tester wireline tool (MDT) in a forearc basin ~50

  14. Modeling of seismic field in porous medium:Simulation study of single pore and pore ensemble effects

    NASA Astrophysics Data System (ADS)

    Shatskaya, A. A.; Nemirovich-Danchenko, M. M.; Terre, D. A.

    2015-11-01

    The article considers the effect of porous media on elastic wave field. Based on numerical modeling, diffraction pattern of the wave propagating through a single pore in carbonates has been produced. Matrix properties (calcite and dolomite) and fluid (water) are modeled based on thin core section image. The qualitative comparison with the available computational data has been performed. Provided that ensemble of pores is involved, the effect of porous medium on seismic field has been studied. For comparison with experimental data the model of porous sintered aluminum Al-6061 has been considered. The processing of numerical modeling results made it possible to estimate average velocities in the model of porous aluminum and compare them with physical modeling data. The provided estimates have indicated qualitative (single pore) and quantitative (ensemble of pores) correlation of simulation and experiment results.

  15. Neutrons measure phase behavior in pores at Angstrom size

    SciTech Connect

    Bardoel, Agatha A; Melnichenko, Yuri B

    2012-01-01

    Researchers have measured the phase behavior of green house gases in pores at the Angstrom-level, using small angle neutron scattering (SANS) at the Oak Ridge National Laboratory's High Flux Isotope Reactor. Yuri Melnichenko, an instrument scientist on the General Purpose Small Angle Neutron Scattering (GP SANS) Diffractometer at ORNL's High Flux Isotope Reactor, his postdoctoral associate Lilin He and collaborators Nidia Gallego and Cristian Contescu from the Material Sciences Division (ORNL) were engaged in the work. They were studying nanoporous carbons to assess their attractiveness as storage media for hydrogen, with a view to potential use for on-board hydrogen storage for transportation applications. Nanoporous carbons can also serve as electrode material for supercapacitors and batteries. The researchers successfully determined that the most efficiently condensing pore size in a carbon nanoporous material for hydrogen storage is less than one nanometer. In a paper recently published by the Journal of the American Chemical Society, the collaborators used small angle neutron scattering to study how hydrogen condenses in small pores at ambient temperature. They discovered that the surface-molecule interactions create internal pressures in pores that may exceed the external gas pressure by a factor of up to 50. 'This is an exciting result,' Melnichenko said, 'as you achieve extreme densification in pores 'for free', i.e. without spending any energy. These results can be used to guide the development of new carbon adsorbents tailored to maximize hydrogen storage capacities.' Another important factor that defines the adsorption capacity of sub-nanometer pores is their shape. In order to get accurate structural information and maximize sorption capacity, it is important that pores are small and of approximately uniform size. In collaboration with Drexel University's Yury Gogotsi who supplied the samples, Melnichenko and his collaborators used the GP SANS

  16. Unified method for the total pore volume and pore size distribution of hierarchical zeolites from argon adsorption and mercury intrusion.

    PubMed

    Kenvin, Jeffrey; Jagiello, Jacek; Mitchell, Sharon; Pérez-Ramírez, Javier

    2015-02-01

    A generalized approach to determine the complete distribution of macropores, mesopores, and micropores from argon adsorption and mercury porosimetry is developed and validated for advanced zeolite catalysts with hierarchically structured pore systems in powder and shaped forms. Rather than using a fragmented approach of simple overlays from individual techniques, a unified approach that utilizes a kernel constructed from model isotherms and model intrusion curves is used to calculate the complete pore size distribution and the total pore volume of the material. An added benefit of a single full-range pore size distribution is that the cumulative pore area and the area distribution are also obtained without the need for additional modeling. The resulting complete pore size distribution and the kernel accurately model both the adsorption isotherm and the mercury porosimetry. By bridging the data analysis of two primary characterization tools, this methodology fills an existing gap in the library of familiar methods for porosity assessment in the design of materials with multilevel porosity for novel technological applications. PMID:25603366

  17. Pore-Filling Ice Diffusively Derived From Atmospheric Water Vapor Under Mars Conditions

    NASA Astrophysics Data System (ADS)

    Hudson, T. L.; Aharonson, O.; Oslund, K.; Siegler, M.; Schorghofer, N.

