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Sample records for pore expansion mediated

  1. Lumenal protein within secretory granules affects fusion pore expansion.

    PubMed

    Weiss, Annita Ngatchou; Anantharam, Arun; Bittner, Mary A; Axelrod, Daniel; Holz, Ronald W

    2014-07-01

    It is often assumed that upon fusion of the secretory granule membrane with the plasma membrane, lumenal contents are rapidly discharged and dispersed into the extracellular medium. Although this is the case for low-molecular-weight neurotransmitters and some proteins, there are numerous examples of the dispersal of a protein being delayed for many seconds after fusion. We have investigated the role of fusion-pore expansion in determining the contrasting discharge rates of fluorescent-tagged neuropeptide-Y (NPY) (within 200 ms) and tissue plasminogen activator (tPA) (over many seconds) in adrenal chromaffin cells. The endogenous proteins are expressed in separate chromaffin cell subpopulations. Fusion pore expansion was measured by two independent methods, orientation of a fluorescent probe within the plasma membrane using polarized total internal reflection fluorescence microscopy and amperometry of released catecholamine. Together, they probe the continuum of the fusion-pore duration, from milliseconds to many seconds after fusion. Polarized total internal reflection fluorescence microscopy revealed that 71% of the fusion events of tPA-cer-containing granules maintained curvature for >10 s, with approximately half of the structures likely connected to the plasma membrane by a short narrow neck. Such events were not commonly observed upon fusion of NPY-cer-containing granules. Amperometry revealed that the expression of tPA-green fluorescent protein (GFP) prolonged the duration of the prespike foot ∼2.5-fold compared to NPY-GFP-expressing cells and nontransfected cells, indicating that expansion of the initial fusion pore in tPA granules was delayed. The t1/2 of the main catecholamine spike was also increased, consistent with a prolonged delay of fusion-pore expansion. tPA added extracellularly bound to the lumenal surface of fused granules. We propose that tPA within the granule lumen controls its own discharge. Its intrinsic biochemistry determines not only

  2. Free energy landscape of rim-pore expansion in membrane fusion.

    PubMed

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

    2014-11-18

    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.

  3. 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

  4. 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.

  5. Two Distinct Modes of Exocytotic Fusion Pore Expansion in Large Astrocytic Vesicles*

    PubMed Central

    Peng, Hong; Kang, Ning; Xu, Jun; Stanton, Patric K.; Kang, Jian

    2013-01-01

    Formation of the fusion pore is a central question for regulated exocytosis by which secretory cells release neurotransmitters or hormones. Here, by dynamically monitoring exocytosis of large vesicles (2–7 μm) in astrocytes with two-photon microscopy imaging, we found that the exocytotic fusion pore was generated from the SNARE-dependent fusion at a ring shape of the docked plasma-vesicular membrane and the movement of a fusion-produced membrane fragment. We observed two modes of fragment movements, 1) a shift fragment that shifted to expand the fusion pore and 2) a fall-in fragment that fell into the collapsed vesicle to expand the fusion pore. Shift and fall-in modes are associated with full and partial collapses of large vesicles, respectively. The astrocytic marker, sulforhodamine 101, stained the fusion-produced membrane fragment more brightly than FM 1-43. Sulforhodamine 101 imaging showed that double fusion pores could simultaneously occur in a single vesicle (16% of large vesicles) to accelerate discharge of vesicular contents. Electron microscopy of large astrocytic vesicles showed shift and fall-in membrane fragments. Two modes of fusion pore formation demonstrate a novel mechanism underlying fusion pore expansion and provide a new explanation for full and partial collapses of large secretory vesicles. PMID:23620588

  6. Isoreticular Expansion of Metal-Organic Frameworks with Multiple Functionalities and Controlled Pore Sizes

    NASA Astrophysics Data System (ADS)

    Deng, Hexiang

    Metal-Organic Frameworks (MOFs) are made by linking organic and inorganic molecular building blocks into extended structures through strong bonds. With a judicious choice of inorganic joints and various functional groups available in organic links, a large number of MOFs have been synthesized in the past decade. Along with the fast expansion of the family of MOFs, important applications emerge including hydrogen storage and carbon dioxide capture, both of which address the most pressing societal demand for clean and sustainable energy resources. Although numerous MOFs are now known and they have found widespread applications, the introduction of more than one kind of building block into their crystal structures remains challenging. One of the main objectives of this study is to demonstrate the successful incorporating of multiple functional groups into MOFs. Here, a new strategy has been developed to achieve the synthesis of a series of eighteen multivariate MOFs (MTV-MOFs) containing up to eight distinct functional groups, while their parent topologies were fully preserved. The backbone of these MTV-MOFs was found to be ordered, while the orientation, number, relative position and ratio of the functionalities along the backbone could be controlled by virtue of the unchanged length of the link and its unaltered connectivity. This strategy allows us to endow the pores of these MOFs with a new level of complexity which far exceeds any held by that of the original mono-functional MOFs---an aspect that makes it possible to fine-tune the pore environment of a porous crystal with favorable implications. Indeed, one member of these MTV-MOFs has already shown an 87% improvement of the hydrogen uptake while another member demonstrated a 400% increase in CO2 selectivity comparing to their mono-functional counterparts. Another goal of this study has been to maximize MOF porosity and pore size. There were three major obstacles against expanding the pore size of porous crystals

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

    PubMed Central

    Haller, Thomas; Dietl, Paul; Pfaller, Kristian; Frick, Manfred; Mair, Norbert; Paulmichl, Markus; Hess, Michael W.; Fürst, Johannes; Maly, Karl

    2001-01-01

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

  8. [Resveratrol promote permeability transition pore opening mediated by Ca2+].

    PubMed

    Tian, Xue-mei; Zhang, Zhan-xia

    2003-02-01

    To investigate the mechanisms of anti-cancer effect of resveratrol (Res), and the effects of Res in cell apoptosis. The role of Res playing in mitochondrial permeability transition pore (PTP) induction was studied. Mitochondria was prepared from the liver of Wistar rats. The effects of Res on oxygen consumption of isolated mitochondria from rat liver was measured with Clark-type electrode and resulted in respiration control rate (RCR). Mitochondrial swelling affected by Res was assessed spectrophotometrically, through the changes in absorbance at 540 nm. The PTP opening was learned from the results. Membrane potential of mitochondia was measured through fluorescence spectrophotometry. Res was shown to inhibit the respiration and decrease the RCR of mitochondria. Res can promote the PTP opening mediated by Ca2+. Res was shown to promote the increase of mitochondial membrane potential mediated by Ca2+ and loss of mitochondial membrane potential. Res was shown to inhibit mitochondial respiration and induce PTP opening of mitochondria. These may be one of the pathways that Res showed anti-cancer action and induce cells apoptosis.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-04-12

    Flickering of fusion pores during exocytotic release of hormones and neurotransmitters is well documented, but without assays that use biochemically defined components and measure single-pore dynamics, the mechanisms remain poorly understood. We used total internal reflection fluorescence microscopy to quantify fusion-pore dynamics in vitro and to separate the roles of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and lipid bilayer properties. When small unilamellar vesicles bearing neuronal v-SNAREs fused with planar bilayers reconstituted with cognate t-SNARES, lipid and soluble cargo transfer rates were severely reduced, suggesting that pores flickered. From the lipid release times we computed pore openness, the fraction of time the pore is open, which increased dramatically with cholesterol. For most lipid compositions tested, SNARE-mediated and nonspecifically nucleated pores had similar openness, suggesting that pore flickering was controlled by lipid bilayer properties. However, with physiological cholesterol levels, SNAREs substantially increased the fraction of fully open pores and fusion was so accelerated that there was insufficient time to recruit t-SNAREs to the fusion site, consistent with t-SNAREs being preclustered by cholesterol into functional docking and fusion platforms. Our results suggest that cholesterol opens pores directly by reducing the fusion-pore bending energy, and indirectly by concentrating several SNAREs into individual fusion events. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Axonal Degeneration Is Mediated by the Mitochondrial Permeability Transition Pore

    PubMed Central

    Barrientos, Sebastian A.; Martinez, Nicolas W.; Yoo, Soonmoon; Jara, Juan S.; Zamorano, Sebastian; Hetz, Claudio; Twiss, Jeffery L.; Alvarez, Jaime; Court, Felipe A.

    2011-01-01

    Axonal degeneration is an active process that has been associated with neurodegenerative conditions triggered by mechanical, metabolic, infectious, toxic, hereditary and inflammatory stimuli. This degenerative process can cause permanent loss of function, so it represents a focus for neuroprotective strategies. Several signaling pathways are implicated in axonal degeneration, but identification of an integrative mechanism for this self-destructive process has remained elusive. Here, we show that rapid axonal degeneration triggered by distinct mechanical and toxic insults is dependent on the activation of the mitochondrial permeability transition pore (mPTP). Both pharmacological and genetic targeting of cyclophilin D, a functional component of the mPTP, protects severed axons and vincristine-treated neurons from axonal degeneration in ex vivo and in vitro mouse and rat model systems. These effects were observed in axons from both the peripheral and central nervous system. Our results suggest that the mPTP is a key effector of axonal degeneration, upon which several independent signaling pathways converge. Since axonal and synapse degeneration are increasingly considered early pathological events in neurodegeneration, our work identifies a potential target for therapeutic intervention in a wide variety of conditions that lead to loss of axons and subsequent functional impairment. PMID:21248121

  13. cAMP-mediated stabilization of fusion pores in cultured rat pituitary lactotrophs

    PubMed Central

    Calejo, Ana Isabel; Jorgačevski, Jernej; Kucka, Marek; Kreft, Marko; Gonçalves, Paula Polónia; Stojilkovic, Stanko S.; Zorec, Robert

    2013-01-01

    Regulated exocytosis mediates the release of hormones and transmitters. The last step of this process is represented by the merger between the vesicle and the plasma membranes, and the formation of a fusion pore. Once formed, the initially stable and narrow fusion pore may reversibly widen (transient exocytosis) or fully open (full-fusion exocytosis). Exocytosis is typically triggered by an elevation in cytosolic calcium activity. However, other second messengers, such as cyclic AMP (cAMP), have been reported to modulate secretion. The way in which cAMP influences the transitions between different fusion pore states remains unclear. Here, hormone release studies show that prolactin release from isolated rat lactotrophs stimulated by forskolin, an activator of adenylyl cyclases, and by membrane-permeable cAMP analog (dbcAMP), exhibit a biphasic concentration dependency. While at lower concentrations (2–10 μM forskolin and 2.5–5 mM dbcAMP) these agents stimulate prolactin release, an inhibition is measured at higher concentrations (50 μM forskolin and 10–15 mM dbcAMP). By using high-resolution capacitance (Cm) measurements, we recorded discrete increases in Cm, which represent elementary exocytic events. An elevation of cAMP leaves the frequency of full-fusion events unchanged, while increasing the frequency of transient events. These exhibited a wider fusion pore as measured by increased fusion pore conductance and a prolonged fusion pore dwell-time. The probability of observing rhythmic reopening of transient fusion pores was elevated by dbcAMP. In conclusion, cAMP-mediated stabilization of wide fusion pores prevents vesicles from proceeding to the full-fusion stage of exocytosis, which hinders vesicle content discharge at high cAMP concentrations. PMID:23637196

  14. Expansion dynamics of a self-avoiding polymer in a cylindrical pore

    NASA Astrophysics Data System (ADS)

    Jung, Youngkyun; Jeon, Chanil; Ha, Meesoon; Ha, Bae-Yeun

    2013-12-01

    Inspired by recent bacterial chromosome experiments in narrow channels, we simulate the expansion (and internal) dynamics of a self-avoiding polymer under cylindrical confinement. The chain is trapped in a piston, compressed up to 20% of its equilibrium length, and released unidirectionally from the right end of the piston. Our results suggest that the chain initially expands like a concentrated hard-sphere system, enters a subdiffusive regime at an intermediate time, and eventually relaxes globally to its equilibrium size. Using our results, we test a few theoretical models (e.g., a Flory-type approach), in which the blob-blob or monomer-monomer interaction determines “expansion forces,” clarifying their applicability. Our results can be used for exploring further the polymer aspect of bacterial chromosomes.

  15. The extracellular EXO protein mediates cell expansion in Arabidopsis leaves.

    PubMed

    Schröder, Florian; Lisso, Janina; Lange, Peggy; Müssig, Carsten

    2009-02-13

    The EXO (EXORDIUM) gene was identified as a potential mediator of brassinosteroid (BR)-promoted growth. It is part of a gene family with eight members in Arabidopsis. EXO gene expression is under control of BR, and EXO overexpression promotes shoot and root growth. In this study, the consequences of loss of EXO function are described. The exo loss of function mutant showed diminished leaf and root growth and reduced biomass production. Light and scanning electron microscopy analyses revealed that impaired leaf growth is due to reduced cell expansion. Epidermis, palisade, and spongy parenchyma cells were smaller in comparison to the wild-type. The exo mutant showed reduced brassinolide-induced cotyledon and hypocotyl growth. In contrast, exo roots were significantly more sensitive to the inhibitory effect of synthetic brassinolide. Apart from reduced growth, exo did not show severe morphological abnormalities. Gene expression analyses of leaf material identified genes that showed robust EXO-dependent expression. Growth-related genes such as WAK1, EXP5, and KCS1, and genes involved in primary and secondary metabolism showed weaker expression in exo than in wild-type plants. However, the vast majority of BR-regulated genes were normally expressed in exo. HA- and GFP-tagged EXO proteins were targeted to the apoplast. The EXO gene is essential for cell expansion in leaves. Gene expression patterns and growth assays suggest that EXO mediates BR-induced leaf growth. However, EXO does not control BR-levels or BR-sensitivity in the shoot. EXO presumably is involved in a signalling process which coordinates BR-responses with environmental or developmental signals. The hypersensitivity of exo roots to BR suggests that EXO plays a diverse role in the control of BR responses in the root.

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

    PubMed Central

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

    2010-01-01

    Paramyxovirus fusion (F) proteins promote both virus-cell fusion, required for viral entry, and cell-cell fusion, resulting in syncytia formation. We used the F-actin stabilizing drug, jasplakinolide, and the G-actin sequestrant, latrunculin A, to examine the role of actin dynamics in cell-cell fusion mediated by the parainfluenza virus 5 (PIV5) F protein. Jasplakinolide treatment caused a dose-dependent increase in cell-cell fusion as measured by both syncytia and reporter gene assays, and latrunculin A treatment also resulted in fusion stimulation. Treatment with jasplakinolide or latrunculin A partially rescued a fusion pore opening defect caused by deletion of the PIV5 F protein cytoplasmic tail, but these drugs had no effect on fusion inhibited at earlier stages by either temperature arrest or by a PIV5 heptad repeat peptide. These data suggest that the cortical actin cytoskeleton is an important regulator of fusion pore enlargement, an energetically costly stage of viral fusion protein-mediated membrane merger. PMID:20537366

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

    SciTech Connect

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

    2010-08-15

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

  18. Metazoan Nuclear Pores Provide a Scaffold for Poised Genes and Mediate Induced Enhancer-Promoter Contacts.

    PubMed

    Pascual-Garcia, Pau; Debo, Brian; Aleman, Jennifer R; Talamas, Jessica A; Lan, Yemin; Nguyen, Nha H; Won, Kyoung J; Capelson, Maya

    2017-04-06

    Nuclear pore complex components (Nups) have been implicated in transcriptional regulation, yet what regulatory steps are controlled by metazoan Nups remains unclear. We identified the presence of multiple Nups at promoters, enhancers, and insulators in the Drosophila genome. In line with this binding, we uncovered a functional role for Nup98 in mediating enhancer-promoter looping at ecdysone-inducible genes. These genes were found to be stably associated with nuclear pores before and after activation. Although changing levels of Nup98 disrupted enhancer-promoter contacts, it did not affect ongoing transcription but instead compromised subsequent transcriptional activation or transcriptional memory. In support of the enhancer-looping role, we found Nup98 to gain and retain physical interactions with architectural proteins upon stimulation with ecdysone. Together, our data identify Nups as a class of architectural proteins for enhancers and supports a model in which animal genomes use the nuclear pore as an organizing scaffold for inducible poised genes.

  19. 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

  20. Dynamin-2 Regulates Fusion Pore Expansion and Quantal Release through a Mechanism that Involves Actin Dynamics in Neuroendocrine Chromaffin Cells

    PubMed Central

    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. PMID:23940613

  1. 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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed Central

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

    2009-01-01

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

  4. Permeability transition pore-mediated mitochondrial superoxide flashes regulate cortical neural progenitor differentiation.

    PubMed

    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 Ca(2+) 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.

  5. Hydrophobic interactions between the voltage sensor and pore mediate inactivation in Kv11.1 channels.

    PubMed

    Perry, Matthew D; Wong, Sophia; Ng, Chai Ann; Vandenberg, Jamie I

    2013-09-01

    Kv11.1 channels are critical for the maintenance of a normal heart rhythm. The flow of potassium ions through these channels is controlled by two voltage-regulated gates, termed "activation" and "inactivation," located at opposite ends of the pore. Crucially in Kv11.1 channels, inactivation gating occurs much more rapidly, and over a distinct range of voltages, compared with activation gating. Although it is clear that the fourth transmembrane segments (S4), within each subunit of the tetrameric channel, are important for controlling the opening and closing of the activation gate, their role during inactivation gating is much less clear. Here, we use rate equilibrium free energy relationship (REFER) analysis to probe the contribution of the S4 "voltage-sensor" helix during inactivation of Kv11.1 channels. Contrary to the important role that charged residues play during activation gating, it is the hydrophobic residues (Leu529, Leu530, Leu532, and Val535) that are the key molecular determinants of inactivation gating. Within the context of an interconnected multi-domain model of Kv11.1 inactivation gating, our REFER analysis indicates that the S4 helix and the S4-S5 linker undergo a conformational rearrangement shortly after that of the S5 helix and S5P linker, but before the S6 helix. Combining REFER analysis with double mutant cycle analysis, we provide evidence for a hydrophobic interaction between residues on the S4 and S5 helices. Based on a Kv11.1 channel homology model, we propose that this hydrophobic interaction forms the basis of an intersubunit coupling between the voltage sensor and pore domain that is an important mediator of inactivation gating.

  6. Substantial Expansion of Detectable Size Range in Ionic Current Sensing through Pores by Using a Microfluidic Bridge Circuit.

    PubMed

    Yasaki, Hirotoshi; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

    2017-09-07

    Measuring ionic currents passing through nano- or micro-pores has shown great promise for the electrical discrimination of various biomolecules, cells, bacteria, and viruses. However, conventional measurements have shown there is an inherent limitation to the detectable particle volume (1% of the pore volume), which critically hinders applications to real mixtures of biomolecule samples with a wide size range of suspended particles. Here we propose a rational methodology which can detect samples with the detectable particle volume of 0.01% of the pore volume by measuring a transient current generated from the potential differences in a microfluidic bridge circuit. Our method substantially suppresses the background ionic current from the µA level to the pA level, which essentially lowers the detectable particle volume limit even for relatively large pore structures. Indeed, utilizing a microscale long pore structure (volume of 5.6 × 10(4) aL; height and width of 2.0 × 2.0 µm; length of 14 µm), we successfully detected various samples including polystyrene nanoparticles (volume: 4 aL), bacteria, cancer cells, and DNA molecules. Our method will expand the applicability of ionic current sensing systems for various mixed biomolecule samples with a wide size range, which have been difficult to measure by previously existing pore technologies.

  7. Pore size and concentration effect of mesoporous silica nanoparticles on the coefficient of thermal expansion and optical transparency of poly(ether sulfone) films.

    PubMed

    Vo, Nhat Tri; Patra, Astam K; Kim, Dukjoon

    2017-01-18

    Mesoporous silica nanoparticles (MSNs) with uniform size (<50 nm) yet with different pore diameters were synthesized, and used as fillers in poly(ether sulfone) (PES) films in order to decrease their coefficient of thermal expansion (CTE) without sacrificing optical transparency. Here, both CTE and optical transparency of the MSN/PES nanocomposite films gradually decreased with increasing MSN concentration. The PES films containing MSNs with larger pores showed the best performance in CTE and optical transparency. While the CTE decreased by 32.3% with increasing MSN content up to 0.5 wt%, the optical transparency decreased by only less than 6.9% because of the small and uniform particle size of less than 50 nm, which minimizes light scattering. This pore size effect is more clearly observed via an annealing process, which enables the polymer chains to slowly move and fill in the free volume in the pores of the MSN, and thus restricts the thermal motion. The effect of the silica nanoparticles was investigated not only on the thermal stability but also on the mechanical stability. We expect the MSNs synthesized in this study to be used as a promising filler to enhance the thermal and mechanical stability of the PES substrate without sacrificing its optical transparency.

  8. RNA-binding proteins in microsatellite expansion disorders: mediators of RNA toxicity.

    PubMed

    Echeverria, Gloria V; Cooper, Thomas A

    2012-06-26

    Although protein-mediated toxicity in neurological disease has been extensively characterized, RNA-mediated toxicity is an emerging mechanism of pathogenesis. In microsatellite expansion disorders, expansion of repeated sequences in noncoding regions gives rise to RNA that produces a toxic gain of function, while expansions in coding regions can disrupt protein function as well as produce toxic RNA. The toxic RNA typically aggregates into nuclear foci and contributes to disease pathogenesis. In many cases, toxicity of the RNA is caused by the disrupted functions of RNA-binding proteins. We will discuss evidence for RNA-mediated toxicity in microsatellite expansion disorders. Different microsatellite expansion disorders are linked with alterations in the same as well as disease-specific RNA-binding proteins. Recent studies have shown that microsatellite expansions can encode multiple repeat-containing toxic RNAs through bidirectional transcription and protein species through repeat-associated non-ATG translation. We will discuss approaches that have characterized the toxic contributions of these various factors.

  9. Anion-mediated negative thermal expansion in lanthanum hexaboride

    NASA Astrophysics Data System (ADS)

    Mattox, Tracy M.; Groome, Chloe; Doran, Andrew; Beavers, Christine M.; Urban, Jeffrey J.

    2017-10-01

    Lanthanum hexaboride (LaB6) is well known for its thermionic emission, mechanical hardness, and intriguing optical properties. Though this material has been studied for decades, it is difficult to design LaB6 to meet application needs because little is understood about the mechanistic details of the synthesis. The ability to observe lattice formation during the reaction through in-situ x-ray diffraction is helping improve our knowledge. We report here the strong influence of anion size of the lanthanum precursor in the solid state reaction of LaX3 (X = Cl or I) and NaBH4. The Cl atom of the precursor remains within LaB6 post-synthesis and causes negative thermal expansion when the lattice is heated. Replacing Cl with the larger I atom has a larger impact on crystal growth; however, I does not remain within the lattice post-synthesis. These results suggest subtle new synthetic knobs may be available to optimize the synthesis of LaB6 that have previously gone unexplored.

  10. 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

  11. Argonaute2 mediates compensatory expansion of the pancreatic β cell.

    PubMed

    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

    2014-01-07

    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. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. 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

  13. A protective antigen mutation increases the pH threshold of anthrax toxin receptor 2-mediated pore formation.

    PubMed

    Dennis, Melissa K; Mogridge, Jeremy

    2014-04-08

    Anthrax toxin protective antigen (PA) binds cellular receptors and self-assembles into oligomeric prepores. A prepore converts to a protein translocating pore after it has been transported to an endosome where the low pH triggers formation of a membrane-spanning β-barrel channel. Formation of this channel occurs after some PA-receptor contacts are broken to allow pore formation, while others are retained to preserve receptor association. The interaction between PA and anthrax toxin receptor 1 (ANTXR1) is weaker than its interaction with ANTXR2 such that the pH threshold of ANTXR1-mediated pore formation is higher by 1 pH unit. Here we examine receptor-specific differences in toxin binding and pore formation by mutating PA residue G342 that selectively abuts ANTXR2. Mutation of G342 to valine, leucine, isoleucine, or tryptophan increased the amount of PA bound to ANTXR1-expressing cells and decreased the amount of PA bound to ANTXR2-expressing cells. The more conservative G342A mutation did not affect the level of binding to ANTXR2, but ANTXR2-bound PA-G342A prepores exhibited a pH threshold higher than that of wild-type prepores. Mixtures of wild-type PA and PA-G342A were functional in toxicity assays, and the pH threshold of ANTXR2-mediated pore formation was dictated by the relative amounts of the two proteins in the hetero-oligomers. These results suggest that PA subunits within an oligomer do not have to be triggered simultaneously for a productive membrane insertion event to occur.

  14. 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.

  15. C9orf72 expansion disrupts ATM-mediated chromosomal break repair.

    PubMed

    Walker, Callum; Herranz-Martin, Saul; Karyka, Evangelia; Liao, Chunyan; Lewis, Katherine; Elsayed, Waheba; Lukashchuk, Vera; Chiang, Shih-Chieh; Ray, Swagat; Mulcahy, Padraig J; Jurga, Mateusz; Tsagakis, Ioannis; Iannitti, Tommaso; Chandran, Jayanth; Coldicott, Ian; De Vos, Kurt J; Hassan, Mohamed K; Higginbottom, Adrian; Shaw, Pamela J; Hautbergue, Guillaume M; Azzouz, Mimoun; El-Khamisy, Sherif F

    2017-09-01

    Hexanucleotide repeat expansions represent the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, though the mechanisms by which such expansions cause neurodegeneration are poorly understood. We report elevated levels of DNA-RNA hybrids (R-loops) and double strand breaks in rat neurons, human cells and C9orf72 ALS patient spinal cord tissues. Accumulation of endogenous DNA damage is concomitant with defective ATM-mediated DNA repair signaling and accumulation of protein-linked DNA breaks. We reveal that defective ATM-mediated DNA repair is a consequence of P62 accumulation, which impairs H2A ubiquitylation and perturbs ATM signaling. Virus-mediated expression of C9orf72-related RNA and dipeptide repeats in the mouse central nervous system increases double strand breaks and ATM defects and triggers neurodegeneration. These findings identify R-loops, double strand breaks and defective ATM-mediated repair as pathological consequences of C9orf72 expansions and suggest that C9orf72-linked neurodegeneration is driven at least partly by genomic instability.

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

    PubMed Central

    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.

