Science.gov

Sample records for pore expansion mediated

  1. 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

  2. Calcium-mediated mechanisms of cystic expansion

    PubMed Central

    Abdul-Majeed, Shakila; Nauli, Surya M.

    2010-01-01

    In this review, we will discuss several well-accepted signaling pathways toward calcium-mediated mechanisms of cystic expansion. The second messenger calcium ion has contributed to a vast diversity of signal transduction pathways. We will dissect calcium signaling as a possible mechanism that contributes to renal cyst formation. Because cytosolic calcium also regulates an array of signaling pathways, we will first discuss cilia-induced calcium fluxes, followed by Wnt signaling that has attributed to much-discussed planar cell polarity. We will then look at the relationship between cytosolic calcium and cAMP as one of the most important aspects of cyst progression. The signaling of cAMP on MAPK and mTOR will also be discussed. We infer that while cilia-induced calcium fluxes may be the initial signaling messenger for various cellular pathways, no single signaling mediator or pathway is implicated exclusively in the progression of the cystic expansion. PMID:20932898

  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. Application of zero-expansion pore-free ceramics to a mirror of an astronomical telescope

    NASA Astrophysics Data System (ADS)

    Akitaya, Hiroshi; Iye, Masanori; Okita, Kiichi; Sato, Motoyasu; Matsuo, Hiroyuki; Itazu, Takeshi; Uno, Takeshi; Yamaguchi, Masao; Tanaka, Zen-ei; Yamashita, Takuya; Kawabata, Koji S.; Uemura, Makoto; Kurita, Mikio

    2008-07-01

    We developed an aspheric convex 33-cm diameter secondary mirror of the Hiroshima University 1.5-m Ritchy-Chretien telescope using Zero-expansion Pore-free ceramics, which has physical properties (thermal expansion, stiffness, thermal conductance, etc.) comparable with or better than existing zero-expansion glasses. After high-precision grinding, polishing, and coating aluminum and silicon monoxide, we obtained the sufficient optical reflecting surface with a figure error within λ/10 and a roughness of about 3 nm rms. The mirror has been attached on the telescope and we confirmed its sufficient performance through a Hartmann test. To date it has shown a good performance in our application and we suggest that this ceramic material has a potential to be used for astronomical telescopes and related area.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. Dynamin-2 regulates fusion pore expansion and quantal release through a mechanism that involves actin dynamics in neuroendocrine chromaffin cells.

    PubMed

    González-Jamett, Arlek M; Momboisse, Fanny; Guerra, María José; Ory, Stéphane; Báez-Matus, Ximena; Barraza, Natalia; Calco, Valerie; Houy, Sébastien; Couve, Eduardo; Neely, Alan; Martínez, Agustín D; Gasman, Stéphane; Cárdenas, Ana M

    2013-01-01

    Over the past years, dynamin has been implicated in tuning the amount and nature of transmitter released during exocytosis. However, the mechanism involved remains poorly understood. Here, using bovine adrenal chromaffin cells, we investigated whether this mechanism rely on dynamin's ability to remodel actin cytoskeleton. According to this idea, inhibition of dynamin GTPase activity suppressed the calcium-dependent de novo cortical actin and altered the cortical actin network. Similarly, expression of a small interfering RNA directed against dynamin-2, an isoform highly expressed in chromaffin cells, changed the cortical actin network pattern. Disruption of dynamin-2 function, as well as the pharmacological inhibition of actin polymerization with cytochalasine-D, slowed down fusion pore expansion and increased the quantal size of individual exocytotic events. The effects of cytochalasine-D and dynamin-2 disruption were not additive indicating that dynamin-2 and F-actin regulate the late steps of exocytosis by a common mechanism. Together our data support a model in which dynamin-2 directs actin polymerization at the exocytosis site where both, in concert, adjust the hormone quantal release to efficiently respond to physiological demands.

  12. 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

  13. 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

  14. LPS-TLR4 Pathway Mediates Ductular Cell Expansion in Alcoholic Hepatitis

    PubMed Central

    Odena, Gemma; Chen, Jiegen; Lozano, Juan Jose; Altamirano, Jose; Rodrigo-Torres, Daniel; Affo, Silvia; Morales-Ibanez, Oriol; Matsushita, Hiroshi; Zou, Jian; Dumitru, Raluca; Caballeria, Juan; Gines, Pere; Arroyo, Vicente; You, Min; Rautou, Pierre-Emmanuel; Valla, Dominique; Crews, Fulton; Seki, Ekihiro; Sancho-Bru, Pau; Bataller, Ramon

    2016-01-01

    Alcoholic hepatitis (AH) is the most severe form of alcoholic liver disease for which there are no effective therapies. Patients with AH show impaired hepatocyte proliferation, expansion of inefficient ductular cells and high lipopolysaccharide (LPS) levels. It is unknown whether LPS mediates ductular cell expansion. We performed transcriptome studies and identified keratin 23 (KRT23) as a new ductular cell marker. KRT23 expression correlated with mortality and LPS serum levels. LPS-TLR4 pathway role in ductular cell expansion was assessed in human and mouse progenitor cells, liver slices and liver injured TLR4 KO mice. In AH patients, ductular cell expansion correlated with portal hypertension and collagen expression. Functional studies in ductular cells showed that KRT23 regulates collagen expression. These results support a role for LPS-TLR4 pathway in promoting ductular reaction in AH. Maneuvers aimed at decreasing LPS serum levels in AH patients could have beneficial effects by preventing ductular reaction development. PMID:27752144

  15. Ultrasound and microbubble mediated drug delivery: acoustic pressure as determinant for uptake via membrane pores or endocytosis.

    PubMed

    De Cock, Ine; Zagato, Elisa; Braeckmans, Kevin; Luan, Ying; de Jong, Nico; De Smedt, Stefaan C; Lentacker, Ine

    2015-01-10

    Although promising results are achieved in ultrasound mediated drug delivery, its underlying biophysical mechanisms remain to be elucidated. Pore formation as well as endocytosis has been reported during ultrasound application. Due to the plethora of ultrasound settings used in literature, it is extremely difficult to draw conclusions on which mechanism is actually involved. To our knowledge, we are the first to show that acoustic pressure influences which route of drug uptake is addressed, by inducing different microbubble-cell interactions. To investigate this, FITC-dextrans were used as model drugs and their uptake was analyzed by flow cytometry. In fluorescence intensity plots, two subpopulations arose in cells with FITC-dextran uptake after ultrasound application, corresponding to cells having either low or high uptake. Following separation of the subpopulations by FACS sorting, confocal images indicated that the low uptake population showed endocytic uptake. The high uptake population represented uptake via pores. Moreover, the distribution of the subpopulations shifted to the high uptake population with increasing acoustic pressure. Real-time confocal recordings during ultrasound revealed that membrane deformation by microbubbles may be the trigger for endocytosis via mechanostimulation of the cytoskeleton. Pore formation was shown to be caused by microbubbles propelled towards the cell. These results provide a better insight in the role of acoustic pressure in microbubble-cell interactions and the possible consequences for drug uptake. In addition, it pinpoints the need for a more rational, microbubble behavior based choice of acoustic parameters in ultrasound mediated drug delivery experiments.

  16. Characterization of Two-pore Channel 2 (TPCN2)-mediated Ca2+ Currents in Isolated Lysosomes*

    PubMed Central

    Schieder, Michael; Rötzer, Katrin; Brüggemann, Andrea; Biel, Martin; Wahl-Schott, Christian A.

    2010-01-01

    Two-pore channels (TPCNs) have been proposed to form lysosomal Ca2+ release channels that are activated by nicotinic acid adenine dinucleotide phosphate. Here, we employ a glass chip-based method to record for the first time nicotinic acid adenine dinucleotide phosphate -dependent currents through a two-pore channel (TPCN2) from intact lysosomes. We show that TPCN2 is a highly selective Ca2+ channel that is regulated by intralysosomal pH. Using site-directed mutagenesis, we identify an amino acid residue in the putative pore region that is crucial for conferring high Ca2+ selectivity. Our glass chip-based method will provide electrophysiological access not only to lysosomal TPCN channels but also to a broad range of other intracellular ion channels. PMID:20495006

  17. Characterization of two-pore channel 2 (TPCN2)-mediated Ca2+ currents in isolated lysosomes.

    PubMed

    Schieder, Michael; Rötzer, Katrin; Brüggemann, Andrea; Biel, Martin; Wahl-Schott, Christian A

    2010-07-01

    Two-pore channels (TPCNs) have been proposed to form lysosomal Ca(2+) release channels that are activated by nicotinic acid adenine dinucleotide phosphate. Here, we employ a glass chip-based method to record for the first time nicotinic acid adenine dinucleotide phosphate -dependent currents through a two-pore channel (TPCN2) from intact lysosomes. We show that TPCN2 is a highly selective Ca(2+) channel that is regulated by intralysosomal pH. Using site-directed mutagenesis, we identify an amino acid residue in the putative pore region that is crucial for conferring high Ca(2+) selectivity. Our glass chip-based method will provide electrophysiological access not only to lysosomal TPCN channels but also to a broad range of other intracellular ion channels.

  18. The Transmembrane Domain Peptide of Vesicular Stomatitis Virus Promotes Both Intermediate and Pore Formation during PEG-Mediated Vesicle Fusion

    PubMed Central

    Sengupta, Tanusree; Chakraborty, Hirak; Lentz, Barry R.

    2014-01-01

    We propose mechanisms by which the transmembrane domain of vesicular stomatitis virus (VSV-TMD) promotes both initiation of fusion and formation of a fusion pore. Time courses of polyethyleneglycol (PEG)-mediated fusion of 25 nm small unilamellar vesicles composed of dioleoylphosphatidylcholine, dioleoylphosphatidylethanolamine (DOPE), bovine brain sphingomyelin, and cholesterol (35:30:15:20 molar ratio) were recorded at pH 7.4 at five different temperatures (from 17°C to 37°C) and compared with time courses obtained with the same vesicles containing the fusion-active TMD of the G protein of VSV. Multiple time courses were fitted globally to a one-intermediate ensemble kinetic model to estimate the rate constants for conversion of the aggregated state to an intermediate hemifused state (k1, stalk, or I1) that rapidly transits to an unstable intermediate (I2 state) that converts to a final fusion pore state with a combined rate k3. The probabilities of lipid mixing, contents mixing, and contents leakage in the three states were also obtained from this analysis. The activation thermodynamics for each step were consistent with previously published models of lipid rearrangements during intermediate and pore formation. The influences of VSV-TMD, hexadecane, and VSV-TMD + hexadecane on the kinetics, activation thermodynamics, and membrane structure support the hypothesis that these two agents do not catalyze fusion by a common mechanism, except possibly at the lowest temperatures examined. VSV-TMD primarily catalyzed initial intermediate formation, although it substantially increased the probability of contents mixing in the intermediate state. Our results support the hypothesis that the catalytic influence of VSV-TMD on the initial-intermediate- and pore-forming steps of PEG-mediated fusion derives from its ability to impose a positive intrinsic curvature and thereby stress small unilamellar vesicle outer leaflets as well as the periphery of intermediate

  19. 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

  20. 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.

  1. 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

  2. The two-pore channel TPCN2 mediates NAADP-dependent Ca(2+)-release from lysosomal stores.

    PubMed

    Zong, Xiangang; Schieder, Michael; Cuny, Hartmut; Fenske, Stefanie; Gruner, Christian; Rötzer, Katrin; Griesbeck, Oliver; Harz, Hartmann; Biel, Martin; Wahl-Schott, Christian

    2009-09-01

    Second messenger-induced Ca(2+)-release from intracellular stores plays a key role in a multitude of physiological processes. In addition to 1,4,5-inositol trisphosphate (IP(3)), Ca(2+), and cyclic ADP ribose (cADPR) that trigger Ca(2+)-release from the endoplasmatic reticulum (ER), nicotinic acid adenine dinucleotide phosphate (NAADP) has been identified as a cellular metabolite that mediates Ca(2+)-release from lysosomal stores. While NAADP-induced Ca(2+)-release has been found in many tissues and cell types, the molecular identity of the channel(s) conferring this release remained elusive so far. Here, we show that TPCN2, a novel member of the two-pore cation channel family, displays the basic properties of native NAADP-dependent Ca(2+)-release channels. TPCN2 transcripts are widely expressed in the body and encode a lysosomal protein forming homomers. TPCN2 mediates intracellular Ca(2+)-release after activation with low-nanomolar concentrations of NAADP while it is desensitized by micromolar concentrations of this second messenger and is insensitive to the NAADP analog nicotinamide adenine dinucleotide phosphate (NADP). Furthermore, TPCN2-mediated Ca(2+)-release is almost completely abolished when the capacity of lysosomes for storing Ca(2+) is pharmacologically blocked. By contrast, TPCN2-specific Ca(2+)-release is unaffected by emptying ER-based Ca(2+) stores. In conclusion, these findings indicate that TPCN2 is a major component of the long-sought lysosomal NAADP-dependent Ca(2+)-release channel.

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

    PubMed

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

    1999-10-12

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

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

    PubMed Central

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

    1999-01-01

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

  5. 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

  6. 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

  7. Ant-mediated expansion of an obligate seeder species during the first years after fire.

    PubMed

    Arnan, X; Rodrigo, A; Molowny-Horas, R; Retana, J

    2010-11-01

    Most obligate seeder species build up a soil seed bank that is associated with massive seed germination in the year immediately after a fire. These species are also shade-intolerant and disappear when vegetation cover closes, creating unsuitable conditions for seedling recruitment. The only way for these plants to expand their populations is when habitats suitable for seedling recruitment arise (i.e. in years immediately after a fire). However, short primary seed dispersal of obligate seeders does not allow these plants to colonise the suitable habitats, and these habitats can only be colonised by secondary seed dispersion. We hypothesised that Fumana ericoides, an obligate-seeding small shrub, not only establishes abundantly in the first year after fire, but also expands its local range in the following years due to secondary dispersal by ants while suitable habitats are still available. We tested this hypothesis using experimental studies and a simulation model of potential population expansion in a recently burned area. Results showed that F. ericoides not only established prolifically in the year immediately after fire, but was also able to recruit new individuals and expand its population in the years following the fire, despite a low germination rate and short primary seed dispersal. Ant-mediated seed dispersal and availability of suitable habitats were key factors in this phenomenon: ants redistributed seeds in suitable habitats while they were available, which accelerated the expansion of F. ericoides because new plants established far away from the core population. PMID:21040299

  8. 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

  9. 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

  10. Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates.

    PubMed

    Martin, Andreas; Baker, Tania A; Sauer, Robert T

    2008-02-29

    ClpX, an archetypal proteolytic AAA+ unfoldase, must engage the ssrA tags of appropriate substrates prior to ATP-dependent unfolding and translocation of the denatured polypeptide into ClpP for degradation. Here, specificity-transplant and disulfide-crosslinking experiments reveal that the ssrA tag interacts with different loops that form the top, middle, and lower portions of the central channel of the ClpX hexamer. Our results support a two-step binding mechanism, in which the top loop serves as a specificity filter and the remaining loops form a binding site for the peptide tag relatively deep within the pore. Crosslinking experiments suggest a staggered arrangement of pore loops in the hexamer and nucleotide-dependent changes in pore-loop conformations. This mechanism of initial tag binding would allow ATP-dependent conformational changes in one or more pore loops to drive peptide translocation, force unfolding, and mediate threading of the denatured protein through the ClpX pore.

  11. The Mitochondrial Permeability Transition Pore Regulates Nitric Oxide-Mediated Apoptosis of Neurons Induced by Target Deprivation

    PubMed Central

    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 days postlesion. We tested the hypothesis that this neuronal apoptosis is initiated by oxidative stress and the mitochondrial permeability transition pore (mPTP). Pre-apoptotic LGN neurons accumulate mitochondria, Zn2+ and Ca2+, and generate higher levels of reactive oxygen species (ROS), including superoxide, nitric oxide (NO) and peroxynitrite, than LGN neurons with an intact cortical target. Pre-apoptosis 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 days after cortical injury. Chemical cross-linking showed that LGN neuron pre-apoptosis 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 and TAT-Bcl-XL-BH4. Manipulation of the mPTP markedly attenuated the early pre-apoptotic 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

  12. Pore orientation mediated control of mechanical behavior of scaffolds and its application in cartilage-mimetic scaffold design.

    PubMed

    Arora, Aditya; Kothari, Anjaney; Katti, Dhirendra S

    2015-11-01

    Scaffolds with aligned pores are being explored in musculoskeletal tissue engineering due to their inherent structural anisotropy. However, influence of their structure on mechanical behavior remains poorly understood. In this work, we elucidate this dependence using chitosan-gelatin based random and aligned scaffolds. For this, scaffolds with horizontally or vertically aligned pores were fabricated using unidirectional freezing technique. Random, horizontal and vertical scaffolds were characterized for their mechanical behavior under compressive, tensile and shear loading regimes. The results revealed conserved trends in compressive, tensile and shear moduli, with horizontal scaffolds showing the least moduli, vertical showing the highest and random showing intermediate. Further, these scaffolds demonstrated a highly viscoelastic behavior under cyclic compressive loading, with a pore orientation dependent relative energy dissipation. These results established that mechanical behavior of porous scaffolds can be modulated by varying pore orientation alone. This finding paved the way to recreate the structural and consequent mechanical anisotropy of articular cartilage tissue using zonally varied pore orientation in scaffolds. To this end, monolithic multizonal scaffolds were fabricated using a novel sequential unidirectional freezing technique. The superficial zone of this scaffold had horizontally aligned pores while the deep zone consisted of vertically aligned pores, with a transition zone between the two having randomly oriented pores. This depth-dependent pore architecture closely mimicked the collagen alignment of native articular cartilage which translated into similar depth-dependent mechanical anisotropy as well. A facile fabrication technique, biomimetic pore architecture and associated mechanical anisotropy make this multizonal scaffold a promising candidate for cartilage tissue engineering.

  13. 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

  14. 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.

  15. 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

  16. Antigen Presenting Cell-Mediated Expansion of Human Umbilical Cord Blood Yields Log-Scale Expansion of Natural Killer Cells with Anti-Myeloma Activity

    PubMed Central

    Shah, Nina; Martin-Antonio, Beatriz; Yang, Hong; Ku, Stephanie; Lee, Dean A.; Cooper, Laurence J. N.; Decker, William K.; Li, Sufang; Robinson, Simon N.; Sekine, Takuya; Parmar, Simrit; Gribben, John; Wang, Michael; Rezvani, Katy; Yvon, Eric; Najjar, Amer; Burks, Jared; Kaur, Indreshpal; Champlin, Richard E.; Bollard, Catherine M.; Shpall, Elizabeth J.

    2013-01-01

    Natural killer (NK) cells are important mediators of anti-tumor immunity and are active against several hematologic malignancies, including multiple myeloma (MM). Umbilical cord blood (CB) is a promising source of allogeneic NK cells but large scale ex vivo expansion is required for generation of clinically relevant CB-derived NK (CB-NK) cell doses. Here we describe a novel strategy for expanding NK cells from cryopreserved CB units using artificial antigen presenting feeder cells (aAPC) in a gas permeable culture system. After 14 days, mean fold expansion of CB-NK cells was 1848-fold from fresh and 2389-fold from cryopreserved CB with >95% purity for NK cells (CD56+/CD3−) and less than 1% CD3+ cells. Though surface expression of some cytotoxicity receptors was decreased, aAPC-expanded CB-NK cells exhibited a phenotype similar to CB-NK cells expanded with IL-2 alone with respect to various inhibitory receptors, NKG2C and CD94 and maintained strong expression of transcription factors Eomesodermin and T-bet. Furthermore, CB-NK cells formed functional immune synapses with and demonstrated cytotoxicity against various MM targets. Finally, aAPC-expanded CB-NK cells showed significant in vivo activity against MM in a xenogenic mouse model. Our findings introduce a clinically applicable strategy for the generation of highly functional CB-NK cells which can be used to eradicate MM. PMID:24204673

  17. Airway epithelial inflammation-induced endoplasmic reticulum Ca2+ store expansion is mediated by X-box binding protein-1.

    PubMed

    Martino, Mary E B; Olsen, John C; Fulcher, Nanette B; Wolfgang, Matthew C; O'Neal, Wanda K; Ribeiro, Carla M P

    2009-05-29

    Inflamed cystic fibrosis (CF) human bronchial epithelia (HBE), or normal HBE exposed to supernatant from mucopurulent material (SMM) from CF airways, exhibit endoplasmic reticulum (ER)/Ca(2+) store expansion and amplified Ca(2+)-mediated inflammation. HBE inflammation triggers an unfolded protein response (UPR) coupled to mRNA splicing of X-box binding protein-1 (XBP-1). Because spliced XBP-1 (XBP-1s) promotes ER expansion in other cellular models, we hypothesized that XBP-1s is responsible for the ER/Ca(2+) store expansion in inflamed HBE. XBP-1s was increased in freshly isolated infected/inflamed CF in comparison with normal HBE. The link between airway epithelial inflammation, XBP-1s, and ER/Ca(2+) store expansion was then addressed in murine airways challenged with phosphate-buffered saline or Pseudomonas aeruginosa. P. aeruginosa-challenged mice exhibited airway epithelial ER/Ca(2+) store expansion, which correlated with airway inflammation. P. aeruginosa-induced airway inflammation triggered XBP-1s in ER stress-activated indicator (ERAI) mice. To evaluate the functional role of XBP-1s in airway inflammation linked to ER/Ca(2+) store expansion, control, XBP-1s, or dominant negative XBP-1 (DN-XBP-1) stably expressing 16HBE14o(-) cell lines were used. Studies with cells transfected with an unfolded protein response element (UPRE) luciferase reporter plasmid confirmed that the UPRE was activated or inhibited by expression of XBP-1s or DN-XBP-1, respectively. Expression of XBP-1s induced ER/Ca(2+) store expansion and potentiated bradykinin-increased interleukin (IL)-8 secretion, whereas expression of DN-XBP-1 inhibited bradykinin-dependent IL-8 secretion. In addition, expression of DN-XBP-1 blunted SMM-induced ER/Ca(2+) store expansion and SMM-induced IL-8 secretion. These findings suggest that, in inflamed HBE, XBP-1s is responsible for the ER/Ca(2+) store expansion that confers amplification of Ca(2+)-dependent inflammatory responses. PMID:19321437

  18. The Pore-Forming Toxin Listeriolysin O Mediates a Novel Entry Pathway of L. monocytogenes into Human Hepatocytes

    PubMed Central

    Vadia, Stephen; Arnett, Eusondia; Haghighat, Anne-Cécile; Wilson-Kubalek, Elisabeth M.; Tweten, Rodney K.; Seveau, Stephanie

    2011-01-01

    Intracellular pathogens have evolved diverse strategies to invade and survive within host cells. Among the most studied facultative intracellular pathogens, Listeria monocytogenes is known to express two invasins-InlA and InlB-that induce bacterial internalization into nonphagocytic cells. The pore-forming toxin listeriolysin O (LLO) facilitates bacterial escape from the internalization vesicle into the cytoplasm, where bacteria divide and undergo cell-to-cell spreading via actin-based motility. In the present study we demonstrate that in addition to InlA and InlB, LLO is required for efficient internalization of L. monocytogenes into human hepatocytes (HepG2). Surprisingly, LLO is an invasion factor sufficient to induce the internalization of noninvasive Listeria innocua or polystyrene beads into host cells in a dose-dependent fashion and at the concentrations produced by L. monocytogenes. To elucidate the mechanisms underlying LLO-induced bacterial entry, we constructed novel LLO derivatives locked at different stages of the toxin assembly on host membranes. We found that LLO-induced bacterial or bead entry only occurs upon LLO pore formation. Scanning electron and fluorescence microscopy studies show that LLO-coated beads stimulate the formation of membrane extensions that ingest the beads into an early endosomal compartment. This LLO-induced internalization pathway is dynamin-and F-actin-dependent, and clathrin-independent. Interestingly, further linking pore formation to bacteria/bead uptake, LLO induces F-actin polymerization in a tyrosine kinase-and pore-dependent fashion. In conclusion, we demonstrate for the first time that a bacterial pathogen perforates the host cell plasma membrane as a strategy to activate the endocytic machinery and gain entry into the host cell. PMID:22072970

  19. 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

  20. 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

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

    PubMed Central

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

    2016-01-01

    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

  2. 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

  3. 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

  4. Inflammation and pyroptosis mediate muscle expansion in an interleukin-1β (IL-1β)-dependent manner.

    PubMed

    Haldar, Subhash; Dru, Christopher; Choudhury, Diptiman; Mishra, Rajeev; Fernandez, Ana; Biondi, Shea; Liu, Zhenqiu; Shimada, Kenichi; Arditi, Moshe; Bhowmick, Neil A

    2015-03-01

    Muscle inflammation is often associated with its expansion. Bladder smooth muscle inflammation-induced cell death is accompanied by hyperplasia and hypertrophy as the primary cause for poor bladder function. In mice, DNA damage initiated by chemotherapeutic drug cyclophosphamide activated caspase 1 through the formation of the NLRP3 complex resulting in detrusor hyperplasia. A cyclophosphamide metabolite, acrolein, caused global DNA methylation and accumulation of DNA damage in a mouse model of bladder inflammation and in cultured bladder muscle cells. In correlation, global DNA methylation and NLRP3 expression was up-regulated in human chronic bladder inflammatory tissues. The epigenetic silencing of DNA damage repair gene, Ogg1, could be reversed by the use of demethylating agents. In mice, demethylating agents reversed cyclophosphamide-induced bladder inflammation and detrusor expansion. The transgenic knock-out of Ogg1 in as few as 10% of the detrusor cells tripled the proliferation of the remaining wild type counterparts in an in vitro co-culture titration experiment. Antagonizing IL-1β with Anakinra, a rheumatoid arthritis therapeutic, prevented detrusor proliferation in conditioned media experiments as well as in a mouse model of bladder inflammation. Radiation treatment validated the role of DNA damage in the NLRP3-associated caspase 1-mediated IL-1β secretory phenotype. A protein array analysis identified IGF1 to be downstream of IL-1β signaling. IL-1β-induced detrusor proliferation and hypertrophy could be reversed with the use of Anakinra as well as an IGF1 neutralizing antibody. IL-1β antagonists in current clinical practice can exploit the revealed mechanism for DNA damage-mediated muscular expansion. PMID:25596528

  5. 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…

  6. 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

  7. IGF-1-mediated osteoblastic niche expansion enhances long-term hematopoietic stem cell engraftment after murine bone marrow transplantation.