    2007-12-01

    Conditions during previous climate epochs on Mars may have allowed subsurface ice to form via diffusion from a moist atmosphere. The deposition and recharge of such reservoirs is driven by subsurface humidity gradients; an atmospheric frostpoint greater than that of the subsurface results in a net influx of vapor which deposits in pore space as ice. Observations of the hydrogen distribution by Mars Odyssey indicate that the ice content of some high-latitude regions (e.g. Olympia Undae) exceeds 70% by volume. Reconciliation of this concentration with typically lower porosities of soils demands a process of ice segregation (lensing) and mechanical expansion, or direct precipitation. We investigate the possibility and consequences of volumetrically significant subsurface ice derived from the Mars atmosphere by vapor diffusion, at present and in the past. Experiments conducted at the Mars Simulation and Ice Laboratory at Caltech demonstrate that diffusion processes produce significant pore-filling ice under controlled lab conditions. Atmospherically derived water vapor is deposited within an initially dry porous medium subject to a strong (~15~K/cm) temperature gradient forcing a humidity gradient. This mimics the humidity gradient caused by time varying temperatures in the shallow subsurface of Mars with a static experimental setup. The vertical profile of water content is determined at the end of the experiment by gravimetric analysis and the thermal conductivity of the ice-bearing sample is calculated. Pore filling fractions up to 100% have been measured. Profiles with a marked transition in ice content at the frostpoint depth are observed corresponding to a subsurface ice table. The data enable calculation of time-varying diffusion coefficients which exhibit a reduction of up to an order of magnitude with respect to ice-free regolith. These are compared to numerical models of vapor diffusion incorporating ice deposition and pore constriction. Formation theories of

  18. Experimental Studies of Dynamic Fault Weakening Due to Thermal Pore-Fluid Pressurization

    NASA Astrophysics Data System (ADS)

    Goldsby, D. L.; Tullis, T. E.; Okazaka, K.; Platt, J. D.; Mitchell, T. M.

    2014-12-01

    Thermal pressurization is a co-seismic weakening mechanism driven by the thermal expansion of native pore fluids, which leads to elevated pore pressures and significant co-seismic weakening. While thermal pressurization has been studied theoretically for many decades, and has been invoked in recent earthquake simulations, its activation in laboratory experiments has remained elusive. Several high-speed friction experiments yield indirect evidence for thermal pressurization, yet none have directly linked with existing theoretical models or the relevant physical parameters -- such as permeability, slip, and slip rate - that control the weakening rate. We are conducting thermal pressurization experiments on fluid-saturated, low-permeability rocks (primarily Fredrick diabase; also SAFOD gouge) at slip rates up to ~5 mm/s, with constant confining pressures in the range 21-149 MPa and initial pore pressures in the range 10-25 MPa. The impractically low permeability of the diabase, ~10-23 m2, is increased prior to the friction test by thermally cracking the samples, yielding measured permeabilities in the range 1.3*10-18 to 6.1*10-19 m2. These permeabilites are high enough to allow sample saturation over one to several days, but also low enough to confine pore pressure rises during rapid sliding and allow thermal pressurization to occur. In recent experiments we also embed a thermocouple ~1-2 mm from the sliding surface, and use the resulting data to calibrate a finite element model that calculates the sliding surface temperature. One experiment revealed a rapid decay of shear stress by ~25% following a step-change in velocity from 10 μm/s to 4.8 mm/s. For the first 28 mm of slip the experimentally measured shear stress agrees closely with the theoretical solution for slip on a plane (Rice [2006]) with an inferred slip weakening distance of ~500 mm, which is in the range predicted by inserting laboratory determined rock and fluid properties into the formula for L* from

  19. The Saccharomyces cerevisiae Mre11-Rad50-Xrs2 complex promotes trinucleotide repeat expansions independently of homologous recombination.