    2016-01-01

    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 1, increases the duration for which patients shed the pathogen in their feces and may on occasion produce a bacteriologic and symptomatic relapse 2,3. These antibiotic-induced changes in the gut microbiota can be studied in mice, where the disruption of a balanced microbial community by treatment with streptomycin leads to an expansion of S. enterica serovars in the large bowel 4. 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 cecal mucosa, streptomycin treatment increased post-antibiotic availability of the oxidation products galactarate and glucarate in the murine cecum. S. Typhimurium utilized galactarate and glucarate within the gut lumen of streptomycin pre-treated mice and genetic ablation of the respective catabolic pathways reduced its competitiveness. Our results identify a host-mediated oxidation of carbohydrates in the gut as a novel mechanism for post-antibiotic pathogen expansion. PMID:27309805

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Caplan, Joshua S; Giménez, Daniel; Subroy, Vandana; Heck, Richard J; Prior, Stephen A; Runion, G Brett; Torbert, H Allen

    2017-04-01

    Soil pore structure has a strong influence on water retention, and is itself influenced by plant and microbial dynamics such as root proliferation and microbial exudation. Although increased nitrogen (N) availability and elevated atmospheric CO2 concentrations (eCO2 ) often have interacting effects on root and microbial dynamics, it is unclear whether these biotic effects can translate into altered soil pore structure and water retention. This study was based on a long-term experiment (7 yr at the time of sampling) in which a C4 pasture grass (Paspalum notatum) was grown on a sandy loam soil while provided factorial additions of N and CO2 . Through an analysis of soil aggregate fractal properties supported by 3D microtomographic imagery, we found that N fertilization induced an increase in intra-aggregate porosity and a simultaneous shift toward greater accumulation of pore space in larger aggregates. These effects were enhanced by eCO2 and yielded an increase in water retention at pressure potentials near the wilting point of plants. However, eCO2 alone induced changes in the opposite direction, with larger aggregates containing less pore space than under control conditions, and water retention decreasing accordingly. Results on biotic factors further suggested that organic matter gains or losses induced the observed structural changes. Based on our results, we postulate that the pore structure of many mineral soils could undergo N-dependent changes as atmospheric CO2 concentrations rise, having global-scale implications for water balance, carbon storage, and related rhizosphere functions. © 2016 John Wiley & Sons Ltd.

  19. Synaptic fusion pore structure and AMPA receptor activation according to Brownian simulation of glutamate diffusion.

    PubMed

    Ventriglia, Francesco; Maio, Vito Di

    2003-03-01

    The rising phase of fast, AMPA-mediated Excitatory Post Synaptic Currents (EPSCs) has a primary role in the computational ability of neurons. The structure and radial expansion velocity of the fusion pore between the vesicle and the presynaptic membrane could be important factors in determining the time course of the EPSC. We have used a Brownian simulation model for glutamate neurotransmitter diffusion to test two hypotheses on the fusion pore structure, namely, the proteinaceous pore and the purely lipidic pore. Three more hypotheses on the radial expansion velocity were also tested. The rising phases of the EPSC, computed under various conditions, were compared with experimental data from the literature. Our present results show that a proteinaceous fusion pore should produce a more marked foot at the beginning of the rising phase of the EPSC. They also confirm the hypothesis that the structure of the fusion pore and its radial expansion velocity play significant roles in shaping the fast EPSC time course.

  20. Alcohol and thiamine deficiency trigger differential mitochondrial transition pore opening mediating cellular death.

    PubMed

    Bâ, Abdoulaye

    2017-06-01

    Accumulating evidence has shown that binge-type alcohol intake in mothers interferes with thiamine deficiency (TD) to promote the fetal alcohol syndrome (FAS). Developmental alcohol or TD exposures act either synergistically or separately to reproduce FAS features e.g. intrauterine growth retardation and related microcephaly characterized by extensive cellular death induced by one another neurotoxicant. However molecular and cellular mechanisms underlying apoptosis in both alcohol and TD toxicities are unknown. The current review addresses mechanisms of apoptosis underlying alcohol and TD toxicities for further understanding FAS pathology. This study indicates two different mitochondria pathways regulating cellular death: The first mechanism may engage alcohol which activates the c-subunit ring of the F0-ATP synthase to form MPT pore-dependent apoptosis; following the second mechanism, TD activates CyP-D translocation from mitochondrial matrix towards the mitochondrial inner membrane to form MPT pore-dependent necrosis. These studies shed light upon molecular and cellular mechanisms underlying apoptosis and necrosis in developemental brain disorders related to alcohol and thiamine deficiency, in hopes of developing new therapeutic strategies for FAS medication.

  1. Intravenous immunoglobulin-induced IL-33 is insufficient to mediate basophil expansion in autoimmune patients

    PubMed Central

    Sharma, Meenu; Schoindre, Yoland; Hegde, Pushpa; Saha, Chaitrali; Maddur, Mohan S.; Stephen-Victor, Emmanuel; Gilardin, Laurent; Lecerf, Maxime; Bruneval, Patrick; Mouthon, Luc; Benveniste, Olivier; Kaveri, Srini V.; Bayry, Jagadeesh

    2014-01-01

    Intravenous immunoglobulin (IVIg) is used in the therapy of various autoimmune and inflammatory diseases. Recent studies in experimental models propose that anti-inflammatory effects of IVIg are mainly mediated by α2,6-sialylated Fc fragments. These reports further suggest that α2,6-sialylated Fc fragments interact with DC-SIGN+ cells to release IL-33 that subsequently expands IL-4-producing basophils. However, translational insights on these observations are lacking. Here we show that IVIg therapy in rheumatic patients leads to significant raise in plasma IL-33. However, IL-33 was not contributed by human DC-SIGN+ dendritic cells and splenocytes. As IL-33 has been shown to expand basophils, we analyzed the proportion of circulating basophils in these patients following IVIg therapy. In contrast to mice data, IVIg therapy led to basophil expansion only in two patients who also showed increased plasma levels of IL-33. Importantly, the fold-changes in IL-33 and basophils were not correlated and we could hardly detect IL-4 in the plasma following IVIg therapy. Thus, our results indicate that IVIg-induced IL-33 is insufficient to mediate basophil expansion in autoimmune patients. Hence, IL-33 and basophil-mediated anti-inflammatory mechanism proposed for IVIg might not be pertinent in humans. PMID:25012067

  2. Bnip3-mediated mitochondrial autophagy is independent of the mitochondrial permeability transition pore

    PubMed Central

    Quinsay, Melissa N; Thomas, Robert L; Lee, Youngil

    2010-01-01

    Bnip3 is a pro-apoptotic BH3-only protein which is associated with mitochondrial dysfunction and cell death. Bnip3 is also a potent inducer of autophagy in many cells. In this study, we have investigated the mechanism by which Bnip3 induces autophagy in adult cardiac myocytes. Overexpression of Bnip3 induced extensive autophagy in adult cardiac myocytes. Fluorescent microscopy studies and ultrastructural analysis revealed selective degradation of mitochondria by autophagy in myocytes overexpressing Bnip3. Oxidative stress and increased levels of intracellular Ca2+ have been reported by others to induce autophagy, but Bnip3-induced autophagy was not abolished by antioxidant treatment or the Ca2+ chelator BAPTA-AM. We also investigated the role of the mitochondrial permeability transition pore (mPTP) in Bnip3-induced autophagy. Although the mPTP has previously been implicated in the induction of autophagy and selective removal of damaged mitochondria by autophagosomes, mitochondria sequestered by autophagosomes in Bnip3-treated cardiac myocytes had not undergone permeability transition and treatment with the mPTP inhibitor cyclosporine A did not inhibit mitochondrial autophagy in cardiac myocytes. Moreover, cyclophilin D (cypD) is an essential component of the mPTP and Bnip3 induced autophagy to the same extent in embryonic fibroblasts isolated from wild-type and cypD-deficient mice. These results support a model where Bnip3 induces selective removal of the mitochondria in cardiac myocytes and that Bnip3 triggers induction of autophagy independent of Ca2+, ROS generation and mPTP opening. PMID:20668412

  3. 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

  4. Improvement of endothelial progenitor outgrowth cell (EPOC)-mediated vascularization in gelatin-based hydrogels through pore size manipulation.

    PubMed

    Fu, Jiayin; Wiraja, Christian; Muhammad, Hamizan B; Xu, Chenjie; Wang, Dong-An

    2017-08-01

    In addition to chemical compositions, physical properties of scaffolds, such as pore size, can also influence vascularization within the scaffolds. A larger pore has been shown to improve host vascular tissue invasion into scaffolds. However, the influence of pore sizes on vascularization by endothelial cells directly encapsulated in hydrogels remains unknown. In this study, micro-cavitary hydrogels with different pore sizes were created in gelatin-methacrylate hydrogels with dissolvable gelatin microspheres (MS) varying in sizes. The effect of pore sizes on vascular network formation by endothelial progenitor outgrowth cells (EPOCs) encapsulated in hydrogels was then investigated both in vitro and in vivo. When cultured in vitro, vascular networks were formed around pore structures in micro-cavitary hydrogels. The middle pore size supported best differentiation of EPOCs and thus best hydrogel vascularization in vitro. When implantation in vivo, functional connections between encapsulated EPOCs and host vasculature micro-cavitary hydrogels were established. Vascularization in vivo was promoted best in hydrogels with the large pore size due to the increased vascular tissue invasion. These results highlight the difference between in vitro and in vivo culture conditions and indicate that pore sizes shall be designed for in vitro and in vivo hydrogel vascularization respectively. Pore sizes for hydrogel vascularization in vitro shall be middle ones and pore sizes for hydrogel vascularization in vivo shall be large ones. This study reveals that the optimal pore size for hydrogel vascularization in vitro and in vivo is different. The middle pore size supported best differentiation of EPOCs and thus best hydrogel vascularization in vitro, while vascularization in vivo was promoted best in hydrogels with the large pore size due to the increased vascular tissue invasion. These results highlight the difference between in vitro and in vivo culture conditions and indicate that

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

    PubMed

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

    2015-08-28

    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.

  6. 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

  7. 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

  8. 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. © 2009 German Botanical Society and The Royal Botanical Society of The Netherlands.

  9. 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.

  10. 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

  11. High surface area Au-SBA-15 and Au-MCM-41 materials synthesis: tryptophan amino acid mediated confinement of gold nanostructures within the mesoporous silica pore walls.

    PubMed

    Selvakannan, Pr; Mantri, Kshudiram; Tardio, James; Bhargava, Suresh K

    2013-03-15

    Advantages of confining the gold nanostructures formation within the mesoporous silica pore walls during its silica condensation and consequent improvement in the textural properties such as specific surface area, pore volume, pore diameter have been demonstrated, while retaining gold nanostructures within the silica walls. This has been achieved by tryptophan mediated confinement of gold nanoparticles formation within the condensing silica framework, to obtain Au-SBA-15 (SSA 1247 m(2)/g, V(t)~1.37 cm(3)/g) and Au-MCM-41 (SSA 1287 m(2)/g, V(t)~1.1 cm(3)/g), mesoporous silica materials having the combination of very high surface area from the porous support as well as gold nanoparticles infiltrated silica walls. Choice of tryptophan for this purpose is that it has an indole group, which was known to reduce gold ions to form gold nanoparticles and its amine and carboxylic acid groups, catalyze the hydrolysis of silica precursors in a wide range of pH. These properties have been utilized in restricting the gold nanostructures formation inside the condensing silica phase without affecting the self assembly between the silica precursors and the triblock copolymer (for SBA-15) or cetyltrimethylammonium bromide template (for MCM-41). The polytryptophan and the gold nanostructures, which were encapsulated within the silica framework and upon removal of the template by calcination resulting in the formation mesoporous materials wherein the silica walls become microporous due to the removal of occluded polytryptophan and the resulting microchannels contain very small gold nanostructures. Hence, the resulting materials have very high surface area, high pore volume and narrow pore size distribution as compared to their parent SBA-15, MCM-41 and SBA-15, MCM-41 post functionalized with gold nanoparticles inside the pores.

  12. 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

  13. 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

  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. 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.

  16. Switch from inhibition to activation of the mitochondrial permeability transition during hematoporphyrin-mediated photooxidative stress. Unmasking pore-regulating external thiols.

    PubMed

    Petronilli, Valeria; Sileikyte, Justina; Zulian, Alessandra; Dabbeni-Sala, Federica; Jori, Giulio; Gobbo, Silvano; Tognon, Giuseppe; Nikolov, Peter; Bernardi, Paolo; Ricchelli, Fernanda

    2009-07-01

    We have studied the mitochondrial permeability transition pore (PTP) under oxidizing conditions with mitochondria-bound hematoporphyrin, which generates reactive oxygen species (mainly singlet oxygen, (1)O(2)) upon UV/visible light-irradiation and promotes the photooxidative modification of vicinal targets. We have characterized the PTP-modulating properties of two major critical sites endowed with different degrees of photosensitivity: (i) the most photovulnerable site comprises critical histidines, whose photomodification by vicinal hematoporphyrin causes a drop in reactivity of matrix-exposed (internal), PTP-regulating cysteines thus stabilizing the pore in a closed conformation; (ii) the most photoresistant site coincides with the binding domains of (external) cysteines sensitive to membrane-impermeant reagents, which are easily unmasked when oxidation of internal cysteines is prevented. Photooxidation of external cysteines promoted by vicinal hematoporphyrin reactivates the PTP after the block caused by histidine photodegradation. Thus, hematoporphyrin-mediated photooxidative stress can either inhibit or activate the mitochondrial permeability transition depending on the site of hematoporphyrin localization and on the nature of the substrate; and selective photomodification of different hematoporphyrin-containing pore domains can be achieved by fine regulation of the sensitizer/light doses. These findings shed new light on PTP modulation by oxidative stress.

  17. 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

  18. Novel Adjuvant Based on the Pore-Forming Protein Sticholysin II Encapsulated into Liposomes Effectively Enhances the Antigen-Specific CTL-Mediated Immune Response.

    PubMed

    Laborde, Rady J; Sanchez-Ferras, Oraly; Luzardo, María C; Cruz-Leal, Yoelys; Fernández, Audry; Mesa, Circe; Oliver, Liliana; Canet, Liem; Abreu-Butin, Liane; Nogueira, Catarina V; Tejuca, Mayra; Pazos, Fabiola; Álvarez, Carlos; Alonso, María E; Longo-Maugéri, Ieda M; Starnbach, Michael N; Higgins, Darren E; Fernández, Luis E; Lanio, María E

    2017-04-01

    Vaccine strategies to enhance CD8(+) CTL responses remain a current challenge because they should overcome the plasmatic and endosomal membranes for favoring exogenous Ag access to the cytosol of APCs. As a way to avoid this hurdle, sticholysin (St) II, a pore-forming protein from the Caribbean Sea anemone Stichodactyla helianthus, was encapsulated with OVA into liposomes (Lp/OVA/StII) to assess their efficacy to induce a CTL response. OVA-specific CD8(+) T cells transferred to mice immunized with Lp/OVA/StII experienced a greater expansion than when the recipients were injected with the vesicles without St, mostly exhibiting a memory phenotype. Consequently, Lp/OVA/StII induced a more potent effector function, as shown by CTLs, in vivo assays. Furthermore, treatment of E.G7-OVA tumor-bearing mice with Lp/OVA/StII significantly reduced tumor growth being more noticeable in the preventive assay. The contribution of CD4(+) and CD8(+) T cells to CTL and antitumor activity, respectively, was elucidated. Interestingly, the irreversibly inactive variant of the StI mutant StI W111C, encapsulated with OVA into Lp, elicited a similar OVA-specific CTL response to that observed with Lp/OVA/StII or vesicles encapsulating recombinant StI or the reversibly inactive StI W111C dimer. These findings suggest the relative independence between StII pore-forming activity and its immunomodulatory properties. In addition, StII-induced in vitro maturation of dendritic cells might be supporting these properties. These results are the first evidence, to our knowledge, that StII, a pore-forming protein from a marine eukaryotic organism, encapsulated into Lp functions as an adjuvant to induce a robust specific CTL response.

  19. 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

  20. HLH-30/TFEB-mediated autophagy functions in a cell-autonomous manner for epithelium intrinsic cellular defense against bacterial pore-forming toxin in C. elegans

    PubMed Central

    Chen, Huan-Da; Kao, Cheng-Yuan; Liu, Bang-Yu; Huang, Shin-Whei; Kuo, Cheng-Ju; Ruan, Jhen-Wei; Lin, Yen-Hung; Huang, Cheng-Rung; Chen, Yu-Hung; Wang, Horng-Dar; Aroian, Raffi V.; Chen, Chang-Shi

    2017-01-01

    ABSTRACT Autophagy is an evolutionarily conserved intracellular system that maintains cellular homeostasis by degrading and recycling damaged cellular components. The transcription factor HLH-30/TFEB-mediated autophagy has been reported to regulate tolerance to bacterial infection, but less is known about the bona fide bacterial effector that activates HLH-30 and autophagy. Here, we reveal that bacterial membrane pore-forming toxin (PFT) induces autophagy in an HLH-30-dependent manner in Caenorhabditis elegans. Moreover, autophagy controls the susceptibility of animals to PFT toxicity through xenophagic degradation of PFT and repair of membrane-pore cell-autonomously in the PFT-targeted intestinal cells in C. elegans. These results demonstrate that autophagic pathways and autophagy are induced partly at the transcriptional level through HLH-30 activation and are required to protect metazoan upon PFT intoxication. Together, our data show a new and powerful connection between HLH-30-mediated autophagy and epithelium intrinsic cellular defense against the single most common mode of bacterial attack in vivo. PMID:27875098

  1. Ah receptor- and TCDD-mediated liver tumor promotion: clonal selection and expansion of cells evading growth arrest and apoptosis.

    PubMed

    Bock, Karl Walter; Köhle, Christoph

    2005-05-15

    The Ah receptor (AhR) has been characterized as a ligand-activated transcription factor which belongs to the bHLH/PAS (basic helix-loop-helix/Per-Arnt-Sim) family of chemosensors. Transgenic mouse models revealed adaptive and developmental functions of the AhR in the absence of exogenous ligands. Use of persistent agonists such as dioxins including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related compounds demonstrated that the AhR mediates a plethora of species- and tissue-dependent toxicities, including chloracne, wasting, teratogenicity, immunotoxicity, liver tumor promotion and carcinogenicity. However, molecular mechanisms underlying most aspects of these toxic responses as well as biological functions of the AhR are currently unknown. Previous studies of liver tumor promotion in the two-stage hepatocarcinogenesis model indicated that TCDD mediates clonal expansion of 'initiated' preneoplastic hepatocytes, identified as enzyme-altered foci (EAF) by inhibiting apoptosis and bypassing AhR-mediated growth arrest. In contrast, the Ah receptor has been shown in cell models to stimulate growth arrest and apoptosis. Possible underlying mechanisms of these AhR responses are discussed, including enhanced metabolism of retinoic acid which attenuates TGFbeta-mediated apoptosis and interaction of the Ah receptor with the hypophosphorylated retinoblastoma tumor suppressor protein. The discrepancy between in vivo findings in EAF and AhR functions may be solved by hypothesizing that sustained activation of the Ah receptor generates a strong selective pressure in liver treated with genotoxic carcinogens leading to selection and expansion of clones evading growth arrest and apoptosis. Models are discussed which may facilitate verification of this hypothesis.

  2. 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

  3. Phosphatidylinositol 3-Kinase Mediates Bronchioalveolar Stem Cell Expansion in Mouse Models of Oncogenic K-ras-Induced Lung Cancer

    PubMed Central

    Yang, Yanan; Iwanaga, Kentaro; Raso, Maria Gabriela; Wislez, Marie; Hanna, Amy E.; Wieder, Eric D.; Molldrem, Jeffrey J.; Wistuba, Ignacio I.; Powis, Garth; Demayo, Francesco J.; Kim, Carla F.; Kurie, Jonathan M.

    2008-01-01

    Background Non-small cell lung cancer (NSCLC) is the most common cause of cancer-related death in Western countries. Developing more effective NSCLC therapeutics will require the elucidation of the genetic and biochemical bases for this disease. Bronchioalveolar stem cells (BASCs) are a putative cancer stem cell population in mouse models of oncogenic K-ras-induced lung adenocarcinoma, an histologic subtype of NSCLC. The signals activated by oncogenic K-ras that mediate BASC expansion have not been fully defined. Methodology/Principal Findings We used genetic and pharmacologic approaches to modulate the activity of phosphatidylinositol 3-kinase (PI3K), a key mediator of oncogenic K-ras, in two genetic mouse models of lung adenocarcinoma. Oncogenic K-ras-induced BASC accumulation and tumor growth were blocked by treatment with a small molecule PI3K inhibitor and enhanced by inactivation of phosphatase and tensin homologue deleted from chromosome 10, a negative regulator of PI3K. Conclusions/Significance We conclude that PI3K is a critical regulator of BASC expansion, supporting treatment strategies to target PI3K in NSCLC patients. PMID:18493606

  4. Inflammation and Pyroptosis Mediate Muscle Expansion in an Interleukin-1β (IL-1β)-dependent Manner*

    PubMed Central

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

    2015-01-01

    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. Ca2+ induces a cyclosporin A-insensitive permeability transition pore in isolated potato tuber mitochondria mediated by reactive oxygen species.

    PubMed

    Fortes, F; Castilho, R F; Catisti, R; Carnieri, E G; Vercesi, A E

    2001-02-01

    Oxidative damage of mammalian mitochondria induced by Ca2+ and prooxidants is mediated by the attack of mitochondria-generated reactive oxygen species on membrane protein thiols promoting oxidation and cross-linkage that leads to the opening of the mitochondrial permeability transition pore (Castilho et al., 1995). In this study, we present evidence that deenergized potato tuber (Solanum tuberosum) mitochondria, which do not possess a Ca2+ uniport, undergo inner membrane permeabilization when treated with Ca2+ (>0.2 mM), as indicated by mitochondrial swelling. Similar to rat liver mitochondria, this permeabilization is enhanced by diamide, a thiol oxidant that creates a condition of oxidative stress by oxidizing pyridine nucleotides. This is inhibited by the antioxidants catalase and dithiothreitol. Potato mitochondrial membrane permeabilization is not inhibited by ADP, cyclosporin A, and ruthenium red, and is partially inhibited by Mg2+ and acidic pH, well known inhibitors of the mammalian mitochondrial permeability transition. The lack of inhibition of potato mitochondrial permeabilization by cyclosporin A is in contrast to the inhibition of the peptidylprolyl cis-trans isomerase activity, that is related to the cyclosporin A-binding protein cyclophilin. Interestingly, the monofunctional thiol reagent mersalyl induces an extensive cyclosporin A-insensitive potato mitochondrial swelling, even in the presence of lower Ca2+ concentrations (>0.01 mM). In conclusion, we have identified a cyclosporin A-insensitive permeability transition pore in isolated potato mitochondria that is induced by reactive oxygen species.

  6. Cell expansion-mediated organ growth is affected by mutations in three EXIGUA genes.

    PubMed

    Rubio-Díaz, Silvia; Pérez-Pérez, José Manuel; González-Bayón, Rebeca; Muñoz-Viana, Rafael; Borrega, Nero; Mouille, Gregory; Hernández-Romero, Diana; Robles, Pedro; Höfte, Herman; Ponce, María Rosa; Micol, José Luis

    2012-01-01

    Organ growth depends on two distinct, yet integrated, processes: cell proliferation and post-mitotic cell expansion. Although the regulatory networks of plant cell proliferation during organ growth have begun to be unveiled, the mechanisms regulating post-mitotic cell growth remain mostly unknown. Here, we report the characterization of three EXIGUA (EXI) genes that encode different subunits of the cellulose synthase complex specifically required for secondary cell wall formation. Despite this highly specific role of EXI genes, all the cells within the leaf, even those that do not have secondary walls, display small sizes in the exi mutants. In addition, we found a positive correlation between cell size and the DNA ploidy levels in exi mutant leaves, suggesting that both processes share some regulatory components. Our results are consistent with the hypothesis that the collapsed xylem vessels of the exi mutants hamper water transport throughout the plant, which, in turn, limits the turgor pressure levels required for normal post-mitotic cell expansion during leaf growth.

  7. IL-33-Mediated Expansion of Type 2 Innate Lymphoid Cells Protects from Progressive Glomerulosclerosis.

    PubMed

    Riedel, Jan-Hendrik; Becker, Martina; Kopp, Kerstin; Düster, Mathis; Brix, Silke R; Meyer-Schwesinger, Catherine; Kluth, Luis A; Gnirck, Ann-Christin; Attar, Madena; Krohn, Sonja; Fehse, Boris; Stahl, Rolf A K; Panzer, Ulf; Turner, Jan-Eric

    2017-07-01

    Innate lymphoid cells (ILCs) have an important role in the immune system's response to different forms of infectious and noninfectious pathologies. In particular, IL-5- and IL-13-producing type 2 ILCs (ILC2s) have been implicated in repair mechanisms that restore tissue integrity after injury. However, the presence of renal ILCs in humans has not been reported. In this study, we show that ILC populations are present in the healthy human kidney. A detailed characterization of kidney-residing ILC populations revealed that IL-33 receptor-positive ILC2s are a major ILC subtype in the kidney of humans and mice. Short-term IL-33 treatment in mice led to sustained expansion of IL-33 receptor-positive kidney ILC2s and ameliorated adriamycin-induced glomerulosclerosis. Furthermore, the expansion of ILC2s modulated the inflammatory response in the diseased kidney in favor of an anti-inflammatory milieu with a reduction of pathogenic myeloid cell infiltration and a marked accumulation of eosinophils that was required for tissue protection. In summary, kidney-residing ILC2s can be effectively expanded in the mouse kidney by IL-33 treatment and are central regulators of renal repair mechanisms. The presence of ILC2s in the human kidney tissue identifies these cells as attractive therapeutic targets for CKD in humans. Copyright © 2017 by the American Society of Nephrology.

  8. IL-17A-mediated neutrophil recruitment limits expansion of segmented filamentous bacteria.

    PubMed

    Flannigan, K L; Ngo, V L; Geem, D; Harusato, A; Hirota, S A; Parkos, C A; Lukacs, N W; Nusrat, A; Gaboriau-Routhiau, V; Cerf-Bensussan, N; Gewirtz, A T; Denning, T L

    2016-09-14

    Specific components of the intestinal microbiota are capable of influencing immune responses such that a mutualistic relationship is established. In mice, colonization with segmented filamentous bacteria (SFB) induces T-helper-17 (Th17) cell differentiation in the intestine, yet the effector functions of interleukin (IL)-17A in response to SFB remain incompletely understood. Here we report that colonization of mice with SFB-containing microbiota induced IL-17A- and CXCR2-dependent recruitment of neutrophils to the ileum. This response required adaptive immunity, as Rag-deficient mice colonized with SFB-containing microbiota failed to induce IL-17A, CXCL1 and CXCL2, and displayed defective neutrophil recruitment to the ileum. Interestingly, neutrophil depletion in wild-type mice resulted in significantly augmented Th17 responses and SFB expansion, which correlated with impaired expression of IL-22 and antimicrobial peptides. These data provide novel insight into a dynamic IL-17A-CXCR2-neutrophil axis during acute SFB colonization and demonstrate a central role for neutrophils in limiting SFB expansion.Mucosal Immunology advance online publication 14 September 2016. doi:10.1038/mi.2016.80.

  9. IL-17A-mediated neutrophil recruitment limits expansion of segmented filamentous bacteria

    PubMed Central

    Flannigan, Kyle L.; Ngo, Vu L.; Geem, Duke; Harusato, Akihito; Hirota, Simon A.; Parkos, Charles A.; Lukacs, Nicholas W.; Nusrat, Asma; Gaboriau-Routhiau, Valérie; Cerf-Bensussan, Nadine; Gewirtz, Andrew T.; Denning, Timothy L.