    PubMed

    Caselli, Anna; Olson, Timothy S; Otsuru, Satoru; Chen, Xiaohua; Hofmann, Ted J; Nah, Hyun-Duck; Grisendi, Giulia; Paolucci, Paolo; Dominici, Massimo; Horwitz, Edwin M

    2013-10-01

    The efficiency of hematopoietic stem cell (HSC) engraftment after bone marrow (BM) transplantation depends largely on the capacity of the marrow microenvironment to accept the transplanted cells. While radioablation of BM damages osteoblastic stem cell niches, little is known about their restoration and mechanisms governing their receptivity to engraft transplanted HSCs. We previously reported rapid restoration and profound expansion of the marrow endosteal microenvironment in response to marrow radioablation. Here, we show that this reorganization represents proliferation of mature endosteal osteoblasts which seem to arise from a small subset of high-proliferative, relatively radio-resistant endosteal cells. Multiple layers of osteoblasts form along the endosteal surface within 48 hours after total body irradiation, concomitant with a peak in marrow cytokine expression. This niche reorganization fosters homing of the transplanted hematopoietic cells to the host marrow space and engraftment of long-term-HSC. Inhibition of insulin-like growth factor (IGF)-1-receptor tyrosine kinase signaling abrogates endosteal osteoblast proliferation and donor HSC engraftment, suggesting that the cytokine IGF-1 is a crucial mediator of endosteal niche reorganization and consequently donor HSC engraftment. Further understanding of this novel mechanism of IGF-1-dependent osteoblastic niche expansion and HSC engraftment may yield clinical applications for improving engraftment efficiency after clinical HSC transplantation.

  8. 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

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

    PubMed

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

    2007-08-15

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

  10. Distinct enhancers of ptf1a mediate specification and expansion of ventral pancreas in zebrafish.

    PubMed

    Pashos, Evanthia; Park, Joon Tae; Leach, Steven; Fisher, Shannon

    2013-09-15

    the requirement of maintained ptf1a expression for normal pancreatic morphogenesis. We also identified a novel enhancer that mediates initiation of ptf1a expression in the pancreas, through which the signals that specify the ventral pancreas are expected to exert their action.

  11. Inhibition of mitotic clonal expansion mediates fisetin-exerted prevention of adipocyte differentiation in 3T3-L1 cells.

    PubMed

    Lee, Youngyi; Bae, Eun Ju

    2013-11-01

    Adipocytes are the key player in adipose tissue inflammation and subsequent systemic insulin resistance and its development involves complex process of proliferation and differentiation of preadipocytes. Fistein, a polyphenol flavonoid, is known to exert anti-inflammatory, anti-carcinogenic and anti-diabetic effects. In this study, we aimed to investigate the effect of fisetin on adipocyte proliferation and differentiation in 3T3-L1 preadipocyte cell line and its mechanism of action. We found that fisetin inhibits adipocyte differentiation in a concentration dependent manner, which were evidenced by Oil Red O staining and the protein expression of mature adipocyte marker genes fatty acid synthase and peroxisome proliferator-activated receptor γ. Moreover, the proliferation of preadipocytes was also markedly suppressed by treatment of fisetin for 24 and 48 h in the differentiation medium. We also found that fisetin inhibition of adipocyte differentiation was largely due to the effect on mitotic clonal expansion. Fisetin suppression of preadipocyte proliferation at early stage of differentiation was accompanied by the changes of expression of a series of cell cycle regulatory proteins. Altogether, our results suggest that the inhibition of adipocyte differentiation by fisetin may be at least in part mediated by cell cycle arrest during adipogenesis.

  12. 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

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

    PubMed

    Rajanala, Kalpana; Nandicoori, Vinay Kumar

    2012-01-01

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

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

    PubMed

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

    2012-09-15

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

  15. Range expansion of house sparrows (Passer domesticus) in Kenya: evidence of genetic admixture and human-mediated dispersal.

    PubMed

    Schrey, Aaron W; Liebl, Andrea L; Richards, Christina L; Martin, Lynn B

    2014-01-01

    Introduced species offer an opportunity to study the ecological process of range expansions. Recently, 3 mechanisms have been identified that may resolve the genetic paradox (the seemingly unlikely success of introduced species given the expected reduction in genetic diversity through bottlenecks or founder effects): multiple introductions, high propagule pressure, and epigenetics. These mechanisms are probably also important in range expansions (either natural or anthropogenic), yet this possibility remains untested in vertebrates. We used microsatellite variation (7 loci) in house sparrows (Passer domesticus), an introduced species that has been spreading across Kenya for ~60 years, to determine if patterns of variation could explain how this human commensal overcame the genetic paradox and expresses such considerable phenotypic differentiation across this new range. We note that in some cases, polygenic traits and epistasis among genes, for example, may not have negative effects on populations. House sparrows arrived in Kenya by a single introduction event (to Mombasa, ~1950) and have lower genetic diversity than native European and introduced North American populations. We used Bayesian clustering of individuals (n = 233) to detect that at least 2 types of range expansion occurred in Kenya: one with genetic admixture and one with little to no admixture. We also found that genetic diversity increased toward a range edge, and the range expansion was consistent with long-distance dispersal. Based on these data, we expect that the Kenyan range expansion was anthropogenically influenced, as the expansions of other introduced human commensals may also be.

  16. 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.

  17. Membrane pores induced by magainin

    SciTech Connect

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

    1996-10-29

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

  18. 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

  19. 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

  20. Forecasting range expansion into ecological traps: climate-mediated shifts in sea turtle nesting beaches and human development.

    PubMed

    Pike, David A

    2013-10-01

    Some species are adapting to changing environments by expanding their geographic ranges. Understanding whether range shifts will be accompanied by increased exposure to other threats is crucial to predicting when and where new populations could successfully establish. If species overlap to a greater extent with human development under climate change, this could form ecological traps which are attractive to dispersing individuals, but the use of which substantially reduces fitness. Until recently, the core nesting range for the Critically Endangered Kemp's ridley sea turtle (Lepidochelys kempii) was ca. 1000 km of sparsely populated coastline in Tamaulipas, Mexico. Over the past twenty-five years, this species has expanded its range into populated areas of coastal Florida (>1500 km outside the historical range), where nesting now occurs annually. Suitable Kemp's ridley nesting habitat has persisted for at least 140 000 years in the western Gulf of Mexico, and climate change models predict further nesting range expansion into the eastern Gulf of Mexico and northern Atlantic Ocean. Range expansion is 6-12% more likely to occur along uninhabited stretches of coastline than are current nesting beaches, suggesting that novel nesting areas will not be associated with high levels of anthropogenic disturbance. Although the high breeding-site fidelity of some migratory species could limit adaptation to climate change, rapid population recovery following effective conservation measures may enhance opportunities for range expansion. Anticipating the interactive effects of past or contemporary conservation measures, climate change, and future human activities will help focus long-term conservation strategies.

  1. 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...

  2. 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

  3. Matrix-mediated retention of osteogenic differentiation potential by human adult bone marrow stromal cells during ex vivo expansion.

    PubMed

    Mauney, Joshua R; Kaplan, David L; Volloch, Vladimir

    2004-07-01

    During prolonged cultivation ex vivo, adult bone marrow stromal stem cells (BMSCs) undergo two probably interdependent processes, replicative aging and a decline in differentiation potential. Recently, our results with primary human fibroblasts indicated that growth on denatured collagen (DC) matrix results in the reduction of the rate of cellular aging. The present study has been undertaken to test whether the growth of human BMSCs under the same conditions would translate into preservation of cellular aging-attenuated functions, such as the ability to express HSP70 in response to stress as well as of osteogenic differentiation potential. We report here that growth of BMSCs on a DC matrix versus tissue culture polystyrene significantly reduced one of the main manifestations of cellular aging, the attenuation of the ability to express a major protective stress response component, HSP70, increased the proliferation capacity of ex vivo expanded BMSCs, reduced the rate of morphological changes, and resulted in a dramatic increase in the retention of the potential to express osteogenic-specific functions and markers upon treatment with osteogenic stimulants. BMSCs are a promising and increasingly important cell source for tissue engineering as well as cell and gene therapeutic strategies. For use of BMSCs in these applications, ex vivo expansion is necessary to obtain a sufficient, therapeutically useful, number of cells; however, this results in the loss of differentiation potential. This problem is especially acute in older patients where more extensive in vitro expansion of smaller number of stem/progenitor cells is needed. The finding that growth on certain biomaterials preserves aging-attenuated functions, enhances proliferation capacity, and maintains differentiation potential of BMSCs indicates a promising approach to address this problem.

  4. Discovery of dual orexin receptor antagonists with rat sleep efficacy enabled by expansion of the acetonitrile-assisted/diphosgene-mediated 2,4-dichloropyrimidine synthesis.

    PubMed

    Roecker, Anthony J; Mercer, Swati P; Harrell, C Meacham; Garson, Susan L; Fox, Steven V; Gotter, Anthony L; Prueksaritanont, Thomayant; Cabalu, Tamara D; Cui, Donghui; Lemaire, Wei; Winrow, Christopher J; Renger, John J; Coleman, Paul J

    2014-05-01

    Recent clinical studies have demonstrated that dual orexin receptor antagonists (OX1R and OX2R antagonists or DORAs) represent a novel treatment option for insomnia patients. Previously we have disclosed several compounds in the diazepane amide DORA series with excellent potency and both preclinical and clinical sleep efficacy. Additional SAR studies in this series were enabled by the expansion of the acetonitrile-assisted, diphosgene-mediated 2,4-dichloropyrimidine synthesis to novel substrates providing an array of Western heterocycles. These heterocycles were utilized to synthesize analogs in short order with high levels of potency on orexin 1 and orexin 2 receptors as well as in vivo sleep efficacy in the rat.

  5. 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

  6. Novel colicin Fy of Yersinia frederiksenii inhibits pathogenic Yersinia strains via YiuR-mediated reception, TonB import, and cell membrane pore formation.

    PubMed

    Bosák, Juraj; Laiblová, Petra; Smarda, Jan; Dedicová, Daniela; Smajs, David

    2012-04-01

    A novel colicin type, designated colicin Fy, was found to be encoded and produced by the strain Yersinia frederiksenii Y27601. Colicin Fy was active against both pathogenic and nonpathogenic strains of the genus Yersinia. Plasmid YF27601 (5,574 bp) of Y. frederiksenii Y27601 was completely sequenced. The colicin Fy activity gene (cfyA) and the colicin Fy immunity gene (cfyI) were identified. The deduced amino acid sequence of colicin Fy was very similar in its C-terminal pore-forming domain to colicin Ib (69% identity in the last 178 amino acid residues), indicating pore forming as its lethal mode of action. Transposon mutagenesis of the colicin Fy-susceptible strain Yersinia kristensenii Y276 revealed the yiuR gene (ykris001_4440), which encodes the YiuR outer membrane protein with unknown function, as the colicin Fy receptor molecule. Introduction of the yiuR gene into the colicin Fy-resistant strain Y. kristensenii Y104 restored its susceptibility to colicin Fy. In contrast, the colicin Fy-resistant strain Escherichia coli TOP10F' acquired susceptibility to colicin Fy only when both the yiuR and tonB genes from Y. kristensenii Y276 were introduced. Similarities between colicins Fy and Ib, similarities between the Cir and YiuR receptors, and the detected partial cross-immunity of colicin Fy and colicin Ib producers suggest a common evolutionary origin of the colicin Fy-YiuR and colicin Ib-Cir systems.

  7. Novel Colicin FY of Yersinia frederiksenii Inhibits Pathogenic Yersinia Strains via YiuR-Mediated Reception, TonB Import, and Cell Membrane Pore Formation

    PubMed Central

    Bosák, Juraj; Laiblová, Petra; Šmarda, Jan; Dědičová, Daniela

    2012-01-01

    A novel colicin type, designated colicin FY, was found to be encoded and produced by the strain Yersinia frederiksenii Y27601. Colicin FY was active against both pathogenic and nonpathogenic strains of the genus Yersinia. Plasmid YF27601 (5,574 bp) of Y. frederiksenii Y27601 was completely sequenced. The colicin FY activity gene (cfyA) and the colicin FY immunity gene (cfyI) were identified. The deduced amino acid sequence of colicin FY was very similar in its C-terminal pore-forming domain to colicin Ib (69% identity in the last 178 amino acid residues), indicating pore forming as its lethal mode of action. Transposon mutagenesis of the colicin FY-susceptible strain Yersinia kristensenii Y276 revealed the yiuR gene (ykris001_4440), which encodes the YiuR outer membrane protein with unknown function, as the colicin FY receptor molecule. Introduction of the yiuR gene into the colicin FY-resistant strain Y. kristensenii Y104 restored its susceptibility to colicin FY. In contrast, the colicin FY-resistant strain Escherichia coli TOP10F′ acquired susceptibility to colicin FY only when both the yiuR and tonB genes from Y. kristensenii Y276 were introduced. Similarities between colicins FY and Ib, similarities between the Cir and YiuR receptors, and the detected partial cross-immunity of colicin FY and colicin Ib producers suggest a common evolutionary origin of the colicin FY-YiuR and colicin Ib-Cir systems. PMID:22343298

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. Fusion pore regulation of transmitter release.

    PubMed

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

    2005-09-01

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

  13. 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)

  14. Velocities in Solar Pores

    NASA Astrophysics Data System (ADS)

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

    1996-05-01

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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion?

    PubMed

    Brown, Rafe M; Linkem, Charles W; Siler, Cameron D; Sukumaran, Jeet; Esselstyn, Jacob A; Diesmos, Arvin C; Iskandar, Djoko T; Bickford, David; Evans, Ben J; McGuire, Jimmy A; Grismer, Lee; Supriatna, Jatna; Andayani, Noviar

    2010-11-01

    Southeast Asia's widespread species offer unique opportunities to explore the effects of geographical barriers to dispersal on patterns of vertebrate lineage diversification. We analyzed mitochondrial gene sequences (16S rDNA) from a geographically widespread sample of 266 Southeast Asian tree frogs, including 244 individuals of Polypedates leucomystax and its close relatives. Our expectation was that lineages on island archipelagos would exhibit more substantial geographic structure, corresponding to the geological history of terrestrial connectivity in this region, compared to the Asian mainland. Contrary to predictions, we found evidence of numerous highly divergent lineages from a limited area on the Asian mainland, but fewer lineages with shallower divergences throughout oceanic islands of the Philippines and Indonesia. Surprisingly and in numerous instances, lineages in the archipelagos span distinct biogeographical provinces. Phylogeographic analyses identified four major haplotype clades; summary statistics, mismatch distributions, and Bayesian coalescent inference of demography provide support for recent range expansion, population growth, and/or admixture in the Philippine and some Sulawesi populations. We speculate that the current range of P. leucomystax in Southeast Asia is much larger now than in the recent past. Conversion of forested areas to monoculture agriculture and transportation of agricultural products between islands may have facilitated unprecedented population and range expansion in P. leucomystax throughout thousands of islands in the Philippine and Indonesian archipelagos.

  3. 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.

  4. Interleukin 1 (IL-1)- and IL-23-Mediated Expansion of Filarial Antigen-Specific Th17 and Th22 Cells in Filarial Lymphedema

    PubMed Central

    Anuradha, R.; George, P. Jovvian; Chandrasekaran, V.; Kumaran, P. Paul; Nutman, Thomas B.

    2014-01-01

    Lymphatic filarial disease is known to be associated with elevated Th1 responses and normal or diminished Th2 responses to parasite-specific antigens. The roles of Th17 cells and the recently described Th22 cells have not been examined in detail in either filarial infection itself or in filarial disease (e.g., lymphedema and elephantiasis). To explore the roles of Th17 and Th22 cells and their subsets, we examined the frequencies of these cells in individuals with filarial lymphedema (chronic pathology [CP]), in clinically asymptomatic infected (INF) individuals, and in uninfected (UN) individuals ex vivo and in response to parasite and nonparasite antigens. Those with disease (CP) had significantly expanded frequencies of Th17 and Th22 cells, compared with either INF or UN individuals, at baseline (ex vivo) and in response to parasite antigens. This antigen-driven expansion of Th17 and Th22 cells was dependent on interleukin 1 (IL-1), IL-23, and, to lesser extent, transforming growth factor β (TGF-β), as blockade of any of these cytokines resulted in significantly diminished frequencies of Th17 and Th22 cells. Our findings, therefore, suggest that filarial parasite-driven expansion of Th17 and Th22 cells is associated with the pathogenesis of filarial infections and disease. PMID:24807054

  5. Expansion of murine periosteal progenitor cells with fibroblast growth factor 2 reveals an intrinsic endochondral ossification program mediated by bone morphogenetic protein 2.

    PubMed

    van Gastel, Nick; Stegen, Steve; Stockmans, Ingrid; Moermans, Karen; Schrooten, Jan; Graf, Daniel; Luyten, Frank P; Carmeliet, Geert

    2014-09-01

    The preservation of the bone-forming potential of skeletal progenitor cells during their ex vivo expansion remains one of the major challenges for cell-based bone regeneration strategies. We report that expansion of murine periosteal cells in the presence of FGF2, a signal present during the early stages of fracture healing, is necessary and sufficient to maintain their ability to organize in vivo into a cartilage template which gives rise to mature bone. Implantation of FGF2-primed cells in a large bone defect in mice resulted in complete healing, demonstrating the feasibility of using this approach for bone tissue engineering purposes. Mechanistically, the enhanced endochondral ossification potential of FGF2-expanded periosteal cells is predominantly driven by an increased production of BMP2 and is additionally linked to an improved preservation of skeletal progenitor cells in the cultures. This characteristic is unique for periosteal cells, as FGF2-primed bone marrow stromal cells formed significantly less bone and progressed exclusively through the intramembranous pathway, revealing essential differences between both cell pools. Taken together, our findings provide insight in the molecular regulation of fracture repair by identifying a unique interaction between periosteal cells and FGF2. These insights may promote the development of cell-based therapeutic strategies for bone regeneration which are independent of the in vivo use of growth factors, thus limiting undesired side effects. PMID:24989687

  6. Pore dynamics in lipid membranes

    NASA Astrophysics Data System (ADS)

    Gozen, I.; Dommersnes, P.

    2014-09-01

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

  7. 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.

  8. 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

  9. Latent fingermark pore area reproducibility.

    PubMed

    Gupta, A; Buckley, K; Sutton, R

    2008-08-01

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

  10. Surge dynamics coupled to pore-pressure evolution in debris flows

    USGS Publications Warehouse

    Savage, S.B.; Iverson, R.M.; ,

    2003-01-01

    Temporally and spatially varying pore-fluid pressures exert strong controls on debris-flow motion by mediating internal and basal friction at grain contacts. We analyze these effects by deriving a one-dimensional model of pore-pressure diffusion explicitly coupled to changes in debris-flow thickness. The new pore-pressure equation is combined with Iverson's (1997) extension of the depth-averaged Savage-Hutter (1989, 1991) granular avalanche equations to predict motion of unsteady debris-flow surges with evolving pore-pressure distributions. Computational results illustrate the profound effects of pore-pressure diffusivities on debris-flow surge depths and velocities. ?? 2003 Millpress,.

  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. Role of Serum Amyloid A, Granulocyte-Macrophage Colony-Stimulating Factor, and Bone Marrow Granulocyte-Monocyte Precursor Expansion in Segmented Filamentous Bacterium-Mediated Protection from Entamoeba histolytica.

    PubMed

    Burgess, Stacey L; Saleh, Mahmoud; Cowardin, Carrie A; Buonomo, Erica; Noor, Zannatun; Watanabe, Koji; Abhyankar, Mayuresh; Lajoie, Stephane; Wills-Karp, Marsha; Petri, William A

    2016-10-01

    Intestinal segmented filamentous bacteria (SFB) protect from ameba infection, and protection is transferable with bone marrow dendritic cells (BMDCs). SFB cause an increase in serum amyloid A (SAA), suggesting that SAA might mediate SFB's effects on BMDCs. Here we further explored the role of bone marrow in SFB-mediated protection. Transient gut colonization with SFB or SAA administration alone transiently increased the H3K27 histone demethylase Jmjd3, persistently increased bone marrow Csf2ra expression and granulocyte monocyte precursors (GMPs), and protected from ameba infection. Pharmacologic inhibition of Jmjd3 H3K27 demethylase activity during SAA treatment or blockade of granulocyte-macrophage colony-stimulating factor (GM-CSF) signaling in SFB-colonized mice prevented GMP expansion, decreased gut neutrophils, and blocked protection from ameba infection. These results indicate that alteration of the microbiota and systemic exposure to SAA can influence myelopoiesis and susceptibility to amebiasis via epigenetic mechanisms. Gut microbiota-marrow communication is a previously unrecognized mechanism of innate protection from infection. PMID:27456830

  13. 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

  14. 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

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

    PubMed

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

    2015-01-01

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

  16. Designed membrane channels and pores.

    PubMed

    Bayley, H

    1999-02-01

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

  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. 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.

  19. Metal structures with parallel pores

    NASA Technical Reports Server (NTRS)

    Sherfey, J. M.

    1976-01-01

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

  20. Weak measure expansive flows

    NASA Astrophysics Data System (ADS)

    Lee, Keonhee; Oh, Jumi

    2016-01-01

    A notion of measure expansivity for flows was introduced by Carrasco-Olivera and Morales in [3] as a generalization of expansivity, and they proved that there were no measure expansive flows on closed surfaces. In this paper we introduce a concept of weak measure expansivity for flows which is really weaker than that of measure expansivity, and show that there is a weak measure expansive flow on a closed surface. Moreover we show that any C1 stably weak measure expansive flow on a C∞ closed manifold M is Ω-stable, and any C1 stably measure expansive flow on M satisfies both Axiom A and the quasi-transversality condition.

  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. Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting.

    PubMed

    Duncombe, Todd A; Kang, Chi-Chih; Maity, Santanu; Ward, Toby M; Pegram, Mark D; Murthy, Niren; Herr, Amy E

    2016-01-13

    Pore-gradient microgel arrays enable thousands of parallel high-resolution single-cell protein electrophoresis separations for targets accross a wide molecular mass (25-289 kDa), yet within 1 mm separation distances. Dual crosslinked hydrogels facilitate gel-pore expansion after electrophoresis for efficient and uniform immunoprobing. The photopatterned, light-activated, and acid-expandable hydrogel underpins single-cell protein analysis, here for oncoprotein-related signaling in human breast biopsy.

  3. Pore size matters for potassium channel conductance.

    PubMed

    Naranjo, David; Moldenhauer, Hans; Pincuntureo, Matías; Díaz-Franulic, Ignacio

    2016-10-01

    Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K(+) channels discriminate K(+) over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K(+) channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K(+) channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K(+) channels, accounting for their diversity in unitary conductance.

  4. Enriching the pore: Splendid complexity from humble origins

    PubMed Central

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

    2014-01-01

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

  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. 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 ...