    PubMed

    Ye, Yanfang; Kirkham-McCarthy, Lucy; Lahue, Robert S

    2016-07-01

    Trinucleotide repeats (TNRs) are tandem arrays of three nucleotides that can expand in length to cause at least 17 inherited human diseases. Somatic expansions in patients can occur in differentiated tissues where DNA replication is limited and cannot be a primary source of somatic mutation. Instead, mouse models of TNR diseases have shown that both inherited and somatic expansions can be suppressed by the loss of certain DNA repair factors. It is generally believed that these repair factors cause misprocessing of TNRs, leading to expansions. Here we extend this idea to show that the Mre11-Rad50-Xrs2 (MRX) complex of Saccharomyces cerevisiae is a causative factor in expansions of short TNRs. Mutations that eliminate MRX subunits led to significant suppression of expansions whereas mutations that inactivate Rad51 had only a minor effect. Coupled with previous evidence, this suggests that MRX drives expansions of short TNRs through a process distinct from homologous recombination. The nuclease function of Mre11 was dispensable for expansions, suggesting that expansions do not occur by Mre11-dependent nucleolytic processing of the TNR. Epistasis between MRX and post-replication repair (PRR) was tested. PRR protects against expansions, so a rad5 mutant gave a high expansion rate. In contrast, the mre11 rad5 double mutant gave a suppressed expansion rate, indistinguishable from the mre11 single mutant. This suggests that MRX creates a TNR substrate for PRR. Protein acetylation was also tested as a mechanism regulating MRX activity in expansions. Six acetylation sites were identified in Rad50. Mutation of all six lysine residues to arginine gave partial bypass of a sin3 HDAC mutant, suggesting that Rad50 acetylation is functionally important for Sin3-mediated expansions. Overall we conclude that yeast MRX helps drive expansions of short TNRs by a mechanism distinct from its role in homologous recombination and independent of the nuclease function of Mre11. PMID:27173583

  20. Pore-pressure gradients, stresses, and induced earthquakes

    SciTech Connect

    Segall, P. . Geophysics Dept. Geological Survey, Menlo Park, CA )

    1992-01-01

    In the theory of poroelasticity, spatial gradients in pore-pressure enter the equilibrium equations in the same way as distributed body forces. Pore-pressure gradients are thus associated with poroelastic stresses in the same way that temperature gradients associated with thermoelastic stresses. The author has suggested that pore-pressure gradients caused by pumping are responsible for earthquakes near some oil and gas fields. Seismic data from a number of active oil and gas fields in California, Texas, Alberta, and elsewhere clearly show that earthquakes are occurring near fields where pore pressures have declined by several 10's of MPa. These observations can not be explained by changes in effective stress alone, which predicts that decreasing pore-fluid pressures tend to stabilize faults. He believes that poro-elastic stresses resulting from pore-fluid extraction are responsible for earthquakes in these situations. Fluid injection also induces poro-elastic stresses, however it is difficult to separate this effect from the destabilizing effect of increased pore-pressure within fault zones. To test the poroelastic model for induced seismicity, theoretical predictions are compared to data from a deep gas field in the Pyrenean foreland. Hundreds of shallow, small to moderate earthquakes have occurred there since 1969. The earthquakes are tightly clustered near the gas field. Reservoir pressure had declined by 30 MPa at the onset of seismicity. The relationship between average reservoir pressure decline and subsidence is remarkably linear, lending support to the linear poroelastic model. Using laboratory derived material parameters and in situ reservoir pressure measurements, it is possible to predict the surface deformations and the change in stress field without adjustable parameters. The computed vertical displacements are in good agreement with the observed subsidence. The poroelastic stress changes at the onset of seismicity are of the order of a few bars.