    2016-01-01

    Specific components of the intestinal microbiota are capable of influencing immune responses such that a mutualistic relationship is established. In mice, colonization with segmented filamentous bacteria (SFB) induces Th17 cell differentiation in the intestine, yet the effector functions of IL-17A in response to SFB remain incompletely understood. Here, we report that colonization of mice with SFB-containing microbiota induced IL-17A- and CXCR2-dependent recruitment of neutrophils to the ileum. This response required adaptive immunity as Rag-deficient mice colonized with SFB-containing microbiota failed to induce IL-17A, CXCL1 and CXCL2, and displayed defective neutrophil recruitment to the ileum. Interestingly, neutrophil depletion in wild-type mice resulted in significantly augmented Th17 responses and SFB expansion, which correlated with impaired expression of IL-22 and antimicrobial peptides. These data provide novel insight into a dynamic IL-17A-CXCR2-neutrophil axis during acute SFB colonization and demonstrate a central role for neutrophils in limiting SFB expansion. PMID:27624780

  10. Intensified wind pollination mediated by pollen dimorphism after range expansion in an ambophilous biennial Aconitum gymnandrum.

    PubMed

    Wang, Lin-Lin; Zhang, Chan; Yang, Ming-Liu; Zhang, Guo-Peng; Zhang, Zhi-Qiang; Yang, Yong-Ping; Duan, Yuan-Wen

    2017-01-01

    Pollination systems and associated floral traits generally differ between core and marginal populations of a species. However, such differences are rarely examined in plants with a mixed wind- and bumblebee-pollination system, and the role of wind pollination during range expansion in ambophilous plants remains unclear. We compared floral traits and the contributions of bumblebee and wind pollination in refugium and marginal populations of the ambophilous plant Aconitum gymnandrum. We found that most floral traits differed between the two populations, and those traits associated with the shift to wind pollination were pronounced in the marginal population. Bumblebee visitation rates varied significantly, but were generally low in the marginal population. Wind pollination occurred in both populations, and the efficiency was lower than that of bumblebee pollination. Two types of pollen grains, namely round and fusiform pollen, were transported to a stigma by bumblebees and wind, but fusiform pollen contributed to wind pollination to a larger degree, especially in the marginal population. Our results suggest that wind pollination was enhanced by pollen dimorphism in the marginal population of A. gymnandrum, and wind pollination may provide reproductive assurance when bumblebee activity is unpredictable during range expansion, indicating that ambophily is stable in this species and shift in pollination system could be common when plants colonize new habitats.

  11. 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…

  12. 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…

  13. Towards an expansive hybrid psychology: integrating theories of the mediated mind.

    PubMed

    Brinkmann, Svend

    2011-03-01

    This article develops an integrative theory of the mind by examining how the mind, understood as a set of skills and dispositions, depends upon four sources of mediators. Harré's hybrid psychology is taken as a meta-theoretical starting point, but is expanded significantly by including the four sources of mediators that are the brain, the body, social practices and technological artefacts. It is argued that the mind is normative in the sense that mental processes do not simply happen, but can be done more or less well, and thus are subject to normative appraisal. The expanded hybrid psychology is meant to assist in integrating theoretical perspectives and research interests that are often thought of as incompatible, among them neuroscience, phenomenology of the body, social practice theory and technology studies. A main point of the article is that these perspectives each are necessary for an integrative approach to the human mind.

  14. 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

  15. α-Tocopherol induces hematopoietic stem/progenitor cell expansion and ERK1/2-mediated differentiation.

    PubMed

    Nogueira-Pedro, Amanda; Barbosa, Christiano M V; Segreto, Helena Regina Comodo; Lungato, Lisandro; D'Almeida, Vania; Moraes, Andrea Aparecida F S; Miranda, Antonio; Paredes-Gamero, Edgar Julian; Ferreira, Alice Teixeira

    2011-12-01

    Tocopherols promote or inhibit growth in different cell types. In the hematopoietic system, the radioprotective property of tocopherols is thought to act through the expansion of primitive hematopoietic cells. However, the mechanisms activated by tocopherols and which HPs are affected remain poorly understood. To better address these questions, mice were treated with α-tocopherol, and its effects were investigated in the BM microenvironment. α-Tocopherol induced increased proliferation in HSC/HP cells, leading to BM hyperplasia. In addition, differentiation to the granulocytic/monocytic lineage was enhanced by α-tocopherol treatment. α-Tocopherol treatment resulted in decreased basal phosphorylation of ERK1/2, PKC, and STAT-5 in HSC/HP cells. In contrast, α-tocopherol enhanced ERK1/2 activation in response to IL-3 stimulation in HSC/HP cells without altering the expression of IL-3Rs. Moreover, α-tocopherol-induced differentiation and ERK1/2 activation were abolished in mice pretreated with a MEK inhibitor (PD98059); however, pretreatment with PD98059 did not reduce the α-tocopherol-mediated increase in HSC/HP cells but instead, further enhanced their proliferation. Therefore, α-tocopherol induces expansion of HSC/HP cells by a nonidentified intracellular pathway and granulocytic/monocytic differentiation through ERK1/2 activation.

  16. 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.

  17. Prolonged expansion of human nucleus pulposus cells expressing human telomerase reverse transcriptase mediated by lentiviral vector.

    PubMed

    Wu, Jianhong; Wang, Deli; Ruan, Dike; He, Qing; Zhang, Yan; Wang, Chaofeng; Xin, Hongkui; Xu, Cheng; Liu, Yue

    2014-01-01

    Human degenerative disc disease (DDD) is characterized by progressive loss of human nucleus pulposus (HNP) cells and extracellular matrix, in which the massive deposition are secreted by HNP cells. Cell therapy to supplement HNP cells to degenerated discs has been thought to be a promising strategy to treat DDD. However, obtaining a large quality of fully functional HNP cells has been severely hampered by limited proliferation capacity of HNP cells in vitro. Previous studies have used lipofectamine or recombinant adeno-associated viral (rAAV) vectors to deliver human telomerase reverse transcriptase (hTERT) into ovine or HNP cells to prolong the activity of nucleus pulposus cells with limited success. Here we developed a lentiviral vector bearing both hTERT and a gene encoding green fluorescence protein (L-hTERT/EGFP). This vector efficiently mediated both hTERT and EGFP into freshly isolated HNP cells. The expressions of both transgenes in L-hTERT/EGFP transduced HNP cells were detected up to day 210 post viral infection, which was twice as long as rAAV vector did. Furthermore, we observed restored telomerase activity, maintained telomere length, delayed cell senescence, and increased cell proliferation rate in those L-hTERT/EGFP transduced HNP cells. Our study suggests that lentiviral vector might be a useful gene delivery vehicle for HNP cell therapy to treat DDD.

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

    PubMed Central

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

    2016-01-01

    demonstrated 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. PMID:23876428

  19. 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.

  20. Localization of Nucleoporin Tpr to the Nuclear Pore Complex Is Essential for Tpr Mediated Regulation of the Export of Unspliced RNA

    PubMed Central

    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. PMID:22253824

  1. HIV cell-to-cell transmission requires the production of infectious virus particles and does not proceed through env-mediated fusion pores.

    PubMed

    Monel, Blandine; Beaumont, Elodie; Vendrame, Daniela; Schwartz, Olivier; Brand, Denys; Mammano, Fabrizio

    2012-04-01

    Direct cell-to-cell transmission of human immunodeficiency virus (HIV) is a more potent and efficient means of virus propagation than infection by cell-free virus particles. The aim of this study was to determine whether cell-to-cell transmission requires the assembly of enveloped virus particles or whether nucleic acids with replication potential could translocate directly from donor to target cells through envelope glycoprotein (Env)-induced fusion pores. To this end, we characterized the transmission properties of viruses carrying mutations in the matrix protein (MA) that affect the incorporation of Env into virus particles but do not interfere with Env-mediated cell-cell fusion. By use of cell-free virus, the infectivity of MA mutant viruses was below the detection threshold both in single-cycle and in multiple-cycle assays. Truncation of the cytoplasmic tail (CT) of Env restored the incorporation of Env into MA mutant viruses and rescued their cell-free infectivity to different extents. In cell-to-cell transmission assays, MA mutations prevented HIV transmission from donor to target cells, despite efficient Env-dependent membrane fusion. HIV transmission was blocked at the level of virus core translocation into the cytosol of target cells. As in cell-free assays, rescue of Env incorporation by truncation of the Env CT restored the virus core translocation and cell-to-cell infectivity of MA mutant viruses. These data show that HIV cell-to-cell transmission requires the assembly of enveloped virus particles. The increased efficiency of this infection route may thus be attributed to the high local concentrations of virus particles at sites of cellular contacts rather than to a qualitatively different transmission process.

  2. 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.

  3. 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.

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

    PubMed

    Dong, Yufeng; Long, Teng; Wang, Cuicui; Mirando, Anthony J; Chen, Jianquan; O'Keefe, Regis J; Hilton, Matthew J

    2014-12-01

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

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

    PubMed Central

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

    2014-01-01

    SUMMARY 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 co-inhibitory receptor on CD8α+ DCs, suppresses, while blocking BTLA enhances both the primary and memory CD8 T cell responses against Listeria. Btla−/− mice have lower effector and memory CD8+ T cells while paradoxically also being more resistant to Listeria. Although bacterial entry into Btla−/− CD8α+ DCs is unaffected, Listeria fails to expand within these cells. BTLA signaling limits Fas/FasL-mediated suppression of Listeria expansion within CD8α+ DCs to more effectively alert adaptive immune cells. This study uncovers a BTLA-mediated strategy used by the host that permits Listeria proliferation to enable increasing T cell responses for long-term protection. PMID:25011109

  6. Intermedilysin-receptor interactions during assembly of the pore complex: assembly intermediates increase host cell susceptibility to complement-mediated lysis.

    PubMed

    LaChapelle, Stephanie; Tweten, Rodney K; Hotze, Eileen M

    2009-05-08

    Intermedilysin (ILY) is an unusual member of the family of cholesterol-dependent cytolysins because it binds to human CD59 (hCD59) rather than directly to cholesterol-rich membranes. Binding of ILY to hCD59 initiates a series of conformational changes within the toxin that result in the conversion of the soluble monomer into an oligomeric membrane-embedded pore complex. In this study the association of ILY with its membrane receptor has been examined throughout the assembly and formation of the pore complex. Using ILY mutants trapped at various stages of pore assembly, we show ILY remains engaged with hCD59 throughout the assembly of the prepore oligomer, but it disengages from the receptor upon the conversion to the pore complex. We further show that the assembly intermediates increase the sensitivity of the host cell to lysis by its complement membrane attack complex, apparently by blocking the hCD59-binding site for complement proteins C8alpha and C9.

  7. EPO-mediated expansion of late-stage erythroid progenitors in the bone marrow initiates recovery from sublethal radiation stress

    PubMed Central

    Peslak, Scott A.; Wenger, Jesse; Bemis, Jeffrey C.; Kingsley, Paul D.; Koniski, Anne D.; McGrath, Kathleen E.

    2012-01-01

    Erythropoiesis is a robust process of cellular expansion and maturation occurring in murine bone marrow and spleen. We previously determined that sublethal irradiation, unlike bleeding or hemolysis, depletes almost all marrow and splenic erythroblasts but leaves peripheral erythrocytes intact. To better understand the erythroid stress response, we analyzed progenitor, precursor, and peripheral blood compartments of mice post–4 Gy total body irradiation. Erythroid recovery initiates with rapid expansion of late-stage erythroid progenitors–day 3 burst-forming units and colony-forming units, associated with markedly increased plasma erythropoietin (EPO). Although initial expansion of late-stage erythroid progenitors is dependent on EPO, this cellular compartment becomes sharply down-regulated despite elevated EPO levels. Loss of EPO-responsive progenitors is associated temporally with a wave of maturing erythroid precursors in marrow and with emergence of circulating erythroid progenitors and subsequent reestablishment of splenic erythropoiesis. These circulating progenitors selectively engraft and mature in irradiated spleen after short-term transplantation, supporting the concept that bone marrow erythroid progenitors migrate to spleen. We conclude that sublethal radiation is a unique model of endogenous stress erythropoiesis, with specific injury to the extravascular erythron, expansion and maturation of EPO-responsive late-stage progenitors exclusively in marrow, and subsequent reseeding of extramedullary sites. PMID:22889760

  8. Nanoscale pore formation dynamics during aluminum anodization.

    PubMed

    Thamida, Sunil Kumar; Chang, Hsueh-Chia

    2002-03-01

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

  9. Toll-like receptor 2 mediates microglia/brain macrophage MT1-MMP expression and glioma expansion

    PubMed Central

    Vinnakota, Katyayni; Hu, Feng; Ku, Min-Chi; Georgieva, Petya B.; Szulzewsky, Frank; Pohlmann, Andreas; Waiczies, Sonia; Waiczies, Helmar; Niendorf, Thoralf; Lehnardt, Seija; Hanisch, Uwe-Karsten; Synowitz, Michael; Markovic, Darko; Wolf, Susanne A.; Glass, Rainer; Kettenmann, Helmut

    2013-01-01

    Background Glioblastomas are the most aggressive primary brain tumors in humans. Microglia/brain macrophage accumulation in and around the tumor correlates with malignancy and poor clinical prognosis of these tumors. We have previously shown that microglia promote glioma expansion through upregulation of membrane type 1 matrix metalloprotease (MT1-MMP). This upregulation depends on signaling via the Toll-like receptor (TLR) adaptor molecule myeloid differentiation primary response gene 88 (MyD88). Methods Using in vitro, ex vivo, and in vivo techniques, we identified TLR2 as the main TLR controlling microglial MT1-MMP expression and promoting microglia-assisted glioma expansion. Results The implantation of mouse GL261 glioma cells into TLR2 knockout mice resulted in significantly smaller tumors, reduced MT1-MMP expression, and enhanced survival rates compared with wild-type control mice. Tumor expansion studied in organotypic brain slices depended on both parenchymal TLR2 expression and the presence of microglia. Glioma-derived soluble factors and synthetic TLR2 specific ligands induced MT1-MMP expression in microglia from wild-type mice, but no such change in MT1-MMP gene expression was observed in microglia from TLR2 knockout mice. We also found evidence that TLR1 and TLR6 cofunction with TLR2 as heterodimers in regulating MT1-MMP expression in vitro. Conclusions Our results thus show that activation of TLR2 along with TLRs 1 and/or 6 converts microglia into a glioma supportive phenotype. PMID:24014382

  10. Donor B cells in Transplants Augment Clonal Expansion and Survival of Pathogenic CD4+ T cells That Mediate Autoimmune-like Chronic GVHD

    PubMed Central

    Young, James S; Wu, Tao; Chen, Yuhong; Zhao, Dongchang; Liu, Hongjun; Yi, Tangsheng; Johnston, Heather; Racine, Jeremy; Li, Xiaofan; Wang, Audrey; Todorov, Ivan; Zeng, Defu

    2013-01-01

    We reported that both donor CD4+ T and B cells in transplants were required for induction of an autoimmune-like chronic graft versus host disease (cGVHD) in a murine model of DBA/2 donor to BALB/c recipient, but mechanisms whereby donor B cells augment cGVHD pathogenesis remain unknown. Here, we report that, although donor B cells have little impact on acute GVHD (aGVHD) severity, they play an important role in augmenting the persistence of tissue damage in the acute and chronic GVHD overlapping target organs (i.e. skin and lung); they also markedly augment damage in a prototypical cGVHD target organ- the salivary gland. During cGVHD pathogenesis, donor B cells are activated by donor CD4+ T cells to upregulate MHC II and co-stimulatory molecules. Acting as efficient APCs, donor B cells augment donor CD4+ T clonal expansion, autoreactivity, IL-7Rα expression, and survival. These qualitative changes markedly augment donor CD4+ T cells' capacity in mediating autoimmune-like cGVHD, so that they mediate disease in the absence of donor B cells in secondary recipients. Therefore, a major mechanism whereby donor B cells augment cGVHD is through augmenting the clonal expansion, differentiation and survival of pathogenic CD4+ T cells. PMID:22649197

  11. 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. © 2013 John Wiley & Sons Ltd.

  12. Hyperbolic regions in flows through three-dimensional pore structures.

    PubMed

    Hyman, Jeffrey D; Winter, C Larrabee

    2013-12-01

    Finite time Lyapunov exponents are used to determine expanding, contracting, and hyperbolic regions in computational simulations of laminar steady-state fluid flows within realistic three dimensional pore structures embedded within an impermeable matrix. These regions correspond approximately to pores where flow converges (contraction) or diverges (expansion), and to throats between pores where the flow mixes (hyperbolic). The regions are sparse and disjoint from one another, occupying only a small percentage of the pore space. Nonetheless, nearly every percolating fluid particle trajectory passes through several hyperbolic regions indicating that the effects of in-pore mixing are distributed throughout an entire pore structure. Furthermore, the observed range of fluid dynamics evidences two scales of heterogeneity within each of these flow fields. There is a larger scale that affects dispersion of fluid particle trajectories across the connected network of pores and a relatively small scale of nonuniform distributions of velocities within an individual pore.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  14. Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2

    PubMed Central

    Occhipinti, Laura; Chang, Yiming; Altvater, Martin; Menet, Anna M.; Kemmler, Stefan; Panse, Vikram G.

    2013-01-01

    Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2’s interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel. PMID:23907389

  15. Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2.

    PubMed

    Occhipinti, Laura; Chang, Yiming; Altvater, Martin; Menet, Anna M; Kemmler, Stefan; Panse, Vikram G

    2013-09-01

    Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2's interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel.

  16. 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.

  17. 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

  18. Novel ABP1-TMK auxin sensing system controls ROP GTPase-mediated interdigitated cell expansion in Arabidopsis.

    PubMed

    Chen, Jisheng; Yang, Zhenbiao

    2014-06-30

    ROP GTPases (Rho-like GTPase from plants), plant counterparts of animal and fungal Rho-family GTPases, have recently been shown to be key components of a novel signaling pathway activated by the plant hormone auxin. Auxin (indole acetic acid) is a key regulator of virtually every aspect of plant growth and development, yet the molecular mechanisms of auxin responses remain largely unknown. AUXIN BINDING PROTEIN1 (ABP1) is an ancient protein that binds auxin and has been implied as a receptor for a number of auxin responses, but its precise mechanism remains unresolved. A paradox for ABP1's action is that it is predominantly found in the endoplasmic reticulum (ER) lumen, while it has been implicated as a cell surface auxin receptor, functionally distinct from the nuclear TIR1/AFB auxin receptor family that regulates transcriptional responses. Since our group reported that ABP1 is required for activating two antagonizing ROP signaling pathways involved in cytoskeletal reorganization and cell shape formation in Arabidopsis leaf pavement cells, we recently further showed that the plasma membrane-localized TMK receptor-like kinases functionally interact in a complex with ABP1 and are required for ABP1-dependent activation of ROP GTPases by auxin. The formation of this cell surface complex is induced by auxin and requires functional ABP1. These exciting findings provide convincing evidence for this novel auxin sensing system on the cell surface and suggest intriguing mechanisms for TMKs being functional partners of ABP1 to transmit extracellular auxin signal to intracellular ROP signaling module during polar cell expansion.

  19. Coordination of cell proliferation and cell expansion mediated by ribosome-related processes in the leaves of Arabidopsis thaliana.

    PubMed

    Fujikura, Ushio; Horiguchi, Gorou; Ponce, María Rosa; Micol, José Luis; Tsukaya, Hirokazu

    2009-08-01

    Co-ordination of cell proliferation and cell expansion is a key regulatory process in leaf-size determination, but its molecular details are unknown. In Arabidopsis thaliana, mutations in a positive regulator of cell proliferation often trigger excessive cell enlargement post-mitotically in leaves. This phenomenon, called compensation syndrome, is seen in the mutant angustifolia3 (an3), which is defective in a transcription co-activator. Such compensation, however, does not occur in response to a decrease in cell number in oligocellula (oli). oli2, oli5 and oli7 did not exhibit compensation and the reduction in cell number in these mutants was moderate. However, when an oli mutation was combined with a different oli mutation to create a double mutant, cell number was further reduced and compensation was induced. Similarly, weak suppression of AN3 expression reduced cell number moderately but did not induce compensation compared with an an3 null mutant. Furthermore, double mutants of either oli2, oli5 or oli7 and an3 showed markedly enhanced compensation. These results suggest that compensation is triggered when cell proliferation regulated by OLI2/OLI5/OLI7 and AN3 is compromised in a threshold-dependent manner. OLI2 encodes a Nop2 homolog in Saccharomyces cerevisiae that is involved in ribosome biogenesis, whereas OLI5 and OLI7 encode ribosome proteins RPL5A and RPL5B, respectively. This suggests that a factor involved in the induction of compensation may be under the dual control of AN3 and a ribosome-related process.

  20. 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.

  1. Lack of CUL4B in Adipocytes Promotes PPARγ-Mediated Adipose Tissue Expansion and Insulin Sensitivity.

    PubMed

    Li, Peishan; Song, Yu; Zan, Wenying; Qin, Liping; Han, Shuang; Jiang, Baichun; Dou, Hao; Shao, Changshun; Gong, Yaoqin

    2017-02-01

    Obesity and obesity-associated diseases are linked to dysregulation of the peroxisome proliferator-activated receptor γ (PPARγ) signaling pathway. Identification of the factors that regulate PPARγ expression and activity is crucial for combating obesity. However, the ubiquitin E3 ligases that target PPARγ for proteasomal degradation have been rarely identified, and their functions in vivo have not been characterized. Here we report that CUL4B-RING E3 ligase (CRL4B) negatively regulates PPARγ by promoting its polyubiquitination and proteasomal degradation. Depletion of CUL4B led to upregulation of PPARγ-regulated genes and facilitated adipogenesis. Adipocyte-specific Cul4b knockout (AKO) mice being fed a high-fat diet exhibited increased body fat accumulation that was mediated by increased adipogenesis. However, AKO mice showed improved metabolic phenotypes, including increased insulin sensitivity and glucose tolerance. Correspondingly, there was a decreased inflammatory response in adipose tissues of AKO mice. Genetic inhibition of CUL4B thus appears to phenocopy the beneficial effects of PPARγ agonists. Collectively, this study establishes a critical role of CRL4B in the regulation of PPARγ stability and insulin sensitivity and suggests that CUL4B could be a potential therapeutic target for combating obesity and metabolic syndromes. © 2017 by the American Diabetes Association.

  2. The heliothis virescens 170 kDa aminopeptidase functions as "receptor A" by mediating specific Bacillus thuringiensis Cry1A delta-endotoxin binding and pore formation.

    PubMed

    Luo, K; Sangadala, S; Masson, L; Mazza, A; Brousseau, R; Adang, M J

    1997-01-01

    The relationship between Bacillus thuringiensis Cry1Aa, Cry1Ab and Cry1Ac delta-endotoxin binding and pore formation was investigated using a purified 170 kDa aminopeptidase N (APN) from Heliothis virescens brush border membranes. Aminopeptidases with molecular sizes of 110, 140 and 170 kDa were eluted from a Cry1Ac toxin affinity column using N-acetylgalactosamine. The 140 kDa aminopeptidase has a cross-reacting determinant typical of a cleaved glycosyl-phosphatidylinositol anchor. After mild base treatment to de-acylate the glycosyl-phosphatidylinositol linkage and incubation in phosphatidyl inositol phospholipase C, anti-cross-reacting determinant antibody recognized the 170 kDa protein. Kinetic binding characteristics of Cry1A toxins to purified 170 kDa APN were determined using surface plasmon resonance. Cry1Aa, Cry1Ab and Cry1Ac, but not Cry1C and Cry1E toxins recognized 170 kDa APN. Each Cry1A toxin recognized two binding sites: a high affinity site with KD ranging from 41 to 95 nM and a lower affinity site with KD in the 325 to 623 nM range. N-acetylgalactosamine inhibited Cry1Ac but not Cry1Aa and Cry1Ab binding to 170 kDa APN. When reconstituted into phospholipid vesicles, the 170 kDa APN promoted toxin-induced 86Rb+ release for Cry1A toxins, but not Cry1C toxin. Furthermore Cry1Ac, the Cry protein most toxic to H. virescens larvae, caused 86Rb+ release at lower concentrations, and to a greater extent than Cry1Aa and Cry1Ab toxins. The correlation between toxin-binding specificity and 86Rb+ release strongly suggests that the purified 170 kDa APN is the functional receptor A in the H. virescens midgut epithelial cell brush border membranes.

  3. 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.

  4. Expansive growth of two glioblastoma stem-like cell lines is mediated by bFGF and not by EGF

    PubMed Central

    Podergajs, Neza; Brekka, Narve; Radlwimmer, Bernhard; Herold-Mende, Christel; Talasila, Krishna M.; Tiemann, Katja; Rajcevic, Uros; Lah, Tamara T.; Bjerkvig, Rolf; Miletic, Hrvoje

    2013-01-01

    Background Patient-derived glioblastoma (GBM) stem-like cells (GSCs) represent a valuable model for basic and therapeutic research. GSCs are usually propagated in serum-free Neural Basal medium supplemented with bFGF and EGF. Yet, the exact influence of these growth factors on GSCs is still unclear. Recently it was suggested that GBM stem-like cells with amplified EGFR should be cultured in stem cell medium without EGF, as the presence of EGF induced rapid loss of EGFR amplification. However, patient biopsies are usually taken into culture before their genomic profiles are defined. Thus, an important question remains whether GBM cells without EGFR amplification also can be cultured in stem cell medium without EGF. Meterials and methods To address this question, we used two heterogeneous glioblastoma GSC lines (NCH421k and NCH644) that lack EGFR amplification. Results Although both cell lines showed very low EGFR expression under standard growth conditions, bFGF stimulation induced higher expression of EGFR in NCH644. In both cell lines, expression of the stem cell markers nestin and CD133 was higher upon stimulation with bFGF compared to EGF. Importantly, bFGF stimulated the growth of both cell lines, whereas EGF had no effect. We verified that the growth stimulation by bFGF was either mediated by proliferation (NCH421k) or resistance to apoptosis (NCH644). Conclusions We demonstrate that GSC cultures without EGFR amplification can be maintained and expanded with bFGF, while the addition of EGF has no significant effect and therefore can be omitted. PMID:24294177

  5. The nuclear pore complex

    PubMed Central

    Adam, Stephen A

    2001-01-01

    Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of components of the complex by proteomics and genomics have provided new insights. PMID:11574060

  6. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. 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

  8. 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)

  9. 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)

  10. 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.