  7. Antimicrobial Peptides in Toroidal and Cylindrical Pores

    PubMed Central

    Mihajlovic, Maja

    2010-01-01

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

  8. Restricted movement of lipid and aqueous dyes through pores formed by influenza hemagglutinin during cell fusion

    PubMed Central

    1994-01-01

    The fusion of cells by influenza hemagglutinin (HA) is the best characterized example of protein-mediated membrane fusion. In simultaneous measurements of pairs of assays for fusion, we determined the order of detectable events during fusion. Fusion pore formation in HA-triggered cell-cell fusion was first detected by changes in cell membrane capacitance, next by a flux of fluorescent lipid, and finally by flux of aqueous fluorescent dye. Fusion pore conductance increased by small steps. A retardation of lipid and aqueous dyes occurred during fusion pore fluctuations. The flux of aqueous dye depended on the size of the molecule. The lack of movement of aqueous dyes while total fusion pore conductance increased suggests that initial HA-triggered fusion events are characterized by the opening of multiple small pores: the formation of a "sieve". PMID:7806567

  9. Pore formation by Cry toxins.

    PubMed

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

    2010-01-01

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

  10. 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.

  11. Novel biometrics based on nose pore recognition

    NASA Astrophysics Data System (ADS)

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

    2009-05-01

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

  12. 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

  13. Diffusive resistance of avian eggshell pores.

    PubMed

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

    1988-12-01

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

  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. Pore-scale spectral induced polarization (SIP) signaturesassociated with FeS biomineral transformations

    SciTech Connect

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

    2007-10-01

    The authors measured Spectral Induced Polarization (SIP) signatures in sand columns during (1) FeS biomineralization produced by sulfate reducing bacteria (D. vulgaris) under anaerboci 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. They find that the modeled time constant is consistent with the polarizable elements being biomineral encrused 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. They conclude that SIP signatures are diagnostic of pore-scale geometrical changes associated with FeS biomineralization by sulfate reducing bacteria.

  16. Glycosylation of the nuclear pore

    PubMed Central

    Li, Bin; Kohler, Jennifer J.

    2014-01-01

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

  17. 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.

  18. 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

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

    PubMed Central

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

    2010-01-01

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

  20. A thermodynamic approach to Alamethicin pore formation

    PubMed Central

    Rahaman, Asif; Lazaridis, Themis

    2013-01-01

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

  1. 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.

  2. Influences on role expansion.

    PubMed

    Bullough, B

    1976-09-01

    Several factors are influencing role expansion for registered nurses, among them the shortage of primary care physicians, the federal government, the physician's assistant movement, the growing complexity of acute hospital care, educational reform, and the women's liberation movement. As state licensure statutes are revised to allow for role expansion, the changing laws themselves become a factor supporting the movement.

  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. Nuclear Pore Proteins and Cancer

    PubMed Central

    Xu, Songli; Powers, Maureen A.

    2009-01-01

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

  5. Fine structures at pore boundary

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  6. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Kuder, Tristan Anselm; Laun, Frederik Bernd

    2015-08-01

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

  9. 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)

  10. 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.

  11. 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.

  12. 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.

  13. A two-dimensional finite difference model of pore pressure evolution within and below a moving thrust sheet

    SciTech Connect

    Smith, R.E.; Wiltschko, D.V. . Dept. of Geology)

    1992-01-01

    The authors have investigated the mechanisms responsible for the evolution of excess pore pressures within and beneath a ramping thrust sheet and the sensitivity of pore pressure to a variety of physical parameters. Coupled pore pressure and temperature equations were solved numerically in two dimensions using a generalized hydrostratigraphy of North American thrust belts; both deposition and thrust loading were modeled. The dominant mechanisms controlling pore pressure evolution were fluid flow and compression of pore space by vertical loading; thermal expansion of the fluids was found to be insignificant in generating excess pore pressures. The results of the modeling predict that it is possible to generate high pore pressure to lithostatic pressure ratios R within thrust belts by depositional loading prior to thrusting. High values of R are generated and maintained during thrust loading for reasonable assumptions about the conditions thought to have existed in thrust belts. Values of R were not constant throughout the model. The highest R values tended to concentrate near the surface of the model and within and below the toe of the thrust sheet. The magnitude and distribution of excess pore pressures and R values were found to be especially sensitive to variations in permeability. Excess pore pressure generation by compression exceeded pore pressure dissipation by fluid flow for permeabilities greater than approximately 10[sup [minus]16] m[sup 2] produced hydrostatic pore pressure gradients. The models demonstrate that permeability anisotropy and inhomogeneity due to lithologic variations may exert a strong control on the magnitude and spatial distribution of excess pore pressures within thrust belts.

  14. 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

  15. MCU encodes the pore conducting mitochondrial calcium currents.

    PubMed

    Chaudhuri, Dipayan; Sancak, Yasemin; Mootha, Vamsi K; Clapham, David E

    2013-06-04

    Mitochondrial calcium (Ca(2+)) import is a well-described phenomenon regulating cell survival and ATP production. Of multiple pathways allowing such entry, the mitochondrial Ca(2+) uniporter is a highly Ca(2+)-selective channel complex encoded by several recently-discovered genes. However, the identity of the pore-forming subunit remains to be established, since knockdown of all the candidate uniporter genes inhibit Ca(2+) uptake in imaging assays, and reconstitution experiments have been equivocal. To definitively identify the channel, we use whole-mitoplast voltage-clamping, the technique that originally established the uniporter as a Ca(2+) channel. We show that RNAi-mediated knockdown of the mitochondrial calcium uniporter (MCU) gene reduces mitochondrial Ca(2+) current (I MiCa ), whereas overexpression increases it. Additionally, a classic feature of I MiCa , its sensitivity to ruthenium red inhibition, can be abolished by a point mutation in the putative pore domain without altering current magnitude. These analyses establish that MCU encodes the pore-forming subunit of the uniporter channel. DOI:http://dx.doi.org/10.7554/eLife.00704.001.

  16. 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

  17. Screening of pi-basic naphthalene and anthracene amplifiers for pi-acidic synthetic pore sensors.

    PubMed

    Hagihara, Shinya; Gremaud, Ludovic; Bollot, Guillaume; Mareda, Jiri; Matile, Stefan

    2008-04-01

    Synthetic ion channels and pores attract current attention as multicomponent sensors in complex matrixes. This application requires the availability of reactive signal amplifiers that covalently capture analytes and drag them into the pore. pi-Basic 1,5-dialkoxynaphthalenes (1,5-DAN) are attractive amplifiers because aromatic electron donor-acceptor (AEDA) interactions account for their recognition within pi-acidic naphthalenediimide (NDI) rich synthetic pores. Focusing on amplifier design, we report here the synthesis of a complete collection of DAN and dialkoxyanthracene amplifiers, determine their oxidation potentials by cyclic voltammetry, and calculate their quadrupole moments. Blockage experiments reveal that subtle structural changes in regioisomeric DAN amplifiers can be registered within NDI pores. Frontier orbital overlap in AEDA complexes, oxidation potentials, and, to a lesser extent, quadrupole moments are shown to contribute to isomer recognition by synthetic pores. Particularly important with regard to practical applications of synthetic pores as multianalyte sensors, we further demonstrate that application of the lessons learned with DAN regioisomers to the expansion to dialkoxyanthracenes provides access to privileged amplifiers with submicromolar activity.

  18. 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

  19. 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

  20. 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Petrishcheva, E.; Renner, J.

    2010-10-01

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

  3. 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

  4. 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.

  5. Optimal Electric Utility Expansion

    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 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. In Vivo Expansion of Regulatory T cells With IL-2/IL-2 mAb Complexes Prevents Anti-factor VIII Immune Responses in Hemophilia A Mice Treated With Factor VIII Plasmid-mediated Gene Therapy

    PubMed Central

    Liu, Chao-Lien; Ye, Peiqing; Yen, Benjamin C; Miao, Carol H

    2011-01-01

    Generation of transgene-specific immune responses can constitute a major complication following gene therapy treatment. An in vivo approach to inducing selective expansion of Regulatory T (Treg) cells by injecting interleukin-2 (IL-2) mixed with a specific IL-2 monoclonal antibody (JES6-1) was adopted to modulate anti-factor VIII (anti-FVIII) immune responses. Three consecutive IL-2 complexes treatments combined with FVIII plasmid injection prevented anti-FVIII formation and achieved persistent, therapeutic-level of FVIII expression in hemophilia A (HemA) mice. The IL-2 complexes treatment expanded CD4+CD25+Foxp3+ Treg cells five- to sevenfold on peak day, and they gradually returned to normal levels within 7–14 days without changing other lymphocyte populations. The transiently expanded Treg cells are highly activated and display suppressive function in vitro. Adoptive transfer of the expanded Treg cells protected recipient mice from generation of high-titer antibodies following FVIII plasmid challenge. Repeated plasmid transfer is applicable in tolerized mice without eliciting immune responses. Mice treated with IL-2 complexes mounted immune responses against both T-dependent and T-independent neoantigens, indicating that IL-2 complexes did not hamper the immune system for long. These results demonstrate the important role of Treg cells in suppressing anti-FVIII immune responses and the potential of developing Treg cell expansion therapies that induce long-term tolerance to FVIII. PMID:21468007

  14. 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).

  15. Uncovering Nuclear Pore Complexity with Innovation

    PubMed Central

    Adams, Rebecca L.; Wente, Susan R.

    2013-01-01

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

  16. 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.)

  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. 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...

  19. 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...

  20. 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.

  1. Colloid dispersion on the pore scale.

    PubMed

    Baumann, Thomas; Toops, Laura; Niessner, Reinhard

    2010-02-01

    Dispersion describes the spreading of a tracer or contaminant in an aquifer. Detailed knowledge of dispersion is the key to successful risk assessment in case of groundwater pollution or groundwater protection. The dispersion of colloids on the pore scale is controlled by flow velocity, ionic strength, colloid size, colloid concentration, and colloid-matrix interactions. The objective of this study was to provide quantitative data and to assess the scale dependency of colloid dispersion on the pore scale. The positions of carboxylated polystyrene microspheres (1 microm, 0.5 microm) were recorded during transport experiments in silicon micromodels with three pore topologies. The positions were combined into particle trajectories revealing the flow path of individual colloids. More than thousand trajectories were evaluated for each experiment to obtain the dispersivity of the colloids for flow distances between 10 and 1000 microm. All experiments were run at high Peclet numbers. The pore scale dispersivity was on the order of 8-30% of the flow distance with pure water, dependent on the heterogeneity of the pore topology. The dispersivity was positively correlated with the ionic strength and inversely correlated with the colloid size and the flow velocity. A coating of the micromodel surface with humic acid also increased dispersivity. The quantitative data set presented here supports the theoretical framework for colloid transport and allows to parametrize colloid transport on the pore scale.

  2. Colloid dispersion on the pore scale.

    PubMed

    Baumann, Thomas; Toops, Laura; Niessner, Reinhard

    2010-02-01

    Dispersion describes the spreading of a tracer or contaminant in an aquifer. Detailed knowledge of dispersion is the key to successful risk assessment in case of groundwater pollution or groundwater protection. The dispersion of colloids on the pore scale is controlled by flow velocity, ionic strength, colloid size, colloid concentration, and colloid-matrix interactions. The objective of this study was to provide quantitative data and to assess the scale dependency of colloid dispersion on the pore scale. The positions of carboxylated polystyrene microspheres (1 microm, 0.5 microm) were recorded during transport experiments in silicon micromodels with three pore topologies. The positions were combined into particle trajectories revealing the flow path of individual colloids. More than thousand trajectories were evaluated for each experiment to obtain the dispersivity of the colloids for flow distances between 10 and 1000 microm. All experiments were run at high Peclet numbers. The pore scale dispersivity was on the order of 8-30% of the flow distance with pure water, dependent on the heterogeneity of the pore topology. The dispersivity was positively correlated with the ionic strength and inversely correlated with the colloid size and the flow velocity. A coating of the micromodel surface with humic acid also increased dispersivity. The quantitative data set presented here supports the theoretical framework for colloid transport and allows to parametrize colloid transport on the pore scale. PMID:20042215

  3. 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.

  4. 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

  5. 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.

  6. Autographa californica Multiple Nucleopolyhedrovirus GP64 Protein: Roles of Histidine Residues in Triggering Membrane Fusion and Fusion Pore Expansion▿†

    PubMed Central

    Li, Zhaofei; Blissard, Gary W.

    2011-01-01

    The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) GP64 protein mediates membrane fusion during entry. Fusion results from a low-pH-triggered conformational change in GP64 and subsequent interactions with the membrane bilayers. The low-pH sensor and trigger of the conformational change are not known, but histidine residues are implicated because the pKa of histidine is near the threshold for triggering fusion by GP64. We used alanine substitutions to examine the roles of all individual and selected clusters of GP64 histidine residues in triggering and mediating fusion by GP64. Three histidine residues (H152, H155, and H156), located in fusion loop 2, were identified as important for membrane fusion. These three histidine residues were important for efficient pore expansion but were not required for the pH-triggered conformational change. In contrast, a cluster of three histidine residues (H245, H304, and H430) located near the base of the central coiled coil was identified as a putative sensor for low pH. Three alanine substitutions in cluster H245/H304/H430 resulted in dramatically reduced membrane fusion and the apparent loss of the prefusion conformation at neutral pH. Thus, the H245/H304/H430 cluster of histidines may function or participate as a pH sensor by stabilizing the prefusion structure of GP64. PMID:21937651

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. Accelerated expansion through interaction

    SciTech Connect

    Zimdahl, Winfried

    2009-05-01

    Interactions between dark matter and dark energy with a given equation of state are known to modify the cosmic dynamics. On the other hand, the strength of these interactions is subject to strong observational constraints. Here we discuss a model in which the transition from decelerated to accelerated expansion of the Universe arises as a pure interaction phenomenon. Various cosmological scenarios that describe a present stage of accelerated expansion, like the {lambda}CDM model or a (generalized) Chaplygin gas, follow as special cases for different interaction rates. This unifying view on the homogeneous and isotropic background level is accompanied by a non-adiabatic perturbation dynamics which can be seen as a consequence of a fluctuating interaction rate.

  13. 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.

  14. Tissue expansion in perspective.

    PubMed Central

    Sharpe, D. T.; Burd, R. M.

    1989-01-01

    Tissue expansion is a recent advance in skin cover technique. Its empirical use has enabled many previously difficult reconstructions to be completed without recourse to distant flaps. Its high complication rate and lack of basic scientific understanding at present restrict its use to selected cases, but the quality of repairs possible by this method encourage further serious scientific study. Images fig. 1 fig. 2 fig. 3 fig. 4 fig. 5 PMID:2589784

  15. Religiosity and the expansion of caregiver stress.

    PubMed

    Leblanc, A J; Driscoll, A K; Pearlin, L I

    2004-09-01

    We present a stress process framework as a model for understanding how religiosity may influence the expansion of stress. Survey data from informal caregivers to a spouse with Alzheimer's disease or a related dementia (n = 200) were analyzed to observe the relationships among three variables: (1) care-related stress, (2) religiosity, and (3) depression. This sample, which has a mean age of 73 years, demonstrates high rates of self-described religiosity, church attendance and frequency of prayer. Using these criteria, women and racial/ethnic minority caregivers are the most religious. In a series of multivariate analyses, we found strong evidence to suggest that there is an expansion of care-related stressors leading to depression in this sample. Religiosity, as measured here, appears to be largely unrelated to stress and stress expansion. We found no evidence to suggest that it moderates stress expansion. However, these data do suggest that one stressor--feelings of role overload--is correlated with greater levels of self-perceived religiosity, which among caregivers who have health problems of their own is associated with greater depressive symptomatology. Thus, for a sub-sample of these caregivers, we find weak evidence of a mediation effect wherein one subjective, non-organizational dimension of religiosity is a conduit of the harmful effects of stress (rather than a suppressor). Results and data limitations are discussed in relation to better assessing the role of religiosity and spirituality in the experience of the stress process.

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

    PubMed

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

    2011-04-01

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

  17. 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

  18. Epidermal Growth Factor Receptor-Mediated Membrane Type 1 Matrix Metalloproteinase Endocytosis Regulates the Transition Between Invasive Versus Expansive Growth of Ovarian Carcinoma Cells in Three-Dimensional Collagen

    PubMed Central

    Moss, Natalie M.; Liu, Yueying; Johnson, Jeff J.; Debiase, Philip; Jones, Jonathan; Hudson, Laurie G.; Munshi, H.G.; Stack, M. Sharon

    2010-01-01

    The epidermal growth factor receptor (EGFR) is overexpressed in ovarian carcinomas and promotes cellular responses that contribute to ovarian cancer pathobiology. In addition to modulation of mitogenic and motogenic behavior, emerging data identify EGFR activation as a novel mechanism for rapid modification of the cell surface proteome. The transmembrane collagenase membrane type 1 matrix metalloproteinase (MT1-MMP, MMP-14) is a major contributor to pericelluar proteolysis in the ovarian carcinoma microenvironment and is subjected to extensive post-translational regulation. In the present study, the contribution of EGFR activation to control of MT1-MMP cell surface dynamics was investigated. Unstimulated ovarian cancer cells display caveolar co-localization of EGFR and MT1-MMP whereas EGFR activation prompts internalization via distinct endocytic pathways. EGF treatment results in phosphorylation of the MT1-MMP cytoplasmic tail and cells expressing a tyrosine mutated form of MT1-MMP (MT1-MMP-Y573F) exhibit defective MT1-MMP internalization. As a result of sustained cell surface MT1-MMP activity, a phenotypic epithelial-mesenchymal transition is observed, characterized by enhanced migration and collagen invasion, whereas growth within three-dimensional collagen gels is inhibited. These data support an EGFR-dependent mechanism for regulation of the transition between invasive and expansive growth of ovarian carcinoma cells via modulation of MT1-MMP cell surface dynamics. PMID:19509114

  19. 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

  20. 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.

  1. 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.

  2. 1.9 μm superficially porous packing material with radially oriented pores and tailored pore size for ultra-fast separation of small molecules and biomolecules.

    PubMed

    Min, Yi; Jiang, Bo; Wu, Ci; Xia, Simin; Zhang, Xiaodan; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

    2014-08-22

    In this work, 1.9 μm reversed-phase packing materials with superficially porous structure were prepared to achieve the rapid and high efficient separation of peptides and proteins. The silica particles were synthesized via three steps, nonporous silica particle preparation by a modified seeded growth method, mesoporous shell formation by a one pot templated dissolution and redeposition strategy, and pore size expansion via acid-refluxing. By such a method, 1.9 μm superficially porous materials with 0.18 μm shell thickness and tailored pore diameter (10 nm, 15 nm) were obtained. After pore enlargement, the formerly dense arrays of mesoporous structure changed, the radially oriented pores dominated the superficially porous structure. The chromatographic performance of such particles was investigated after C18 derivatization. For packing materials with 1.9 μm diameter and 10 nm pore size, the column efficiency could reach 211,300 plates per m for naphthalene. To achieve the high resolution separation of peptides and proteins, particles with pore diameter of 15 nm were tailored, by which the baseline separation of 5 peptides and 5 intact proteins could be respectively achieved within 1 min, demonstrating the superiority in the high efficiency and high throughput analysis of biomolecules. Furthermore, BSA digests were well separated with peak capacity of 120 in 30 min on a 15 cm-long column. Finally, we compared our columns with a 1.7 μm Kinetex C18 column under the same conditions, our particles with 10nm pore size demonstrated similar performance for separation of the large intact proteins. Moreover, the particles with 15 nm pore size showed more symmetrical peaks for the separation of large proteins (BSA, OVA and IgG) and provided rapid separation of protein extracts from Escherichia coli in 5 min. All these results indicated that the synthesized 1.9 μm superficially porous silica packing materials would be promising in the ultra-fast and high

  3. Energetics of Transport through the Nuclear Pore Complex

    PubMed Central

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

    2016-01-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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…

  10. Tailoring particle translocation via dielectrophoresis in pore channels

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  11. 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

  12. 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

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

    PubMed

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

    2015-10-01

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

  14. 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.

  15. 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

  16. 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.

  17. Nuclear pores protect genome integrity by assembling a premitotic and Mad1-dependent anaphase inhibitor

    PubMed Central

    Rodriguez-Bravo, Veronica; Maciejowski, John; Corona, Jennifer; Buch, Håkon Kirkeby; Collin, Philippe; Kanemaki, Masato T.; Shah, Jagesh V.; Jallepalli, Prasad V.

    2014-01-01

    Summary The spindle assembly checkpoint (SAC) delays anaphase until all chromosomes are bi-oriented on the mitotic spindle. Under current models, unattached kinetochores transduce the SAC by catalyzing the intramitotic production of a diffusible APC/CCdc20 inhibitor. Here we show that nuclear pore complexes (NPCs) in interphase cells also function as scaffolds for anaphase-inhibitory signaling. This role is mediated by Mad1-Mad2 complexes tethered to the nuclear basket, which activate soluble Mad2 as a binding partner and inhibitor of Cdc20 in the cytoplasm. Displacing Mad1-Mad2 from nuclear pores accelerated anaphase onset, prevented effective correction of merotelic errors, and increased the threshold of kinetochore-dependent signaling needed to halt mitosis in response to spindle poisons. A heterologous Mad1-NPC tether restored Cdc20 inhibitor production and normal M phase control. We conclude that nuclear pores and kinetochores both emit “wait anaphase” signals that preserve genome integrity. PMID:24581499

  18. 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

  19. 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

  20. Operator product expansion algebra

    SciTech Connect

    Holland, Jan; Hollands, Stefan

    2013-07-15

    We establish conceptually important properties of the operator product expansion (OPE) in the context of perturbative, Euclidean φ{sup 4}-quantum field theory. First, we demonstrate, generalizing earlier results and techniques of hep-th/1105.3375, that the 3-point OPE, =Σ{sub C}C{sub A{sub 1A{sub 2A{sub 3}{sup C}}}}, usually interpreted only as an asymptotic short distance expansion, actually converges at finite, and even large, distances. We further show that the factorization identity C{sub A{sub 1A{sub 2A{sub 3}{sup B}}}}=Σ{sub C}C{sub A{sub 1A{sub 2}{sup C}}}C{sub CA{sub 3}{sup B}} is satisfied for suitable configurations of the spacetime arguments. Again, the infinite sum is shown to be convergent. Our proofs rely on explicit bounds on the remainders of these expansions, obtained using refined versions, mostly due to Kopper et al., of the renormalization group flow equation method. These bounds also establish that each OPE coefficient is a real analytic function in the spacetime arguments for non-coinciding points. Our results hold for arbitrary but finite loop orders. They lend support to proposals for a general axiomatic framework of quantum field theory, based on such “consistency conditions” and akin to vertex operator algebras, wherein the OPE is promoted to the defining structure of the theory.

  1. 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.

  2. 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.

  3. 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.

  4. Metalloprotein design using genetic code expansion.

    PubMed

    Hu, Cheng; Chan, Sunney I; Sawyer, Elizabeth B; Yu, Yang; Wang, Jiangyun

    2014-09-21

    More than one third of all proteins are metalloproteins. They catalyze important reactions such as photosynthesis, nitrogen fixation and CO2 reduction. Metalloproteins such as the olfactory receptors also serve as highly elaborate sensors. Here we review recent developments in functional metalloprotein design using the genetic code expansion approach. We show that, through the site-specific incorporation of metal-chelating unnatural amino acids (UAAs), proton and electron transfer mediators, and UAAs bearing bioorthogonal reaction groups, small soluble proteins can recapitulate and expand the important functions of complex metalloproteins. Further developments along this route may result in cell factories and live-cell sensors with unprecedented efficiency and selectivity.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. Pore-scale studies of gas shale

    NASA Astrophysics Data System (ADS)

    Silin, D.; Ajo Franklin, J. B.; Cabrini, S.; Kneafsey, T. J.; MacDowell, A.; Nico, P. S.; Radmilovic, V.

    2010-12-01

    Natural gas is the cleanest hydrocarbon fuel. The contribution of natural gas produced from shale to the United States energy portfolio has been steadily increasing over the past several years. The projections into the coming decades expect this trend to remain stable. Although the advancements in well stimulation technologies have made it possible to convert huge resources into recoverable reserves, the mechanisms of gas recovery from these practically impermeable rocks are not yet fully understood. We employed the powerful imaging facilities at Lawrence Berkeley National Laboratory to gain insights into the pore geometry and structure of shale at micron and submicron scales. The X-ray micro-tomography facility at the Advanced Light Source produces 3D reconstructions of the pore space at resolutions approaching one micron. The Focused Ion-Beam sequential milling and imaging at the Molecular Foundry and National Center for Electron Microscopy allows for 3D shale structure and mineral composition at a resolution on the order of ten nanometers. We find that even a miniscule volume of reservoir shale includes an extremely rich diversity of minerals and geometries. Organic matter is consistently present as pore filling among solid grains. Some samples show a connected networks of pores in kerogen, apparently indicating its thermal maturity. Understanding the features controlling gas flow will help increase the ultimate recovery and extend the productive lifetime of a given well.