  11. Amphotericin B-Induced Renal Tubular Cell Injury Is Mediated by Na+ Influx through Ion-Permeable Pores and Subsequent Activation of Mitogen-Activated Protein Kinases and Elevation of Intracellular Ca2+ Concentration▿

    PubMed Central

    Yano, Takahisa; Itoh, Yoshinori; Kawamura, Eiko; Maeda, Asuka; Egashira, Nobuaki; Nishida, Motohiro; Kurose, Hitoshi; Oishi, Ryozo

    2009-01-01

    Amphotericin B (AMB) is one of the most effective antifungal agents; however, its use is often limited by the occurrence of adverse events, especially nephrotoxicity. The present study was designed to determine the possible mechanisms underlying the nephrotoxic action of AMB. The exposure of a porcine proximal renal tubular cell line (LLC-PK1 cells) to AMB caused cell injury, as assessed by mitochondrial enzyme activity, the leakage of lactate dehydrogenase, and tissue ATP depletion. Propidium iodide uptake was enhanced, while terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling was not affected by AMB, suggesting a lack of involvement of apoptosis in AMB-induced cell injury. The cell injury was inhibited by the depletion of membrane cholesterol with methyl-β-cyclodextrin, which lowered the extracellular Na+ concentration or the chelation of intracellular Ca2+. The rise in the intracellular Ca2+ concentration may be mediated through the activation of the ryanodine receptor (RyR) on the endoplasmic reticulum and the mitochondrial Na+-Ca2+ exchanger, since cell injury was attenuated by dantrolene (an RyR antagonist) and CGP37157 (an Na+-Ca2+ exchanger inhibitor). Moreover, AMB-induced cell injury was reversed by PD169316 (a p38 mitogen-activated protein [MAP] kinase inhibitor), c-Jun N-terminal kinase inhibitor II, and PD98059 (a MEK1/2 inhibitor). The phosphorylations of these MAP kinases were enhanced by AMB in a calcium-independent manner, suggesting the involvement of MAP kinases in AMB-induced cell injury. These findings suggest that Na+ entry through membrane pores formed by the association of AMB with membrane cholesterol leads to the activation of MAP kinases and the elevation of the intracellular Ca2+ concentration, leading to renal tubular cell injury. PMID:19139282

  12. Proteasome-independent major histocompatibility complex class I cross-presentation mediated by papaya mosaic virus-like particles leads to expansion of specific human T cells.

    PubMed

    Leclerc, Denis; Beauseigle, Diane; Denis, Jérome; Morin, Hélène; Paré, Christine; Lamarre, Alain; Lapointe, Réjean

    2007-02-01

    The development of versatile vaccine platforms is a priority that is recognized by health authorities worldwide; such platforms should induce both arms of the immune system, the humoral and cytotoxic-T-lymphocyte responses. In this study, we have established that a vaccine platform based on the coat protein of papaya mosaic virus (PapMV CP), previously shown to induce a humoral response, can induce major histocompatibility complex (MHC) class I cross-presentation of HLA-A*0201 epitopes from gp100, a melanoma antigen, and from influenza virus M1 matrix protein. PapMV proteins were able to assemble into stable virus-like particles (VLPs) in a crystalline and repetitive structure. When we pulsed HLA-A*0201+ antigen-presenting cells (APCs) with the recombinant PapMV FLU or gp100, we noted that antigen-specific CD8+ T cells were highly reactive to these APCs, demonstrating that the epitope from the VLPs were processed and loaded on the MHC class I complex. APCs were preincubated with two different proteasome inhibitors, which did not affect the efficiency of peptide presentation on MHC class I. Classical presentation from an endogenous antigen was abolished in the same conditions. Clearly, antigen presentation mediated by the PapMV system was proteasome independent. Finally, PapMV-pulsed APCs had the capacity to expand highly avid antigen-specific T cells against the influenza virus M1 HLA-A*0201 epitope when cocultured with autologous peripheral blood mononuclear cells. This study demonstrates the potential of PapMV for MHC class I cross-presentation and for the expansion of human antigen-specific T cells. It makes VLPs from PapMV CP a very attractive platform to trigger cellular responses for vaccine development against chronic infectious diseases and cancers.

  13. Development of maternal seed tissue in barley is mediated by regulated cell expansion and cell disintegration and coordinated with endosperm growth.

    PubMed

    Radchuk, Volodymyr; Weier, Diana; Radchuk, Ruslana; Weschke, Winfriede; Weber, Hans

    2011-01-01

    After fertilization, filial grain organs are surrounded by the maternal nucellus embedded within the integuments and pericarp. Rapid early endosperm growth must be coordinated with maternal tissue development. Parameters of maternal tissue growth and development were analysed during early endosperm formation. In the pericarp, cell proliferation is accomplished around the time of fertilization, followed by cell elongation predominantly in longitudinal directions. The rapid cell expansion coincides with endosperm cellularization. Distribution of TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling)-positive nuclei reveals distinct patterns starting in the nucellus at anthesis and followed later by the inner cell rows of the pericarp, then spreading to the whole pericarp. The pattern suggests timely and spatially regulated programmed cell death (PCD) processes in maternal seed tissues. When the endosperm is coenocytic, PCD events are only observed within the nucellus. Thereby, remobilization of nucellar storage compounds by PCD could nourish the early developing endosperm when functional interconnections are absent between maternal and filial seed organs. Specific proteases promote PCD events. Characterization of the barley vacuolar processing enzyme (VPE) gene family identified seven gene members specifically expressed in the developing grain. HvVPE2a (known as nucellain) together with closely similar HvVPE2b and HvVPE2d might be involved in nucellar PCD. HvVPE4 is strongly cell specific for pericarp parenchyma. Correlative evidence suggests that HvVPE4 plays a role in PCD events in the pericarp. Possible functions of PCD in the maternal tissues imply a potential nutritive role or the relief of a physical restraint for endosperm growth. PCD could also activate post-phloem transport functions.

  14. Induced rupture of vesicles adsorbed on glass by pore formation at the surface-bilayer interface.

    PubMed

    Kataoka-Hamai, Chiho; Yamazaki, Tomohiko

    2015-02-03

    Supported lipid bilayers (SLBs) are often formed by spontaneous vesicle rupture and fusion on a solid surface. A well-characterized rupture mechanism for isolated vesicles is pore nucleation and expansion in the solution-exposed nonadsorbed area. In contrast, pore formation in the adsorbed bilayer region has not been investigated to date. In this work, we studied the detailed mechanisms of asymmetric rupture of giant unilamellar vesicles (GUVs) adsorbed on glass using fluorescence microscopy. Asymmetric rupture is the pathway where a rupture pore forms in a GUV near the edge of the glass-bilayer interface with high curvature and then expansion of the pore yields a planar bilayer patch. We show that asymmetric rupture occasionally resulted in SLB patches bearing a defect pore. The defect formation probability depended on lipid composition, salt concentration, and pH. Approximately 40% of negatively charged GUVs under physiological conditions formed pore-containing SLB patches, while negatively charged GUVs at low salt concentration or pH 4.0 and positively charged GUVs exhibited a low probability of defect inclusion. The edge of the defect pore was either in contact with (on-edge) or away from (off-edge) the edge of the planar bilayer. On-edge pores were predominantly formed over off-edge defects. Pores initially formed in the glass-adsorbed region before rupture, most frequently in close contact with the edge of the adsorbed region. When a pore formed near the edge of the adsorbed area or when the edge of a pore reached that of the adsorbed area by pore expansion, asymmetric rupture was induced from the defect site. These induced rupture mechanisms yielded SLB patches with an on-edge pore. In contrast, off-edge pores were produced when defect pore generation and subsequent vesicle rupture were uncoupled. The current results demonstrate that pore formation in the surface-adsorbed region of GUVs is not a negligible event.

  15. With minimal systemic T-cell expansion, CD8+ T Cells mediate protection of rhesus macaques immunized with attenuated simian-human immunodeficiency virus SHIV89.6 from vaginal challenge with simian immunodeficiency virus.

    PubMed

    Genescà, Meritxell; Skinner, Pamela J; Hong, Jung Joo; Li, Jun; Lu, Ding; McChesney, Michael B; Miller, Christopher J

    2008-11-01

    The presence, at the time of challenge, of antiviral effector T cells in the vaginal mucosa of female rhesus macaques immunized with live-attenuated simian-human immunodeficiency virus 89.6 (SHIV89.6) is associated with consistent and reproducible protection from pathogenic simian immunodeficiency virus (SIV) vaginal challenge (18). Here, we definitively demonstrate the protective role of the SIV-specific CD8(+) T-cell response in SHIV-immunized monkeys by CD8(+) lymphocyte depletion, an intervention that abrogated SHIV-mediated control of challenge virus replication and largely eliminated the SIV-specific T-cell responses in blood, lymph nodes, and genital mucosa. While in the T-cell-intact SHIV-immunized animals, polyfunctional and degranulating SIV-specific CD8(+) T cells were present in the genital tract and lymphoid tissues from the day of challenge until day 14 postchallenge, strikingly, expansion of SIV-specific CD8(+) T cells in the immunized monkeys was minimal and limited to the vagina. Thus, protection from uncontrolled SIV replication in animals immunized with attenuated SHIV89.6 is primarily mediated by CD8(+) T cells that do not undergo dramatic systemic expansion after SIV challenge. These findings demonstrate that despite, and perhaps because of, minimal systemic expansion of T cells at the time of challenge, a stable population of effector-cytotoxic CD8(+) T cells can provide significant protection from vaginal SIV challenge.

  16. Exocytotic fusion pores as a target for therapy.

    PubMed

    Jorgačevski, Jernej; Kreft, Marko; Zorec, Robert

    2017-09-01

    Regulated exocytosis can be split into a sequence of steps ending with the formation and the dilation of a fusion pore, a neck-like connection between the vesicle and the plasma membrane. Each of these steps is precisely controlled to achieve the optimal spatial and temporal profile of the release of signalling molecules. At the level of the fusion pore, tuning of the exocytosis can be achieved by preventing its formation, by stabilizing the unproductive narrow fusion pore, by altering the speed of fusion pore expansion and by completely closing the fusion pore. The molecular structure and dynamics of fusion pores have become a major focus of cell research, especially as a promising target for therapeutic strategies. Electrophysiological, optical and electrochemical methods have been used extensively to illuminate how cells regulate secretion at the level of a single fusion pore. Here, we describe recent advances in the structure and mechanisms of the initial fusion pore formation and the progress in therapeutic strategies with the focus on exocytosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Hampered cumulus expansion of porcine cumulus-oocyte complexes by excessive presence of alpha2 -macroglobulin is likely mediated via inhibition of zinc-dependent metalloproteases.

    PubMed

    Appeltant, Ruth; Beek, Josine; Maes, Dominiek; Bijttebier, Jo; Van Steendam, Katleen; Nauwynck, Hans; Van Soom, Ann

    2017-09-01

    In vitro maturation (IVM) in serum causes hampered expansion of porcine cumulus-oocyte complexes (COCs) due to excessive alpha2 -macroglobulin (A2M). This study investigated two hypotheses that could explain the effect of A2M: (i) binding of epidermal growth factor (EGF) to A2M, followed by its decreased availability; and (ii) inhibition of zinc-dependent metalloproteases. Cumulus expansion was evaluated based on the diameter of the COCs, the proportion of COCs participating in a floating cloud and the proportion of COCs with loss of cumulus cells. The first hypothesis of decreased EGF availability was tested by increasing the EGF concentration (20 and 50 ng/mL vs. 10 ng/mL), but was not confirmed because cumulus expansion did not improve. To verify the second hypothesis of inhibited zinc-dependent metalloproteases, the effect of tissue inhibitor of metalloproteases-3 (TIMP-3) on cumulus expansion during IVM with and without A2M was investigated. To immuno-neutralize A2M, serum was pre-incubated with A2M antibodies. Impaired cumulus expansion because of TIMP-3 could only be observed during IVM in 10% of serum with A2M antibodies. No effect of TIMP-3 was observed in medium without A2M antibodies. These results indicate that A2M and TIMP-3 share a common target, a zinc-dependent metalloprotease. Future research is directed toward the identification of the protease involved. © 2017 Japanese Society of Animal Science.

  18. 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

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

    PubMed

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

    2013-12-01

    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.

  20. 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.

  1. Donor bone marrow cells are essential for iNKT cell-mediated Foxp3+ Treg cell expansion in a murine model of transplantation tolerance.

    PubMed

    Miyairi, Satoshi; Hirai, Toshihito; Ishii, Rumi; Okumi, Masayoshi; Nunoda, Shinichi; Yamazaki, Kenji; Ishii, Yasuyuki; Tanabe, Kazunari

    2017-01-26

    Mixed chimerism induction is the most reliable method for establishing transplantation tolerance. We previously described a novel treatment using a suboptimal dose of anti-CD40 ligand (anti-CD40L) and liposomal formulation of a ligand for invariant natural killer T cells administered to sub-lethally irradiated recipient mice after donor bone marrow cell (BMC) transfer. Recipient mice treated with this regimen showed expansion of a Foxp3-positive regulatory T(Treg) cell phenotype, and formation of mixed chimera. However, the mechanism of expansion and bioactivity of Treg cells remains unclear. Here, we examine the role of donor BMCs in the expansion of bioactive Treg cells. The mouse model was transplanted with a heart allograft the day after treatment. The results showed that transfer of spleen cells in place of BMCs failed to deplete host interferon (IFN)-γ-producing CD8(+) T cells, expand host Ki67(+) CD4(+) CD25(+) Foxp3(+) Treg cells, and prolong graft survival. Severe combined immunodeficiency mice who received Treg cells obtained from BMC-recipients accepted skin grafts in an allo-specific manner. Myeloid-derived suppressor cells, which were a copious cell subset in BMCs, enhanced the Ki67 expression of Treg cells. This suggests that donor BMCs are indispensable for the expansion of host bioactive Treg cells in our novel treatment for transplant tolerance induction.

  2. Model Pores of Molecular Dimension

    PubMed Central

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

    1972-01-01

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

  3. 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

  4. 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

  5. Open-closed switching of synthetic tubular pores

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  6. Hydrate formation and growth in pores

    NASA Astrophysics Data System (ADS)

    Jung, Jong-Won; Santamarina, J. Carlos

    2012-04-01

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

  7. Matrix-mediated retention of adipogenic differentiation potential by human adult bone marrow-derived mesenchymal stem cells during ex vivo expansion.

    PubMed

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

    2005-11-01

    Recently, cell-based approaches utilizing adipogenic progenitor cells for fat tissue engineering have been developed and reported to have success in promoting in vivo adipogenesis and the repair of defect sites. For autologous applications, human bone marrow-derived mesenchymal stem cells (MSCs) have been suggested as a potential cell source for adipose tissue engineering applications due to their ability to be isolated and ex vivo expanded from adult bone marrow aspirates and their versatility for pluripotent differentiation into various mesenchymal lineages including adipogenic. Due to the relatively low frequency of MSCs present within bone marrow, extensive ex vivo expansion of these cells is necessary to obtain therapeutic cell populations for tissue engineering strategies. Currently, utilization of MSCs for adipose tissue engineering is limited due to the attenuation of their adipogenic differentiation potential following extensive ex vivo expansion on conventional tissue culture plastic (TCP) substrates. In the present study, the ability of a denatured collagen type I (DC) matrix to preserve MSC adipogenic potential during ex vivo expansion was examined. Adipocyte-related markers and functions were examined in vitro in response to adipogenic culture conditions for 21 days in comparison to early passage MSCs and late passage MSCs ex vivo expanded on TCP. The results demonstrated significant preservation of the ability of late passage MSCs ex vivo expanded on the DC matrix to express adipogenic markers (fatty acid-binding protein-4, lipoprotein lipase, acyl-CoA synthetase, adipsin, facilitative glucose transporter-4, and accumulation of lipids) similar to the early passage cells and in contrast to late passage MSCs expanded on TCP. The ability of the DC matrix to preserve adipocyte-related markers and functions of MSCs following extensive ex vivo expansion represents a novel culture technique to expand functional adipogenic progenitors for tissue engineering

  8. 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.

  9. Experimental study on the response characteristics of coal permeability to pore pressure under loading and unloading conditions

    NASA Astrophysics Data System (ADS)

    Ye, Zhiwei; Zhang, Lei; Hao, Dingyi; Zhang, Cun; Wang, Chen

    2017-10-01

    In order to study the response characteristics of coal permeability to pore pressure, seepage experiments under different simulated in situ stresses on loading and unloading paths are carried out using the self-developed Gas Flow and Displacement Testing Apparatus (GFDTA) system. Based on the analysis of the experimental data, the relationship between average pore pressure and permeability is found to basically obey the function distribution of a two degree polynomial. In this paper, two aspects of the relationship between permeability and pore pressure are explained: the Klinbenberg effect and expansion, and the penetration of the initial fracture. Under low pore pressure, the decrease in the Klinbenberg effect is the main reason for the decrease in permeability with increased pore pressure. Under relatively high pore pressure, the increase in pore pressure leads to the initial fracture expansion and penetration of the coal sample, which causes an increase in permeability. In order to evaluate the sensitivity of the permeability response to pore pressure changes, the permeability dispersion and pore pressure sensitivity coefficients are defined. After the sensitivity analysis, it was concluded that the loading history changed the fracture structure of the original coal sample and reduced its permeability sensitivity to pore pressure. Under low pore pressure, the Klinbenberg effect is the reason for the decrease in pore pressure sensitivity. Lastly, the permeability-pore pressure relationship is divided into three stages to describe the different response characteristics individually.

  10. Expansion Microscopy

    PubMed Central

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

    2014-01-01

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

  11. Interleukin 1 (IL-1)- and IL-23-mediated expansion of filarial antigen-specific Th17 and Th22 cells in filarial lymphedema.

    PubMed

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

    2014-07-01

    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. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  12. 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

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

    PubMed Central

    Peters, Nathaniel C.

    2015-01-01

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

  14. 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.

  15. Push-and-pull regulation of the fusion pore by synaptotagmin-7.

    PubMed

    Segovia, Margarita; Alés, Eva; Montes, María Angeles; Bonifas, Imelda; Jemal, Imane; Lindau, Manfred; Maximov, Anton; Südhof, Thomas C; Alvarez de Toledo, Guillermo

    2010-11-02

    In chromaffin cells, Ca(2+) binding to synaptotagmin-1 and -7 triggers exocytosis by promoting fusion pore opening and fusion pore expansion. Synaptotagmins contain two C2 domains that both bind Ca(2+) and contribute to exocytosis; however, it remains unknown whether the C2 domains act similarly or differentially to promote opening and expansion of fusion pores. Here, we use patch amperometry measurements in WT and synaptotagmin-7-mutant chromaffin cells to analyze the role of Ca(2+) binding to the two synaptotagmin-7 C2 domains in exocytosis. We show that, surprisingly, Ca(2+) binding to the C2A domain suffices to trigger fusion pore opening but that the resulting fusion pores are unstable and collapse, causing a dramatic increase in kiss-and-run fusion events. Thus, synaptotagmin-7 controls fusion pore dynamics during exocytosis via a push-and-pull mechanism in which Ca(2+) binding to both C2 domains promotes fusion pore opening, but the C2B domain is selectively essential for continuous expansion of an otherwise unstable fusion pore.

  16. Push-and-pull regulation of the fusion pore by synaptotagmin-7

    PubMed Central

    Segovia, Margarita; Alés, Eva; Montes, María Angeles; Bonifas, Imelda; Jemal, Imane; Lindau, Manfred; Maximov, Anton; Südhof, Thomas C.; Alvarez de Toledo, Guillermo

    2010-01-01

    In chromaffin cells, Ca2+ binding to synaptotagmin-1 and -7 triggers exocytosis by promoting fusion pore opening and fusion pore expansion. Synaptotagmins contain two C2 domains that both bind Ca2+ and contribute to exocytosis; however, it remains unknown whether the C2 domains act similarly or differentially to promote opening and expansion of fusion pores. Here, we use patch amperometry measurements in WT and synaptotagmin-7–mutant chromaffin cells to analyze the role of Ca2+ binding to the two synaptotagmin-7 C2 domains in exocytosis. We show that, surprisingly, Ca2+ binding to the C2A domain suffices to trigger fusion pore opening but that the resulting fusion pores are unstable and collapse, causing a dramatic increase in kiss-and-run fusion events. Thus, synaptotagmin-7 controls fusion pore dynamics during exocytosis via a push-and-pull mechanism in which Ca2+ binding to both C2 domains promotes fusion pore opening, but the C2B domain is selectively essential for continuous expansion of an otherwise unstable fusion pore. PMID:20956309

  17. 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,.

  18. Pore-forming proteins with built-in triggers and switches

    NASA Astrophysics Data System (ADS)

    Bayley, Hagan

    1996-02-01

    Genetic engineering and targeted chemical modification are being used to produce polypeptides with pore-forming activity that can be triggered or switched on-and-off by biochemical, chemical or physical stimuli. The principal target of our studies has been the (alpha) -hemolysin ((alpha) HL) from the bacterium Staphylococcus aureus. The remodeled hemolysins include protease-activated pores, metal-regulated pores, pores that are activated by chemical alkylation and pores that are turned on with light. These polypeptides have several potential applications. For example, they might serve as components of sensors or they might be useful for mediating the controlled release of encapsulated drugs.

  19. Thermal Expansion

    NASA Astrophysics Data System (ADS)

    Ventura, Guglielmo; Perfetti, Mauro

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

  20. Stimulus-responsive track pores

    NASA Astrophysics Data System (ADS)

    Yoshida, Masaru; Tamada, Masao; Asano, Masaharu; Omichi, Hideki; Kubota, Hitoshi; Katakai, Ryoichi; Spohr, Reimar; Vetter, Johann

    1993-03-01

    Ion track grafting enables the manufacture of chemically responsive track pores analogous to the discrete membrane channels found in biology. For this purpose etched ion tracks generated in CR-39 are surface-grafted by methacryloyl-L-alaninemethylester. In the future, the responsive track pores could be used to model the actively controlled channels in biomembranes and may lead to interesting technological applications.

  1. 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.

  2. 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

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

    PubMed Central

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

    2010-01-01

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

  4. What is the mitochondrial permeability transition pore?

    PubMed

    Halestrap, Andrew P

    2009-06-01

    Under conditions of mitochondrial calcium overload, especially when accompanied by oxidative stress, elevated phosphate concentrations and adenine nucleotide depletion, a non-specific pore, the mitochondrial permeability transition pore (MPTP), opens in the inner mitochondrial membrane. MPTP opening enables free passage into the mitochondria of molecules of <1.5 kDa including protons. The resulting uncoupling of oxidative phosphorylation leads to ATP depletion and necrotic cell death and it is now widely recognised that MPTP opening is a major cause of reperfusion injury and an effective target for cardioprotection. The properties of the MPTP are well defined, but despite extensive research in many laboratories, its exact molecular identity remains uncertain. Knockout studies have confirmed a role for cyclophilin-D (CyP-D), probably mediated by its peptidyl-prolyl cis-trans isomerase activity facilitating a conformational change of an inner membrane protein. However, the identity of the membrane component(s) remains controversial. Knockout studies have eliminated an essential role for either the voltage dependent anion channel (VDAC) or the adenine nucleotide translocase (ANT), although a regulatory role for the ANT was confirmed. Our own studies implicate the mitochondrial phosphate carrier (PiC) in MPTP formation and are consistent with a calcium-triggered conformational change of the PiC, facilitated by CyP-D, inducing pore opening. We propose that this is enhanced by an association of the PiC with the "c" conformation of the ANT. Agents that modulate pore opening may act on either or both the PiC and the ANT. However, knockdown and reconstitution studies are awaited to confirm or refute this model.

  5. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-02-18

    The response to DNA double-strand breaks (DSBs) requires alterations in chromatin structure to promote the assembly of repair complexes on broken chromosomes. Non-homologous end-joining (NHEJ) is the dominant DSB repair pathway in human cells, but our understanding of how it operates in chromatin is limited. Here, we define a mechanism that plays a crucial role in regulating NHEJ in chromatin. This mechanism is initiated by DNA damage-associated poly(ADP-ribose) polymerase 1 (PARP1), which recruits the chromatin remodeler CHD2 through a poly(ADP-ribose)-binding domain. CHD2 in turn triggers rapid chromatin expansion and the deposition of histone variant H3.3 at sites of DNA damage. Importantly, we find that PARP1, CHD2, and H3.3 regulate the assembly of NHEJ complexes at broken chromosomes to promote efficient DNA repair. Together, these findings reveal a PARP1-dependent process that couples ATP-dependent chromatin remodeling with histone variant deposition at DSBs to facilitate NHEJ and safeguard genomic stability. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Chemomechanical evolution of pore space in carbonate microstructures upon dissolution: Linking pore geometry to bulk elasticity

    NASA Astrophysics Data System (ADS)

    Arson, C.; Vanorio, T.

    2015-10-01

    One of the challenges faced today in a variety of geophysical applications is the need to understand the changes of elastic properties due to time-variant chemomechanical processes. The objective of this work is to model carbonate rock elastic properties as functions of pore geometry changes that occur when the solid matrix is dissolved by carbon dioxide. We compared two carbonate microstructures: porous micrite ("mudstone") and grain-supported carbonate ("packstone"). We formulated a mathematical model that distinguishes the effects of microporosity and macroporosity on stiffness changes. We used measures of mechanical and chemical porosity changes recorded during injection tests to compute elastic moduli and compare them to moduli obtained from wave velocity measurements. In mudstones, both experimental and numerical results indicate that bulk moduli change by less than 5%. The evolution of elastic moduli is controlled by macropore enlargement. In packstones, model predictions underestimate changes of elastic moduli with total porosity by 10% to 80%. The total porosity variation is 60% to 75% smaller than the chemical porosity variation, which indicates that pore expansion due to dissolution is counterbalanced by pore shrinkage due to compaction. Packstone elastic properties are controlled by grain sliding. The methodology presented in this paper can be generalized to other chemomechanical processes studied in rocks, such as dislocations, glide, diffusive mass transfer, recrystallization, and precipitation.

  10. Dynamics and regulation of endocytotic fission pores: role of calcium and dynamin.

    PubMed

    Cabeza, José María; Acosta, Jorge; Alés, Eva

    2010-12-01

    Although endocytosis involves the fission pore, a transient structure that produces the scission between vesicle and plasma membranes, the dimensions and dynamics of fission pores remain unclear. Here we report that the pore resistance changes proceed in three distinct phases: an initial phase where the resistance increases at 31.7 ± 2.9 GΩ/second, a slower linear phase with an overall slope of 11.7 ± 1.9 GΩ/second and a final increase in resistance more steeply (1189 ± 136 GΩ/second). The kinetics of these changes was calcium dependent. These sequential stages of the fission pore may be interpreted in terms of pore geometry as changes, first in pore diameter and then in pore length, according to which, before fission, the pore diameter consistently decreased to a value near 4 nm, whereas the pore length ranged between 20 and 300 nm. Dynamin, a mechanochemical GTPase, plays an important role in accelerating the fission event, preferentially in endocytotic vesicles of regular size, by increasing the rates of pore closure during the first and second phases of the fission pore, but hardly affected larger and longer-lived endocytotic events. These results suggest that fission pores are dynamic structures that form thin and long membrane necks regulated by intracellular calcium. Between calcium mediators, dynamin functions as a catalyst to increase the speed of single vesicle endocytosis.

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

    PubMed Central

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

    2008-01-01

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

  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. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. 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 Central

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

    2016-01-01

    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

  14. 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

  15. 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.

  16. Toxic PRn poly-dipeptides encoded by the C9orf72 repeat expansion block nuclear import and export

    PubMed Central

    Shi, Kevin Y.; Mori, Eiichiro; Nizami, Zehra F.; Lin, Yi; Kato, Masato; Xiang, Siheng; Wu, Leeju C.; Ding, Ming; Yu, Yonghao; Gall, Joseph G.; McKnight, Steven L.