  12. 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

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

    PubMed Central

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

    2010-01-01

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

  14. 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

  15. 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

  16. Tracking S4 movement by gating pore currents in the bacterial sodium channel NaChBac.

    PubMed

    Gamal El-Din, Tamer M; Scheuer, Todd; Catterall, William A

    2014-08-01

    Voltage-gated sodium channels mediate the initiation and propagation of action potentials in excitable cells. Transmembrane segment S4 of voltage-gated sodium channels resides in a gating pore where it senses the membrane potential and controls channel gating. Substitution of individual S4 arginine gating charges (R1-R3) with smaller amino acids allows ionic currents to flow through the mutant gating pore, and these gating pore currents are pathogenic in some skeletal muscle periodic paralysis syndromes. The voltage dependence of gating pore currents provides information about the transmembrane position of the gating charges as S4 moves in response to membrane potential. Here we studied gating pore current in mutants of the homotetrameric bacterial sodium channel NaChBac in which individual arginine gating charges were replaced by cysteine. Gating pore current was observed for each mutant channel, but with different voltage-dependent properties. Mutating the first (R1C) or second (R2C) arginine to cysteine resulted in gating pore current at hyperpolarized membrane potentials, where the channels are in resting states, but not at depolarized potentials, where the channels are activated. Conversely, the R3C gating pore is closed at hyperpolarized membrane potentials and opens with channel activation. Negative conditioning pulses revealed time-dependent deactivation of the R3C gating pore at the most hyperpolarized potentials. Our results show sequential voltage dependence of activation of gating pore current from R1 to R3 and support stepwise outward movement of the substituted cysteines through the narrow portion of the gating pore that is sealed by the arginine side chains in the wild-type channel. This pattern of voltage dependence of gating pore current is consistent with a sliding movement of the S4 helix through the gating pore. Through comparison with high-resolution models of the voltage sensor of bacterial sodium channels, these results shed light on the

  17. 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.

  18. Optical imaging. Expansion microscopy.

    PubMed

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

    2015-01-30

    In optical microscopy, fine structural details are resolved by using refraction to magnify images of a specimen. We discovered 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 superresolution microscopy with diffraction-limited microscopes. We demonstrate ExM with apparent ~70-nanometer lateral resolution in both cultured cells and brain tissue, performing three-color superresolution imaging of ~10(7) cubic micrometers of the mouse hippocampus with a conventional confocal microscope.

  19. 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

  20. 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.

  1. 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

  2. Fabrication and electrical characterization of a pore-cavity-pore device

    NASA Astrophysics Data System (ADS)

    Pedone, D.; Langecker, M.; Münzer, A. M.; Wei, R.; Nagel, R. D.; Rant, U.

    2010-11-01

    We present a solid state nanopore device structure comprising two nanopores which are stacked above each other and connected via a pyramidal cavity of 10 fl volume. The process of fabrication of the pore-cavity-pore device (PCP) relies on the formation of one pore in a Si3N4 membrane by electron beam lithography, while the other pore is chemically etched into the Si carrier by a feedback controlled process. The dimensions of the two nanopores as well as the cavity can be adjusted independently, which is confirmed by transmission electron microscopy. The PCP device is characterized with respect to its electrical properties, including noise analysis and impedance spectroscopy. An equivalent circuit model is identified and resistance, capacitance, and dielectric loss factors are obtained. Potential and electric field distributions inside the electrically biased device are simulated by finite element methods. The low noise characteristics of the PCP device (comparable to a single solid state nanopore) make it suitable for the stochastic sensing of single molecules; moreover, the pore-cavity-pore architecture allows for novel kinds of experiments including the trapping of single nano-objects and single molecule time-of-flight measurements.

  3. 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.

  4. 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

  5. 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

  6. 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

  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. The effective pore radius of screen wicks

    SciTech Connect

    Imura, Hideaki; Kozai, Hiroaki; Ikeda, Yuji

    1994-10-01

    The effective pore radius in screen-wick heat pipes was investigated, which is very important for the prediction of maximum heat transfer rates due to capillary limitation. An equation for the effective pore radius of the screen wicks was derived based on the model of the screen geometry. The capillary height for stainless steel and phosphor bronze screens was measured using water, ethyl alcohol, and Freon 113 as the test liquids. The effect of surface treatment (acid cleaning and oxidation) on the capillary height was also examined. From the comparison of the experimental data for water and ethyl alcohol with those for Freon 113, it was indicated that the contact angle was 24.2{degree} for water and 16.9{degree} for ethyl alcohol. Consequently, it was found that the effective pore radius of the screen wicks could be predicted fairly well from the expression presented in this study, and that the contact angle should be taken into consideration to evaluate the maximum capillary pressure accurately.

  9. 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.

  10. On the Bantu expansion.

    PubMed

    Rowold, Daine J; Perez-Benedico, David; Stojkovic, Oliver; Garcia-Bertrand, Ralph; Herrera, Rene J

    2016-11-15

    Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups. PMID:27451076

  11. On the Bantu expansion.

    PubMed

    Rowold, Daine J; Perez-Benedico, David; Stojkovic, Oliver; Garcia-Bertrand, Ralph; Herrera, Rene J

    2016-11-15

    Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.

  12. 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...

  13. 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.

  14. 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

  15. 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

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Or, D.; Moebius, F.

    2014-12-01

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

  18. 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.

  19. 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

  20. 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

  1. Unraveling the potential and pore-size dependent capacitance of slit-shaped graphitic carbon pores in aqueous electrolytes.

    PubMed

    Kalluri, R K; Biener, M M; Suss, M E; Merrill, M D; Stadermann, M; Santiago, J G; Baumann, T F; Biener, J; Striolo, A

    2013-02-21

    Understanding and leveraging physicochemical processes at the pore scale are believed to be essential to future performance improvements of supercapacitors and capacitive desalination (CD) cells. Here, we report on a combination of electrochemical experiments and fully atomistic simulations to study the effect of pore size and surface charge density on the capacitance of graphitic nanoporous carbon electrodes. Specifically, we used cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) to study the effect of potential and pore size on the capacitance of nanoporous carbon foams. Molecular dynamics simulations were performed to study the pore-size dependent accumulation of aqueous electrolytes in slit-shaped graphitic carbon pores of different widths (0.65 to 1.6 nm). Experimentally, we observe a pronounced increase of the capacitance of sub-nm pores as the applied potential window gets wider, from a few F g(-1) for narrow potential ranges (-0.3 to 0.3 V vs. Ag/AgCl) to ~40 F g(-1) for wider potential windows (-0.9 V to 0.9 V vs. Ag/AgCl). By contrast, the capacitance of wider pores does not depend significantly on the applied potential window. Molecular dynamics simulations confirm that the penetration of ions into pores becomes more difficult with decreasing pore width and increasing strength of the hydration shell. Consistent with our experimental results, we observe a pore- and ion-size dependent threshold-like charging behavior when the pore width becomes comparable to the size of the hydrated ion (0.65 nm pores for Na(+) and 0.79 nm pores for Cl(-) ions). The observed pore-size and potential dependent accumulation of ions in slit-shaped carbon pores can be explained by the hydration structure of the ions entering the charged pores. The results are discussed in view of their effect on energy-storage and desalination efficiency.

  2. 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.

  3. 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.

  4. Genus expansion of HOMFLY polynomials

    NASA Astrophysics Data System (ADS)

    Mironov, A. D.; Morozov, A. Yu.; Sleptsov, A. V.

    2013-11-01

    In the planar limit of the' t Hooft expansion, the Wilson-loop vacuum average in the three-dimensional Chern-Simons theory (in other words, the HOMFLY polynomial) depends very simply on the representation (Young diagram), HR(A|q)|q=1 = (σ1(A)|R|. As a result, the (knot-dependent) Ooguri-Vafa partition function becomes a trivial τ -function of the Kadomtsev-Petviashvili hierarchy. We study higher-genus corrections to this formula for HR in the form of an expansion in powers of z = q - q-1. The expansion coefficients are expressed in terms of the eigenvalues of cut-and-join operators, i.e., symmetric group characters. Moreover, the z-expansion is naturally written in a product form. The representation in terms of cut-and-join operators relates to the Hurwitz theory and its sophisticated integrability. The obtained relations describe the form of the genus expansion for the HOMFLY polynomials, which for the corresponding matrix model is usually given using Virasoro-like constraints and the topological recursion. The genus expansion differs from the better-studied weak-coupling expansion at a finite number N of colors, which is described in terms of Vassiliev invariants and the Kontsevich integral.

  5. 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.

  6. Simulations of Membrane-Disrupting Peptides I: Alamethicin Pore Stability and Spontaneous Insertion.

    PubMed

    Perrin, B Scott; Pastor, Richard W

    2016-09-20

    An all-atom molecular dynamics simulation of the archetype barrel-stave alamethicin (alm) pore in a 1,2-dioleoyl-sn-glycero-3-phosphocholine bilayer at 313 K indicates that ∼7 μs is required for equilibration of a preformed 6-peptide pore; the pore remains stable for the duration of the remaining 7 μs of the trajectory, and the structure factors agree well with experiment. A 5 μs simulation of 10 surface-bound alm peptides shows significant peptide unfolding and some unbinding, but no insertion. Simulations at 363 and 413 K with a -0.2 V electric field yield peptide insertion in 1 μs. Insertion is initiated by the folding of residues 3-11 into an α-helix, and mediated by membrane water or by previously inserted peptides. The stability of five alm pore peptides at 413 K with a -0.2 V electric field demonstrates a significant preference for a transmembrane orientation. Hence, and in contrast to the cationic antimicrobial peptide described in the following article, alm shows a strong preference for the inserted over the surface-bound state. PMID:27653483

  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. Precipitation in pores: A geochemical frontier

    DOE PAGESBeta

    Stack, Andrew G.

    2015-07-29

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

  9. 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

  10. 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

  11. Comparison of unimodal versus bimodal pore catalysts in residues hydrotreating

    SciTech Connect

    Absi-Halabi, M.; Stanislaus, A.; Al-Zaid, H.

    1994-12-31

    Catalyst pore structure is a critical factor influencing the performance of residues hydroprocessing catalysts. The effect is reflected in both hydrodesulfurization activity of the catalyst and its rate of deactivation. In this paper, the pore size distributions of two categories of catalysts, unimodal and bimodal, were systematically varied. Performance evaluation tests in a fixed bed reactor using vacuum residues under conditions comparable to typical refinery operations were conducted. Two series of unimodal and bimodal catalyst extrudates were prepared starting from boehmite gel, whereby the pore structure was systematically varied using hydrothermal treatment and organic additives. For the unimodal catalysts, the pore maxima ranged between 50 and 500 {angstrom} with 70--80% of the pore volume in the desired pore diameter range. The bimodal catalysts had narrow pores with pore diameters less than 100 {angstrom} and wide pres with pore diameter around 5,000 {angstrom}. For bimodal catalyst, an increase in the average wide pore diameter, while maintaining the narrow pore constant, had no significant effect on the catalyst performance. For monomodal catalyst, the activity of the catalyst was noted to have an optimum between 150--350 {angstrom} diameter. Furthermore, the performance of the catalyst concerning its desulfurization activity and deactivation was superior to that of the bimodal catalysts.

  12. 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

  13. 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.

  14. Bacterial accumulation mediated by flow compression-expansion

    NASA Astrophysics Data System (ADS)

    Miño, Gastón L.; Altshuler, Ernesto; Lindner, Anke; Stocker, Roman; Condat, Carlos A.; Banchio, Adolfo J.; Marconi, Veronica I.; Clément, Eric

    2014-11-01

    Swimming bacteria can be concentrated using a suitable microfluidic device. The combination of flow rate and surface shape can have significant impact on the microorganisms' behavior. In those processes rheotaxis, accumulation caused by ratchets and even attachment to surfaces leading biofilm formation can be observed. Under these conditions, the transport of the active suspension is deeply modified, and differs significantly from passive suspensions. In this work, we present experimental evidence of Escherichia coli suspension flowing in a straight channel with a funnel-like constriction in the middle. This constriction is characterized by the aperture (wf) and its angle (Θf). We explore how the modification of wf and Θf affects the accumulation of bacteria in the channel. Concentrations of bacteria passing the constriction were observed for all the cases. However, the range of the flow rate that produced such accumulation varied with the geometry. In order to obtain a better understanding of this phenomenon, experiments are compared with a simple phenomenological model.

  15. Micromechanics of expansive mechanisms in expansive cement concretes

    NASA Astrophysics Data System (ADS)

    Cohen, M. D.

    The kinetics of hydration were studied by monitoring the presence of various compounds by X-ray diffractometer, a chemical extraction method, and scanning electron microscope. These studies indicated that the rates of depletion of the expanding particles and sulfates are higher in the finer blends, which is why expansion stops earlier in these blends. It is shown that the double curvature phenomenon (strength-drop and sudden increase in the rate of expansion) is caused by mechanical failure (e.g., microcracking) of the matrix surrounding the expanding particles that are producing ettringite crystals. The theory of protective and partial protective coating is reviewed. A hypothesis is introduced which assumes that monosulfate is not formed immediately when ettringite stops forming but is preceded by an intermediate phase. Shrinkage studies show that expansive cements shrink more than portland cements. The results of these studies were used to develop a modified model of the expansive process. It was shown theoretically that the time of expansion is inversely proportional to the surface area of the expansive clinker and directly proportional to the amount of sulfate used.

  16. 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.

  17. 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

  18. 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

  19. Structure of the N-terminal domain of the protein Expansion: an 'Expansion' to the Smad MH2 fold.

    PubMed

    Beich-Frandsen, Mads; Aragón, Eric; Llimargas, Marta; Benach, Jordi; Riera, Antoni; Pous, Joan; Macias, Maria J

    2015-04-01

    Gene-expression changes observed in Drosophila embryos after inducing the transcription factor Tramtrack led to the identification of the protein Expansion. Expansion contains an N-terminal domain similar in sequence to the MH2 domain characteristic of Smad proteins, which are the central mediators of the effects of the TGF-β signalling pathway. Apart from Smads and Expansion, no other type of protein belonging to the known kingdoms of life contains MH2 domains. To compare the Expansion and Smad MH2 domains, the crystal structure of the Expansion domain was determined at 1.6 Å resolution, the first structure of a non-Smad MH2 domain to be characterized to date. The structure displays the main features of the canonical MH2 fold with two main differences: the addition of an α-helical region and the remodelling of a protein-interaction site that is conserved in the MH2 domain of Smads. Owing to these differences, to the new domain was referred to as Nα-MH2. Despite the presence of the Nα-MH2 domain, Expansion does not participate in TGF-β signalling; instead, it is required for other activities specific to the protostome phyla. Based on the structural similarities to the MH2 fold, it is proposed that the Nα-MH2 domain should be classified as a new member of the Smad/FHA superfamily.

  20. Structural alterations, pore generation, and deacetylation of α- and β-chitin submitted to steam explosion.

    PubMed

    Tan, Too Shen; Chin, Hui Yen; Tsai, Min-Lang; Liu, Chao-Lin

    2015-05-20

    The purpose of this study was to use an environmentally friendly steam explosion method to achieve α- and β-chitin structural alterations, pore generation, and deacetylation, enhancing the degree of deacetylation (DD) in chitin and extending its applications. The samples of α- and β-chitin possessing various moisture contents that were exploded at 9 kg/cm(2) exhibited higher DDs, lower densities, lower crystallinity and more porous structures compared to unexploded chitin. After explosion, β-chitin exhibited a larger expansion ratio, lower crystallinity and contained a larger proportion of small-sized particles compared to α-chitin. The highest DD values of exploded α- and β-chitin with 75% moisture content were 42.9% and 43.7%, respectively. The exploded chitin samples with lower moisture content exhibited lower DDs, densities, crystallinity indices, smaller particle sizes, and higher expansion ratios than the chitin samples with higher moisture content. The chitin samples with lower moisture content also contained larger and more numerous pores.

  1. Range expansion of heterogeneous populations.

    PubMed

    Reiter, Matthias; Rulands, Steffen; Frey, Erwin

    2014-04-11

    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. PMID:24766021

  2. 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.

  3. 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.

  4. Computational modeling of electrokinetic transport in random networks of micro-pores and nano-pores

    NASA Astrophysics Data System (ADS)

    Alizadeh, Shima; Mani, Ali

    2014-11-01

    A reduced order model has been developed to study the nonlinear electrokinetic behaviors emerging in the transport of ionic species through micro-scale and nano-scale porous media. In this approach a porous structure is modeled as a network of long and thin pores. By assuming transport equilibrium in the thin dimensions for each pore, a 1D transport equation is developed in the longitudinal direction covering a wide range of conditions including extreme limits of thick and thin electric double layers. This 1D model includes transport via diffusion, electromigration and wide range of advection mechanisms including pressure driven flow, electroosmosis, and diffusion osmosis. The area-averaged equations governing the axial transport from different pores are coupled at the pore intersections using the proper conservation laws. Moreover, an asymptotic treatment has been included in order to remove singularities in the limit of small concentration. The proposed method provides an efficient framework for insightful simulations of porous electrokinetic systems with applications in water desalination and energy storage. PhD student in Mechanical Engineering, Stanford University. She received her Master's degree in Mechanical Engineering from Stanford at 2013. Her research interests include CFD, high performance computing, and optimization.

  5. 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.

  6. 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.

  7. Primary Biliary Cirrhosis and the Nuclear Pore Complex

    PubMed Central

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

    2012-01-01

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

  8. Two-pore Domain Potassium Channels in Astrocytes

    PubMed Central

    Ryoo, Kanghyun

    2016-01-01

    Two-pore domain potassium (K2P) channels have a distinct structure and channel properties, and are involved in a background K+ current. The 15 members of the K2P channels are identified and classified into six subfamilies on the basis of their sequence similarities. The activity of the channels is dynamically regulated by various physical, chemical, and biological effectors. The channels are expressed in a wide variety of tissues in mammals in an isoform specific manner, and play various roles in many physiological and pathophysiological conditions. To function as channels, the K2P channels form dimers, and some isoforms form heterodimers that provide diversity in channel properties. In the brain, TWIK1, TREK1, TREK2, TRAAK, TASK1, and TASK3 are predominantly expressed in various regions, including the cerebral cortex, dentate gyrus, CA1-CA3, and granular layer of the cerebellum. TWIK1, TREK1, and TASK1 are highly expressed in astrocytes, where they play specific cellular roles. Astrocytes keep leak K+ conductance, called the passive conductance, which mainly involves TWIK1-TREK1 heterodimeric channel. TWIK1 and TREK1 also mediate glutamate release from astrocytes in an exocytosis-independent manner. The expression of TREK1 and TREK2 in astrocytes increases under ischemic conditions, that enhance neuroprotection from ischemia. Accumulated evidence has indicated that astrocytes, together with neurons, are involved in brain function, with the K2P channels playing critical role in these astrocytes. PMID:27790056

  9. Nuclear pore ion channel activity in live syncytial nuclei.

    PubMed

    Bustamante, Jose Omar

    2002-05-01

    Nuclear pore complexes (NPCs) are important nanochannels for the control of gene activity and expression. Most of our knowledge of NPC function has been derived from isolated nuclei and permeabilized cells in cell lysates/extracts. Since recent patch-clamp work has challenged the dogma that NPCs are freely permeable to small particles, a preparation of isolated living nuclei in their native liquid environment was sought and found: the syncytial nuclei in the water of the coconut Cocos nucifera. These nuclei have all properties of NPC-mediated macromolecular transport (MMT) and express foreign green fluorescent protein (GFP) plasmids. They display chromatin movement, are created by particle aggregation or by division, can grow by throwing filaments to catch material, etc. This study shows, for the first time, that living NPCs engaged in MMT do not transport physiological ions - a phenomenon that explains observations of nucleocytoplasmic ion gradients. Since coconuts are inexpensive (less than US$1/nut per litre), this robust preparation may contribute to our understanding of NPCs and cell nucleus and to the development of biotechnologies for the production of DNA, RNA and proteins.

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

    PubMed

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

    2014-06-17

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2015-11-03

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

  13. Cytosol-dependent membrane fusion in ER, nuclear envelope and nuclear pore assembly: biological implications.

    PubMed

    Rafikova, Elvira R; Melikov, Kamran; Chernomordik, Leonid V

    2010-01-01

    Endoplasmic reticulum and nuclear envelope rearrangements after mitosis are often studied in the reconstitution system based on Xenopus egg extract. In our recent work we partially replaced the membrane vesicles in the reconstitution mix with protein-free liposomes to explore the relative contributions of cytosolic and transmembrane proteins. Here we discuss our finding that cytosolic proteins mediate fusion between membranes lacking functional transmembrane proteins and the role of membrane fusion in endoplasmic reticulum and nuclear envelope reorganization. Cytosol-dependent liposome fusion has allowed us to restore, without adding transmembrane nucleoporins, functionality of nuclear pores, their spatial distribution and chromatin decondensation in nuclei formed at insufficient amounts of membrane material and characterized by only partial decondensation of chromatin and lack of nuclear transport. Both the mechanisms and the biological implications of the discovered coupling between spatial distribution of nuclear pores, chromatin decondensation and nuclear transport are discussed.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. THE SIZE OF SONOPORATION PORES ON THE CELL MEMBRANE

    PubMed Central

    Zhou, Yun; Kumon, Ronald E.; Cui, Jianmin; Deng, Cheri X.

    2009-01-01

    Sonoporation uses ultrasound (US) to generate transient non-selective pores on the cell membrane and has been exploited as a non-viral intracellular drug and gene delivery strategy. The pore size determines the size of agents that can be delivered into the cytoplasm using the technique. However, measurements of the dynamic, submicron-scale pores have not been readily available. Electron microscopy or atomic force microscopy has been used to gauge pore size but such techniques are intrinsically limited to post US measurements that may not accurately reveal the relevant information. As previously demonstrated, changes of the transmembrane current (TMC) of a single cell under voltage clamp can be used for monitoring sonoporation in real time. Because the TMC is related to the diffusion of ions through the pores on the membrane, it can potentially provide information of the pore size generated in sonoporation. Using Xenopus laevis oocytes as the model system, the TMC of single cells under voltage clamp was measured in real time to assess formation of pores on the membrane in sonoporation. The cells were exposed to US (0.2 s, 0.3 MPa, 1.075 MHz) in the presence of Definity™ microbubbles. Experiments were designed to obtain the TMC corresponding to a single pore on the membrane. The size of the pores was estimated from an electro-diffusion model that relates the TMC with pore size from the ion transport through the pores on the membrane. The mean radius of single pores was determined to be 110 nm with standard deviation of 40 nm. This study reports the first results of pore size from the TMC measured using the voltage clamp technique. PMID:19647924

  19. A Stereolithography Pore-Throat Model

    NASA Astrophysics Data System (ADS)

    Crandall, D.; Ahmadi, G.; Ferer, M.; Smith, D. H.

    2007-12-01

    A new experimental, heterogeneous pore-throat model has been designed and fabricated using stereolithography (SL). In SL production, a laser cures a thin layer of photo-sensitive resin on the surface of a vat of liquid resin; a moveable platform then submerges the cured layer and a new layer is cured on top of the previous one, creating a physical model from a computer generated model. This layered fabrication of a computer generated model has enabled the production of an experimental porous medium with improved fluid resistance properties, as compared to previously studied, constant-height etched cells. A uniform distribution of throat widths was randomly placed throughout the pore-throat matrix and the throat height of each throat was assigned to increase the range of viscous and capillary resistances within the physical model. This variation in both throat height and width generated a porous medium with fairly low porosity (43%), permeability (~400 D), and wide range of geometric resistance properties. Experimental, two-phase immiscible drainage studies in the porous flowcell were performed. Analysis of the captured images was performed with open-source image processing software. These analysis techniques utilized the capability of both ImageJ and the Gnu Image Manipulation Program to be customized with ancillary codes. This enabled batch procedures to be created that converted the original grey-scale bitmaps to binary data sets, which were then analyzed with in-house codes. The fractal dimension, Df, (measured with box-counting) and percent saturation of these experiments were calculated and shown to compare favorably to fractal predictions and previous flowcell studies. Additionally, using the computer generated pore-throat geometry, a computational fluid dynamics model of two- phase flow through the porous medium was created. This model was created using FLUENT code and the Volume of Fluid method. The percent saturation of the less-viscous invading fluid

  20. Global Functional Analyses of Cellular Responses to Pore-Forming Toxins

    PubMed Central

    Kao, Cheng-Yuan; 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.