    2017-01-01

    The toxic proline:arginine (PRn) poly-dipeptide encoded by the (GGGGCC)n repeat expansion in the C9orf72 form of heritable amyotrophic lateral sclerosis (ALS) binds to the central channel of the nuclear pore and inhibits the movement of macromolecules into and out of the nucleus. The PRn poly-dipeptide binds to polymeric forms of the phenylalanine:glycine (FG) repeat domain, which is shared by several proteins of the nuclear pore complex, including those in the central channel. A method of chemical footprinting was used to characterize labile, cross-β polymers formed from the FG domain of the Nup54 protein. Mutations within the footprinted region of Nup54 polymers blocked both polymerization and binding by the PRn poly-dipeptide. The aliphatic alcohol 1,6-hexanediol melted FG domain polymers in vitro and reversed PRn-mediated enhancement of the nuclear pore permeability barrier. These data suggest that toxicity of the PRn poly-dipeptide results in part from its ability to lock the FG repeats of nuclear pore proteins in the polymerized state. Our study offers a mechanistic interpretation of PRn poly-dipeptide toxicity in the context of a prominent form of ALS. PMID:28069952

  17. Pore-forming activity of clostridial binary toxins.

    PubMed

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

    2016-03-01

    Clostridial binary toxins (Clostridium perfringens Iota toxin, Clostridium difficile transferase, Clostridium spiroforme toxin, Clostridium botulinum C2 toxin) as Bacillus binary toxins, including Bacillus anthracis toxins consist of two independent proteins, one being the binding component which mediates the internalization into cell of the intracellularly active component. Clostridial binary toxins induce actin cytoskeleton disorganization through mono-ADP-ribosylation of globular actin and are responsible for enteric diseases. Clostridial and Bacillus binary toxins share structurally and functionally related binding components which recognize specific cell receptors, oligomerize, form pores in endocytic vesicle membrane, and mediate the transport of the enzymatic component into the cytosol. Binding components retain the global structure of pore-forming toxins (PFTs) from the cholesterol-dependent cytotoxin family such as perfringolysin. However, their pore-forming activity notably that of clostridial binding components is more related to that of heptameric PFT family including aerolysin and C. perfringens epsilon toxin. This review focuses upon pore-forming activity of clostridial binary toxins compared to other related PFTs. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Mauro Dalla Serra and Franco Gambale. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Low-Thermal-Expansion Filled Polytetrafluoroethylene

    NASA Technical Reports Server (NTRS)

    Shapiro, Sanford S.

    1989-01-01

    PTFE made thermally compatible with aluminum without changing dielectric constant. Manufactured with fillers and pores to reduce coefficient of thermal expansion by factor of 6 to match aluminum. Material retains 2.1 dielectric constant of pure PTFE. Combines filler and micropore concepts. Particles and voids embedded in PTFE matrix function cooperatively. Particles take up compressive stress imposed by contracting PTFE, and voids take up expanding material. Increases dielectric constant, while voids reduce it.

  19. Low-Thermal-Expansion Filled Polytetrafluoroethylene

    NASA Technical Reports Server (NTRS)

    Shapiro, Sanford S.

    1989-01-01

    PTFE made thermally compatible with aluminum without changing dielectric constant. Manufactured with fillers and pores to reduce coefficient of thermal expansion by factor of 6 to match aluminum. Material retains 2.1 dielectric constant of pure PTFE. Combines filler and micropore concepts. Particles and voids embedded in PTFE matrix function cooperatively. Particles take up compressive stress imposed by contracting PTFE, and voids take up expanding material. Increases dielectric constant, while voids reduce it.

  20. IL1RAP antibodies block IL-1-induced expansion of candidate CML stem cells and mediate cell killing in xenograft models.

    PubMed

    Ågerstam, Helena; Hansen, Nils; von Palffy, Sofia; Sandén, Carl; Reckzeh, Kristian; Karlsson, Christine; Lilljebjörn, Henrik; Landberg, Niklas; Askmyr, Maria; Högberg, Carl; Rissler, Marianne; Porkka, Kimmo; Wadenvik, Hans; Mustjoki, Satu; Richter, Johan; Järås, Marcus; Fioretos, Thoas

    2016-12-08

    Chronic myeloid leukemia (CML) is currently treated with tyrosine kinase inhibitors, but these do not effectively eliminate the CML stem cells. As a consequence, CML stem cells persist and cause relapse in most patients upon drug discontinuation. Furthermore, no effective therapy exists for the advanced stages of the disease. Interleukin-1 receptor accessory protein (IL1RAP; IL1R3) is a coreceptor of interleukin-1 receptor type 1 and has been found upregulated on CML stem cells. Here, we show that primitive (CD34(+)CD38(-)) CML cells, in contrast to corresponding normal cells, express a functional interleukin-1 (IL-1) receptor complex and respond with NF-κB activation and marked proliferation in response to IL-1. IL1RAP antibodies that inhibit IL-1 signaling could block these effects. In vivo administration of IL1RAP antibodies in mice transplanted with chronic and blast phase CML cells resulted in therapeutic effects mediated by murine effector cells. These results provide novel insights into the role of IL1RAP in CML and a strong rationale for the development of an IL1RAP antibody therapy to target residual CML stem cells. © 2016 by The American Society of Hematology.

  1. EZH2-mediated repression of GSK-3β and TP53 promotes Wnt/β-catenin signaling-dependent cell expansion in cervical carcinoma.

    PubMed

    Chen, Qian; Zheng, Peng-Sheng; Yang, Wen-Ting

    2016-06-14

    Enhancer of zeste homolog 2 (EZH2), a catalytic core component of the Polycomb repressive complex 2 (PRC2), stimulates the silencing of target genes through histone H3 lysine 27 trimethylation (H3K27me3). Recent findings have indicated EZH2 is involved in the development and progression of various human cancers. However, the exact mechanism of EZH2 in the promotion of cervical cancer is largely unknown. Here, we show that EZH2 expression gradually increases during the progression of cervical cancer. We identified a significant positive correlation between EZH2 expression and cell proliferation in vitro and tumor formation in vivo by the up-regulation or down-regulation of EZH2 using CRISPR-Cas9-mediated gene editing technology and shRNA in HeLa and SiHa cells. Further investigation indicated that EZH2 protein significantly accelerated the cell cycle transition from the G0/G1 to S phase. TOP/FOP-Flash reporter assay revealed that EZH2 significantly activated Wnt/β-catenin signaling and the target genes of Wnt/β-catenin pathway were up-regulated, including β-catenin, cyclin D1, and c-myc. Moreover, dual-luciferase reporter and chromatin immunoprecipitation (ChIP) assays confirmed that EZH2 inhibited the expression of glycogen synthase kinase-3β (GSK-3β) and TP53 through physically interacting with motifs in the promoters of the GSK-3β and TP53 genes. Additionally, blockage of the Wnt/β-catenin pathway resulted in significant inhibition of cell proliferation, and activation of the Wnt/β-catenin pathway resulted in significant enhancement of cell proliferation, as induced by EZH2. Taken together, our data demonstrate that EZH2 promotes cell proliferation and tumor formation in cervical cancer through activating the Wnt/β-catenin pathway by epigenetic silencing via GSK-3β and TP53.

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

    PubMed Central

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

    2012-01-01

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

  3. 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

  4. Geostatistical Modeling of Pore Velocity

    SciTech Connect

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

    1981-06-01

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

  5. Restricted Transport in Small Pores

    PubMed Central

    Anderson, John L.; Quinn, John A.

    1974-01-01

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

  6. Heterogeneous nucleation in and out of pores.

    PubMed

    Page, Amanda J; Sear, Richard P

    2006-08-11

    We study the nucleation of a new thermodynamic phase in pores and find that the nucleation often proceeds via two steps: nucleation of pore filling, and nucleation out of the pore. These two rates have opposing dependencies on pore size, resulting in a pore size at which the nucleation rate of the new phase is maximal. This finding is relevant to attempts to design and use porous media to crystallize proteins.

  7. Pore size matters for potassium channel conductance

    PubMed Central

    Moldenhauer, Hans; Pincuntureo, Matías

    2016-01-01

    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. PMID:27619418

  8. 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.

  9. Mitochondrial permeability transition pore and calcium handling.

    PubMed

    Wong, Renee; Steenbergen, Charles; Murphy, Elizabeth

    2012-01-01

    Opening of a large conductance channel in the inner mitochondrial membrane, known as the mitochondrial permeability transition (MPT) pore, has been shown to be a primary mediator of cell death in the heart subjected to ischemia-reperfusion injury. Inhibitors of the MPT have been shown to reduce cardiac ischemia-reperfusion injury. Furthermore, most cardioprotective strategies appear to reduce ischemic cell death either by reducing the triggers for the opening of the MPT, such as reducing calcium overload or reactive oxygen species, or by more direct inhibition of the MPT. This chapter focuses on key issues in the study of the MPT and provides some methods for measuring MPT opening in isolated mitochondria.

  10. GATED PORES IN THE FERRITIN PROTEIN NANOCAGE

    PubMed Central

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

    2008-01-01

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

  11. 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.

  12. Smectic pores and defect cores

    PubMed Central

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

    2012-01-01

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

  13. Pore volume is most highly correlated with the visual assessment of skin pores.

    PubMed

    Kim, S J; Shin, M K; Back, J H; Koh, J S

    2014-11-01

    Many studies have been focused on evaluating assessment techniques for facial pores amid growing attention on skin care. Ubiquitous techniques used to assess the size of facial pores include visual assessment, cross-section images of the skin surface, and profilometric analysis of silicone replica of the facial skin. In addition, there are indirect assessment methods, including observation of pores based on confocal laser scanning microscopy and the analysis of sebum secretion and skin elasticity. The aim of this study was to identify parameters useful in estimating pore of surface in normal skin. The severity of pores on the cheek area by frontal optical images was divided on a 0-6 scale with '0' being faint and small pore and '6' being obvious and large pore. After the photos of the frontal cheek of 32 women aged between 35 and 49 were taken, the size of their pores was measured on a 0-6 scale; and the correlation between visual grading of pore and various evaluations (pore volume by 3-D image, pore area and number by Optical Image Analyzer) contributing to pore severity investigated using direct, objective, and noninvasive evaluations. The visual score revealed that the size of pores was graded on a 1-6 scale. Visual grading of pore was highly correlated with pore volume measured from 3-D images and pore area measured from 2-D optical images in the order (P < 0.01). Visual grading of pore was also slightly correlated with the number of pores in size of over 0.04 mm(2) (P < 0.05). High correlation between pore score and pore volume can be explained by 3-D structural characteristics of pores. It is concluded that pore volume and area serve as useful parameters in estimating pore of skin surface. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Protein crystal nucleation in pores

    PubMed Central

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

    2017-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  16. 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 ...

  17. Pore size--a key property for selective toxin removal in blood purification.

    PubMed

    Harm, Stephan; Falkenhagen, Dieter; Hartmann, Jens

    2014-09-01

    Extracorporeal blood purification systems based on combined membrane/adsorption technologies are used in acute liver failure to replace detoxification as well as to remove inflammatory mediators in sepsis patients. In addition to coating and chemical modification of the surface, pore size significantly controls the selectivity of adsorption materials. This study addresses the adsorption of albumin bound liver toxins, cytokines, and representative plasma compounds on three adsorbents which differ only in pore size distribution. All three adsorbents are based on hydrophobic poly(styrene-divinylbenzene) copolymer matrices and have mean pore sizes of 15, 30, and 100 nm. The pores of adsorbents act as molecular sieves and prevent the entry of molecules that are larger than their molecular cut-off. The results of this study reveal that adsorbents based on styrene-divinylbenzene polymers with 15 nm pores are suitable for cytokine removal, and the same adsorbents with 30-40 nm pores are the best choice for the removal of albumin-bound toxins in the case of liver failure. Adsorbents with very large pores lack selectivity which leads to uncontrolled adsorption of all plasma proteins. Therefore, hydrophobic adsorbents with large pores offer inadequate plasma compatibility and do not fulfill the requirements for blood purification. Biocompatibility and efficiency of adsorbents used for blood purification can improved by fine tuning of adsorbent surface pore distributions.

  18. Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

    NASA Astrophysics Data System (ADS)

    Chen, M.; Kocar, B. D.

    2016-12-01

    Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

  19. The energy expansions of evolution.

    PubMed

    Judson, Olivia P

    2017-04-28

    The history of the life-Earth system can be divided into five 'energetic' epochs, each featuring the evolution of life forms that can exploit a new source of energy. These sources are: geochemical energy, sunlight, oxygen, flesh and fire. The first two were present at the start, but oxygen, flesh and fire are all consequences of evolutionary events. Since no category of energy source has disappeared, this has, over time, resulted in an expanding realm of the sources of energy available to living organisms and a concomitant increase in the diversity and complexity of ecosystems. These energy expansions have also mediated the transformation of key aspects of the planetary environment, which have in turn mediated the future course of evolutionary change. Using energy as a lens thus illuminates patterns in the entwined histories of life and Earth, and may also provide a framework for considering the potential trajectories of life-planet systems elsewhere.

  20. 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.

  1. Capillary Properties of Model Pores.

    NASA Astrophysics Data System (ADS)

    Walsh, Tim J.

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

  2. 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.

  3. 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.

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

    PubMed

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

    2014-12-02

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

  5. 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

  6. Bax and Bif-1 proteins interact on Bilayer Lipid Membrane and form pore.

    PubMed

    Gupta, Rajeev; Ghosh, Subhendu

    2015-08-07

    Bax and Bax interacting factor-1(Bif-1) are cytosolic proteins, which translocate towards mitochondria during mitochondria-mediated apoptosis. Bif-1 has been identified to co-immunoprecipitate with Bax in apoptotic cells. We have studied the interaction of Bax and Bif-1 on Bilayer Lipid Membrane (BLM) through electrophysiological experiments. It has been observed that Bax-Bif-1 equimolar mixture can form a pore. The pore conductance is in the range of 4.96-5.41 nS. It also displays a sub-state with a conductance of 2.6 nS. No pore activity is observed on BLM when monomeric Bax and Bif-1 proteins are tested independently. The above-mentioned pore forming activity could be relevant in mitochondria-mediated apoptosis. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    SciTech Connect

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

    1999-10-01

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

  8. Particle Trajectory-Dependent Ionic Current Blockade in Low-Aspect-Ratio Pores.

    PubMed

    Tsutsui, Makusu; He, Yuhui; Yokota, Kazumichi; Arima, Akihide; Hongo, Sadato; Taniguchi, Masateru; Washio, Takashi; Kawai, Tomoji

    2016-01-26

    Resistive pulse sensing with nanopores having a low thickness-to-diameter aspect-ratio structure is expected to enable high-spatial-resolution analysis of nanoscale objects in a liquid. Here we investigated the sensing capability of low-aspect-ratio pore sensors by monitoring the ionic current blockades during translocation of polymeric nanobeads. We detected numerous small current spikes due to partial occlusion of the pore orifice by particles diffusing therein reflecting the expansive electrical sensing zone of the low-aspect-ratio pores. We also found wide variations in the ion current line-shapes in the particle capture stage suggesting random incident angle of the particles drawn into the pore. In sharp contrast, the ionic profiles were highly reproducible in the post-translocation regime by virtue of the spatial confinement in the pore that effectively constricts the stochastic capture dynamics into a well-defined ballistic motion. These results, together with multiphysics simulations, indicate that the resistive pulse height is highly dependent on the nanoscopic single-particle trajectories involved in ultrathin pore sensors. The present finding indicates the importance of regulating the translocation pathways of analytes in low-aspect-ratio pores for improving the discriminability toward single-bioparticle tomography in liquid.

  9. 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.

  10. 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

  11. A thermodynamic approach to alamethicin pore formation.

    PubMed

    Rahaman, Asif; Lazaridis, Themis

    2014-01-01

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

  12. A thermodynamic approach to alamethicin pore formation.

    PubMed

    Rahaman, Asif; Lazaridis, Themis

    2014-05-01

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

  13. Tiny Pores observed by HINODE/SOT

    NASA Astrophysics Data System (ADS)

    Cho, K.; Bong, S.; Chae, J.; Kim, Y.; Park, Y.

    2010-12-01

    The study of pores, small penumbraless sunspots, can give us a chance to understand how strong magnetic fields interact with convective motions in the photosphere. For a better understanding of this interaction, we investigate the temporal variation of several tiny pores smaller than 2“. These pores were observed by the Solar Optical Telescope (SOT) onboard Hinode on 2006 December 29. We have analyzed the high resolution spectropolarimetric (SP) data and the G-band filtergrams taken during the observation. Magnetic flux density and Doppler velocities of the pores are estimated by applying the center of gravity (COG) method to the SP data. The horizontal motions in and around the pores are tracked by adopting the Nonlinear Affine Velocity Estimator (NAVE) method to the G-band filter images. As results, we found the followings. (1) Darkness of pores is positively correlated with magnetic flux density. (2) Downflows always exist inside and around the pores. (3) The speed of downflows inside the pores is negatively correlated with their darkness. (4) The pores are surrounded by strong downflows. (5) Brightness changes of the pores are correlated with the divergence of mass flow (correlation coefficient > 0.9). (6) The pores in the growing phase are associated with the converging flow pattern and the pores in the decay phase with the diverging flow pattern. Our results support the idea that a pore grows as magnetic flux density increases due to the convergence of ambient mass flow and it decays with the decrease of the flux density due to the diverging mass flow.

  14. Gating of two pore domain potassium channels

    PubMed Central

    Mathie, Alistair; Al-Moubarak, Ehab; Veale, Emma L

    2010-01-01

    Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their activity is modulated by a variety of chemical and physical stimuli which act to increase or decrease the open probability of individual K2P channels. Crystallographic data and homology modelling suggest that all K+ channels possess a highly conserved structure for ion selectivity and gating mechanisms. Like other K+ channels, K2P channels are thought to have two primary conserved gating mechanisms: an inactivation (or C-type) gate at the selectivity filter close to the extracellular side of the channel and an activation gate at the intracellular entrance to the channel involving key, identified, hinge glycine residues. Zinc and hydrogen ions regulate Drosophila KCNK0 and mammalian TASK channels, respectively, by interacting with the inactivation gate of these channels. In contrast, the voltage dependence of TASK3 channels is mediated through its activation gate. For KCNK0 it has been shown that the gates display positive cooperativity. It is of much interest to determine whether other K2P regulatory compounds interact with either the activation gate or the inactivation gate to alter channel activity or, indeed, whether additional regulatory gating pathways exist. PMID:20566661

  15. Gating of two pore domain potassium channels.

    PubMed

    Mathie, Alistair; Al-Moubarak, Ehab; Veale, Emma L

    2010-09-01

    Two-pore-domain potassium (K2P) channels are responsible for background leak currents which regulate the membrane potential and excitability of many cell types. Their activity is modulated by a variety of chemical and physical stimuli which act to increase or decrease the open probability of individual K2P channels. Crystallographic data and homology modelling suggest that all K(+) channels possess a highly conserved structure for ion selectivity and gating mechanisms. Like other K(+) channels, K2P channels are thought to have two primary conserved gating mechanisms: an inactivation (or C-type) gate at the selectivity filter close to the extracellular side of the channel and an activation gate at the intracellular entrance to the channel involving key, identified, hinge glycine residues. Zinc and hydrogen ions regulate Drosophila KCNK0 and mammalian TASK channels, respectively, by interacting with the inactivation gate of these channels. In contrast, the voltage dependence of TASK3 channels is mediated through its activation gate. For KCNK0 it has been shown that the gates display positive cooperativity. It is of much interest to determine whether other K2P regulatory compounds interact with either the activation gate or the inactivation gate to alter channel activity or, indeed, whether additional regulatory gating pathways exist.

  16. Recoverable gas from hydrate-bearing sediments: Pore network model simulation and macroscale analyses

    NASA Astrophysics Data System (ADS)

    Jang, Jaewon; Santamarina, J. Carlos

    2011-08-01

    The volume of hydrate expands into a significantly larger volume of water and gas upon dissociation. Gas recovery and capillary-trapped residual gas saturation are investigated by simulating hydrate dissociation within pore networks. A fluid pressure-controlled boundary condition is used to determine the amount of recovered gas as a function of volume expansion; in this form, results are applicable to gas production by either thermal stimulation or depressurization when production rates prevent secondary hydrate or ice formation. Simulation results show that gas recovery is proportional to gas expansion, initial hydrate saturation, and the sediment pore size distribution (i.e., capillary pressure). Gas recovery is not affected by pore size in coarse-grained sediments with pores larger than 1 μm. Hydrate-bearing sediments with low hydrate saturation yield low gas recovery. Macroscale close form solutions, validated using the numerical results, provide estimates for recoverable gas as a function of the initial hydrate saturation and the fluid expansion factor.

  17. 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)

  18. 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.

  19. 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

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

    PubMed Central

    Jackson, Meyer B.

    2010-01-01

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

  1. Translocation of knotted proteins through a pore

    NASA Astrophysics Data System (ADS)

    Szymczak, P.

    2014-09-01

    We report the results of molecular dynamics simulations of translocation of knotted proteins through pores. The protein is pulled into the pore with a constant force, which in many cases leads to the tightening of the knot. Since the radius of tightened knot is larger than that of the pore opening, the tight knot can block the pore thus preventing further translocation of the chain. Analyzing six different proteins, we show that the stuck probability increases with the applied force and that final positions of the tightened knot along the protein backbone are not random but are usually associated with sharp turns in the polypeptide chain. The combined effect of the confining geometry of the pore and the inhomogeneous character of the protein chain leads thus to the appearance of topological traps, which can immobilize the knot and lead to the jamming of the pore.

  2. Pore network extraction for fractured porous media

    NASA Astrophysics Data System (ADS)

    Jiang, Z.; van Dijke, M. I. J.; Geiger, S.; Ma, J.; Couples, G. D.; Li, X.

    2017-09-01

    Although flow through fractured rocks involves many different length-scales, it is crucial for the prediction of continuum-scale single- and multi-phase flow functions to understand, at the pore-scale, the interaction between the rock matrix and fractures. Here we present a pore-network extraction method in which the pore diameters and fracture apertures are of similar size. The method involves a shrinking algorithm to extract a hybrid skeleton of medial axes and surfaces, and it includes a workflow to convert the medial surfaces of fractures into dense networks of virtual medial axes, allowing generation of an integrated pore-network for the entire pore space. Appropriate single- and two-phase flow properties are assigned to network elements representing the fractures. We validate the method via comparisons between pore network flow simulations and an analytical solution, direct flow simulations and experimental observations. The network calculations are several orders of magnitude faster than the direct simulations.

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

    PubMed Central

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

    1996-01-01

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

  4. 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.

  5. Alkali-silica reaction and pore solution composition in mortars in sea water

    SciTech Connect

    Kawamura, Mitsunori; Takeuchi, Katsunobu

    1996-12-01

    The promotion of expansion of mortars containing a reactive aggregate in 1N NaCl solution at 38 C was attributed to a rise of OH{sup {minus}} ion concentration in the pore solution in the mortars. However, it is ambiguous whether the promotion of expansion of mortars in sea water at a room temperature can be explained in the same way as in NaCl solution at an elevated temperature. This study aims at pursuing the expansion behavior of mortars containing a reactive aggregate relating it to their pore solution composition and the extent of alkali-silica reaction occurring within reactive grains. The alkali-silica reaction in mortars in sea water and 0.5 1N NaCl solution at 20 C appears to progress differently from that in mortars in 1N NaCl solution at an elevated temperature of 38 C. The promotion of expansion of mortars in sea water at 20 C was found to be responsible for an effect of Cl{sup {minus}} ions in the alkali-silica reaction at early stages of immersion. Only when OH{sup {minus}} ion concentration in the pore solution was relatively high, NaCl and sea water could accelerate the alkali-silica reaction in mortars at 20 C.

  6. 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.

  7. 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.

  8. 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 Central

    Gao, Junping

    2013-01-01

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

  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. 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)

  13. Thermal-Expansion Measurement

    NASA Technical Reports Server (NTRS)

    Davis, J. H.; Rives, C.

    1985-01-01

    Precise stable laser system determines coefficients of thermal expansion. Dual-beam interferometer arrangement monitors changes in sample length as function of temperature by following changes inoptical path lengths.

  14. Optimal Electric Utility Expansion

    SciTech Connect

    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 expansion 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.

  15. The Effect of the Pore Entrance on Particle Motion in Slit Pores: Implications for Ultrathin Membranes

    PubMed Central

    Delavari, Armin; Baltus, Ruth

    2017-01-01

    Membrane rejection models generally neglect the effect of the pore entrance on intrapore particle transport. However, entrance effects are expected to be particularly important with ultrathin membranes, where membrane thickness is typically comparable to pore size. In this work, a 2D model was developed to simulate particle motion for spherical particles moving at small Re and infinite Pe from the reservoir outside the pore into a slit pore. Using a finite element method, particles were tracked as they accelerated across the pore entrance until they reached a steady velocity in the pore. The axial position in the pore where particle motion becomes steady is defined as the particle entrance length (PEL). PELs were found to be comparable to the fluid entrance length, larger than the pore size and larger than the thickness typical of many ultrathin membranes. Results also show that, in the absence of particle diffusion, hydrodynamic particle–membrane interactions at the pore mouth result in particle “funneling” in the pore, yielding cross-pore particle concentration profiles focused at the pore centerline. The implications of these phenomena on rejection from ultrathin membranes are examined. PMID:28796197

  16. The Effect of the Pore Entrance on Particle Motion in Slit Pores: Implications for Ultrathin Membranes.

    PubMed

    Delavari, Armin; Baltus, Ruth

    2017-08-10

    Membrane rejection models generally neglect the effect of the pore entrance on intrapore particle transport. However, entrance effects are expected to be particularly important with ultrathin membranes, where membrane thickness is typically comparable to pore size. In this work, a 2D model was developed to simulate particle motion for spherical particles moving at small Re and infinite Pe from the reservoir outside the pore into a slit pore. Using a finite element method, particles were tracked as they accelerated across the pore entrance until they reached a steady velocity in the pore. The axial position in the pore where particle motion becomes steady is defined as the particle entrance length (PEL). PELs were found to be comparable to the fluid entrance length, larger than the pore size and larger than the thickness typical of many ultrathin membranes. Results also show that, in the absence of particle diffusion, hydrodynamic particle-membrane interactions at the pore mouth result in particle "funneling" in the pore, yielding cross-pore particle concentration profiles focused at the pore centerline. The implications of these phenomena on rejection from ultrathin membranes are examined.