    2011-01-01

    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

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

    PubMed Central

    1990-01-01

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

  2. 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.

  3. 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.

  4. Viruses Challenge Selectivity Barrier of Nuclear Pores

    PubMed Central

    Labokha, Aksana A.; Fassati, Ariberto

    2013-01-01

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

  5. 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.

  6. Active genes at the nuclear pore complex.

    PubMed

    Taddei, Angela

    2007-06-01

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

  7. Stacking of silicon pore optics for IXO

    NASA Astrophysics Data System (ADS)

    Collon, Maximilien J.; Guenther, Ramses; Ackermann, Marcelo; Partapsing, Rakesh; Kelly, Chris; Beijersbergen, Marco W.; Bavdaz, Marcos; Wallace, Kotska; Olde Riekerink, Mark; Mueller, Peter; Krumrey, Michael

    2009-08-01

    Silicon pore optics is a technology developed to enable future large area X-ray telescopes, such as the International Xray Observatory (IXO), a candidate mission in the ESA Space Science Programme 'Cosmic Visions 2015-2025'. IXO uses nested mirrors in Wolter-I configuration to focus grazing incidence X-ray photons on a detector plane. The IXO mirrors will have to meet stringent performance requirements including an effective area of ~3 m2 at 1.25 keV and ~1 m2 at 6 keV and angular resolution better than 5 arc seconds. To achieve the collecting area requires a total polished mirror surface area of ~1300 m2 with a surface roughness better than 0.5 nm rms. By using commercial high-quality 12" silicon wafers which are diced, structured, wedged, coated, bent and stacked the stringent performance requirements of IXO can be attained without any costly polishing steps. Two of these stacks are then assembled into a co-aligned mirror module, which is a complete X-ray imaging system. Included in the mirror module are the isostatic mounting points, providing a reliable interface to the telescope. Hundreds of such mirror modules are finally integrated into petals, and mounted onto the spacecraft to form an X-ray optic of four meters in diameter. In this paper we will present the silicon pore optics assembly process and latest X-ray results. The required metrology is described in detail and experimental methods are shown, which allow to assess the quality of the HPOs during production and to predict the performance when measured in synchrotron radiation facilities.

  8. 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

  9. Application of real rock pore-throat statistics to a regular pore network model

    SciTech Connect

    Sarker, M.R.; McIntyre, D.; Ferer, M.; Siddigui, S.; Bromhal. G.

    2011-01-01

    This work reports the application of real rock statistical data to a previously developed regular pore network model in an attempt to produce an accurate simulation tool with low computational overhead. A core plug from the St. Peter Sandstone formation in Indiana was scanned with a high resolution micro CT scanner. The pore-throat statistics of the three-dimensional reconstructed rock were extracted and the distribution of the pore-throat sizes was applied to the regular pore network model. In order to keep the equivalent model regular, only the throat area or the throat radius was varied. Ten realizations of randomly distributed throat sizes were generated to simulate the drainage process and relative permeability was calculated and compared with the experimentally determined values of the original rock sample. The numerical and experimental procedures are explained in detail and the performance of the model in relation to the experimental data is discussed and analyzed. Petrophysical properties such as relative permeability are important in many applied fields such as production of petroleum fluids, enhanced oil recovery, carbon dioxide sequestration, ground water flow, etc. Relative permeability data are used for a wide range of conventional reservoir engineering calculations and in numerical reservoir simulation. Two-phase oil water relative permeability data are generated on the same core plug from both pore network model and experimental procedure. The shape and size of the relative permeability curves were compared and analyzed and good match has been observed for wetting phase relative permeability but for non-wetting phase, simulation results were found to be deviated from the experimental ones. Efforts to determine petrophysical properties of rocks using numerical techniques are to eliminate the necessity of regular core analysis, which can be time consuming and expensive. So a numerical technique is expected to be fast and to produce reliable results

  10. Application of real rock pore-threat statistics to a regular pore network model

    SciTech Connect

    Rakibul, M.; Sarker, H.; McIntyre, D.; Ferer, M.; Siddiqui, S.; Bromhal. G.

    2011-01-01

    This work reports the application of real rock statistical data to a previously developed regular pore network model in an attempt to produce an accurate simulation tool with low computational overhead. A core plug from the St. Peter Sandstone formation in Indiana was scanned with a high resolution micro CT scanner. The pore-throat statistics of the three-dimensional reconstructed rock were extracted and the distribution of the pore-throat sizes was applied to the regular pore network model. In order to keep the equivalent model regular, only the throat area or the throat radius was varied. Ten realizations of randomly distributed throat sizes were generated to simulate the drainage process and relative permeability was calculated and compared with the experimentally determined values of the original rock sample. The numerical and experimental procedures are explained in detail and the performance of the model in relation to the experimental data is discussed and analyzed. Petrophysical properties such as relative permeability are important in many applied fields such as production of petroleum fluids, enhanced oil recovery, carbon dioxide sequestration, ground water flow, etc. Relative permeability data are used for a wide range of conventional reservoir engineering calculations and in numerical reservoir simulation. Two-phase oil water relative permeability data are generated on the same core plug from both pore network model and experimental procedure. The shape and size of the relative permeability curves were compared and analyzed and good match has been observed for wetting phase relative permeability but for non-wetting phase, simulation results were found to be deviated from the experimental ones. Efforts to determine petrophysical properties of rocks using numerical techniques are to eliminate the necessity of regular core analysis, which can be time consuming and expensive. So a numerical technique is expected to be fast and to produce reliable results

  11. 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.

  12. 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.

  13. A lipocentric view of peptide-induced pores.

    PubMed

    Fuertes, Gustavo; Giménez, Diana; Esteban-Martín, Santi; Sánchez-Muñoz, Orlando L; Salgado, Jesús

    2011-04-01

    Although lipid membranes serve as effective sealing barriers for the passage of most polar solutes, nonmediated leakage is not completely improbable. A high activation energy normally keeps unassisted bilayer permeation at a very low frequency, but lipids are able to self-organize as pores even in peptide-free and protein-free membranes. The probability of leakage phenomena increases under conditions such as phase coexistence, external stress or perturbation associated to binding of nonlipidic molecules. Here, we argue that pore formation can be viewed as an intrinsic property of lipid bilayers, with strong similarities in the structure and mechanism between pores formed with participation of peptides, lipidic pores induced by different types of stress, and spontaneous transient bilayer defects driven by thermal fluctuations. Within such a lipocentric framework, amphipathic peptides are best described as pore-inducing rather than pore-forming elements. Active peptides bound to membranes can be understood as a source of internal surface tension which facilitates pore formation by diminishing the high activation energy barrier. This first or immediate action of the peptide has some resemblance to catalysis. However, the presence of membrane-active peptides has the additional effect of displacing the equilibrium towards the pore-open state, which is then maintained over long times, and reducing the size of initial individual pores. Thus, pore-inducing peptides, regardless of their sequence and oligomeric organization, can be assigned a double role of increasing the probability of pore formation in membranes to high levels as well as stabilizing these pores after they appear.

  14. On genus expansion of superpolynomials

    NASA Astrophysics Data System (ADS)

    Mironov, Andrei; Morozov, Alexei; Sleptsov, Alexei; Smirnov, Andrey

    2014-12-01

    Recently it was shown that the (Ooguri-Vafa) generating function of HOMFLY polynomials is the Hurwitz partition function, i.e. that the dependence of the HOMFLY polynomials on representation R is naturally captured by symmetric group characters (cut-and-join eigenvalues). The genus expansion and expansion through Vassiliev invariants explicitly demonstrate this phenomenon. In the present paper we claim that the superpolynomials are not functions of such a type: symmetric group characters do not provide an adequate linear basis for their expansions. Deformation to superpolynomials is, however, straightforward in the multiplicative basis: the Casimir operators are β-deformed to Hamiltonians of the Calogero-Moser-Sutherland system. Applying this trick to the genus and Vassiliev expansions, we observe that the deformation is fully straightforward only for the thin knots. Beyond the family of thin knots additional algebraically independent terms appear in the Vassiliev and genus expansions. This can suggest that the superpolynomials do in fact contain more information about knots than the colored HOMFLY and Kauffman polynomials. However, even for the thin knots the beta-deformation is non-innocent: already in the simplest examples it seems inconsistent with the positivity of colored superpolynomials in non-(anti)symmetric representations, which also happens in I. Cherednik's (DAHA-based) approach to the torus knots.

  15. The spatial, temporal and contrast properties of expansion and rotation flight optomotor responses in Drosophila.

    PubMed

    Duistermars, Brian J; Chow, Dawnis M; Condro, Michael; Frye, Mark A

    2007-09-01

    Fruit flies respond to panoramic retinal patterns of visual expansion with robust steering maneuvers directed away from the focus of expansion to avoid collisions and maintain an upwind flight posture. Panoramic rotation elicits comparatively weak syndirectional steering maneuvers, which also maintain visual stability. Full-field optic flow patterns like expansion and rotation are elicited by distinct flight maneuvers such as body translation during straight flight or body rotation during hovering, respectively. Recent analyses suggest that under some experimental conditions the rotation optomotor response reflects the linear sum of different expansion response components. Are expansion and rotation-mediated visual stabilization responses part of a single optomotor response subserved by a neural circuit that is differentially stimulated by the two flow fields, or rather do the two behavioral responses reflect two distinct control systems? Guided by the principle that the properties of neural circuits are revealed in the behaviors they mediate, we systematically varied the spatial, temporal and contrast properties of expansion and rotation stimuli, and quantified the time course and amplitude of optomotor responses during tethered flight. Our results support the conclusion that expansion and rotation optomotor responses are indeed two separate reflexes, which draw from the same system of elementary motion detectors, but are likely mediated by separate pre-motor circuits having different spatial integration properties, low-pass characteristics and contrast sensitivity.

  16. 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

  17. 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.

  18. Extraction of pores from microtomographic reconstructions of intact soil aggregates

    SciTech Connect

    Albee, P. B.; Stockman, G. C.; Smucker, A. J. M.

    2000-02-29

    Segmentation of features is often a necessary step in the analysis of volumetric data. The authors have developed a simple technique for extracting voids from irregular volumetric data sets. In this work they look at extracting pores from soil aggregates. First, they identify a threshold that gives good separability of the object from the background. They then segment the object, and perform connected components analysis on the pores within the object. Using their technique pores that break the surface can be segmented along with pores completely contained in the initially segmented object.

  19. Characterisation of pore structures in nanoporous materials for advanced bionanotechnology.

    PubMed

    Heo, K; Yoon, J; Jin, K S; Jin, S; Ree, M

    2006-08-01

    Porous materials are potential candidates for applications in various fields, such as bionanotechnology, gas separation, catalysts and micro-electronics. In particular, their applications in bionanotechnology include biosensors, biomedical implants and microdevices, biosupporters, bio-encapsules, biomolecule separations and biomedical therapy. All these bionanotechnology applications utilise the shape, size and size distribution of pores in porous materials. Therefore the controlled creation of pores with desired shape, size and size distribution is most important in the development of nanoporous materials. Accordingly, the accurate evaluation of pore structure is necessary in the development of nanoporous materials and their applications. This article reviews recent developments in analytical techniques to characterise the pore structures of nanoporous materials.

  20. 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.

  1. 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.

  2. Enzyme screening with synthetic multifunctional pores: Focus on biopolymers

    PubMed Central

    Sordé, Nathalie; Das, Gopal; Matile, Stefan

    2003-01-01

    This report demonstrates that a single set of identical synthetic multifunctional pores can detect the activity of many different enzymes. Enzymes catalyzing either synthesis or degradation of DNA (exonuclease III or polymerase I), RNA (RNase A), polysaccharides (heparinase I, hyaluronidase, and galactosyltransferase), and proteins (papain, ficin, elastase, subtilisin, and pronase) are selected to exemplify this key characteristic of synthetic multifunctional pore sensors. Because anionic, cationic, and neutral substrates can gain access to the interior of complementarily functionalized pores, such pores can be the basis for very user-friendly screening of a broad range of enzymes. PMID:14530413

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Trichomonas vaginalis haemolysis: evidence of functional pores formation on red cell membranes.

    PubMed

    Fiori, P L; Rappelli, P; Rocchigiani, A M; Cappuccinelli, P

    1993-05-01

    We have investigated the mechanisms used by Trichomonas vaginalis to damage cellular membranes, using human erythrocytes as target cells. Haemolysis is a contact- and temperature-dependent phenomenon, and is inhibited in 4 mM EGTA. Osmotic protection experiments using carbohydrates with different molecular diameters as protectants demonstrated that the cytolytic activity of T. vaginalis is inhibited in 75 mM stachyose. On the basis of our data, we hypothesize a cytopathic mechanism mediated by the formation of functional pores into the target membrane. Some of the Trichomonas protein involved in haemolysis have been immunologically characterized. PMID:8319880

  9. Cosmological expansion and local physics

    SciTech Connect

    Faraoni, Valerio; Jacques, Audrey

    2007-09-15

    The interplay between cosmological expansion and local attraction in a gravitationally bound system is revisited in various regimes. First, weakly gravitating Newtonian systems are considered, followed by various exact solutions describing a relativistic central object embedded in a Friedmann universe. It is shown that the 'all or nothing' behavior recently discovered (i.e., weakly coupled systems are comoving while strongly coupled ones resist the cosmic expansion) is limited to the de Sitter background. New exact solutions are presented which describe black holes perfectly comoving with a generic Friedmann universe. The possibility of violating cosmic censorship for a black hole approaching the big rip is also discussed.

  10. 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.

  11. 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...

  12. 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,...

  13. 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...

  14. 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,...

  15. 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...

  16. 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...

  17. 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,...

  18. 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...

  19. 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,...

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

    PubMed

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

    2002-02-18

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

  1. 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

  2. Evidence that histidine protonation of receptor-bound anthrax protective antigen is a trigger for pore formation

    PubMed Central

    Wimalasena, D. Shyamali; Janowiak, Blythe E.; Lovell, Scott; Miyagi, Masaru; Sun, Jianjun; Zhou, Haiying; Hajduch, Jan; Pooput, Chaya; Kirk, Kenneth L.; Battaile, Kevin P.; Bann, James G.

    2010-01-01

    The protective antigen (PA) component of the anthrax toxin forms pores within the low pH environment of host endosomes, through mechanisms that are poorly understood. It has been proposed that pore formation is dependent on histidine protonation. In previous work, we biosynthetically incorporated 2-fluorohistidine (2-FHis), an isosteric analog of histidine with a significantly reduced pKa (~1), into PA, and showed that the pH-dependent conversion from the soluble prepore to a pore was unchanged. However, we also observed that 2-FHisPA was non-functional in the ability to mediate cytotoxicity of CHO-K1 cells by LFN-DTA, and was defective in translocation through planar lipid bilayers. Here, we show that the defect in cytotoxicity is due to both a defect in translocation and, when bound to the host cellular receptor, an inability to undergo low pH-induced pore formation. Combining X-ray crystallography with hydrogen-deuterium (H-D) exchange mass spectrometry, our studies lead to a model in which hydrogen bonds to the histidine ring are strengthened by receptor binding. The combination of both fluorination and receptor binding is sufficient to block low pH-induced pore formation. PMID:20672855

  3. 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

  4. Removable Type Expansion Bolt Innovative Design

    NASA Astrophysics Data System (ADS)

    Wang, Feng-Lan; Zhang, Bo; Gao, Bo; Liu, Yan-Xin; Gao, Bo

    2016-05-01

    Expansion bolt is a kind of the most common things in our daily life. Currently, there are many kinds of expansion bolts in the market. However, they have some shortcomings that mainly contain underuse and unremovement but our innovation of design makes up for these shortcomings very well. Principle of working follows this: expansion tube is fixed outside of bolt, steel balls and expansion covers are fixed inside. Meanwhile, the steel balls have 120° with each other. When using it ,expansion cover is moved in the direction of its internal part. So the front part of expansion bolt cover is increasingly becoming big and steel halls is moved outside. Only in this way can it be fixed that steel balls make expansion tube expand. When removing them, expansion bolt is moved outside. So the front part of expansion bolt cover is gradually becoming small and steel balls moves inside, after expansion tube shrinks, we can detach them.

  5. 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.

  6. 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

  7. The nuclear pore complex and nuclear transport.

    PubMed

    Wente, Susan R; Rout, Michael P

    2010-10-01

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

  8. Blood, blebs and lumen expansion.

    PubMed

    Reichman-Fried, Michal; Raz, Erez

    2016-04-01

    A powerful combination of cell labelling, genetic tools and rapid imaging techniques in vivo has now led to a high-resolution description of lumen formation during angiogenesis in zebrafish. The study reveals a haemodynamic-force-driven and myosin-II-dependent cellular mechanism (termed inverse membrane blebbing) as the basis for lumen expansion in unicellular and multicellular angiogenic sprouts. PMID:27027487

  9. French Expansion in North America.

    ERIC Educational Resources Information Center

    Jaenen, Cornelius J.

    2001-01-01

    Explores the French colonization in North America. Presents background information on New France, focusing on the French in Canada. Covers topics, such as how the French became interested in North American expansion, the French in Louisiana, colonial economics, and the reasons for the collapse of New France. Includes a bibliography. (CMK)

  10. 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.

  11. 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.

  12. 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.

  13. 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)

  14. Blood, blebs and lumen expansion.

    PubMed

    Reichman-Fried, Michal; Raz, Erez

    2016-04-01

    A powerful combination of cell labelling, genetic tools and rapid imaging techniques in vivo has now led to a high-resolution description of lumen formation during angiogenesis in zebrafish. The study reveals a haemodynamic-force-driven and myosin-II-dependent cellular mechanism (termed inverse membrane blebbing) as the basis for lumen expansion in unicellular and multicellular angiogenic sprouts.

  15. 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...

  16. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  18. Effect of pore pressure buildup on slowness of rupture propagation

    NASA Astrophysics Data System (ADS)

    Ougier-Simonin, A.; Zhu, W.

    2015-12-01

    Pore fluid pressure is known to play an important role in brittle fracture initiation and propagation, yet the underlying mechanisms remain unclear. We conducted triaxial experiments on saturated porous sandstones to investigate effects of pore pressure buildup on the slowness of shear rupture propagation at different confining pressures. At low to intermediate confinements, rocks fail by brittle faulting, and pore pressure buildup causes a reduction in rock's shear strength but does not induce measurable differences in slip behavior. When the confinement is high enough to prohibit dynamic faulting, rocks fail in the brittle-ductile transitional regime. In the transitional regime, pore pressure buildup promotes slip instability on an otherwise stably sliding fracture. Compared to those observed in the brittle regime, the slip rate, stress drop, and energy dissipated during rupture propagation with concurrent pore pressure buildup in the transitional regime are distinctively different. When decreasing confining pressure instead, the slip behavior resembles the ones of the brittle regime, emphasizing how the observed slowness is related to excess pore pressure beyond the effective pressure phenomenon. Analysis of the mechanical data using existing theoretical models confirms these observations. Quantitative microstructural analyses reveal that increasing pore pressure lessens the dilatancy hardening during failure, thus enhances slip along the localized zone in the transitional regime. Our experimental results suggest that pore pressure buildup induces slow slip in the transitional regime, and slip rates along a shear fracture may vary considerably depending on effective stress states.

  19. Partitioning of habitable pore space in earthworm burrows

    PubMed Central

    Amador, Jose A.

    2010-01-01

    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, Vs, 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 Vs 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

  20. Antimicrobial peptides bind more strongly to membrane pores

    PubMed Central

    Mihajlovic, Maja

    2010-01-01

    Antimicrobial peptides (AMPs) are small, usually cationic peptides, which permeabilize bacterial membranes. Understanding their mechanism of action might help design better antibiotics. Using an implicit membrane model, modified to include pores of different shapes, we show that four AMPs (alamethicin, melittin, a magainin analogue, MG-H2, and piscidin 1) bind more strongly to membrane pores, consistent with the idea that they stabilize them. The effective energy of alamethicin in cylindrical pores is similar to that in toroidal pores, whereas the effective energy of the other three peptides is lower in toroidal pores. Only alamethicin intercalates into the membrane core; MG-H2, melittin and piscidin are located exclusively at the hydrophobic/hydrophilic interface. In toroidal pores, the latter three peptides often bind at the edge of the pore, and are in an oblique orientation. The calculated binding energies of the peptides are correlated with their hemolytic activities. We hypothesize that one distinguishing feature of AMPs may be the fact that they are imperfectly amphipathic which allows them to bind more strongly to toroidal pores. An initial test on a melittin-based mutant seems to support this hypothesis. PMID:20188066

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. HIV-1 capsid undergoes coupled binding and isomerization by the nuclear pore protein NUP358

    PubMed Central

    2013-01-01

    Background Lentiviruses such as HIV-1 can be distinguished from other retroviruses by the cyclophilin A-binding loop in their capsid and their ability to infect non-dividing cells. Infection of non-dividing cells requires transport through the nuclear pore but how this is mediated is unknown. Results Here we present the crystal structure of the N-terminal capsid domain of HIV-1 in complex with the cyclophilin domain of nuclear pore protein NUP358. The structure reveals that HIV-1 is positioned to allow single-bond resonance stabilisation of exposed capsid residue P90. NMR exchange experiments demonstrate that NUP358 is an active isomerase, which efficiently catalyzes cis-trans isomerization of the HIV-1 capsid. In contrast, the distantly related feline lentivirus FIV can bind NUP358 but is neither isomerized by it nor requires it for infection. Conclusion Isomerization by NUP358 may be preserved by HIV-1 to target the nuclear pore and synchronize nuclear entry with capsid uncoating. PMID:23902822

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  10. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore.

    PubMed

    Rizzi, F; Jones, R E; Debusschere, B J; Knio, O M

    2013-05-21

    In this article, uncertainty quantification is applied to molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. We consider a silica pore model connecting two reservoirs containing a solution of sodium (Na(+)) and chloride (Cl(-)) ions in water. An ad hoc concentration control algorithm is developed to simulate a concentration driven counter flow of ions through the pore, with the ionic flux being the main observable extracted from the MD system. We explore the sensitivity of the system to two physical parameters of the pore, namely, the pore diameter and the gating charge. First we conduct a quantitative analysis of the impact of the pore diameter on the ionic flux, and interpret the results in terms of the interplay between size effects and ion mobility. Second, we analyze the effect of gating charge by treating the charge density over the pore surface as an uncertain parameter in a forward propagation study. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of intrinsic noise and quantify the impact of parametric uncertainty on the MD predictions. We highlight the challenges arising from the heterogeneous nature of the system, given the several components involved, and from the substantial effect of the intrinsic thermal noise.

  11. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore

    NASA Astrophysics Data System (ADS)

    Rizzi, F.; Jones, R. E.; Debusschere, B. J.; Knio, O. M.

    2013-05-01

    In this article, uncertainty quantification is applied to molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. We consider a silica pore model connecting two reservoirs containing a solution of sodium (Na+) and chloride (Cl-) ions in water. An ad hoc concentration control algorithm is developed to simulate a concentration driven counter flow of ions through the pore, with the ionic flux being the main observable extracted from the MD system. We explore the sensitivity of the system to two physical parameters of the pore, namely, the pore diameter and the gating charge. First we conduct a quantitative analysis of the impact of the pore diameter on the ionic flux, and interpret the results in terms of the interplay between size effects and ion mobility. Second, we analyze the effect of gating charge by treating the charge density over the pore surface as an uncertain parameter in a forward propagation study. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of intrinsic noise and quantify the impact of parametric uncertainty on the MD predictions. We highlight the challenges arising from the heterogeneous nature of the system, given the several components involved, and from the substantial effect of the intrinsic thermal noise.

  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. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  15. 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.

  16. 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.

  17. Influence of Pore Structure on Compressive Strength of Cement Mortar

    PubMed Central

    Zhao, Haitao; Xiao, Qi; Huang, Donghui

    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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

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

    PubMed

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

    2015-07-01

    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

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

    PubMed

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

    2015-07-01

    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.

  9. Entropic pulling: how Hsp70 chaperones translocate proteins through membrane pores

    NASA Astrophysics Data System (ADS)

    de Los Rios, Paolo; Ben-Zvi, Anat; Slutsky, Olga; Azem, Abdussalam; Goloubinoff, Pierre

    2006-03-01

    Hsp70s are highly conserved ATPase molecular chaperones mediating the translocation of proteins across membranes and the active unfolding and disassembly of stress-induced protein aggregates. Here, we introduce a mechanism named entropic pulling, based on entropy loss due to excluded volume effects, by which Hsp70 molecules can convert the energy of ATP hydrolysis into a force capable to drive the translocation of polypeptides into mitochondria. Entropic pulling represents a possible solution to the long-standing debate between the power-stroke and the Brownian ratchet models for Hsp70-mediated protein translocation across membranes. Moreover, in a very different context devoid of membrane and components of the import pore, the same physical principles apply to the forceful unfolding, solubilization and assisted native refolding of stable protein aggregates by individual Hsp70 molecules, thus providing a unifying mechanism for the different Hsp70 functions.

  10. Self-assembling organic nanotubes with precisely defined, sub-nanometer pores: formation and mass transport characteristics.

    PubMed

    Gong, Bing; Shao, Zhifeng

    2013-12-17

    The transport of molecules and ions across nanometer-scaled pores, created by natural or artificial molecules, is a phenomenon of both fundamental and practical significance. Biological channels are the most remarkable examples of mass transport across membranes and demonstrate nearly exclusive selectivity and high efficiency with a diverse collection of molecules. These channels are critical for many basic biological functions, such as membrane potential, signal transduction, and osmotic homeostasis. If such highly specific and efficient mass transport or separation could be achieved with artificial nanostructures under controlled conditions, they could create revolutionary technologies in a variety of areas. For this reason, investigators from diverse disciplines have vigorously studied small nondeformable nanopores. The most exciting studies have focused on carbon nanotubes (CNTs), which have exhibited fast mass transport and high ion selectivity despite their very simple structure. However, the limitations of CNTs and the dearth of other small (≤2 nm) nanopores have severely hampered the systematic investigation of nanopore-mediated mass transport, which will be essential for designing artificial nanopores with desired functions en masse. Researchers can overcome the difficulties associated with CNT and other artificial pores by stacking macrocyclic building blocks with persistent shapes to construct tunable, self-assembling organic pores. This effort started when we discovered a highly efficient, one-pot macrocyclization process to efficiently prepare several classes of macrocycles with rigid backbones containing nondeformable cavities. Such macrocycles, if stacked atop one another, should lead to nanotubular assemblies with defined inner pores determined by their constituent macrocycles. One class of macrocycles with aromatic oligoamide backbones had a very high propensity for directional assembly, forming nanotubular structures containing nanometer and sub

  11. Investigating Hydrophilic Pores in Model Lipid Bilayers Using Molecular Simulations: Correlating Bilayer Properties with Pore-Formation Thermodynamics.

    PubMed

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2015-06-23

    Cell-penetrating and antimicrobial peptides show a 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 porelike membrane configurations during the solute transfer process into vesicles and cells. The initiation and formation of pores are associated with a nontrivial free-energy cost, thus necessitating a consideration of the factors associated with pore formation and the attendant free energies. Because of experimental and modeling challenges related to the long time scales 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 headgroups, charge states, acyl chain lengths, and saturation. We probe the dependence of pore-formation barriers on the area per lipid, lipid bilayer thickness, and 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. The pore-formation free energy is higher in peptide-lipid systems than in peptide-free lipid systems due to penalties to maintain the solvation of charged hydrophilic solutes within the membrane environment.

  12. Pore Water Convection in Carbonaceous Chondrite Planetesimals

    NASA Astrophysics Data System (ADS)

    Travis, B. J.; Schubert, G.

    2004-12-01

    initial temperature, we use 170 K, assume a constant exterior temperature of 170 K, and apply a radiation surface temperature boundary condition. We then consider variations from the reference case for three variables: permeability (10 darcys), radius (80 km) and radiogenic heat content (50 % increase). Our simulations demonstrate that hydrothermal convection should occur for a range of parameter values and would last for several millions of years. In all of the simulations, radiogenic heating creates a water phase in about 0.6 Myr. The liquid phase lasts at least 4, to over 20 Myr, depending on the case. The center warms to peak temperatures of 360 to 450 K. Convection starts after sufficient cooling at the outer regions (but inside the outer frozen shell) has occurred to create a sufficiently strong radial temperature gradient. In these simulations, boiling does not occur, but, for a time, the systems are not far from that state. In all the simulations the convection is characterized by a mix of plumes and sheets, with plumes sharply defined for the more strongly convecting cases (10 darcys, and 50% increased heating cases). Roughly half the interior experiences water fluxes of 100--200 pore volumes. High pore volume flux facilitates extensive chemical reactions.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. Resolving single membrane fusion events on planar pore-spanning membranes.

    PubMed

    Schwenen, Lando L G; Hubrich, Raphael; Milovanovic, Dragomir; Geil, Burkhard; Yang, Jian; Kros, Alexander; Jahn, Reinhard; Steinem, Claudia

    2015-07-13

    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.

  18. 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

  19. 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.

  20. Impedance nanopore biosensor: influence of pore dimensions on biosensing performance.

    PubMed

    Kant, Krishna; Yu, Jingxian; Priest, Craig; Shapter, Joe G; Losic, Dusan

    2014-03-01

    Knowledge about electrochemical and electrical properties of nanopore structures and the influence of pore dimensions on these properties is important for the development of nanopore biosensing devices. The aim of this study was to explore the influence of nanopore dimensions (diameter and length) on biosensing performance using non-faradic electrochemical impedance spectroscopy (EIS). Nanoporous alumina membranes (NPAMs) prepared by self-ordered electrochemical anodization of aluminium were used as model nanopore sensing platforms. NPAMs with different pore diameters (25-65 nm) and lengths (4-18 μm) were prepared and the internal pore surface chemistry was modified by covalently attaching streptavidin and biotin. The performance of this antibody nanopore biosensing platform was evaluated using various concentrations of biotin as a model analyte. EIS measurements of pore resistivity and conductivity were carried out for pores with different diameters and lengths. The results showed that smaller pore dimensions of 25 nm and pore lengths up to 10 μm provide better biosensing performance.

  1. 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.

  2. Pore Structure Reconstruction and Moisture Migration in Porous Media

    NASA Astrophysics Data System (ADS)

    Zheng, Jiayi; Shi, Xing; Shi, Juan; Chen, Zhenqian

    2014-09-01

    Three kinds of porous media (isotropic, perpendicular anisotropic and parallel anisotropic porous media) with the same porosity, different pore size distributions and fractal spectral dimensions were reconstructed by random growth method. It was aimed to theoretically study the impact of microscopic pore structure on water vapor diffusion process in porous media. The results show that pore size distribution can only denote the static characteristics of porous media but cannot effectively reflect the dynamic transport characteristics of porous media. Fractal spectral dimension can effectively analyze and reflect pores connectivity and moisture dynamic transport properties of porous media from the microscopic perspective. The pores connectivity and water vapor diffusion performance in pores of porous media get better with the increase of fractal spectral dimension of porous media. Fractal spectral dimension of parallel anisotropic porous media is more than that of perpendicular anisotropic porous media. Fractal spectral dimension of isotropic porous media is between parallel anisotropic porous media and perpendicular anisotropic porous media. Other macroscopic parameters such as equilibrium diffusion coefficient of water vapor, water vapor concentration variation at right boundary in equilibrium, the time when water vapor diffusion process reaches a stable state also can characterize the pores connectivity and water vapor diffusion properties of porous media.

  3. 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

  4. Optimization of a pressurization methodology for extracting pore-water.

    PubMed

    Lopes, Isabel; Ribeiro, Rui

    2005-12-01

    Sediment toxicity can be assessed by conducting pore-water toxicity assays with standard water column organisms. Several methods have been developed for sampling pore-water. Centrifugation and pressurization methods are recommended when large volumes of pore-water are required to perform toxicity assays. Nevertheless, these methods involve sediment transportation and storage in laboratory, which can alter sediment toxicity. Therefore, an extraction method for large volumes that could be employed in the field site would be highly desirable. This study aimed to optimize and further evaluate an existing sediment pressurizing device with low construction costs, easy to carry and operate in the field, and presenting minimal chemical reactivity. The latter characteristic was achieved by lining the device interior with Teflon, by using large pore filters (50 microm), and by using an inert gas (nitrogen). Pore-water extraction efficiency and the toxicities of pore-water samples obtained by pressurization and by refrigerated centrifugation were compared. An artificial sediment (70% sand, 20% kaolin and 10% alpha-cellulose) spiked with an alcohol (phenol), a surfactant (SDS), a metal (copper), an organophosphate pesticide (parathion), and a natural sediment contaminated with acid mine drainage, were assayed for toxicity using Microtox assays. Sediment pressurization was found to be as efficient to extract pore-water as centrifugation, being more cost effective and adequate for field use.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. Differential tangential expansion as a mechanism for cortical gyrification.

    PubMed

    Ronan, Lisa; Voets, Natalie; Rua, Catarina; Alexander-Bloch, Aaron; Hough, Morgan; Mackay, Clare; Crow, Tim J; James, Anthony; Giedd, Jay N; Fletcher, Paul C

    2014-08-01

    Gyrification, the developmental buckling of the cortex, is not a random process-the forces that mediate expansion do so in such a way as to generate consistent patterns of folds across individuals and even species. Although the origin of these forces is unknown, some theories have suggested that they may be related to external cortical factors such as axonal tension. Here, we investigate an alternative hypothesis, namely, whether the differential tangential expansion of the cortex alone can account for the degree and pattern-specificity of gyrification. Using intrinsic curvature as a measure of differential expansion, we initially explored whether this parameter and the local gyrification index (used to quantify the degree of gyrification) varied in a regional-specific pattern across the cortical surface in a manner that was replicable across independent datasets of neurotypicals. Having confirmed this consistency, we further demonstrated that within each dataset, the degree of intrinsic curvature of the cortex was predictive of the degree of cortical folding at a global and regional level. We conclude that differential expansion is a plausible primary mechanism for gyrification, and propose that this perspective offers a compelling mechanistic account of the co-localization of cytoarchitecture and cortical folds.

  10. 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.

  11. 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.

  12. 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

  13. 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...

  14. 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

  15. 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

  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. 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.

  18. 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.

  19. 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.

  20. Modeling permeability evolution by precipitation and dissolution: from a single-pore channel to heterogeneous multi-pore systems

    NASA Astrophysics Data System (ADS)

    Silin, D.; Molins, S.

    2011-12-01

    Permeability modification by mineral precipitation or dissolution can significantly affect injection well performance in a bioremediation project. Well clogging may occur due to massive mineral deposition on the pore walls near the wellbore. Although the size of a cleanup site can be measured in hundreds of meters or even kilometers, the underlying geochemical and hydrologic processes in individual pores eventually define where and how fast the permeability will decline. Therefore, it is important to understand these pore-scale mechanisms in order to reduce the hindering effect of pore clogging and develop efficient well treatment procedures when its injectivity drops below the minimal-tolerance level. Additionally, model-based permeability-porosity correlations for pore space evolution caused by precipitation or dissolution are needed for realistic reservoir-scale numerical simulations. To gain insights into the pore-scale mechanisms of permeability modification by mineral precipitation and dissolution, we have developed a model describing the dynamic coupling between flow and reactive transport. The model relies on a sequential approach where alternating finite-volume multicomponent reactive transport and flow simulations evaluate the local precipitation-dissolution rates, update the pore space geometry from the mass balance considerations, the re-compute the flow field on the updated sample model. Segmented three dimensional micro-tomography images of the sediment, the chemical composition of the fluid, and the mineral composition of the rock are the input data for simulations. Some model details were reported at previous AGU meetings. We validate the model against a single-pore calcite dissolution experiment. Building on this problem, we use the model to evaluate the precipitation-dissolution patterns for a range of flow rates. We then simulate multi-pore systems to qualitatively reproduce the pattern of precipitation observed in experiments. For that purpose

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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...

  6. Hydrochromic conjugated polymers for human sweat pore mapping.

    PubMed

    Lee, Joosub; Pyo, Minkyeong; Lee, Sang-hwa; Kim, Jaeyong; Ra, Moonsoo; Kim, Whoi-Yul; Park, Bum Jun; Lee, Chan Woo; Kim, Jong-Man

    2014-04-29

    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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. A pore segment in DEG/ENaC Na(+) channels.

    PubMed

    Snyder, P M; Olson, D R; Bucher, D B

    1999-10-01

    DEG/ENaC Na(+) channels have diverse functions, including Na(+) absorption, neurotransmission, and sensory transduction. The ability of these channels to discriminate between different ions is critical for their normal function. Several findings suggest that DEG/ENaC channels have a pore structure similar to K(+) channels. To test this hypothesis, we examined the accessibility of native and introduced cysteines in the putative P loop of ENaC. We identified residues that span a barrier that excludes amiloride as well as anionic and large methanethiosulfonate reagents from the pore. This segment contains a structural element ((S/G)CS) involved in selectivity of ENaC. The results are not consistent with predictions from the K(+) channel pore, suggesting that DEG/ENaC Na(+) channels have a novel pore structure. PMID:10497211

  13. 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.

  14. Nitrocellulose Templated Hierarchical Pore Structure in Mesoporous Thin Films

    SciTech Connect

    Li, Xiaohong S.; Fryxell, Glen E.; Wang, Chong M.; Young, James S.

    2006-01-01

    Over the last decade, a great deal of effort has been expended on the templated synthesis of nanoporous materials. Many different templates have been used to create this nanostructure (surfactants, polymers, latex spheres, etc.), but by far the most widely used has been micelles composed of surfactants. This is a versatile, and highly useful, synthetic method, capable of producing a wide variety of materials and structures. More recently, the synthesis of hierarchical pore structures (i.e. small pores leading to large pores) has been of great interest as a means of enhancing mass transport within these materials.[1] Such hierarchical pore structures have been made by combining surfactant templating methods with latex beads [2], by assembling as-synthesized MCM-41 particles around block co-polymer micelles, followed by crosslinking and calcination [3], by spray drying MCM-41 and MCM-48 agglomerates [4], and by using ''evaporation induced self-assembly'' [5-9].

  15. Dynamic pore-pressure fluctuations in rapidly shearing granular materials

    USGS Publications Warehouse

    Iverson, R.M.; LaHusen, R.G.

    1989-01-01

    Results from two types of experiments show that intergranular pore pressures fluctuated dynamically during rapid, steady shear deformation of water-saturated granular materials. During some fluctuations, the pore water locally supported all normal and shear stresses, while grain-contact stresses transiently fell to zero. Fluctuations also propagated outward from the shear zone; this process modifies grain-contact stresses in adjacent areas and potentially instigates shear-zone growth.

  16. 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.

  17. 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...

  18. 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.

  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. Multiscale pore-network representation of heterogeneous carbonate rocks

    NASA Astrophysics Data System (ADS)

    Pak, Tannaz; Butler, Ian B.; Geiger, Sebastian; van Dijke, Marinus I. J.; Jiang, Zeyun; Surmas, Rodrigo

    2016-07-01

    A multiscale network integration approach introduced by Jiang et al. (2013) is used to generate a representative pore-network for a carbonate rock with a pore size distribution across several orders of magnitude. We predict the macroscopic flow parameters of the rock utilising (i) 3-D images captured by X-ray computed microtomography and (ii) pore-network flow simulations. To capture the multiscale pore size distribution of the rock, we imaged four different rock samples at different resolutions and integrated the data to produce a pore-network model that combines information at several length-scales that cannot be recovered from a single tomographic image. A workflow for selection of the number and length-scale of the required input networks for the network integration process, as well as fine tuning the model parameters is presented. Mercury injection capillary-pressure data were used to evaluate independently the multiscale networks. We explore single-scale, two-scale, and three-scale network models and discuss their representativeness by comparing simulated capillary-pressure versus saturation curves with laboratory measurements. We demonstrate that for carbonate rocks with wide pore size distributions, it may be required to integrate networks extracted from two or three discrete tomographic data sets in order to simulate macroscopic flow parameters.

  1. 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.

  2. 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.

  3. 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.

  4. Pore size effect of collagen scaffolds on cartilage regeneration.

    PubMed

    Zhang, Qin; Lu, Hongxu; Kawazoe, Naoki; Chen, Guoping

    2014-05-01

    Scaffold pore size is an important factor affecting tissue regeneration efficiency. The effect of pore size on cartilage tissue regeneration was compared by using four types of collagen porous scaffolds with different pore sizes. The collagen porous scaffolds were prepared by using pre-prepared ice particulates that had diameters of 150-250, 250-355, 355-425 and 425-500μm. All the scaffolds had spherical large pores with good interconnectivity and high porosity that facilitated cell seeding and spatial cell distribution. Chondrocytes adhered to the walls of the spherical pores and showed a homogeneous distribution throughout the scaffolds. The in vivo implantation results indicated that the pore size did not exhibit any obvious effect on cell proliferation but exhibited different effects on cartilage regeneration. The collagen porous scaffolds prepared with ice particulates 150-250μm in size best promoted the expression and production of type II collagen and aggrecan, increasing the formation and the mechanical properties of the cartilage.

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

    PubMed

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

    2014-01-01

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

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

    PubMed Central

    Niether, Doreen; Afanasenkau, Dzmitry; Dhont, Jan K. G.

    2016-01-01

    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 USA 104(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 10−3 wt % that is typical for concentrations in shallow lakes on early Earth. PMID:27044100

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

    PubMed Central

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

    2014-01-01

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

  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. 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.

  14. 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.

  15. Structural Basis for Recognition of the Pore-Forming Toxin Intermedilysin by Human Complement Receptor CD59

    PubMed Central

    Johnson, Steven; Brooks, Nicholas J.; Smith, Richard A.G.; Lea, Susan M.; Bubeck, Doryen

    2013-01-01

    Summary Pore-forming proteins containing the structurally conserved membrane attack complex/perforin fold play an important role in immunity and host-pathogen interactions. Intermedilysin (ILY) is an archetypal member of a cholesterol-dependent cytolysin subclass that hijacks the complement receptor CD59 to make cytotoxic pores in human cells. ILY directly competes for the membrane attack complex binding site on CD59, rendering cells susceptible to complement lysis. To understand how these bacterial pores form in lipid bilayers and the role CD59 plays in complement regulation, we determined the crystal structure of human CD59 bound to ILY. Here, we show the ILY-CD59 complex at 3.5 Å resolution and identify two interfaces mediating this host-pathogen interaction. An ILY-derived peptide based on the binding site inhibits pore formation in a CD59-containing liposome model system. These data provide insight into how CD59 coordinates ILY monomers, nucleating an early prepore state, and suggest a potential mechanism of inhibition for the complement terminal pathway. PMID:23665225

  16. 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

  17. Determining pore length scales and pore surface relaxivity of rock cores by internal magnetic fields modulation at 2MHz NMR.

    PubMed

    Liu, Huabing; Nogueira d'Eurydice, Marcel; Obruchkov, Sergei; Galvosas, Petrik

    2014-09-01

    Pore length scales and pore surface relaxivities of rock cores with different lithologies were studied on a 2MHz Rock Core Analyzer. To determine the pore length scales of the rock cores, the high eigenmodes of spin bearing molecules satisfying the diffusion equation were detected with optimized encoding periods in the presence of internal magnetic fields Bin. The results were confirmed using a 64MHz NMR system, which supports the feasibility of high eigenmode detection at fields as low as 2MHz. Furthermore, this methodology was combined with relaxometry measurements to a two-dimensional experiment, which provides correlation between pore length and relaxation time. This techniques also yields information on the surface relaxivity of the rock cores. The estimated surface relaxivities were then compared to the results using an independent NMR method.

  18. 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

  19. 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

  20. Phase-field modeling of temperature gradient driven pore migration coupling with thermal conduction

    SciTech Connect

    Liangzhe Zhang; Michael R Tonks; Paul C Millett; Yongfeng Zhang; Karthikeyan Chockalingam; Bulent Biner

    2012-04-01

    Pore migration in a temperature gradient (Soret effect) is investigated by a phase-field model coupled with a heat transfer calculation. Pore migration is observed towards the high temperature domain with velocities that agree with analytical solution. Due to the low thermal conductivity of the pores, the temperature gradient across individual pores is increased, which in turn, accelerates the pore migration. In particular, for pores filled with xenon and helium, the pore velocities are increased by a factor of 2.2 and 2.1, respectively. A quantitative equation is then derived to predict the influence of the low thermal conductivity of pores.

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

    NASA Astrophysics Data System (ADS)

    Asakuma, Yusuke; Yamamoto, Tsuyoshi

    2016-10-01

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

  2. 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.

  3. 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

  4. Evolutionary expansion of the Monogenea.

    PubMed

    Kearn, G C

    1994-12-01

    The evolutionary expansion of the monogeneans has taken place in parallel with the diversification of the fish-like vertebrates. In this article the main trends in monogenean evolution are traced from a hypothetical skin-parasitic ancestor on early vertebrates. Special consideration is given to the following topics: early divergence between skin feeders and blood feeders; diversification and specialization of the haptor for attachment to skin; transfer from host to host, viviparity and the success of the gyrodactylids; predation on skin parasites and camouflage; colonization of the buccal and branchial cavities; diversification and specialization of the haptor for attachment to the gills; phoresy in gill parasites; the development of endoparasitism and the origin of the cestodes; the success of dactylogyroidean gill parasites; the uniqueness of the polyopisthocotyleans; ovoviviparity and the colonization of the tetrapods. Host specificity has been the guiding force of coevolution between monogeneans and their vertebrate hosts, but the establishment of monogeneans on unrelated hosts sharing the same environment (host-switching) may have been underestimated. Host-switching has provided significant opportunities for evolutionary change of direction and is probably responsible for the establishment of monogeneans on cephalopod molluscs, on the hippopotamus and possibly on chelonians. There are indications that host-switching may be more common in monogeneans that spread by direct transfer of adults/juveniles from host to host. A limitation on the further expansion of monogeneans is the need for water for the dispersal of the infective larva (oncomiracidium).

  5. 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

  6. 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.

  7. 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.

  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. 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

  10. 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.

  11. Pore-structure models of hydraulic conductivity for permeable pavement

    NASA Astrophysics Data System (ADS)

    Kuang, X.; Sansalone, J.; Ying, G.; Ranieri, V.

    2011-03-01

    SummaryPermeable pavement functions as a porous infrastructure interface allowing the infiltration and evaporation of rainfall-runoff while functioning as a relatively smooth load-bearing surface for vehicular transport. Hydraulic conductivity ( k) of permeable pavement is an important hydraulic property and is a function of the pore structure. This study examines k for a cementitious permeable pavement (CPP) through a series of pore-structure models. Measurements utilized include hydraulic head as well as total porosity, ( ϕ t), effective porosity ( ϕ e), tortuosity ( L e/ L) and pore size distribution (PSD) indices generated through X-ray tomography (XRT). XRT results indicate that the permeable pavement pore matrix is hetero-disperse, with high tortuosity and ϕ t ≠ ϕ e. Power law models of k- ϕ t and k- ϕ e relationships are developed for a CPP mix design. Results indicate that the Krüger, Fair-Hatch, Hazen, Slichter, Beyer and Terzaghi models based on simple pore-structure indices do not reproduce measured k values. The conventional Kozeny-Carman model (KCM), a more parameterized pore-structure model, did not reproduce measured k values. This study proposes a modified KCM utilizing ϕ e, specific surface area (SSA) pe and weighted tortuosity ( L e/ L) w. Results demonstrate that such permeable pavement pore-structure parameters with the modified KCM can predict k. The k results are combined with continuous simulation modeling using historical rainfall to provide nomographs examining permeable pavement as a low impact development (LID) infrastructure component.

  12. A robust model for pore-water chemistry of clayrock

    NASA Astrophysics Data System (ADS)

    Gaucher, E. C.; Tournassat, C.; Pearson, F. J.; Blanc, P.; Crouzet, C.; Lerouge, C.; Altmann, S.

    2009-11-01

    The chemistry of pore water is an important property of clayrocks being considered as host rocks for long-term storage of radioactive waste. It may be difficult, if not impossible, to obtain water samples for chemical analysis from such rocks because of their low hydraulic conductivity. This paper presents an approach for calculating the pore-water compositions of clayrocks from laboratory-measured properties of core samples, including their leachable Cl and SO 4 concentrations and analysed exchangeable cations, and from mineral and cation exchange equilibria based on the formation mineralogy. New core sampling and analysis procedures are presented that reduce or quantify side reactions such as sample oxidation (e.g. pyrite) and soluble mineral dissolution (celestite, SrSO 4) that affect measured SO 4 concentrations and exchangeable cation distributions. The model considers phase equilibria only with minerals that are observed in the formation including the principal clay phases. The model has been used to calculate the composition of mobile pore water in the Callovo-Oxfordian clayrock and validated against measurements of water chemistry made in an underground research laboratory in that formation. The model reproduces the measured, in situ pore-water composition without any estimated parameters. All required parameters can be obtained from core sample analysis. We highlight the need to consider only those mineral phases which can be shown to be in equilibrium with contacting pore water. The consequence of this is that some conceptual models available in the literature appear not to be appropriate for modelling clayrocks, particularly those considering high temperature and/or high pressure detrital phases as chemical buffers of pore water. The robustness of our model with respect to uncertainties in the log K values of clay phases is also demonstrated. Large uncertainties in log K values for clay minerals have relatively small effects on modelled pore

  13. Extending electromagnetic methods to map coastal pore water salinities

    USGS Publications Warehouse

    Greenwood, Wm. J.; Kruse, S.; Swarzenski, P.