  17. 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

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

    PubMed

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

    2008-04-02

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

  19. The Rab3A-22A Chimera Prevents Sperm Exocytosis by Stabilizing Open Fusion Pores.

    PubMed

    Quevedo, María F; Lucchesi, Ornella; Bustos, Matías A; Pocognoni, Cristian A; De la Iglesia, Paola X; Tomes, Claudia N

    2016-10-28

    At the final stage of exocytotis, a fusion pore opens between the plasma and a secretory vesicle membranes; typically, when the pore dilates the vesicle releases its cargo. Sperm contain a large dense-core secretory granule (the acrosome) whose contents are secreted by regulated exocytosis at fertilization. Minutes after the arrival of the triggering signal, the acrosomal and plasma membranes dock at multiple sites and fusion pores open at the contact points. It is believed that immediately afterward, fusion pores dilate spontaneously. Rab3A is an essential component of human sperm exocytotic machinery. Yet, recombinant, persistently active Rab3A halts calcium-triggered secretion when introduced after docking into streptolysin O-permeabilized cells; so does a Rab3A-22A chimera. Here, we applied functional assays, electron and confocal microscopy to show that the secretion blockage is due to the stabilization of open fusion pores. Other novel findings are that sperm SNAREs engage in α-SNAP/NSF-sensitive complexes at a post-fusion stage. Complexes are disentangled by these chaperons to achieve vesiculation and acrosomal contents release. Thus, post-fusion regulation of the pores determines their expansion and the success of the acrosome reaction. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Pore pressure prediction in laminated shaly sand reservoir: A case study of Bintuni Basin

    NASA Astrophysics Data System (ADS)

    Haris, A.; Parlindungan, E.; Riyanto, A.

    2017-07-01

    Pore pressure prediction has been carried out using well log and seismic velocity data to evaluate pore pressure character of the laminated shally sand reservoir in Bintuni Basin, West Papua. The majority of the thin laminated reservoir are below resolving power of logging tool. The main factor of reservoir behavior, which typically exhibits composition mineral of lithic, micaceous and glauconitic, has a strong relationship with conductive mineral. Based on total gas mud logging data, there is some potential gas reservoir. In this study, non-normal high pore pressure was identified in some intervals and designed for cases where compaction disequilibrium is the cause of fluid expansion on the compaction state of the impermeable sediments. We used Eaton's method to estimate pore pressure gradient. We also performed seismic velocity model analysis to estimate the effective stress using empirical Bowers and Terzaghi method, where horizontal and vertical pressure data were distributed using probabilistic neural network method. Our analysis on the pore pressure distribution map, which is combined with the time structure, shows that the correlation of non normal pore pressure is found not only in height structure but also in the low structure, particularly at the southern part of the study area.

  1. Fluctuation of surface charge in membrane pores.

    PubMed Central

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

    2002-01-01

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

  2. On seismically induced pore pressure and settlement

    USGS Publications Warehouse

    Chen, Albert T.F.

    1988-01-01

    Two different approaches are used to estimate pore pressures and settlement in a 50-ft (15.2-m) sand deposit subjected to a variety of earthquake loadings. Although the two approaches seem consistent in predicting the occurrence of liquefaction, the results show that they are quite divergent in estimating pore-pressure build-ups and magnitude of ground settlement.

  3. Cavitation and pore blocking in nanoporous glasses.

    PubMed

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

    2011-09-06

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

  4. A New Path through the Nuclear Pore.

    PubMed

    Gozalo, Alejandro; Capelson, Maya

    2016-11-17

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

  5. Recovery from cyclophosphamide-induced lymphopenia results in expansion of immature dendritic cells which can mediate enhanced prime-boost vaccination antitumor responses in vivo when stimulated with the TLR3 agonist poly(I:C).

    PubMed

    Salem, Mohamed L; Díaz-Montero, C Marcela; Al-Khami, Amir A; El-Naggar, Sabry A; Naga, Osama; Montero, Alberto J; Khafagy, Ahmed; Cole, David J

    2009-02-15

    Recent preclinical studies suggest that vaccination following adoptive transfer of CD8(+) T cells into a lymphopenic host can augment the therapeutic antitumor responses of the transferred cells. However, the mechanism by which the lymphopenic microenvironment benefits Ag-specific CD8(+) T cell responses remains elusive. We show herein that induction of lymphodepletion by a single 4 mg cyclophosphamide (CTX) treatment induces a marked expansion of immature dendritic cells (DCs) in the peripheral blood on days 8-16 post-CTX (termed restoration phase). In vitro, these DCs were functional, because they showed normal phagocytosis and effective Ag presentation capability upon activation. In vivo, administration of the TLR3 agonist poly(I:C) at the peak of DC expansion (day 12 postlymphopenia) induced inflammatory cytokine production and increases in the number of activated DCs in lymph nodes. Importantly, boosting with gp100(25-33) melanoma peptide combined with poly(I:C) 12 days after an initial priming with the same regimen significantly increased the expansion and the antitumor efficacy of adoptively transferred pmel-1 CD8(+) T cells. These responses were abrogated after depletion of activated DCs during Ag boosting. In conclusion, our data show that CTX treatment induces, during the restoration phase, expansion of immature DCs, which are functional and can be exploited in vivo to foster more effective antitumor adoptive immunotherapy strategies.

  6. Probing the SecYEG translocation pore size with preproteins conjugated with sizable rigid spherical molecules.

    PubMed

    Bonardi, Francesco; Halza, Erik; Walko, Martin; Du Plessis, François; Nouwen, Nico; Feringa, Ben L; Driessen, Arnold J M

    2011-05-10

    Protein translocation in Escherichia coli is mediated by the translocase that in its minimal form consists of the protein-conducting channel SecYEG, and the motor protein, SecA. SecYEG forms a narrow pore in the membrane that allows passage of unfolded proteins only. Molecular dynamics simulations suggest that the maximal width of the central pore of SecYEG is limited to . To access the functional size of the SecYEG pore, the precursor of outer membrane protein A was modified with rigid spherical tetraarylmethane derivatives of different diameters at a unique cysteine residue. SecYEG allowed the unrestricted passage of the precursor of outer membrane protein A conjugates carrying tetraarylmethanes with diameters up to , whereas a sized molecule blocked the translocation pore. Translocation of the protein-organic molecule hybrids was strictly proton motive force-dependent and occurred at a single pore. With an average diameter of an unfolded polypeptide chain of , the pore accommodates structures of at least , which is vastly larger than the predicted maximal width of a single pore by molecular dynamics simulations.

  7. Proapoptotic Bax and Bak Proteins Form Stable Protein-permeable Pores of Tunable Size

    PubMed Central

    Bleicken, Stephanie; Landeta, Olatz; Landajuela, Ane; Basañez, Gorka; García-Sáez, Ana J.

    2013-01-01

    The Bcl-2 proapoptotic proteins Bax and Bak mediate the permeabilization of the mitochondrial outer membrane during apoptosis. Current models consider that Bax and Bak form pores at the mitochondrial outer membrane that are responsible for the release of cytochrome c and other larger mitochondrial apoptotic factors (i.e. Smac/DIABLO, AIF, and endoglycosidase G). However, the properties and nature of Bax/Bak apoptotic pores remain enigmatic. Here, we performed a detailed analysis of the membrane permeabilizing activity of Bax and Bak at the single vesicle level. We directly visualized that cBid-activated Bax and BakΔC21 can form membrane pores large enough to release not only cytochrome c, but also allophycocyanine, a protein of 104 kDa. Interestingly, the size of Bax and BakΔC21 pores is not constant, as typically observed in purely proteinaceous channels, but evolves with time and depends on protein concentration. We found that Bax and BakΔC21 formed long-lived pores, whose areas changed with the amount of Bax/BakΔC21 but not with cardiolipin concentration. Altogether, our results demonstrate that Bax and BakΔC21 follow similar mechanisms of membrane permeabilization characterized by the formation of protein-permeable pores of dynamic size, in agreement with the proteolipidic nature of these apoptotic pores. PMID:24100034

  8. Relocalization of DNA lesions to the nuclear pore complex

    PubMed Central

    Freudenreich, Catherine H.; Su, Xiaofeng A.

    2016-01-01

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

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

    PubMed Central

    2015-01-01

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

  10. 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

  11. Role of heparan sulfates and glycosphingolipids in the pore formation of basic polypeptides of cobra cardiotoxin.

    PubMed

    Wu, Wen-Guey; Tjong, Siu-Cin; Wu, Po-Long; Kuo, Je-Hung; Wu, Karen

    2010-01-01

    Cobra venom contains cardiotoxins (CTXs) that induce tissue necrosis and systolic heart arrest in bitten victims. CTX-induced membrane pore formation is one of the major mechanisms responsible for the venom's designated cytotoxicity. This chapter examines how glycoconjugates such as heparan sulfates (HS) and glycosphingolipids, located respectively in the extracellular matrix and lipid bilayers of the cell membranes, facilitate CTX pore formation. Evidences for HS-facilitated cell surface retention and glycosphingolipid-facilitated membrane bilayer insertion of CTX are reviewed. We suggest that similar physical steps could play a role in the mediation of other pore forming toxins (PFT). The membrane pores formed by PFT are expected to have limited lifetime on biological cell surface as a result of membrane dynamics during endocytosis and/or rearrangement of lipid rafts.

  12. Modelling the influence of pore size on the response of materials to infrared lasers An application to human enamel

    NASA Astrophysics Data System (ADS)

    Vila Verde, A.; Ramos, Marta M. D.

    2005-07-01

    We present an analytical model for a ceramic material (hydroxyapatite, HA) containing nanometre-scale water pores, and use it to estimate the pressure at the pore as a function of temperature at the end of a single 0.35 μs laser pulse by Er:YAG (2.94 μm) and CO 2 (10.6 μm) lasers. Our results suggest that the pressure at the pore is directly related to pore temperature, and that very high pressures can be generated simply by the thermal expansion of liquid water. Since the temperature reached in the pores at the end of the laser pulse is a strong function of pore size for Er:YAG lasers, but is independent of pore size for CO 2 lasers, our present results provide a possible explanation for the fact that human dental enamel threshold ablation fluences vary more for Er:YAG lasers than for CO 2 lasers. This suggests that experimentalists should analyse their results accounting for factors, like age or type of tooth, that may change the pore size distribution in their samples.

  13. 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.

  14. The great human expansion.

    PubMed

    Henn, Brenna M; Cavalli-Sforza, L L; Feldman, Marcus W

    2012-10-30

    Genetic and paleoanthropological evidence is in accord that today's human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth's habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the "serial founder effect." In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution.

  15. Virial Expansion Bounds

    NASA Astrophysics Data System (ADS)

    Tate, Stephen James

    2013-10-01

    In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

  16. 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.

  17. Supercritical fluid removal of hydrocarbons adsorbed on wide pore zeolite catalysts

    SciTech Connect

    Lucia M. Petkovic; Daniel M. Ginosar; Kyle C. Burch

    2005-06-01

    The effect of zeolite pore structure on coke removal by supercritical fluid regeneration (SFR) was studied on a series of wide pore zeolite catalysts, which included acidic Y, beta, L, and mordenite zeolites. Catalyst samples were deactivated under liquid phase isobutane/butene alkylation reaction conditions and treated under flowing supercritical isobutane for 60 min. The chemical nature of the species remaining on the catalyst surface before and after SFR was analyzed by temperature-programmed oxidation (TPO), diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), and ultraviolet-visible (UV-Vis) spectroscopy. Zeolite pore structure played an important role not only in hydrocarbon deposition during alkylation but also in hydrocarbon transformation and removal during SFR. During SFR, the formation of unsaturated cyclic or polycyclic compounds, which likely affects catalyst long-term activity after cyclic alkylation/SFR treatments, was hindered on beta zeolites and favored on catalysts containing periodic expansions or cages, such as Y and L zeolites.

  18. 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

  19. 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 C.; 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.

  20. 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.

  1. Steppe expansion in Patagonia?

    NASA Astrophysics Data System (ADS)

    Veblen, Thomas T.; Markgraf, Vera

    1988-11-01

    Westward expansion of the Patagonian steppe and retrocession of Andean forests due to increasing aridity over the past one or two millennia has been a persistent theme in the ecological and paleoecological literature for at least half a century. New evidence from pollen profiles, tree-ring analysis, vegetation structure, and photographic and documentary historical sources does not show the expansion of the steppe. Instead, over the past century trees have invaded the steppe as a consequence mainly of human-induced changes in the fire regime, and trees have regenerated in forest areas that were heavily burnt at the onset of European colonization.

  2. 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.

  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. Cytolysis by Ca-permeable transmembrane channels. Pore formation causes extensive DNA degradation and cell lysis

    PubMed Central

    1989-01-01

    This study investigates the effect of the purified membrane pore formers, staphylococcal alpha-toxin and CTL perforin, on target cell lysis as measured by 51Cr release and on nuclear damage as measured by DNA degradation and 125IUdR release. Both pore formers cause dose- dependent cell lysis, which is accompanied by DNA release. The ratio of DNA/Cr release depends on the nature of target cell and shows the same pattern as the ratio of release of the two markers reported for CTL- mediated lysis of the same targets. DNA degradation is dependent on the presence of intracellular Ca in the target cell and is totally blocked if Ca is chelated by Quin 2 intracellularly and EGTA extracellularly. DNA degradation, in addition, is inhibited by the lysosomotropic agents NH4Cl, chloroquine, and monensin. rTNF doubles the degree of DNA degradation mediated by alpha-toxin in 3-h assays. We conclude that pore formers alone can mediate DNA degradation. In addition, they may promote the uptake of other factors and thereby accelerate their time course of action. DNA degradation by pore formers requires active target participation in a pathway that is dependent on intracellular Ca and lysosomes. These aspects of target lysis resemble CTL- and NK cell- mediated cytolysis. PMID:2538546

  5. Pore network extraction from pore space images of various porous media systems

    NASA Astrophysics Data System (ADS)

    Yi, Zhixing; Lin, Mian; Jiang, Wenbin; Zhang, Zhaobin; Li, Haishan; Gao, Jian

    2017-04-01

    Pore network extraction, which is defined as the transformation from irregular pore space to a simplified network in the form of pores connected by throats, is significant to microstructure analysis and network modeling. A physically realistic pore network is not only a representation of the pore space in the sense of topology and morphology, but also a good tool for predicting transport properties accurately. We present a method to extract pore network by employing the centrally located medial axis to guide the construction of maximal-balls-like skeleton where the pores and throats are defined and parameterized. To validate our method, various rock samples including sand pack, sandstones, and carbonates were used to extract pore networks. The pore structures were compared quantitatively with the structures extracted by medial axis method or maximal ball method. The predicted absolute permeability and formation factor were verified against the theoretical solutions obtained by lattice Boltzmann method and finite volume method, respectively. The two-phase flow was simulated through the networks extracted from homogeneous sandstones, and the generated relative permeability curves were compared with the data obtained from experimental method and other numerical models. The results show that the accuracy of our network is higher than that of other networks for predicting transport properties, so the presented method is more reliable for extracting physically realistic pore network.

  6. Pore dynamics in a liquid membrane

    NASA Astrophysics Data System (ADS)

    Nepomnyashchy, Alexander; Volpert, Vladimir

    2014-11-01

    It is known that vesicles formed from lipid bilayer membranes are used for transportation of a toxic drug to a target, where the drug is released by pore creation. The pores in a membrane show a rather nontrivial dynamics, which thus far has been studied by means of simplified models. In the present talk, we describe the pore dynamics in a stretched membrane, which is considered as a two-dimensional viscous or viscoelastic liquid medium surrounded by a three-dimensional ambient viscous liquid. In the case of a viscoelastic membrane, a Lagrangian approach, which allows to account for large displacements, is applied. A closed equation for the pore radius is derived and investigated. The work has been partially supported by the US-Israel Binational Science Foundation (Grant No. 2008122).

  7. 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).

  8. OBSERVATIONS OF SAUSAGE MODES IN MAGNETIC PORES

    SciTech Connect

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

    2011-03-10

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

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

    NASA Astrophysics Data System (ADS)

    Im, J.; Lee, Y.

    2013-12-01

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

  10. 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.)

  11. 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.

  12. 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.

  13. 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.)

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. Adsorption hysteresis in ink-bottle pore

    NASA Astrophysics Data System (ADS)

    Morishige, Kunimitsu; Tateishi, Noriko

    2003-07-01

    To examine the mechanism of the adsorption hysteresis in ink-bottle pores, we measured the temperature dependence of the adsorption-desorption isotherms of argon, oxygen, and carbon dioxide onto SBA-16 ordered mesoporous material with cagelike pores. The hysteresis loop always shrank with increasing temperature and eventually disappeared at a hysteresis temperature (Th), well below the bulk critical temperature (Tc). When the relative pressures p/p0 of the capillary condensation and evaporation are plotted as a function of reduced temperature T/Tc, all the data including the transition pressures for nitrogen reported previously are represented by a common curve. We also calculated the temperature dependence of the capillary condensation and evaporation pressures of nitrogen under the assumption that adsorption and desorption in an ink-bottle pore may be regarded as the process of the disappearance and formation of a gas bubble in a liquid droplet confined to the pore. A fit between the observed and calculated transition pressures in a wide temperature range was reasonable in light of several assumptions and approximations used. This clearly indicates that the energy barrier for the formation and disappearance of vapor bubbles in the liquid confined to the pores is responsible for the appearance of the adsorption hysteresis and the hysteresis temperature is not concerned with the so-called capillary criticality. At temperatures higher than Th, the reversible capillary condensation takes place, because the energy barrier between a full liquid pore and the vapor coexisting with the liquid film becomes surmountable.

  19. Polymer Melt Diffusion inside Nanoscale Cylindrical Pores

    NASA Astrophysics Data System (ADS)

    Winey, Karen

    Polymers in composites and inside porous media are frequently confined to spaces that are comparable to or even smaller than their mean end-to-end distances in the unconfined bulk state. Understanding the impact of nanoscale confinement on both polymer structure and dynamics is critical during processing and in applications. Anodized aluminum oxide (AAO) membranes with uniform cylindrical pores (diameters 18, 35, 55 or 80 nm) were filled with polystyrene (200 kDa) and then a thin layer of deuterated polystyrene was deposited on top. After annealing the concentration profile of the deuterated polymer was measured using elastic recoil detection and the center-of-mass polymer diffusion coefficient was determined. Melt diffusion is faster in AAO membranes with smaller pore diameters. This experimental finding is corroborated by coarse grain simulations with neutral interactions with the pore walls, although the increase is more pronounced in the simulations. Our simulations previously found that chain conformations slightly elongated parallel to the cylinder axis and compressed perpendicular to the cylinder and the number of entanglements per chain decreases as the cylinder diameter decreases. It is primarily the reduction in polymer entanglements that allows polymers to diffuse faster when the pore diameter is smaller in an athermal or weakly interacting system. Segmental dynamics have been measured using quasielastic neutron scattering. Polymer diffusion is cylindrical pores is now being studied at a fixed pore diameter as a function of molecular weight.

  20. 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.

  1. The great human expansion

    PubMed Central

    Henn, Brenna M.; Cavalli-Sforza, L. L.; Feldman, Marcus W.

    2012-01-01

    Genetic and paleoanthropological evidence is in accord that today’s human population is the result of a great demic (demographic and geographic) expansion that began approximately 45,000 to 60,000 y ago in Africa and rapidly resulted in human occupation of almost all of the Earth’s habitable regions. Genomic data from contemporary humans suggest that this expansion was accompanied by a continuous loss of genetic diversity, a result of what is called the “serial founder effect.” In addition to genomic data, the serial founder effect model is now supported by the genetics of human parasites, morphology, and linguistics. This particular population history gave rise to the two defining features of genetic variation in humans: genomes from the substructured populations of Africa retain an exceptional number of unique variants, and there is a dramatic reduction in genetic diversity within populations living outside of Africa. These two patterns are relevant for medical genetic studies mapping genotypes to phenotypes and for inferring the power of natural selection in human history. It should be appreciated that the initial expansion and subsequent serial founder effect were determined by demographic and sociocultural factors associated with hunter-gatherer populations. How do we reconcile this major demic expansion with the population stability that followed for thousands years until the inventions of agriculture? We review advances in understanding the genetic diversity within Africa and the great human expansion out of Africa and offer hypotheses that can help to establish a more synthetic view of modern human evolution. PMID:23077256

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

    PubMed

    Ros, Uris; García-Sáez, Ana J

    2015-06-01

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

  3. STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate

    NASA Astrophysics Data System (ADS)

    Yamashita, Megumi; Yeung, Priscilla S.-W.; Ing, Christopher E.; McNally, Beth A.; Pomès, Régis; Prakriya, Murali

    2017-02-01

    Store-operated Ca2+ release-activated Ca2+ (CRAC) channels constitute a major pathway for Ca2+ influx and mediate many essential signalling functions in animal cells, yet how they open remains elusive. Here, we investigate the gating mechanism of the human CRAC channel Orai1 by its activator, stromal interacting molecule 1 (STIM1). We find that two rings of pore-lining residues, V102 and F99, work together to form a hydrophobic gate. Mutations of these residues to polar amino acids produce channels with leaky gates that conduct ions in the resting state. STIM1-mediated channel activation occurs through rotation of the pore helix, which displaces the F99 residues away from the pore axis to increase pore hydration, allowing ions to flow through the V102-F99 hydrophobic band. Pore helix rotation by STIM1 also explains the dynamic coupling between CRAC channel gating and ion selectivity. This hydrophobic gating mechanism has implications for CRAC channel function, pharmacology and disease-causing mutations.

  4. STIM1 activates CRAC channels through rotation of the pore helix to open a hydrophobic gate

    PubMed Central

    Yamashita, Megumi; Yeung, Priscilla S.-W.; Ing, Christopher E.; McNally, Beth A.; Pomès, Régis; Prakriya, Murali

    2017-01-01

    Store-operated Ca2+ release-activated Ca2+ (CRAC) channels constitute a major pathway for Ca2+ influx and mediate many essential signalling functions in animal cells, yet how they open remains elusive. Here, we investigate the gating mechanism of the human CRAC channel Orai1 by its activator, stromal interacting molecule 1 (STIM1). We find that two rings of pore-lining residues, V102 and F99, work together to form a hydrophobic gate. Mutations of these residues to polar amino acids produce channels with leaky gates that conduct ions in the resting state. STIM1-mediated channel activation occurs through rotation of the pore helix, which displaces the F99 residues away from the pore axis to increase pore hydration, allowing ions to flow through the V102-F99 hydrophobic band. Pore helix rotation by STIM1 also explains the dynamic coupling between CRAC channel gating and ion selectivity. This hydrophobic gating mechanism has implications for CRAC channel function, pharmacology and disease-causing mutations. PMID:28220789

  5. Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials.

    PubMed

    Van Eyndhoven, G; Kurttepeli, M; Van Oers, C J; Cool, P; Bals, S; Batenburg, K J; Sijbers, J

    2015-01-01

    Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm "POre REconstruction and Segmentation" is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    PubMed Central

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

    2016-01-01

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

  7. 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.

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

    PubMed Central

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

    2013-01-01

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

  9. 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

  10. 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.

  11. 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

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

    2011-08-01

    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.

  12. 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.

  13. Low Pore Connectivity in Natural Rock

    SciTech Connect

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

    2012-05-15

    As repositories for CO₂ and radioactive waste, as oil and gas reservoirs, and as contaminated sites needing remediation, rock formations play a central role in energy and environmental management. The connectivity of the rock's porespace strongly affects fluid flow and solute transport. This work examines pore connectivity and its implications for fluid flow and chemical transport. Three experimental approaches (imbibition, tracer concentration profiles, and imaging) were used in combination with network modeling. In the imbibition results, three types of imbibition slope [log (cumulative imbibition) vs. log (imbibition time)] were found: the classical 0.5, plus 0.26, and 0.26 transitioning to 0.5. The imbibition slope of 0.26 seen in Indiana sandstone, metagraywacke, and Barnett shale indicates low pore connectivity, in contrast to the slope of 0.5 seen in the well-connected Berea sandstone. In the tracer profile work, rocks exhibited different distances to the plateau porosity, consistent with the pore connectivity from the imbibition tests. Injection of a molten metal into connected pore spaces, followed by 2-D imaging of the solidified alloy in polished thin sections, allowed direct assessment of pore structure and lateral connection in the rock samples. Pore-scale network modeling gave results consistent with measurements, confirming pore connectivity as the underlying cause of both anomalous behaviors: imbibition slope not having the classical value of 0.5, and accessible porosity being a function of distance from the edge. A poorly connected porespace will exhibit anomalous behavior in fluid flow and chemical transport, such as a lower imbibition slope (in air–water system) and diffusion rate than expected from classical behavior.

  14. 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.

  15. Deposition Nucleation or Pore Condensation and Freezing?

    NASA Astrophysics Data System (ADS)

    David, Robert O.; Mahrt, Fabian; Marcolli, Claudia; Fahrni, Jonas; Brühwiler, Dominik; Lohmann, Ulrike; Kanji, Zamin A.

    2017-04-01

    Ice nucleation plays an important role in moderating Earth's climate and precipitation formation. Over the last century of research, several mechanisms for the nucleation of ice have been identified. Of the known mechanisms for ice nucleation, only deposition nucleation occurs below water saturation. Deposition nucleation is defined as the formation of ice from supersaturated water vapor on an insoluble particle without the prior formation of liquid. However, recent work has found that the efficiency of so-called deposition nucleation shows a dependence on the homogeneous freezing temperature of water even though no liquid phase is presumed to be present. Additionally, the ability of certain particles to nucleate ice more efficiently after being pre-cooled (pre-activation) raises questions on the true mechanism when ice nucleation occurs below water saturation. In an attempt to explain the dependence of the efficiency of so-called deposition nucleation on the onset of homogeneous freezing of liquid water, pore condensation and freezing has been proposed. Pore condensation and freezing suggests that the liquid phase can exist under sub-saturated conditions with respect to liquid in narrow confinements or pores due to the inverse Kelvin effect. Once the liquid-phase condenses, it is capable of nucleating ice either homogeneously or heterogeneously. The role of pore condensation and freezing is assessed in the Zurich Ice Nucleation Chamber, a continuous flow diffusion chamber, using spherical nonporous and mesoporous silica particles. The mesoporous silica particles have a well-defined particle size range of 400 to 600nm with discreet pore sizes of 2.5, 2.8, 3.5 and 3.8nm. Experiments conducted between 218K and 238K show that so-called deposition nucleation only occurs below the homogenous freezing temperature of water and is highly dependent on the presence of pores and their size. The results strongly support pore condensation and freezing, questioning the role of

  16. Bigravity from gradient expansion

    SciTech Connect

    Yamashita, Yasuho; Tanaka, Takahiro

    2016-05-04

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

  17. Range expansion of mutualists

    NASA Astrophysics Data System (ADS)

    Muller, Melanie J. I.; Korolev, Kirill S.; Murray, Andrew W.; Nelson, David R.

    2012-02-01

    The expansion of a species into new territory is often strongly influenced by the presence of other species. This effect is particularly striking for the case of mutualistic species that enhance each other's proliferation. Examples range from major events in evolutionary history, such as the spread and diversification of flowering plants due to their mutualism with pollen-dispersing insects, to modern examples like the surface colonisation of multi-species microbial biofilms. Here, we investigate the spread of cross-feeding strains of the budding yeast Saccharomyces cerevisiae on an agar surface as a model system for expanding mutualists. Depending on the degree of mutualism, the two strains form distinctive spatial patterns during their range expansion. This change in spatial patterns can be understood as a phase transition within a stepping stone model generalized to two mutualistic species.