    2006-01-01

    The feasibility of mapping pore water salinity based on surface electromagnetic (EM) methods over land and shallow marine water is examined in a coastal wetland on Tampa Bay, Florida. Forward models predict that useful information on seabed conductivity can be obtained through <1.5 m of saline water, using floating EM-31 and EM-34 instruments from Geonics Ltd. The EM-31 functioned as predicted when compared against resistivity soundings and pore water samples and proved valuable for profiling in otherwise inaccessible terrain due to its relatively small size. Experiments with the EM-34 in marine water, however, did not reproduce the theoretical instrument response. The most effective technique for predicting pore water conductivities based on EM data entailed (1) computing formation factors from resistivity surveys and pore water samples at representative sites and (2) combining these formation factors with onshore and offshore EM-31 readings for broader spatial coverage. This method proved successful for imaging zones of elevated pore water conductivities/ salinities associated with mangrove forests, presumably caused by salt water exclusion by mangrove roots. These zones extend 5 to 10 m seaward from mangrove trunks fringing Tampa Bay. Modeling indicates that EM-31 measurements lack the resolution necessary to image the subtle pore water conductivity variations expected in association with diffuse submarine ground water discharge of fresher water in the marine water of Tampa Bay. The technique has potential for locating high-contrast zones and other pore water salinity anomalies in areas not accessible to conventional marine- or land-based resistivity arrays and hence may be useful for studies of coastal-wetland ecosystems. Copyright ?? 2005 National Ground Water Association.

  14. 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.

  15. Pore networks in continental and marine mudstones: Characteristics and controls on sealing behavior

    USGS Publications Warehouse

    Heath, J.E.; Dewers, T.A.; McPherson, B.J.O.L.; Petrusak, R.; Chidsey, T.C.; Rinehart, A.J.; Mozley, P.S.

    2011-01-01

    Mudstone pore networks are strong modifiers of sedimentary basin fluid dynamics and have a critical role in the distribution of hydrocarbons and containment of injected fluids. Using core samples from continental and marine mudstones, we investigate properties of pore types and networks from a variety of geologic environments, together with estimates of capillary beam- scanning electron microscopy, suggest seven dominant mudstone pore types distinguished by geometry and connectivity. A dominant planar pore type occurs in all investigated mudstones and generally has high coordination numbers (i.e., number of neighboring connected pores). Connected networks of pores of this type contribute to high mercury capillary pressures due to small pore throats at the junctions of connected pores and likely control most matrix transport in these mudstones. Other pore types are related to authigenic (e.g., replacement or pore-lining precipitation) clay minerals and pyrite nodules; pores in clay packets adjacent to larger, more competent clastic grains; pores in organic phases; and stylolitic and microfracture-related pores. Pores within regions of authigenic clay minerals often form small isolated networks (<3 ??m). Pores in stringers of organic phases occur as tubular pores or slit- and/or sheet-like pores. These form short, connected lengths in 3D reconstructions, but appear to form networks no larger than a few microns in size. Sealing efficiency of the studied mudstones increases with greater distal depositional environments and greater maximum depth of burial. ?? 2011 Geological Society of America.

  16. Strain-based in-situ study of anion and cation insertion into porous carbon electrodes with different pore sizes

    SciTech Connect

    Black, Jennifer M; Feng, Guang; Fulvio, Pasquale F; Hillesheim, Patrick C; Dai, Sheng; Gogotsi, Yury G.; Cummings, Peter T; Kalinin, Sergei V; Balke, Nina

    2013-01-01

    The expansion of porous carbon electrodes in a room temperature ionic liquid (RTIL) is studied using in-situ atomic force microscopy (AFM). The effect of carbon surface area and pore size/pore size distribution on the observed strain profile and ion kinetics is examined. Also, the influence of potential scan rate on the strain response is investigated. By analyzing the strain data at various potential scan rates information on ion kinetics in the different carbon materials is obtained. Molecular dynamics (MD) simulations are performed to compare with and provide molecular insights into experimental results, which is the first MD work investigating the pressure exerted on porous electrodes under applied potential in a RTIL electrolyte. Using MD, the pressure exerted on the pore wall is calculated as a function of potential/charge for both a micropore (1.2 nm) and a mesopore (7.0 nm). The shape of the calculated pressure profile matches closely with the strain profiles observed experimentally.

  17. Idealized Shale Sorption Isotherm Measurements to Determine Pore Volume, Pore Size Distribution, and Surface Area

    NASA Astrophysics Data System (ADS)

    Holmes, R.; Wang, B.; Aljama, H.; Rupp, E.; Wilcox, J.

    2014-12-01

    One method for mitigating the impacts of anthropogenic CO2-related climate change is the sequestration of CO2 in depleted gas and oil reservoirs, including shale. The accurate characterization of the heterogeneous material properties of shale, including pore volume, surface area, pore size distributions (PSDs) and composition is needed to understand the interaction of CO2 with shale. Idealized powdered shale sorption isotherms were created by varying incremental amounts of four essential components by weight. The first two components, organic carbon and clay, have been shown to be the most important components for CO2 uptake in shales. Organic carbon was represented by kerogen isolated from a Silurian shale, and clay groups were represented by illite from the Green River shale formation. The rest of the idealized shale was composed of equal parts by weight of SiO2 to represent quartz and CaCO3 to represent carbonate components. Baltic, Eagle Ford, and Barnett shale sorption measurements were used to validate the idealized samples. The idealized and validation shale sorption isotherms were measured volumetrically using low pressure N2 (77K) and CO2 (273K) adsorbates on a Quantachrome Autosorb IQ2. Gravimetric isotherms were also produced for a subset of these samples using CO2 and CH4adsorbates under subsurface temperature and pressure conditions using a Rubotherm magnetic suspension balance. Preliminary analyses were inconclusive in validating the idealized samples. This could be a result of conflicting reports of total organic carbon (TOC) content in each sample, a problem stemming from the heterogeneity of the samples and different techniques used for measuring TOC content. The TOC content of the validation samples (Eagle Ford and Barnett) was measured by Rock-Eval pyrolysis at Weatherford Laboratories, while the TOC content in the Baltic validation samples was determined by LECO TOC. Development of a uniform process for measuring TOC in the validation samples is

  18. Final Report for Subcontract B541028, Pore-Scale Modeling to Support "Pore Connectivity" Research Work

    SciTech Connect

    Ewing, R P

    2009-02-25

    This report covers modeling aspects of a combined experimental and modeling task in support of the DOE Science and Technology Program (formerly OSTI) within the Office of Civilian Radioactive Waste Management (OCRWM). Research Objectives The research for this project dealt with diffusive retardation: solute moving through a fracture diffuses into and out of the rock matrix. This diffusive exchange retards overall solute movement, and retardation both dilutes waste being released, and allows additional decay. Diffusive retardation involves not only fracture conductivity and matrix diffusion, but also other issues and processes: contaminants may sorb to the rock matrix, fracture flow may be episodic, a given fracture may or may not flow depending on the volume of flow and the fracture's connection to the overall fracture network, the matrix imbibes water during flow episodes and dries between episodes, and so on. The objective of the project was to improve understanding of diffusive retardation of radionuclides due to fracture / matrix interactions. Results from combined experimental/modeling work were to (1) determine whether the current understanding and model representation of matrix diffusion is valid, (2) provide insights into the upscaling of laboratory-scale diffusion experiments, and (3) help in evaluating the impact on diffusive retardation of episodic fracture flow and pore connectivity in Yucca Mountain tuffs. Questions explored included the following: (1) What is the relationship between the diffusion coefficient measured at one scale, to that measured or observed at a different scale? In classical materials this relationship is trivial; in low-connectivity materials it is not. (2) Is the measured diffusivity insensitive to the shape of the sample? Again, in classical materials there should be no sample shape effect. (3) Does sorption affect diffusive exchange in low-connectivity media differently than in classical media? (4) What is the effect of matrix

  19. Network representation of pore scale imagery for percolation models

    NASA Astrophysics Data System (ADS)

    Klise, K. A.; McKenna, S. A.; Read, E.; Karpyn, Z. T.; Celauro, J.

    2012-12-01

    Multiphase flow under capillary dominated flow regimes is driven by an intricate relationship between pore geometry, material and fluid properties. In this research, high-resolution micro-computed tomography (CT) imaging experiments are used to investigate structural and surface properties of bead packs, and how they influence percolation pathways. Coreflood experiments use a mix of hydrophilic and hydrophobic beads to track the influence of variable contact angle on capillary flow. While high-resolution CT images can render micron scale representation of the pore space, data must be upscaled to capture pore and pore throat geometry for use in percolation models. In this analysis, the pore space is upscaled into a network representation based on properties of the medial axis. Finding the medial axis using micron scale images is computationally expensive. Here, we compare the efficiency and accuracy of medial axes using erosion-based and watershed algorithms. The resulting network representation is defined as a ball-and-stick model which represents pores and pore throats. The ball-and-stick model can be further reduced by eliminating sections of the network that fall below a capillary pressure threshold. In a system of mixed hydrophilic and hydrophobic beads, capillary pressure can change significantly throughout the network based on the interaction between surface and fluid properties. The upscaled network representations are used in percolation models to estimate transport pathway. Current results use a basic percolation model that sequentially fills neighboring pores with the highest potential. Future work will expand the percolation model to include additional mechanics, such as trapping, vacating pores, and viscous fingering. Results from the coreflood experiments will be used to validate upscaling techniques and percolation models. Preliminary results show that the relative strength of water-wet and oil-wet surfaces has a significant impact on percolation

  20. Bilinear Expansion For Redistribution Functions

    NASA Astrophysics Data System (ADS)

    Harutyunian, Haik; Alecian, Georges; Khachatryan, Knarik; Vardanyan, Ani

    2016-11-01

    We suggest here a method for construction of a bilinear expansion for an angle-averaged redistribution function. This function describes the elementary act of a photon scattering by a model two-level atom with the upper level broadened due to radiation damping. An eigenvalue and eigenvector determination problem is formulated and the relevant matrices are found analytically. Numerical procedures for their computations are elaborated as well. A simple method for the numerical calculations accuracy evaluation is suggested. It is shown that a family of redistribution functions describing the light scattering process within the spectral line frequencies can be constructed if the eigenvalue problem for the considered function is solved. It becomes possible if the eigenvalues and eigenvectors with the appropriate basic functions are used. The Voigt function and its derivatives used as basic functions are studied in detail as well.

  1. PORE CONNECTIVITY, EPISODIC FLOW, AND UNSATURATED DIFFUSION IN FRACTURED TUFF

    SciTech Connect

    Q. Hu; R.P. Ewing; L. Tomutsa; M.J. Singleton

    2006-02-21

    We use an integrated approach consisting of experiments and complementary pore-scale network modeling to investigate the occurrence of sparsely connected pore spaces in rock matrices at Yucca Mountain, Nevada, and their implications for matrix diffusion. Imbibition results indicate that pore spaces in devitrified tuff are not well-connected, and that this lack of connectivity is further compounded by episodic flow in fractured devitrified tuff with low matrix permeability. A rigorous methodology for investigating chemical transport in fractured rock under episodic conditions, employing a suite of both sorbing and non-sorbing tracers (including radionuclides U-235, Np-237, and Pu-242), has been developed and implemented. In addition, gas diffusion and synchrotron microtomography techniques have been under development to examine the scaling issues of diffusion and pore connectivity. Preliminary results from experiments and modeling work are presented in this paper, confirming the need to reexamine our understanding of matrix diffusion and to evaluate the impact on diffusive radionuclide retardation of episodic fracture flow and low pore connectivity.

  2. The mitochondrial permeability transition pore in AD 2016: An update.

    PubMed

    Biasutto, Lucia; Azzolini, Michele; Szabò, Ildikò; Zoratti, Mario

    2016-10-01

    Over the past 30years the mitochondrial permeability transition - the permeabilization of the inner mitochondrial membrane due to the opening of a wide pore - has progressed from being considered a curious artifact induced in isolated mitochondria by Ca(2+) and phosphate to a key cell-death-inducing process in several major pathologies. Its relevance is by now universally acknowledged and a pharmacology targeting the phenomenon is being developed. The molecular nature of the pore remains to this day uncertain, but progress has recently been made with the identification of the FOF1 ATP synthase as the probable proteic substrate. Researchers sharing this conviction are however divided into two camps: these believing that only the ATP synthase dimers or oligomers can form the pore, presumably in the contact region between monomers, and those who consider that the ring-forming c subunits in the FO sector actually constitute the walls of the pore. The latest development is the emergence of a new candidate: Spastic Paraplegia 7 (SPG7), a mitochondrial AAA-type membrane protease which forms a 6-stave barrel. This review summarizes recent developments of research on the pathophysiological relevance and on the molecular nature of the mitochondrial permeability transition pore. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:26902508

  3. The role of pore geometry in single nanoparticle detection

    SciTech Connect

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; Teslich, Nick; Cabrini, Stefano; Morrison, Alan P.; Siwy, Zuzanna S.; Letant, Sonia E.

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the applied voltage and the pore’s geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.

  4. The role of pore geometry in single nanoparticle detection

    DOE PAGESBeta

    Davenport, Matthew; Healy, Ken; Pevarnik, Matthew; Teslich, Nick; Cabrini, Stefano; Morrison, Alan P.; Siwy, Zuzanna S.; Letant, Sonia E.

    2012-08-22

    In this study, we observe single nanoparticle translocation events via resistive pulse sensing using silicon nitride pores described by a range of lengths and diameters. Pores are prepared by focused ion beam milling in 50 nm-, 100 nm-, and 500 nm-thick silicon nitride membranes with diameters fabricated to accommodate spherical silica nanoparticles with sizes chosen to mimic that of virus particles. In this manner, we are able to characterize the role of pore geometry in three key components of the detection scheme, namely, event magnitude, event duration, and event frequency. We find that the electric field created by the appliedmore » voltage and the pore’s geometry is a critical factor. We develop approximations to describe this field, which are verified with computer simulations, and interactions between particles and this field. In so doing, we formulate what we believe to be the first approximation for the magnitude of ionic current blockage that explicitly addresses the invariance of access resistance of solid-state pores during particle translocation. These approximations also provide a suitable foundation for estimating the zeta potential of the particles and/or pore surface when studied in conjunction with event durations. We also verify that translocation achieved by electro-osmostic transport is an effective means of slowing translocation velocities of highly charged particles without compromising particle capture rate as compared to more traditional approaches based on electrophoretic transport.« less

  5. Pore-throat sizes in sandstones, tight sandstones, and shales

    USGS Publications Warehouse

    Nelson, Philip H.

    2009-01-01

    Pore-throat sizes in silidclastic rocks form a continuum from the submillimeter to the nanometer scale. That continuum is documented in this article using previously published data on the pore and pore-throat sizes of conventional reservoir rocks, tight-gas sandstones, and shales. For measures of central tendency (mean, mode, median), pore-throat sizes (diameters) are generally greater than 2 μm in conventional reservoir rocks, range from about 2 to 0.03 μm in tight-gas sandstones, and range from 0.1 to 0.005 μm in shales. Hydrocarbon molecules, asphaltenes, ring structures, paraffins, and methane, form another continuum, ranging from 100 Å (0.01 μm for asphaltenes to 3.8 A (0.00038 μm) for methane. The pore-throat size continuum provides a useful perspective for considering (1) the emplacement of petroleum in consolidated siliciclastics and (2) fluid flow through fine-grained source rocks now being exploited as reservoirs.

  6. Pore Water Collection, Analysis and Evolution: The Need for Standardization.

    PubMed

    Gruzalski, Jacob G; Markwiese, James T; Carriker, Neil E; Rogers, William J; Vitale, Rock J; Thal, David I

    2016-01-01

    Investigating the ecological impacts of contaminants released into the environment requires integration of multiple lines of evidence. Collection and analysis of interstitial water is an often-used line of evidence for developing benthic exposure estimates in aquatic ecosystems. It is a well-established principle that chemical and toxicity data on interstitial water samples should represent in-situ conditions; i.e., sample integrity must be maintained throughout the sample collection process to avoid alteration of the in-situ geochemical conditions. Unfortunately, collection and processing of pore water is not standardized to address possible geochemical transformations introduced by atmospheric exposure. Furthermore, there are no suitable benchmarks (ecological or human health) against which to evaluate adverse effects from chemicals in pore water; i.e., empirical data is lacking on the toxicity of inorganic contaminants in sediment interstitial water. It is clear that pore water data is best evaluated by considering the bioavailability of trace elements and the partitioning of contaminants between the aqueous and solid phases. It is also evident that there is a need for sediment researchers and regulatory agencies to collaborate in developing a standardized approach for sediment/pore water collection and data evaluation. Without such guidelines, the number of different pore water collection and extraction techniques will continue to expand, and investigators will continue to evaluate potentially questionable data by comparison to inappropriate criteria. PMID:26613987

  7. The mitochondrial permeability transition pore in AD 2016: An update.

    PubMed

    Biasutto, Lucia; Azzolini, Michele; Szabò, Ildikò; Zoratti, Mario

    2016-10-01

    Over the past 30years the mitochondrial permeability transition - the permeabilization of the inner mitochondrial membrane due to the opening of a wide pore - has progressed from being considered a curious artifact induced in isolated mitochondria by Ca(2+) and phosphate to a key cell-death-inducing process in several major pathologies. Its relevance is by now universally acknowledged and a pharmacology targeting the phenomenon is being developed. The molecular nature of the pore remains to this day uncertain, but progress has recently been made with the identification of the FOF1 ATP synthase as the probable proteic substrate. Researchers sharing this conviction are however divided into two camps: these believing that only the ATP synthase dimers or oligomers can form the pore, presumably in the contact region between monomers, and those who consider that the ring-forming c subunits in the FO sector actually constitute the walls of the pore. The latest development is the emergence of a new candidate: Spastic Paraplegia 7 (SPG7), a mitochondrial AAA-type membrane protease which forms a 6-stave barrel. This review summarizes recent developments of research on the pathophysiological relevance and on the molecular nature of the mitochondrial permeability transition pore. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.

  8. The Bicomponent Pore-Forming Leucocidins of Staphylococcus aureus

    PubMed Central

    Alonzo, Francis

    2014-01-01

    SUMMARY The ability to produce water-soluble proteins with the capacity to oligomerize and form pores within cellular lipid bilayers is a trait conserved among nearly all forms of life, including humans, single-celled eukaryotes, and numerous bacterial species. In bacteria, some of the most notable pore-forming molecules are protein toxins that interact with mammalian cell membranes to promote lysis, deliver effectors, and modulate cellular homeostasis. Of the bacterial species capable of producing pore-forming toxic molecules, the Gram-positive pathogen Staphylococcus aureus is one of the most notorious. S. aureus can produce seven different pore-forming protein toxins, all of which are believed to play a unique role in promoting the ability of the organism to cause disease in humans and other mammals. The most diverse of these pore-forming toxins, in terms of both functional activity and global representation within S. aureus clinical isolates, are the bicomponent leucocidins. From the first description of their activity on host immune cells over 100 years ago to the detailed investigations of their biochemical function today, the leucocidins remain at the forefront of S. aureus pathogenesis research initiatives. Study of their mode of action is of immediate interest in the realm of therapeutic agent design as well as for studies of bacterial pathogenesis. This review provides an updated perspective on our understanding of the S. aureus leucocidins and their function, specificity, and potential as therapeutic targets. PMID:24847020

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  10. Evidence for excess pore pressures in southwest Indian Ocean sediments

    SciTech Connect

    Abbott, D.; Menke, W.; Hobart, M.; Anderson, R.

    1981-03-10

    Brown clay cores from the Madagascar and Crozet basins show the following evidence of excess pore pressures: large amounts of flow-in, increasing average sedimentation rate with age, and nonlinear temperature gradients. Additionally, many hilltops in these basins have no visible sediment cover. The bare hilltops may result from periodic slumping caused by excess pore pressures. Calculated excess pore pressures which equal or exceed the overburden pressure were inferred from water fluxes predicted by nonlinear temperature gradients and laboratory permeability measurements by using Darcy's law. Since pore pressures which exceed the overburden pressure are unreasonable, we attribute this discrepancy to laboratory measures which underestimate the in situ permeability. The widespread presence of overpressured sediments in areas of irregular topography provides a process for resuspension of clay-sized particles. This mechanism does not require high current velocities for the erosion of clay and therefore can be applied to many areas where no strong currents are evident. Carbonate-rich sediments from the Madagascar Ridge, the Mozambique Ridge, and the Agulhas Plateau had almost no flow-in and occurred in areas where all topography was thickly draped with sediment, Since the age and tectonic location of the ridges and plateaus preclude water circulation in the basement, we attribute these differences between the brown clay and the carbonate-rich material to an absence of significant excess pore pressures in the plateau and ridge sediments.

  11. Pore fluid pressure, apparent friction, and Coulomb failure

    USGS Publications Warehouse

    Beeler, N.M.; Simpson, R.W.; Hickman, S.H.; Lockner, D.A.

    2000-01-01

    Many recent studies of stress-triggered seismicity rely on a fault failure model with a single free parameter, the apparent coefficient of friction, presumed to be a material constant with possible values 0 ≤ μ′ ≤ 1. These studies may present a misleading view of fault strength and the role of pore fluid pressure in earthquake failure. The parameter μ′ is intended to incorporate the effects of both friction and pore pressure, but is a material constant only if changes in pore fluid pressure induced by changes in stress are proportional to the normal stress change across the potential failure plane. Although specific models of fault zones permit such a relation, neither is it known that fault zones within the Earth behave this way, nor is this behavior expected in all cases. In contrast, for an isotropic homogeneous poroelastic model the pore pressure changes are proportional to changes in mean stress, μ′ is not a material constant, and −∞ ≤ μ′ ≤ +∞. Analysis of the change in Coulomb failure stress for tectonically loaded reverse and strike-slip faults shows considerable differences between these two pore pressure models, suggesting that such models might be distinguished from one another using observations of triggered seismicity (e.g., aftershocks). We conclude that using the constant apparent friction model exclusively in studies of Coulomb failure stress is unwise and could lead to significant errors in estimated stress change and seismic hazard.

  12. Tunable ultrathin membranes with nonvolatile pore shape memory.

    PubMed

    Kuroki, Hidenori; Islam, Crescent; Tokarev, Igor; Hu, Heng; Liu, Guojun; Minko, Sergiy

    2015-05-20

    The concept of a responsive nanoporous thin-film gel membranes whose pores could be tuned to a desired size by a specific "molecular signal" and whose pore geometry becomes "memorized" by the gel is reported. The ∼100 nm thick membranes were prepared by dip-coating from a solution mixture of a random copolymer comprising responsive and photo-cross-linkable units and monodisperse latex nanoparticles used as a sacrificial colloidal template. After stabilization of the films by photo-cross-linking the latex template was removed, yielding nanoporous structures with a narrow pore size distribution and a high porosity. The thin-film membranes could be transferred onto porous supports to serve as tunable size-selective barriers in various colloids separation applications. The pore dimensions and hence the membrane's colloidal-particle-size cutoff were reversibly regulated by swelling-shrinking of the polymer network with a specially selected low-molar-mass compound. The attained pore shape was "memorized" in aqueous media and "erased" by treatment in special solvents reverting the membrane to the original state.

  13. Pore Connectivity, Episodic Flow, and Unsaturated Diffusion in Fractured Tuff

    SciTech Connect

    Hu, Q; Ewing, R P; Tomutsa, L; Singleton, M J

    2006-01-30

    We use an integrated approach consisting of experiments and complementary pore-scale network modeling to investigate the occurrence of sparsely connected pore spaces in rock matrices at Yucca Mountain, Nevada, and its implication to matrix diffusion. Imbibition results indicate that pore spaces in devitrified tuff are not well-connected, and that this lack of connectivity is further compounded by episodic flow in fractured devitrified tuff with low matrix permeability. A rigorous methodology for investigating chemical transport in fractured rock under episodic conditions, employing a suite of both sorbing and non-sorbing tracers (including radionuclides U-235, Np-237, and Pu-242), has been developed and implemented. In addition, gas diffusion and synchrotron microtomography techniques have been under development to examine the scaling issues of diffusion and pore connectivity. Preliminary results from experiments and modeling work are presented in this paper, in order to reexamine our understanding of matrix diffusion and to evaluate the impact on diffusive radionuclide retardation of episodic fracture flow and low pore connectivity.