  18. Genetic Control of Fusion Pore Expansion in the Epidermis of Caenorhabditis elegans

    PubMed Central

    Gattegno, Tamar; Mittal, Aditya; Valansi, Clari; Nguyen, Ken C.Q.; Hall, David H.; Chernomordik, Leonid V.

    2007-01-01

    Developmental cell fusion is found in germlines, muscles, bones, placentae, and stem cells. In Caenorhabditis elegans 300 somatic cells fuse during development. Although there is extensive information on the early intermediates of viral-induced and intracellular membrane fusion, little is known about late stages in membrane fusion. To dissect the pathway of cell fusion in C. elegans embryos, we use genetic and kinetic analyses using live-confocal and electron microscopy. We simultaneously monitor the rates of multiple cell fusions in developing embryos and find kinetically distinct stages of initiation and completion of membrane fusion in the epidermis. The stages of cell fusion are differentially blocked or retarded in eff-1 and idf-1 mutants. We generate kinetic cell fusion maps for embryos grown at different temperatures. Different sides of the same cell differ in their fusogenicity: the left and right membrane domains are fusion-incompetent, whereas the anterior and posterior membrane domains fuse with autonomous kinetics in embryos. All but one cell pair can initiate the formation of the largest syncytium. The first cell fusion does not trigger a wave of orderly fusions in either direction. Ultrastructural studies show that epidermal syncytiogenesis require eff-1 activities to initiate and expand membrane merger. PMID:17229888

  19. Role of hydrocarbons in pore expansion and contraction of a flexible metal-organic framework

    SciTech Connect

    Motkuri, Radha K.; Thallapally, Praveen K.; Nune, Satish K.; Fernandez, Carlos A.; McGrail, B. Peter; Atwood, Jerry L.

    2011-05-06

    A flexible metal organic framework obtained from a flexible organic linker shows a breathing phenomenon upon adsorption of polar protic and non-polar solvents. Sorption profiles indicate favorable interactions with non-polar solvents over polar solvents.

  20. 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

  1. Modeling branching pore structures in membrane filters

    NASA Astrophysics Data System (ADS)

    Sanaei, Pejman; Cummings, Linda J.

    2016-11-01

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

  2. Modeling tissue growth within nonwoven scaffolds pores.

    PubMed

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

    2011-02-01

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

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2003-02-25

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

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

    PubMed

    Ustinov, Eugene A

    2009-07-07

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

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

    PubMed

    Vollmer, Benjamin; Antonin, Wolfram

    2014-05-01

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

  10. Thermal expansion of glassy polymers.

    PubMed

    Davy, K W; Braden, M

    1992-01-01

    The thermal expansion of a number of glassy polymers of interest in dentistry has been studied using a quartz dilatometer. In some cases, the expansion was linear and therefore the coefficient of thermal expansion readily determined. Other polymers exhibited non-linear behaviour and values appropriate to different temperature ranges are quoted. The linear coefficient of thermal expansion was, to a first approximation, a function of both the molar volume and van der Waal's volume of the repeating unit.

  11. Pore-forming toxins in Cnidaria.

    PubMed

    Podobnik, Marjetka; Anderluh, Gregor

    2017-07-24

    The ancient phylum of Cnidaria contains many aquatic species with peculiar lifestyle. In order to survive, these organisms have evolved attack and defense mechanisms that are enabled by specialized cells and highly developed venoms. Pore-forming toxins are an important part of their venomous arsenal. Along some other types, the most representative are examples of four protein families that are commonly found in other kingdoms of life: actinoporins, Cry-like proteins, aerolysin-like toxins and MACPF/CDC toxins. Some of the homologues of pore-forming toxins may serve other functions, such as in food digestion, development and response against pathogenic organisms. Due to their interesting physico-chemical properties, the cnidarian pore-forming toxins may also serve as tools in medical research and nanobiotechnological applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Moving Magnetic Features around a Pore

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  13. Foam invasion through a single pore.

    PubMed

    Delbos, Aline; Pitois, Olivier

    2011-07-01

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

  14. Unplugging the callose plug from sieve pores.

    PubMed

    Xie, Bo; Hong, Zonglie

    2011-04-01

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

  15. Unplugging the callose plug from sieve pores

    PubMed Central

    Xie, Bo

    2011-01-01

    The presence of callose in sieve plates has been known for a long time, but how this polysaccharide plug is synthesized has remained unsolved. Two independent laboratories have recently reported the identification of callose synthase 7 (CalS7), also known as glucan synthase-like 7 (GSL7), as the enzyme responsible for callose deposition in sieve plates. Mutant plants defective in this enzyme failed to synthesize callose in developing sieve plates during phloem formation and were unable to accumulate callose in sieve pores in response to stress treatments. The mutant plants developed less open pores per sieve plate and the pores were smaller in diameter. As a result, phloem conductivity was reduced significantly and the mutant plants were shorter and set fewer seeds. PMID:21386663

  16. 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…

  17. 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…

  18. Assessing Coating Reliability Through Pore Architecture Evaluation

    NASA Astrophysics Data System (ADS)

    Paul, S.

    2010-06-01

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

  19. Active Polymer Translocation through Flickering Pores

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  20. Membrane injury by pore-forming proteins.

    PubMed

    Bischofberger, Mirko; Gonzalez, Manuel R; van der Goot, F Gisou

    2009-08-01

    The plasma membrane defines the boundary of every living cell, and its integrity is essential for life. The plasma membrane may, however, be challenged by mechanical stress or pore-forming proteins produced by the organism itself or invading pathogens. We will here review recent findings about pore-forming proteins from different organisms, highlighting their structural and functional similarities, and describe the mechanisms that lead to membrane repair, since remarkably, cells can repair breaches in their plasma membrane of up to 10,000 microm(2).

  1. The Pore-Forming Haemolysins of Bacillus Cereus: A Review

    PubMed Central

    Ramarao, Nalini; Sanchis, Vincent

    2013-01-01

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

  2. The selective permeability barrier in the nuclear pore complex

    PubMed Central

    Li, Christina; Goryaynov, Alexander; Yang, Weidong

    2016-01-01

    ABSTRACT The nuclear pore complex (NPC) mediates the shuttle transport of macromolecules between the nucleus and cytoplasm in eukaryotic cells. The permeability barrier formed by intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG-Nups) in the NPC functions as the critical selective control for nucleocytoplasmic transport. Signal-independent small molecules (< 40 kDa) passively diffuse through the pore, but passage of large cargo molecules is inhibited unless they are chaperoned by nuclear transport receptors (NTRs). NTRs are capable of interacting with FG-Nups and guide the cargos to cross the barrier by facilitated diffusion. The native conformation of the FG-Nups permeability barrier and the competition among multiple NTRs interacting with this barrier in the native NPCs are the 2 core questions still being highly debated in the field. Recently, we applied high-speed super-resolution fluorescence microscopy to map out the natural structure of the FG-Nups barrier and determined the competition among multiple NTRs as they interact with the barrier in the native NPCs. In this extra-view article, we will review the current understanding in the configuration and function of FG-Nups barrier and highlight the new evidence obtained recently to answer the core questions in nucleocytoplasmic transport. PMID:27673359

  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. 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.

  5. 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.

  6. Expansion in condensates

    SciTech Connect

    Chakrabarti, J.; Sajjad Zahir, M.

    1985-03-01

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

  7. Thrust expansion engine

    NASA Astrophysics Data System (ADS)

    Zovko, Carl T.

    1993-03-01

    Break-up activity of water by injection of hot propellant gas into channels of a thrust expansion engine is suppressed to prevent rapid cooling of the gas utilizing one or more methods including injection of a secondary inflow of the propellant gas and/or the water under lower pressures into the channels, injection of a viscosity enhancer and/or surfactant into the inflow stream of the water, and restricting outflow of the water from the channels by means of convergent nozzles.

  8. 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.

  9. 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

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

    DOE PAGES

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

    2017-01-11

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

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

    DOE PAGES

    Bailey, V. L.; Smith, A. P.; Tfaily, M.; ...

    2017-04-01

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

  12. 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.

  13. 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.

  14. Bax and Bak Pores: Are We Closing the Circle?

    PubMed

    Cosentino, Katia; García-Sáez, Ana J

    2017-04-01

    Bax and its homolog Bak are key regulators of the mitochondrial pathway of apoptosis. On cell stress Bax and Bak accumulate at distinct foci on the mitochondrial surface where they undergo a conformational change, oligomerize, and mediate cytochrome c release, leading to cell death. The molecular mechanisms of Bax and Bak assembly and mitochondrial permeabilization have remained a longstanding question in the field. Recent structural and biophysical studies at several length scales have shed light on key aspects of Bax and Bak function that have shifted how we think this process occurs. These discoveries reveal an unexpected molecular mechanism in which Bax (and likely Bak) dimers assemble into oligomers with an even number of molecules that fully or partially delineate pores of different sizes to permeabilize the mitochondrial outer membrane (MOM) during apoptosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. 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

  16. 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.

  17. 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

  18. 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.

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

    PubMed

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

    2015-10-02

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

  20. Transport Selectivity of Nuclear Pores, Phase Separation, and Membraneless Organelles.

    PubMed

    Schmidt, H Broder; Görlich, Dirk

    2016-01-01

    Nuclear pore complexes (NPCs) provide a selective passageway for receptor-mediated active transport between nucleus and cytoplasm, while maintaining the distinct molecular compositions of both compartments at large. In this review we discuss how NPCs gain a remarkable sorting selectivity from non-globular FG domains and their phase separation into dense polymer meshworks. The resulting sieve-like FG hydrogels are effective barriers to normal macromolecules but are at the same time highly permeable to shuttling nuclear transport receptors, which bind to FG motifs as well as to their designated cargoes. Phase separation driven by disordered protein domains was recently also recognized as being pivotal to the formation of membraneless organelles, making it an important emerging principle in cell biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Pore pressure estimation from velocity data: Accounting for overpressure mechanisms besides undercompaction

    SciTech Connect

    Bowers, G.L.

    1995-06-01

    A new method for estimating pore pressure from formation sonic velocity data is presented. Unlike previous techniques, this method accounts for excess pressure generated by both undercompaction, and fluid expansion mechanisms such as aquathermal pressuring, hydrocarbon maturation, clay diagenesis, and charging from other zones. The method is an effective stress approach; the effective stress is computed from the velocity, and the result is subtracted from the overburden stress to obtain pore pressure. to include multiple sources of overpressure, a pair of velocity-vs.-effective-stress relations are introduced. One relation accounts for normal pressure and overpressure caused by undercompaction. The second is applied inside velocity reversal zones caused by fluid expansion mechanisms. Example applications of the method are presented from the U.S. gulf coast, the Gulf of Mexico, and the Central North Sea. some other pore pressure estimation approaches are also examined to demonstrate how these techniques have unknowingly accounted for overpressure mechanisms other than undercompaction. It is also explained how velocity-vs.-effective-stress data can be used to identify the general cause of overpressure in an area. For instance, the empirical correlation of Hottman and Johnson indicates that overpressure along the US gulf coast cannot be due only to undercompaction.

  2. 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.

  3. Blastocoel expansion in the preimplantation mouse embryo

    SciTech Connect

    Manejwala, F.M.

    1989-01-01

    Since cAMP can regulate fluid transport in many types of epithelia, the mechanism of fluid transport and the role of cAMP in the mouse blastocyst were examined. Results described here indicate an increase in the ability of mouse embryos to elevate cAMP levels in response to activators of adenylate cyclase, which is the enzyme that synthesizes cAMP, during the transition from morula to blastocyst. In addition, a positive correlation is observed between the increase in activatable adenylate cyclase and the presence of a blastocoel. Moreover, elevating intracellular cAMP in nascent cavitating embryos stimulates the rate of fluid transport in the blastocoel. Accumulation of fluid in the blastocoel is a function of the tight permeability seal around the embryo and the vectorial flow of ions into the blastocoel. Results reported here indicate that extracellular Na{sup +} and Cl{sup {minus}} are required for expansion of the blastocoel in nascent cavitating blastocysts. Sodium uptake into the embryo is carrier-mediated and probably occurs through multiple routes which include the Na{sup +}-channel and the Na{sup +}/H{sup +} exchanger. Chloride uptake is non-carrier mediated and may occur by a paracellular route. In addition, cAMP, which stimulates blastocoel expansion, also stimulates uptake of {sup 22}Na{sup +}. This effect may be mediated by a cAMP-dependent protein kinase, since inhibition of this enzyme inhibits both the cAMP-stimulated rate of blastocoel expansion and {sup 22}Na{sup +} uptake.

  4. Modification of the Cytoplasmic Domain of Influenza Virus Hemagglutinin Affects Enlargement of the Fusion Pore

    PubMed Central

    Kozerski, Christine; Ponimaskin, Evgeni; Schroth-Diez, Britta; Schmidt, Michael F. G.; Herrmann, Andreas

    2000-01-01

    The fusion activity of chimeras of influenza virus hemagglutinin (HA) (from A/fpv/Rostock/34; subtype H7) with the transmembrane domain (TM) and/or cytoplasmic tail (CT) either from the nonviral, nonfusogenic T-cell surface protein CD4 or from the fusogenic Sendai virus F-protein was studied. Wild-type or chimeric HA was expressed in CV-1 cells by the transient T7-RNA-polymerase vaccinia virus expression system. Subsequently, the fusion activity of the expression products was monitored with red blood cells or ghosts as target cells. To assess the different steps of fusion, target cells were labeled with the fluorescent membrane label octadecyl rhodamine B-chloride (R18) (membrane fusion) and with the cytoplasmic fluorophores calcein (molecular weight [MW], 623; formation of small aqueous fusion pore) and tetramethylrhodamine-dextran (MW, 10,000; enlargement of fusion pore). All chimeric HA/F-proteins, as well as the chimera with the TM of CD4 and the CT of HA, were able to mediate the different steps of fusion very similarly to wild-type HA. Quite differently, chimeric proteins with the CT of CD4 were strongly impaired in mediating pore enlargement. However, membrane fusion and formation of small pores were similar to those of wild-type HA, indicating that the conformational change of the ectodomain and earlier fusion steps were not inhibited. Various properties of the CT which may affect pore enlargement are considered. We surmise that the hydrophobicity of the sequence adjacent to the transmembrane domain is important for pore dilation. PMID:10906206

  5. Pore-Forming Toxins Trigger the Purge.

    PubMed

    Bonfini, Alessandro; Buchon, Nicolas

    2016-12-14

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

  6. Channel gating pore: a new therapeutic target.

    PubMed

    Kornilov, Polina; Peretz, Asher; Attali, Bernard

    2013-09-01

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

  7. Molecular Sensing with an Artificial Pore

    NASA Astrophysics Data System (ADS)

    Saleh, Omar A.

    2002-03-01

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

  8. Drainage Studies Using Pore-Scale Approaches

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  9. Real Time Pore Structure Evolution during Olivine Mineral Carbonation

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    SciTech Connect

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

    2015-08-19

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

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

    DOE PAGES

    Kong, Xian; Gallegos, Alejandro; Lu, Diannan; ...

    2015-08-19

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

  12. α-Toxin Regulates Local Granulocyte Expansion from Hematopoietic Stem and Progenitor Cells in Staphylococcus aureus-Infected Wounds.

    PubMed

    Falahee, Patrick C; Anderson, Leif S; Reynolds, Mack B; Pirir, Mauricio; McLaughlin, Bridget E; Dillen, Carly A; Cheung, Ambrose L; Miller, Lloyd S; Simon, Scott I

    2017-09-01

    The immune response to Staphylococcus aureus infection in skin involves the recruitment of polymorphonuclear neutrophils (PMNs) from the bone marrow via the circulation and local granulopoiesis from hematopoietic stem and progenitor cells (HSPCs) that also traffic to infected skin wounds. We focus on regulation of PMN number and function and the role of pore-forming α-toxin (AT), a virulence factor that causes host cell lysis and elicits inflammasome-mediated IL-1β secretion in wounds. Infection with wild-type S. aureus enriched in AT reduced PMN recruitment and resulted in sustained bacterial burden and delayed wound healing. In contrast, PMN recruitment to wounds infected with an isogenic AT-deficient S. aureus strain was unimpeded, exhibiting efficient bacterial clearance and hastened wound resolution. HSPCs recruited to infected wounds were unaffected by AT production and were activated to expand PMN numbers in proportion to S. aureus abundance in a manner regulated by TLR2 and IL-1R signaling. Immunodeficient MyD88-knockout mice infected with S. aureus experienced lethal sepsis that was reversed by PMN expansion mediated by injection of wild-type HSPCs directly into wounds. We conclude that AT-induced IL-1β promotes local granulopoiesis and effective resolution of S. aureus-infected wounds, revealing a potential antibiotic-free strategy for tuning the innate immune response to treat methicillin-resistant S. aureus infection in immunodeficient patients. Copyright © 2017 by The American Association of Immunologists, Inc.

  13. 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

  14. Neutron Scattering Measurements of Carbon Dioxide Adsorption in Pores within the Marcellus Shale: Implications for Sequestration.

    PubMed

    Stefanopoulos, Konstantinos L; Youngs, Tristan G A; Sakurovs, Richard; Ruppert, Leslie F; Bahadur, Jitendra; Melnichenko, Yuri B

    2017-06-06

    Shale is an increasingly viable source of natural gas and a potential candidate for geologic CO2 sequestration. Understanding the gas adsorption behavior on shale is necessary for the design of optimal gas recovery and sequestration projects. In the present study neutron diffraction and small-angle neutron scattering measurements of adsorbed CO2 in Marcellus Shale samples were conducted on the Near and InterMediate Range Order Diffractometer (NIMROD) at the ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory along an adsorption isotherm of 22 °C and pressures of 25 and 40 bar. Additional measurements were conducted at approximately 22 and 60 °C at the same pressures on the General-Purpose Small-Angle Neutron Scattering (GP-SANS) instrument at Oak Ridge National Laboratory. The structures investigated (pores) for CO2 adsorption range in size from Å level to ∼50 nm. The results indicate that, using the conditions investigated densification or condensation effects occurred in all accessible pores. The data suggest that at 22 °C the CO2 has liquid-like properties when confined in pores of around 1 nm radius at pressures as low as 25 bar. Many of the 2.5 nm pores, 70% of 2 nm pores, most of the <1 nm pores, and all pores <0.25 nm, are inaccessible or closed to CO2, suggesting that despite the vast numbers of micropores in shale, the micropores will be unavailable for storage for geologic CO2 sequestration.

  15. 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.

  16. Hydration properties of mechanosensitive channel pores define the energetics of gating

    NASA Astrophysics Data System (ADS)

    Anishkin, A.; Akitake, B.; Kamaraju, K.; Chiang, C.-S.; Sukharev, S.

    2010-11-01

    Opening of ion channels directly by tension in the surrounding membrane appears to be the most ancient and simple mechanism of gating. Bacterial mechanosensitive channels MscL and MscS are the best-studied tension-gated nanopores, yet the key physical factors that define their gating are still hotly debated. Here we present estimations, simulations and experimental results showing that hydration of the pore might be one of the major parameters defining the thermodynamics and kinetics of mechanosensitive channel gating. We associate closing of channel pores with complete dehydration of the hydrophobic gate (occlusion by 'vapor lock') and formation of two water-vapor interfaces above and below the constriction. The opening path is the expansion of these interfaces, ultimately leading to wetting of the hydrophobic pore, which does not appear to be the exact reverse of the closing path, thus producing hysteresis. We discuss specifically the role of polar groups (glycines) buried in narrow closed conformations but exposed in the open states that change the wetting characteristics of the pore lining and stabilize conductive states of the channels.

  17. 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

  18. Pore-scale evaporation-condensation dynamics resolved by synchrotron x-ray tomography

    NASA Astrophysics Data System (ADS)

    Shahraeeni, Ebrahim; Or, Dani

    2012-01-01

    Capillary processes greatly influence vapor mediated transport dynamics and associated changes in liquid phase content of porous media. Rapid x-ray synchrotron tomography measurements were used to resolve liquid-vapor interfacial dynamics during evaporation and condensation within submillimetric pores forming between sintered glass bead samples subjected to controlled ambient temperature and relative humidity. Evolution of gas-liquid interfacial shapes were in agreement with predictions based on our analytical model for interfacial dynamics in confined wedge-shaped pores. We also compared literature experimental data at the nanoscale to illustrate the capability of our model to describe early stages of condensation giving rise to the onset of capillary forces between rough surfaces. The study provides high resolution, synchrotron-based observations of capillary evaporation-condensation dynamics at the pore scale as the confirmation of the pore scale analytical model for capillary condensation in a pore and enables direct links with evolution of macroscopic vapor gradients within a sintered glass bead sample through their effect on configuration and evolution of the local interfaces. Rapid condensation processes play a critical role in the onset of capillary-induced friction affecting mechanical behavior of physical systems and industrial applications.

  19. Disentangling the roles of cholesterol and CD59 in intermedilysin pore formation

    PubMed Central

    Boyd, Courtney M.; Parsons, Edward S.; Smith, Richard A. G.; Seddon, John M.; Ces, Oscar; Bubeck, Doryen

    2016-01-01

    The plasma membrane provides an essential barrier, shielding a cell from the pressures of its external environment. Pore-forming proteins, deployed by both hosts and pathogens alike, breach this barrier to lyse target cells. Intermedilysin is a cholesterol-dependent cytolysin that requires the human immune receptor CD59, in addition to cholesterol, to form giant β-barrel pores in host membranes. Here we integrate biochemical assays with electron microscopy and atomic force microscopy to distinguish the roles of these two receptors in mediating structural transitions of pore formation. CD59 is required for the specific coordination of intermedilysin (ILY) monomers and for triggering collapse of an oligomeric prepore. Movement of Domain 2 with respect to Domain 3 of ILY is essential for forming a late prepore intermediate that releases CD59, while the role of cholesterol may be limited to insertion of the transmembrane segments. Together these data define a structural timeline for ILY pore formation and suggest a mechanism that is relevant to understanding other pore-forming toxins that also require CD59. PMID:27910935

  20. Multi-scale fractal analysis of pores in shale rocks

    NASA Astrophysics Data System (ADS)

    Liu, Kouqi; Ostadhassan, Mehdi

    2017-05-01

    Pore structures is a very critical parameter that affects the physical, mechanical and chemical properties of the reservoir rock. Pore shapes and pore size distributions can impact the transport and storage capacity of the reservoir rocks. This necessitates the adequate knowledge of the pore structures of the rocks. In this paper, we characterized and quantified the pore structures of rock samples from the Bakken Formation which is a typical unconventional shale oil reservoir. Samples of Upper and Middle Bakken were collected and studied based on the Scanning Electron Microscope (SEM) images. First, the threshold of each image was determined from overflow criteria and then the related pores were extracted from the corresponding image. In the next step, the pore microstructures such as pore size, pore shape distributions of different samples were calculated and compared. Finally, we used fractal theory to describe the pore structures of the shale formation and investigated the relationship between fractal dimension and pore structures. The results showed that pores with various sizes and shapes were widely distributed in the shale samples. Compared with samples from Middle Bakken, samples from Upper Bakken Formation with higher clay content showed higher fractal dimension and more complex pore structures. Finally, the fractal dimension was used to quantify the impact of the magnification on the pore structures.

  1. Regulation of Fusion Pore Closure and Compound Exocytosis in Neuroendocrine PC12 Cells by SCAMP1

    PubMed Central

    Zhang, Jie; Castle, David

    2011-01-01

    During exocytosis, neuroendocrine cells can achieve partial release of stored secretory products from dense core vesicles (DCVs) by coupling endocytosis directly at fusion sites and without full discharge. The physiological role of partial secretion is of substantial interest. Much is known about SNARE-mediated initiation of exocytosis and dynamin-mediated completion of endocytosis, but little is known about coupling events. We have used real-time microscopy to examine the role of secretory carrier membrane protein SCAMP1 in exo-endocytic coupling in PC12 cells. While reduced SCAMP1 expression is known to impede dilation of newly opened fusion pores during onset of DCV exocytosis, we now show that SCAMP1 deficiency also inhibits closure of fusion pores after they have opened. Inhibition causes accumulation of fusion figures at the plasma membrane. Closure is recovered by restoring expression and accelerated slightly by overexpression. Interestingly, inhibited pore closure resulting from loss of SCAMP1 appears to increase secondary fusion of DCVs to already-fused DCVs (compound exocytosis). Unexpectedly, reinternalization of expanded DCV membranes following compound exocytosis appears to proceed normally in SCAMP1-deficient cells. SCAMP1’s apparent dual role in facilitating dilation and closure of fusion pores implicates its function in exo-endocytic coupling and in the regulation of partial secretion. Secondarily, SCAMP1 may serve to limit the extent of compound exocytosis. PMID:21272170

  2. 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.

  3. 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.

  4. The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics.

    PubMed Central

    Sankararamakrishnan, R; Adcock, C; Sansom, M S

    1996-01-01

    The pore domain of the nicotinic acetylcholine receptor has been modeled as a bundle of five kinked M2 helices. Models were generated via molecular dynamics simulations incorporating restraints derived from 9-A resolution cryoelectron microscopy data (Unwin, 1993; 1995), and from mutagenesis data that identify channel-lining side chains. Thus, these models conform to current experimental data but will require revision as higher resolution data become available. Models of the open and closed states of a homopentameric alpha 7 pore are compared. The minimum radius of the closed-state model is less than 2 A; the minimum radius of the open-state models is approximately 6 A. It is suggested that the presence of "bound" water molecules within the pore may reduce the effective minimum radii below these values by up to approximately 3 A. Poisson-Boltzmann calculations are used to obtain a first approximation to the potential energy of a monovalent cation as it moves along the pore axis. The differences in electrostatic potential energy profiles between the open-state models of alpha 7 and of a mutant of alpha 7 are consistent with the experimentally observed change in ion selectivity from cationic to anionic. Models of the open state of the heteropentameric Torpedo nicotinic acetylcholine receptor pore domain are also described. Relatively small differences in pore radius and electrostatic potential energy profiles are seen when the Torpedo and alpha 7 models are compared. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 5 PMID:8889144

  5. Indicator Expansion with Analysis Pipeline

    DTIC Science & Technology

    2015-01-13

    2014 Carnegie Mellon University Indicator Expansion with Analysis Pipeline Dan Ruef 1/13/15 Report Documentation Page Form ApprovedOMB No. 0704...4. TITLE AND SUBTITLE Indicator Expansion with Analysis Pipeline 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...Mellon®, CERT® and FloCon® are registered marks of Carnegie Mellon University. DM-0002067 3 Definition “Indicator expansion is a process of using one or

  6. Relativistic Sommerfeld Low Temperature Expansion

    NASA Astrophysics Data System (ADS)

    Lourenço, O.; Dutra, M.; Delfino, A.; Sá Martins, J. S.

    We derive a relativistic Sommerfeld expansion for thermodynamic quantities in many-body fermionic systems. The expansion is used to generate the equation of state of the Walecka model and its isotherms. We find that these results are in good agreement with numerical calculations, even when the expansion is truncated at its lowest order, in the low temperature regime, defined by T/xf ≪ 1. Although the interesting region near the liquid-gas phase transition is excluded by this criterion, the expansion may still find usefulness in the study of very cold nuclear matter systems, such as neutron stars.