  14. Ion exclusion by sub-2-nm carbon nanotube pores

    PubMed Central

    Fornasiero, Francesco; Park, Hyung Gyu; Holt, Jason K.; Stadermann, Michael; Grigoropoulos, Costas P.; Noy, Aleksandr; Bakajin, Olgica

    2008-01-01

    Biological pores regulate the cellular traffic of a large variety of solutes, often with high selectivity and fast flow rates. These pores share several common structural features: the inner surface of the pore is frequently lined with hydrophobic residues, and the selectivity filter regions often contain charged functional groups. Hydrophobic, narrow-diameter carbon nanotubes can provide a simplified model of membrane channels by reproducing these critical features in a simpler and more robust platform. Previous studies demonstrated that carbon nanotube pores can support a water flux comparable to natural aquaporin channels. Here, we investigate ion transport through these pores using a sub-2-nm, aligned carbon nanotube membrane nanofluidic platform. To mimic the charged groups at the selectivity region, we introduce negatively charged groups at the opening of the carbon nanotubes by plasma treatment. Pressure-driven filtration experiments, coupled with capillary electrophoresis analysis of the permeate and feed, are used to quantify ion exclusion in these membranes as a function of solution ionic strength, pH, and ion valence. We show that carbon nanotube membranes exhibit significant ion exclusion that can be as high as 98% under certain conditions. Our results strongly support a Donnan-type rejection mechanism, dominated by electrostatic interactions between fixed membrane charges and mobile ions, whereas steric and hydrodynamic effects appear to be less important. PMID:18539773

  15. SCAM analysis of Panx1 suggests a peculiar pore structure.

    PubMed

    Wang, Junjie; Dahl, Gerhard

    2010-11-01

    Vertebrates express two families of gap junction proteins: the well-characterized connexins and the pannexins. In contrast to connexins, pannexins do not appear to form gap junction channels but instead function as unpaired membrane channels. Pannexins have no sequence homology to connexins but are distantly related to the invertebrate gap junction proteins, innexins. Despite the sequence diversity, pannexins and connexins form channels with similar permeability properties and exhibit similar membrane topology, with two extracellular loops, four transmembrane (TM) segments, and cytoplasmic localization of amino and carboxy termini. To test whether the similarities extend to the pore structure of the channels, pannexin 1 (Panx1) was subjected to analysis with the substituted cysteine accessibility method (SCAM). The thiol reagents maleimidobutyryl-biocytin and 2-trimethylammonioethyl-methanethiosulfonate reacted with several cysteines positioned in the external portion of the first TM segment (TM1) and the first extracellular loop. These data suggest that portions of TM1 and the first extracellular loop line the outer part of the pore of Panx1 channels. In this aspect, the pore structures of Panx1 and connexin channels are similar. However, although the inner part of the pore is lined by amino-terminal amino acids in connexin channels, thiol modification was detected in carboxyterminal amino acids in Panx1 channels by SCAM analysis. Thus, it appears that the inner portion of the pores of Panx1 and connexin channels may be distinct.

  16. Statistical geometry of pores and statistics of porous nanofibrous assemblies

    PubMed Central

    Eichhorn, Stephen J; Sampson, William W

    2005-01-01

    The application of theoretical models to describe the structure of the types of fibrous network produced by the electrospinning of polymers for use in tissue engineering and a number of other applications is presented. Emphasis is placed on formal analyses of the pore size distribution and porosities that one would encounter with such structures and the nature of their relationships with other structural characteristics likely to be important for the performance of nanofibrous materials. The theoretical structures considered result from interactions between randomly placed straight rods that represent fibres with nanoscale dimensions. The dominant role of fibre diameter in controlling the pore diameter of the networks is shown and we discuss the perhaps counter-intuitive finding that at a given network mass per unit area and porosity, increasing fibre diameter results in an increase in mean pore radius. Larger pores may be required for ingrowth of cells to nanofibrous networks, hence this study clarifies that simply making the diameters of the fibres smaller might not be the way to improve cell proliferation on such substrates. An extensive review of structural features of the network such as the distribution of mass, inter-fibre contacts and available surface for cell attachment, fibre contact distributions for integrity of the networks and the porosity and pore size distributions is given, with emphasis placed on nanofibre dimensions for the first time. PMID:16849188

  17. YaxAB, a Yersinia enterocolitica Pore-Forming Toxin Regulated by RovA

    PubMed Central

    Wagner, Nikki J.; Lin, Carolina P.; Borst, Luke B.

    2013-01-01

    The transcriptional regulator RovA positively regulates transcription of the Yersinia enterocolitica virulence gene inv. Invasin, encoded by inv, is important for establishment of Y. enterocolitica infection. However, a rovA mutant is more attenuated for virulence than an inv mutant, implying that RovA regulates additional virulence genes. When the Y. enterocolitica RovA regulon was defined by microarray analysis, YE1984 and YE1985 were among the genes identified as being upregulated by RovA. Since these genes are homologous to Xenorhabdus nematophila cytotoxin genes xaxA and xaxB, we named them yaxA and yaxB, respectively. In this work, we demonstrate the effects of YaxAB on the course of infection in the murine model. While a yaxAB mutant (ΔyaxAB) is capable of colonizing mice at the same level as the wild type, it slightly delays the course of infection and results in differing pathology in the spleen. Further, we found that yaxAB encode a probable cytotoxin capable of lysing mammalian cells, that both YaxA and YaxB are required for cytotoxic activity, and that the two proteins associate. YaxAB-mediated cell death occurs via osmotic lysis through the formation of distinct membrane pores. In silico tertiary structural analysis identified predicted structural homology between YaxA and proteins in pore-forming toxin complexes from Bacillus cereus (HBL-B) and Escherichia coli (HlyE). Thus, it appears that YaxAB function as virulence factors by inducing cell lysis through the formation of pores in the host cell membrane. This characterization of YaxAB supports the hypothesis that RovA regulates expression of multiple virulence factors in Y. enterocolitica. PMID:24002058

  18. A voltage-gated pore for translocation of tRNA

    SciTech Connect

    Koley, Sandip; Adhya, Samit

    2013-09-13

    Highlights: •A tRNA translocating complex was assembled from purified proteins. •The complex translocates tRNA at a membrane potential of ∼60 mV. •Translocation requires Cys and His residues in the Fe–S center of RIC6 subunit. -- Abstract: Very little is known about how nucleic acids are translocated across membranes. The multi-subunit RNA Import Complex (RIC) from mitochondria of the kinetoplastid protozoon Leishmania tropica induces translocation of tRNAs across artificial or natural membranes, but the nature of the translocation pore remains unknown. We show that subunits RIC6 and RIC9 assemble on the membrane in presence of subunit RIC4A to form complex R3. Atomic Force Microscopy of R3 revealed particles with an asymmetric surface groove of ∼20 nm rim diameter and ∼1 nm depth. R3 induced translocation of tRNA into liposomes when the pH of the medium was lowered to ∼6 in the absence of ATP. R3-mediated tRNA translocation could also be induced at neutral pH by a K{sup +} diffusion potential with an optimum of 60–70 mV. Point mutations in the Cys{sub 2}–His{sub 2} Fe-binding motif of RIC6, which is homologous to the respiratory Complex III Fe–S protein, abrogated import induced by low pH but not by K{sup +} diffusion potential. These results indicate that the R3 complex forms a pore that is gated by a proton-generated membrane potential and that the Fe–S binding region of RIC6 has a role in proton translocation. The tRNA import complex of L. tropica thus contains a novel macromolecular channel distinct from the mitochondrial protein import pore that is apparently involved in tRNA import in some species.

  19. To the pore and through the pore: a story of mRNA export kinetics.

    PubMed

    Oeffinger, Marlene; Zenklusen, Daniel

    2012-06-01

    The evolutionary 'decision' to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transport mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing. PMID:22387213

  20. To the Pore and Through the Pore: A Story of mRNA Export Kinetics

    PubMed Central

    Oeffinger, Marlene; Zenklusen, Daniel

    2012-01-01

    Summary The evolutionary ‘decision’ to store genetic information away from the place of protein synthesis, in a separate compartment, has forced eukaryotic cells to establish a system to transports mRNAs from the nucleus to the cytoplasm for translation. To ensure export to be fast and efficient, cells have evolved a complex molecular interplay that is tightly regulated. Over the last few decades, many of the individual players in this process have been described, starting with the composition of the nuclear pore complex to proteins that modulate co-transcriptional events required to prepare an mRNP for export to the cytoplasm. How the interplay between all the factors and processes results in the efficient and selective export of mRNAs from the nucleus and how the export process itself is executed within cells, however, is still not fully understood. Recent advances in using proteomic and single molecule microscopy approaches have provided important insights into the process and its kinetics. This review summarizes these recent advances and how they led to the current view on how cells orchestrate the export of mRNAs. PMID:22387213

  1. Breathing Stimulant Compounds Inhibit TASK-3 Potassium Channel Function Likely by Binding at a Common Site in the Channel Pore

    PubMed Central

    Chokshi, Rikki H.; Larsen, Aaron T.; Bhayana, Brijesh

    2015-01-01

    Compounds PKTHPP (1-{1-[6-(biphenyl-4-ylcarbonyl)-5,6,7,8-tetrahydropyrido[4,3-d]-pyrimidin-4-yl]piperidin-4-yl}propan-1-one), A1899 (2ʹ′-[(4-methoxybenzoylamino)methyl]biphenyl-2-carboxylic acid 2,4-difluorobenzylamide), and doxapram inhibit TASK-1 (KCNK3) and TASK-3 (KCNK9) tandem pore (K2P) potassium channel function and stimulate breathing. To better understand the molecular mechanism(s) of action of these drugs, we undertook studies to identify amino acid residues in the TASK-3 protein that mediate this inhibition. Guided by homology modeling and molecular docking, we hypothesized that PKTHPP and A1899 bind in the TASK-3 intracellular pore. To test our hypothesis, we mutated each residue in or near the predicted PKTHPP and A1899 binding site (residues 118–128 and 228–248), individually, to a negatively charged aspartate. We quantified each mutation's effect on TASK-3 potassium channel concentration response to PKTHPP. Studies were conducted on TASK-3 transiently expressed in Fischer rat thyroid epithelial monolayers; channel function was measured in an Ussing chamber. TASK-3 pore mutations at residues 122 (L122D, E, or K) and 236 (G236D) caused the IC50 of PKTHPP to increase more than 1000-fold. TASK-3 mutants L122D, G236D, L239D, and V242D were resistant to block by PKTHPP, A1899, and doxapram. Our data are consistent with a model in which breathing stimulant compounds PKTHPP, A1899, and doxapram inhibit TASK-3 function by binding at a common site within the channel intracellular pore region, although binding outside the channel pore cannot yet be excluded. PMID:26268529

  2. Nitrogen-mediated effects of elevated CO2 on intra-aggregate soil pore structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While previous elevated atmospheric CO2 research has addressed changes in belowground processes, its effects on soil structure remain virtually undescribed. This study examined the long-term effects of elevated CO2 and N fertilization on soil structural changes in a bahiagrass pasture grown on a san...

  3. Pressurized electrolysis stack with thermal expansion capability

    SciTech Connect

    Bourgeois, Richard Scott

    2015-07-14

    The present techniques provide systems and methods for mounting an electrolyzer stack in an outer shell so as to allow for differential thermal expansion of the electrolyzer stack and shell. Generally, an electrolyzer stack may be formed from a material with a high coefficient of thermal expansion, while the shell may be formed from a material having a lower coefficient of thermal expansion. The differences between the coefficients of thermal expansion may lead to damage to the electrolyzer stack as the shell may restrain the thermal expansion of the electrolyzer stack. To allow for the differences in thermal expansion, the electrolyzer stack may be mounted within the shell leaving a space between the electrolyzer stack and shell. The space between the electrolyzer stack and the shell may be filled with a non-conductive fluid to further equalize pressure inside and outside of the electrolyzer stack.

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

    PubMed Central

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

    2010-01-01

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

  5. Injectable, Pore-Forming Hydrogels for In Vivo Enrichment of Immature Dendritic Cells.

    PubMed

    Verbeke, Catia S; Mooney, David J

    2015-12-01

    Biomaterials-based vaccines have emerged as a powerful method to evoke potent immune responses directly in vivo, without the need for ex vivo cell manipulation, and modulating dendritic cell (DC) responses in a noninflammatory context could enable the development of tolerogenic vaccines to treat autoimmunity. This study describes the development of a noninflammatory, injectable hydrogel system to locally enrich DCs in vivo without inducing their maturation or activation, as a first step toward this goal. Alginate hydrogels that form pores in situ are characterized and used as a physical scaffold for cell infiltration. These gels are also adapted to control the release of granulocyte-macrophage colony stimulating factor (GM-CSF), a potent inducer of DC recruitment and proliferation. In vivo, sustained release of GM-CSF from the pore-forming gels leads to the accumulation of millions of cells in the material. These cells are highly enriched in CD11b(+) CD11c(+) DCs, and further analysis of cell surface marker expression indicates these DCs are immature. This study demonstrates that a polymeric delivery system can mediate the accumulation of a high number and percentage of immature DCs, and may provide the basis for further development of materials-based, therapeutic vaccines.

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

    PubMed Central

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

    2009-01-01

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

  7. Characterization of the Decision Network for Wing Expansion in Drosophila Using Targeted Expression of the TRPM8 Channel

    PubMed Central

    Peabody, Nathan C.; Pohl, Jascha B.; Diao, Fengqiu; Vreede, Andrew P.; Sandstrom, David J.; Wang, Howard; Zelensky, Paul K.; White, Benjamin H.

    2009-01-01

    After emergence, adult flies and other insects select a suitable perch and expand their wings. Wing expansion is governed by the hormone bursicon and can be delayed under adverse environmental conditions. How environmental factors delay bursicon release and alter perch selection and expansion behaviors has not been investigated in detail. Here we provide evidence that in Drosophila the motor programs underlying perch selection and wing expansion have different environmental dependencies. Using physical manipulations, we demonstrate that the decision to perch is based primarily on environmental valuations and is incrementally delayed under conditions of increasing perturbation and confinement. In contrast, the all-or-none motor patterns underlying wing expansion are relatively invariant in length regardless of environmental conditions. Using a novel technique for targeted activation of neurons, we show that the highly stereotyped wing expansion motor patterns can be initiated by stimulation of NCCAP, a small network of central neurons that regulates the release of bursicon. Activation of this network using the cold-sensitive rat TRPM8 channel is sufficient to trigger all essential behavioral and somatic processes required for wing expansion. The delay of wing expansion under adverse circumstances thus couples an environmentally-sensitive decision network to a command-like network that initiates a fixed action pattern. Because NCCAP mediates environmentally-insensitive ecdysis-related behaviors in Drosophila development prior to adult emergence, the study of wing expansion promises insights not only into how networks mediate behavioral choices, but also into how decision networks develop. PMID:19295141

  8. The Mediator complex and transcription regulation

    PubMed Central

    Poss, Zachary C.; Ebmeier, Christopher C.

    2013-01-01

    The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module. PMID:24088064

  9. Pore-scale studies of unconventional reservoir rocks

    NASA Astrophysics Data System (ADS)

    Silin, D.; Ajo Franklin, J. B.; Cabrini, S.; Kneafsey, T. J.; MacDowell, A.; Nico, P. S.; Tomutsa, L.

    2009-12-01

    Our overall objective is the development of a technique for predicting reservoir behavior from the pore structure of low-permeability rock. Gas shale and tight sands are examples of low-permeability formations containing enormous quantities of natural gas. As the availability of energy resources in conventional reservoirs is declining, the importance of these unconventional reservoirs is increasing. Our approach is based on acquiring micro- and nanometer-scale images of the pore structure of natural rocks using synchrotron X-ray microtomography (Advanced Light Source) and Focused Ion Beam milling (Molecular Foundry), Lawrence Berkeley National Laboratory. These techniques provide three dimensional images of the rich diversity of pore structures present in so called “unconventional resources.” Using these images as input data, Maximal Inscribed Spheres simulations are used to evaluate the two-phase flow properties of the rock.

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

    PubMed

    Juckers, Myra; Watmough, Shaun A

    2014-01-01

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

  11. Nanometer to Centimeter Scale Analysis and Modeling of Pore Structures

    NASA Astrophysics Data System (ADS)

    Wesolowski, D. J.; Anovitz, L.; Vlcek, L.; Rother, G.; Cole, D. R.

    2011-12-01

    The microstructure and evolution of pore space in rocks is a critically important factor controlling fluid flow. The size, distribution and connectivity of these confined geometries dictate how fluids including H2O and CO2, migrate into and through these micro- and nano-environments, wet and react with the solid. (Ultra)small-angle neutron scattering and autocorrelations derived from BSE imaging provide a method of quantifying pore structures in a statistically significant manner from the nanometer to the centimeter scale. Multifractal analysis provides additional constraints. These methods were used to characterize the pore features of a variety of potential CO2 geological storage formations and geothermal systems such as the shallow buried quartz arenites from the St. Peter Sandstone and the deeper Mt. Simon quartz arenite in Ohio as well as the Eau Claire shale and mudrocks from the Cranfield MS CO2 injection test and the normal temperature and high-temperature vapor-dominated parts of the Geysers geothermal system in California. For example, analyses of samples of St. Peter sandstone show total porosity correlates with changes in pores structure including pore size ratios, surface fractal dimensions, and lacunarity. These samples contain significant large-scale porosity, modified by quartz overgrowths, and neutron scattering results show significant sub-micron porosity, which may make up fifty percent or more of the total pore volume. While previous scattering data from sandstones suggest scattering is dominated by surface fractal behavior, our data are both fractal and pseudo-fractal. The scattering curves are composed of steps, modeled as polydispersed assemblages of pores with log-normal distributions. In some samples a surface-fractal overprint is present. There are also significant changes in the mono and multifractal dimensions of the pore structure as the pore fraction decreases. There are strong positive correlations between D(0) and image and total

  12. Pore sizes and filtration rates from two alumina slips

    SciTech Connect

    Smith, P.A. . Materials Science Dept.); Kerch, H.; Krueger, S.; Long, G.G. . Ceramics Div.); Keller, J.; Haber, R.A. . Dept. of Ceramics)

    1994-07-01

    The relationship between filtration rate and the resultant green body microstructure was examined for aqueous alumina slips cast at two different deflocculation states. The volume loading of both slips was 40%. Slip viscosities of 500 and 60 mPa[center dot]s were produced by different tetrasodium pyrophosphate additions. The filtration rate of these slips varied by a factor of 2; however, mercury porosimetry results showed the same average pore size for both samples. Single and multiple small-angle neutron scattering results showed the specimen cast with the higher-viscosity slip to possess a bimodal pore size distribution. The body cast with the low-viscosity slip showed unimodal porosity and, consequently, the filtration is attributed to the toroidal region between the packed particles. These results showed that mercury porosimetry does not provide a pore size that predicts filtration behavior of slips with different degrees of dispersion.

  13. Translocation of an Incompressible Vesicle through a Pore

    PubMed Central

    Shojaei, Hamid R.; Muthukumar, Murugappan

    2016-01-01

    We have derived the free energy landscape for the translocation of a single vesicle through a narrow pore by accounting for bending and stretching of the vesicle, and the deformation of the vesicle by the pore. Emergence of a free energy barrier for translocation is a general result, and the magnitude of the barrier is calculated in terms of the various material parameters. The extent of the reduction in the barrier by the presence of an external constant force is calculated. Using the Fokker–Planck formalism, we have calculated the average translocation time corresponding to the various free energy landscapes representing different parameter sets. The dependencies of the average translocation time on the strength of the external force, vesicle size, bending and stretching moduli of the vesicle, and radius and length of the pore are derived, and the computed results are discussed. PMID:27089012

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

    PubMed

    Bird, Sean P; Baker, Lane A

    2011-09-12

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

  15. Integration of pore features into the evaluation of fingerprint evidence.

    PubMed

    Anthonioz, Alexandre; Champod, Christophe

    2014-01-01

    Fingerprint practitioners rely on level 3 features to make decisions in relation to the source of an unknown friction ridge skin impression. This research proposes to assess the strength of evidence associated with pores when shown in (dis)agreement between a mark and a reference print. Based upon an algorithm designed to automatically detect pores, a metric is defined in order to compare different impressions. From this metric, the weight of the findings is quantified using a likelihood ratio. The results obtained on four configurations and 54 donors show the significant contribution of the pore features and translate into statistical terms what latent fingerprint examiners have developed holistically through experience. The system provides LRs that are indicative of the true state under both the prosecution and the defense propositions. Not only such a system brings transparency regarding the weight to assign to such features, but also forces a discussion in relation to the risks of such a model to mislead.

  16. An engineered dimeric protein pore that spans adjacent lipid bilayers

    PubMed Central

    Mantri, Shiksha; Sapra, K. Tanuj; Cheley, Stephen; Sharp, Thomas H.; Bayley, Hagan

    2013-01-01

    The bottom-up construction of artificial tissues is an underexplored area of synthetic biology. An important challenge is communication between constituent compartments of the engineered tissue and between the engineered tissue and additional compartments, including extracellular fluids, further engineered tissue and living cells. Here we present a dimeric transmembrane pore that can span two adjacent lipid bilayers and thereby allow aqueous compartments to communicate. Two heptameric staphylococcal α-hemolysin (αHL) pores were covalently linked in an aligned cap-to-cap orientation. The structure of the dimer, (α7)2, was confirmed by biochemical analysis, transmission electron microscopy (TEM) and single-channel electrical recording. We show that one of two β barrels of (α7)2 can insert into the lipid bilayer of a small unilamellar vesicle, while the other spans a planar lipid bilayer. (α7)2 pores spanning two bilayers were also observed by TEM. PMID:23591892

  17. Pore-scale simulation of calcium carbonate precipitation and dissolution under highly supersaturated conditions in a microfludic pore network

    NASA Astrophysics Data System (ADS)

    Yoon, H.; Dewers, T. A.; Valocchi, A. J.; Werth, C. J.

    2011-12-01

    Dissolved CO2 during geological CO2 storage may react with minerals in fractured rocks or confined aquifers and cause mineral precipitation. The overall rate of reaction can be affected by coupled processes among hydrodynamics, transport, and reactions at pore-scale. Pore-scale models of coupled fluid flow, reactive transport, and CaCO3 precipitation and dissolution are applied to account for transient experimental results of CaCO3 precipitation and dissolution under highly supersaturated conditions in a microfluidic pore network (i.e., micromodel). Pore-scale experiments in the micromodel are used as a basis for understanding coupled physics of systems perturbed by geological CO2 injection. In the micromodel, precipitation is induced by transverse mixing along the centerline in pore bodies. Overall, the pore-scale model qualitatively captured the governing physics of reactions such as precipitate morphology, precipitation rate, and maximum precipitation area in first few pore spaces. In particular, we found that proper estimation of the effective diffusion coefficient and the reactive surface area is necessary to adequately simulate precipitation and dissolution rates. As the model domain increases, the effect of flow patterns affected by precipitation on the overall reaction rate also increases. The model is also applied to account for the effect of different reaction rate laws on mineral precipitation and dissolution at pore-scale. Reaction rate laws tested include the linear rate law, nonlinear power law, and newly-developed rate law based on in-situ measurements at nano scale in the literature. Progress on novel methods for upscaling pore-scale models for reactive transport are discussed, and are being applied to mineral precipitation patterns observed in natural analogues. H.Y. and T. D. were supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of

  18. Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion.

    PubMed

    Krull, Sandra; Dörries, Julia; Boysen, Björn; Reidenbach, Sonja; Magnius, Lars; Norder, Helene; Thyberg, Johan; Cordes, Volker C

    2010-05-19

    Amassments of heterochromatin in somatic cells occur in close contact with the nuclear envelope (NE) but are gapped by channel- and cone-like zones that appear largely free of heterochromatin and associated with the nuclear pore complexes (NPCs). To identify proteins involved in forming such heterochromatin exclusion zones (HEZs), we used a cell culture model in which chromatin condensation induced by poliovirus (PV) infection revealed HEZs resembling those in normal tissue cells. HEZ occurrence depended on the NPC-associated protein Tpr and its large coiled coil-forming domain. RNAi-mediated loss of Tpr allowed condensing chromatin to occur all along the NE's nuclear surface, resulting in HEZs no longer being established and NPCs covered by heterochromatin. These results assign a central function to Tpr as a determinant of perinuclear organization, with a direct role in forming a morphologically distinct nuclear sub-compartment and delimiting heterochromatin distribution.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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