  7. 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.

  8. 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

  9. Pore configuration landscape of granular crystallization

    NASA Astrophysics Data System (ADS)

    Saadatfar, M.; Takeuchi, H.; Robins, V.; Francois, N.; Hiraoka, Y.

    2017-05-01

    Uncovering grain-scale mechanisms that underlie the disorder-order transition in assemblies of dissipative, athermal particles is a fundamental problem with technological relevance. To date, the study of granular crystallization has mainly focussed on the symmetry of crystalline patterns while their emergence and growth from irregular clusters of grains remains largely unexplored. Here crystallization of three-dimensional packings of frictional spheres is studied at the grain-scale using X-ray tomography and persistent homology. The latter produces a map of the topological configurations of grains within static partially crystallized packings. Using numerical simulations, we show that similar maps are measured dynamically during the melting of a perfect crystal. This map encodes new information on the formation process of tetrahedral and octahedral pores, the building blocks of perfect crystals. Four key formation mechanisms of these pores reproduce the main changes of the map during crystallization and provide continuous deformation pathways representative of the crystallization dynamics.

  10. 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

  11. Mechanics of membrane fusion/pore formation.

    PubMed

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

    2015-01-01

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

  12. 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.

  13. Pore collapse and hot spots in HMX

    SciTech Connect

    Menikoff, Ralph

    2003-01-01

    The computing power now available has led researchers to reconsider mesoscale simulations as a means to develop a detailed understanding of detonation waves in a heterogeneous explosive. Since chemical reaction rates are sensitive to temperature, hot spots are of critical importance for initiation. In a plastic-bonded explosive, shock desensitization experiments imply that hot spots generated by pore collapse dominate shock initiation. Here, for the collapse of a single pore driven by a shock, the dependence of the temperature distribution on numerical resolution and dissipative mechanism i s investigated. An inert material (with the constibtive properties of HMX) is used to better focus on the mechanics of pore collapse. ' h o important findings resulted from this study. Eust, too low a resolution can significantly enhance the hot-spot mass. Second, at even moderate piston velocities (< 1W s),s hock dissipation alone does not generate sufficient hot-spot mass. ' b oo ther dissipative mechanism investigated are plastic work and viscous heating. In the cases studied, the integrated lempera!xre distribution has a power-law tail with exponent related to a parameter with dimensions of viscosity. For a particular case, the parameter of either dissipative mechanism can be fit to obtain quantitatively the hot-spot mass needed for initiation. But the dissipative mechanisms scale differently with shock strength and pore size. Consequently, to predict initiation behavior over a range of stimuli and as the micro-stmcture properties of a PBX am varied, sufficient numerical resolution and the correct physical dissipative mechanism are essential.

  14. Further characterization of Closed Pore Insulation (CPI)

    NASA Technical Reports Server (NTRS)

    Russak, M.; Feldman, C.

    1973-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  16. 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.

  17. 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...

  18. 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...

  19. Dilation of fusion pores by crowding of SNARE proteins.

    PubMed

    Wu, Zhenyong; Bello, Oscar D; Thiyagarajan, Sathish; Auclair, Sarah Marie; Vennekate, Wensi; Krishnakumar, Shyam S; O'Shaughnessy, Ben; Karatekin, Erdem

    2017-03-27

    Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v- and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed dilation of single fusion pores using v-SNARE-reconstituted ~23 nm diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, 'flipped' t-SNAREs. Pore nucleation required a minimum of 2, and reached a maximum above ~4 copies per face, but the probability of pore dilation was far from saturating at 15 copies, the NLP capacity. Our experimental and computational results suggest SNARE availability may be pivotal in determining whether neurotransmitters or hormones are released through a transient (kiss & run) or an irreversibly dilating pore (full fusion).

  20. Singularity Expansion Method

    NASA Astrophysics Data System (ADS)

    Riggs, Lloyd Stephen

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

  1. Expansive Northern Volcanic Plains

    NASA Image and Video Library

    2015-04-16

    Mercury northern region is dominated by expansive smooth plains, created by huge amounts of volcanic material flooding across Mercury surface in the past, as seen by NASA MESSENGER spacecraft. The volcanic lava flows buried craters, leaving only traces of their rims visible. Such craters are called ghost craters, and there are many visible in this image, including a large one near the center. Wrinkle ridges cross this scene and small troughs are visible regionally within ghost craters, formed as a result of the lava cooling. The northern plains are often described as smooth since their surface has fewer impact craters and thus has been less battered by such events. This indicates that these volcanic plains are younger than Mercury's rougher surfaces. Instrument: Mercury Dual Imaging System (MDIS) Center Latitude: 60.31° N Center Longitude: 36.87° E Scale: The large ghost crater at the center of the image is approximately 103 kilometers (64 miles) in diameter http://photojournal.jpl.nasa.gov/catalog/PIA19415

  2. Lattice harmonics expansion revisited

    NASA Astrophysics Data System (ADS)

    Kontrym-Sznajd, G.; Holas, A.

    2017-04-01

    The main subject of the work is to provide the most effective way of determining the expansion of some quantities into orthogonal polynomials, when these quantities are known only along some limited number of sampling directions. By comparing the commonly used Houston method with the method based on the orthogonality relation, some relationships, which define the applicability and correctness of these methods, are demonstrated. They are verified for various sets of sampling directions applicable for expanding quantities having the full symmetry of the Brillouin zone of cubic and non-cubic lattices. All results clearly show that the Houston method is always better than the orthogonality-relation one. For the cubic symmetry we present a few sets of special directions (SDs) showing how their construction and, next, a proper application depend on the choice of various sets of lattice harmonics. SDs are important mainly for experimentalists who want to reconstruct anisotropic quantities from their measurements, performed at a limited number of sampling directions.

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

    PubMed

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

    2013-01-01

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

  4. Local Adaptation Interacts with Expansion Load during Range Expansion: Maladaptation Reduces Expansion Load.

    PubMed

    Gilbert, Kimberly J; Sharp, Nathaniel P; Angert, Amy L; Conte, Gina L; Draghi, Jeremy A; Guillaume, Frédéric; Hargreaves, Anna L; Matthey-Doret, Remi; Whitlock, Michael C

    2017-04-01

    The biotic and abiotic factors that facilitate or hinder species range expansions are many and complex. We examine the impact of two genetic processes and their interaction on fitness at expanding range edges: local maladaptation resulting from the presence of an environmental gradient and expansion load resulting from increased genetic drift at the range edge. Results from spatially explicit simulations indicate that the presence of an environmental gradient during range expansion reduces expansion load; conversely, increasing expansion load allows only locally adapted populations to persist at the range edge. Increased maladaptation reduces the speed of range expansion, resulting in less genetic drift at the expanding front and more immigration from the range center, therefore reducing expansion load at the range edge. These results may have ramifications for species being forced to shift their ranges because of climate change or other anthropogenic changes. If rapidly changing climate leads to faster expansion as populations track their shifting climatic optima, populations may suffer increased expansion load beyond previous expectations.

  5. Fabrication of colloidal crystals composed of pore-expanded mesoporous silica nanoparticles prepared by a controlled growth method.

    PubMed

    Yamamoto, Eisuke; Mori, Seiya; Shimojima, Atsushi; Wada, Hiroaki; Kuroda, Kazuyuki

    2017-02-16

    Colloidal crystals composed of mesoporous silica nanoparticles (MSNs) are expected to have various applications because of their unique hierarchical structures and tunable functions. The expansion of the mesopore size is important for introducing guest species which cannot be accommodated by using conventional colloidal crystals of MSNs; however, the preparation of MSNs with a controllable pore size, suitable for the fabrication of colloidal crystals, still remains a challenge. In this study, we fabricated colloidal crystals composed of pore-expanded MSNs using a sophisticated particle growth method to control the pore size of colloidal MSNs while retaining their monodispersity high enough to form colloidal crystals. By adding triisopropylbenzene (TIPB) only during the growth process with the stepwise addition of tetrapropoxysilane (TPOS), the particle size can be tuned from 60 nm to 100 nm, while the pore size can be tuned from 3 nm to ten plus several nm which is the largest size among the previous MSNs capable of forming colloidal crystals. These novel colloidal crystals should contribute to the expansion of nanomaterials science.

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

    DOE PAGES

    Kim, Hyea; Lee, Jung Tae; Magasinski, Alexandre; ...

    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

  7. Effect of pore size on the performance of immobilised enzymes.

    PubMed

    Bayne, Lauren; Ulijn, Rein V; Halling, Peter J

    2013-12-07

    Porous materials are widely employed as supports in the immobilisation of enzymes. Traditionally macroporous materials with pore diameters >50 nm were believed to be the most suitable support material, ensuring no spatial restrictions upon enzyme molecules entering such large pores. In recent years however, there has been growing emphasis in the use of mesoporous supports with pore diameters ranging between 2 and 50 nm. It is thought this smaller pore range may offer enhanced conformational stability to immobilised enzymes while not being so small as to restrict enzyme access. Despite their increasing popularity, many argue that mesoporous materials have not yet proven superior to traditional macroporous supports for enzyme immobilisation. Through the design and application of a unique confidence rating system we were able to accurately compare data and establish trends between pore characteristics and protein loading. By analysing published data (182 experiments in total) and extracting pore characteristics and protein loading values, we have described three categories of pore diameters in which correlations between pore characteristics and protein loading are noted. With pore diameters less than 10 nm we see a general decrease in protein loading as the enzymes find physical restrictions in accessing the high surface offered in this pore diameter range. At pore sizes greater than 100 nm, protein loading generally decreases due to a concomitant reduction in available surface area. In the pore range of 10-100 nm there it is expected to see a decrease in protein loading level with increasing pore diameter. In fact protein loading in this range remains largely constant, suggesting some degree of protein-protein interaction blocking pores and restricting access to the increasing surface area available at decreasing pore diameters. No trends were established between pore characteristics and retention of activity.

  8. Physical Pore Properties and Grain Interactions of SAX04 Sands

    DTIC Science & Technology

    2010-07-01

    serve as flow junctions and ac- count for void volume in these models, while pore throats serve as conduits between the pore bodies and provide...properties can be addressed and quantified using a network, similar to an electrical circuit, of interconnected pore bodies ( junctions ) and pore...Berger, M. J. Buckingham, N. P. Chotiros, P. H. Dahl, N. T. Dewitt, P. Fleischer, R. Flood, C. F. Greenlaw. D. V. Holliday , M. H. Hulbert. M. P. Hutnak

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

    PubMed

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

    2015-09-01

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

  10. 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.

  11. 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.

  12. Molecular dynamics of narrow, liquid-filled pores

    NASA Astrophysics Data System (ADS)

    Magda, J. J.; Tirrell, M.; Davis, H. T.

    1985-08-01

    Molecular dynamics studies are reported for a 6-12 Lennard-Jones liquid in pore channels ranging from about 2-12 molecules wide. The pore walls are modeled as flat surfaces interacting with the fluid molecules via a continuous potential varying only with perpendicular distance from the wall. Liquid density profiles, solvation forces, interfacial tensions, and self-diffusion coefficients along the pore axis were computed. The density profiles indicate multilayer adsorption in the pore, whereas the locally defined diffusion coefficients do not vary significantly across the pore. The pore-averaged diffusivity as well as the solvation force oscillate with varying pore width at constant chemical potential. For pore widths greater than ten molecular diameters, the average diffusion coefficient is almost equal to its bulk value, and the solvation force equals the bulk pressure. In the smaller pores the mean square displacement normal to the pore walls never achieves linearity in time, and thus does not reach a diffusive limit. Thermodynamic equations relating the solvation force to the interfacial tension are derived, and the appropriate mechanical expressions for these quantities are identified. Simulation results are shown to be consistent with these thermodynamic equations. The simulations presented here will be useful in the development of the theory of fluid structure and transport in the tight pores occurring in such materials as vicor glass, clay dispersions, and biological pores and membranes.

  13. 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.

  14. Activation, Permeability, and Inhibition of Astrocytic and Neuronal Large Pore (Hemi)channels*♦

    PubMed Central

    Hansen, Daniel Bloch; Ye, Zu-Cheng; Calloe, Kirstine; Braunstein, Thomas Hartig; Hofgaard, Johannes Pauli; Ransom, Bruce R.; Nielsen, Morten Schak; MacAulay, Nanna

    2014-01-01

    Astrocytes and neurons express several large pore (hemi)channels that may open in response to various stimuli, allowing fluorescent dyes, ions, and cytoplasmic molecules such as ATP and glutamate to permeate. Several of these large pore (hemi)channels have similar characteristics with regard to activation, permeability, and inhibitor sensitivity. Consequently, their behaviors and roles in astrocytic and neuronal (patho)physiology remain undefined. We took advantage of the Xenopus laevis expression system to determine the individual characteristics of several large pore channels in isolation. Expression of connexins Cx26, Cx30, Cx36, or Cx43, the pannexins Px1 or Px2, or the purinergic receptor P2X7 yielded functional (hemi)channels with isoform-specific characteristics. Connexin hemichannels had distinct sensitivity to alterations of extracellular Ca2+ and their permeability to dyes and small atomic ions (conductance) were not proportional. Px1 and Px2 exhibited conductance at positive membrane potentials, but only Px1 displayed detectable fluorescent dye uptake. P2X7, in the absence of Px1, was permeable to fluorescent dyes in an agonist-dependent manner. The large pore channels displayed overlapping sensitivity to the inhibitors Brilliant Blue, gadolinium, and carbenoxolone. These results demonstrated isoform-specific characteristics among the large pore membrane channels; an open (hemi)channel is not a nonselective channel. With these isoform-specific properties in mind, we characterized the divalent cation-sensitive permeation pathway in primary cultured astrocytes. We observed no activation of membrane conductance or Cx43-mediated dye uptake in astrocytes nor in Cx43-expressing C6 cells. Our data underscore that although Cx43-mediated transport is observed in overexpressing cell systems, such transport may not be detectable in native cells under comparable experimental conditions. PMID:25086040

  15. Pore-forming peptides induce rapid phospholipid flip-flop in membranes.

    PubMed

    Fattal, E; Nir, S; Parente, R A; Szoka, F C

    1994-05-31

    A kinetic model for pore-mediated and perturbation-mediated flip-flop is presented and used to characterize the mechanism of peptide-induced phospholipid flip-flop in bilayers. The model assumes that certain peptides can bind to and aggregate within the membrane. When the aggregate attains a critical size (M peptides), a channel is created that results in a fast flip-flop of phospholipids. In addition, certain peptides induce flip-flop through perturbation of the membrane without forming a pore. Donor phospholipid vesicles with an asymmetrical distribution of the fluorescent phospholipid 1-oleoyl-2-[12-[(7-nitro-1,2,3-benzoxadiazol-4- yl)amino]dodecanoyl]phosphatidylcholine (NBD-PC) were used to measure the extent of flip-flop by quantitating the decrease in fluorescence as the NBD-PC exchanged from the donor vesicles to acceptor vesicles that contained a quencher of the NBD fluorescence. Flip-flop curves generated at lipid/peptide ratios ranging from 30/1 to 300000/1 could be well-simulated by the model. Pore-forming peptides, such as melittin or the synthetic peptide GALA (WEAALAEALAEALAEHLAEALAEALEALAA), induce rapid phospholipid flip-flop with half-times for flip-flop of seconds at low peptide/vesicle ratios. The deduced pore sizes are M = 10 +/- 2 for GALA and M = 2 - 4 for melittin. The synthetic peptide LAGA (WEAALAEAEALALAEHEALALAEAELALAA) can catalyze flip-flop via bilayer perturbation. In contrast, hydrophobic peptides such as gramicidin A and valinomycin intercalate into the membrane, but induce little flip-flop. Modeling of the kinetics of phospholipid translocation supports pore formation as the key factor in accelerating phospholipid flip-flop. Thus, amphipathic segments from membrane proteins may account for non-energy-dependent phospholipid flip-flop in biological membranes.

  16. Salt Templating with Pore Padding: Hierarchical Pore Tailoring towards Functionalised Porous Carbons.

    PubMed

    Kumar, K Vasanth; Gadipelli, Srinivas; Preuss, Kathrin; Porwal, Harshit; Zhao, Tingting; Guo, Zheng Xiao; Titirici, Maria-Magdalena

    2017-01-10

    We propose a new synthetic route towards nanoporous functional carbon materials based on salt templating with pore-padding approach (STPP). STPP relies on the use of a pore-padding agent that undergoes an initial polymerisation/ condensation process prior to the formation of a solid carbon framework. The pore-padding agent allows tailoring hierarchically the pore-size distribution and controlling the amount of heteroatom (nitrogen in this case) functionalities as well as the type of nitrogen (graphitic, pyridinic, oxides of nitrogen) incorporated within the carbon framework in a single-step-process. Our newly developed STPP method offers a unique pathway and new design principle to create simultaneously high surface area, microporosity, functionality and pore hierarchy. The functional carbon materials produced by STPP showed a remarkable CO2 /N2 selectivity. At 273 K, a carbon with only micropores offered an exceptionally high CO2 adsorption capacity whereas a carbon with only mesopores showed promising CO2 -philicity with high CO2 /N2 selectivity in the range of 46-60 %, making them excellent candidates for CO2 capture from flue gas or for CO2 storage.

  17. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. 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

  19. Pore network and pore scale modeling of reactive transport in porous media

    NASA Astrophysics Data System (ADS)

    Adler, P. M.; Vu, T. M.; Varloteaux, C.; Bekri, S.

    2012-12-01

    The study of the evolution of a porous medium where a reactive fluid flows is conditioned by the accurate determination of three macroscopic parameters governing the solute displacement, namely the solute velocity, dispersion and mean reaction rate. Of course, a possible application of such studies is CO2 sequestration. This presentation proposes to approach the determination of these parameters by two different ways and to compare them; both are on the pore scale. In the first one called PNM (for pore-network model), a pore-network is extracted from micro tomography images of a real porous medium. This network is composed of spherical pores joined by circular tubes; it is used to calculate transport macroscopic parameters and porosity-permeability evolution during the reactive transport flow as functions of dimensionless numbers representing the reaction and flow rate regimes. The flow is calculated by using Kirchhoff laws. Transport is determined in the asymptotic regime where the solute concentration undergoes an exponential evolution with time. In the second approach called PSM (for pore scale model), the pore-network model is used as a three dimensional medium which is discretized by the Level Set Method. The Stokes equations are solved in order to determine the local flow field and the corresponding permeability. The solute concentration is obtained by solving the local convection-diffusion equation in the 3D pore-network; numerical dispersion is reduced by a Flux Limiting Scheme. Two different geometries of porous media are addressed by both numerical codes. The first pore-network geometry is used to validate the PNM assumptions, whereas the second pore-network is defined for a better understanding of the dominant solute distribution. One of the main results obtained with the first pore-network is the dependence of the concentration profile on the Péclet number Pe in the pore-bodies. When this number increases, one has to switch from an assumption of

  20. 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

  1. 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.

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

    PubMed

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

    2013-02-01

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

  3. Displacement of soil pore water by trichloroethylene

    SciTech Connect

    Wershaw, R.L.; Aiken, G.R.; Imbrigiotta, T.E.

    1994-07-01

    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 am 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. 15 refs., 6 figs., 4 tabs.

  4. 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.

  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. 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

  7. Precipitation in pores: A geochemical frontier

    DOE PAGES

    Stack, Andrew G.

    2015-07-29

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

  8. 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

  9. Catalytic reforming catalyst with modified pore size distribution

    SciTech Connect

    Unmuth, E.E.; Fleming, B.A.

    1987-10-27

    In a naphtha reforming catalyst having at least one catalytic metal deposited on a porous solid catalyst support, an improvement is described which comprises the catalyst having the following in combination: (A) a surface area above about 250M/sup 2//gram of catalyst; (B) A pore volume above about 0.4 cc/gram of catalyst in pores having diameters of from about 30 angstroms to about 38,000 angstroms; and (C) A pore volume distribution wherein about 70 percent or less of the pore volume is in pores having diameters of from about 30 angstroms to about 400 angstroms, and 30 percent or more of the pore volume is in pores having diameters of from about 400 angstroms to about 38,000 angstroms.

  10. Quantifying similarity of pore-geometry in nanoporous materials.

    PubMed

    Lee, Yongjin; Barthel, Senja D; Dłotko, Paweł; Moosavi, S Mohamad; Hess, Kathryn; Smit, Berend

    2017-05-23

    In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. However, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify them using topological data analysis. This allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.

  11. Quantifying similarity of pore-geometry in nanoporous materials

    NASA Astrophysics Data System (ADS)

    Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; Moosavi, S. Mohamad; Hess, Kathryn; Smit, Berend

    2017-05-01

    In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. However, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify them using topological data analysis. This allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.

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

    PubMed

    Salinas, Dino G

    2016-01-01

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

  13. Pedotransfer functions for permeability: A computational study at pore scales

    NASA Astrophysics Data System (ADS)

    Hyman, Jeffrey D.; Smolarkiewicz, Piotr K.; Larrabee Winter, C.

    2013-04-01

    Three phenomenological power law models for the permeability of porous media are derived from computational experiments with flow through explicit pore spaces. The pore spaces are represented by three-dimensional pore networks in 63 virtual porous media along with 15 physical pore networks. The power laws relate permeability to (i) porosity, (ii) squared mean hydraulic radius of pores, and (iii) their product. Their performance is compared to estimates derived via the Kozeny equation, which also uses the product of porosity with squared mean hydraulic pore radius to estimate permeability. The power laws provide tighter estimates than the Kozeny equation even after adjusting for the extra parameter they each require. The best fit is with the power law based on the Kozeny predictor, that is, the product of porosity with the square of mean hydraulic pore radius.

  14. Quantifying similarity of pore-geometry in nanoporous materials

    DOE PAGES

    Lee, Yongjin; Barthel, Senja D.; Dłotko, Paweł; ...

    2017-05-23

    In most applications of nanoporous materials the pore structure is as important as the chemical composition as a determinant of performance. For example, one can alter performance in applications like carbon capture or methane storage by orders of magnitude by only modifying the pore structure. For these applications it is therefore important to identify the optimal pore geometry and use this information to find similar materials. But, the mathematical language and tools to identify materials with similar pore structures, but different composition, has been lacking. We develop a pore recognition approach to quantify similarity of pore structures and classify themmore » using topological data analysis. This then allows us to identify materials with similar pore geometries, and to screen for materials that are similar to given top-performing structures. Using methane storage as a case study, we also show that materials can be divided into topologically distinct classes requiring different optimization strategies.« less

  15. 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

  16. 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.

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

    PubMed

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

    2013-02-05

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

  18. 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.

  19. 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.

  20. Designing biomimetic pores based on carbon nanotubes

    PubMed Central

    García-Fandiño, Rebeca; Sansom, Mark S. P.

    2012-01-01

    Biomimetic nanopores based on membrane-spanning single-walled carbon nanotubes have been designed to include selectivity filters based on combinations of anionic and cationic groups mimicking those present in bacterial porins and in voltage-gated sodium and calcium channels. The ion permeation and selectivity properties of these nanopores when embedded in a phospholipid bilayer have been explored by molecular dynamics simulations and free energy profile calculations. The interactions of the nanopores with sodium, potassium, calcium, and chloride ions have been explored as a function of the number of anionic and cationic groups within the selectivity filter. Unbiased molecular dynamics simulations show that the overall selectivity is largely determined by the net charge of the filter. Analysis of distribution functions reveals considerable structuring of the distribution of ions and water within the nanopores. The distributions of ions along the pore axis reveal local selectivity for cations around filter, even in those nanopores (C0) where the net filter charge is zero. Single ion free energy profiles also reveal clear evidence for cation selectivity, even in the C0 nanopores. Detailed analysis of the interactions of the C0 nanopore with Ca2+ ions reveals that local interactions with the anionic (carboxylate) groups of the selectivity filter lead to (partial) replacement of solvating water as the ion passes through the pore. These studies suggest that a computational biomimetic approach can be used to evaluate our understanding of the design principles of nanopores and channels. PMID:22509000

  1. Multimodal pore formation in calcium phosphate cements.

    PubMed

    Lodoso-Torrecilla, Irene; van Gestel, Nicole A P; Diaz-Gomez, Luis; Grosfeld, Eline-Claire; Laperre, Kjell; Wolke, Joop G C; Smith, Brandon T; Arts, Jacobus J; Mikos, AntoniosG; Jansen, John A; Hofmann, Sandra; van den Beucken, Jeroen J J P

    2017-09-23

    Calcium phosphate cements (CPCs) are commonly used as bone substitute materials. However, their slow degradation rate and lack of macroporosity hinders new bone formation. Poly(DL-lactic-co-glycolic acid) (PLGA) incorporation is of great interest as, upon degradation, produces acidic by-products that enhance CPC degradation. Yet, new bone formation is delayed until PLGA degradation occurs a few weeks after implantation. Therefore, the aim of this study was to accelerate the early stage pore formation within CPCs in vitro. With that purpose, we incorporated the water-soluble porogen sucrose at different weight percentages (10 or 20 wt.%) to CPC and CPC/PLGA composites. The results revealed that incorporation of sucrose porogens increased mass loss within the first week of in vitro degradation in groups containing sucrose compared to control groups. After week 1, a further mass loss was observed related to PLGA and CPC degradation. Macroporosity analysis confirmed that macroporosity formation is influenced by the dissolution of sucrose at an early stage and by the degradation of PLGA and CPC at a later stage. We concluded that the combination of sucrose and PLGA porogens in CPC is a promising approach to promote early stage bone tissue ingrowth and complete replacement of CPC via multimodal pore formation. This article is protected by copyright. All rights reserved. © 2017 Wiley Periodicals, Inc.

  2. Size of diffusion pore of Alcaligenes faecalis.

    PubMed Central

    Ishii, J; Nakae, T

    1988-01-01

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

  3. Exo-endocytosis and closing of the fission pore during endocytosis in single pituitary nerve terminals internally perfused with high calcium concentrations.

    PubMed Central

    Rosenboom, H; Lindau, M

    1994-01-01

    An increase in free Ca2+ triggers exocytosis in pituitary nerve terminals leading to an increase in membrane area and membrane capacitance. When Ca2+ is increased by step depolarization, an instantaneous capacitance increase during the first 80 ms is followed by a slow increase extending over several seconds. We measured capacitance changes associated with exocytosis and endocytosis in single pituitary nerve terminals internally perfused with high Ca2+. At 50 microM Ca2+ the capacitance increased by up to 2%/s, similar to the slow phase observed during depolarization. Our results indicate that at the site of fusion very high Ca2+ is required. Following exocytosis, large downward capacitance steps were measured, reflecting endocytosis of large vacuoles. These events were not abrupt but reflected a gradual decrease of fission pore conductance from 8 nS to < 40 pS during 500 ms, revealing the dynamics of individual fission pore closures. Above 300 pS, narrowing of the endocytotic fission pore was approximately 10 times slower than the previously reported expansion of the exocytotic fusion pore. The transition between 300 pS and 0 pS took approximately 200 ms, whereas it has been reported that the exocytotic fusion pore measured in mast cells opens from 0 to 280 pS in < 100 microseconds. The time course of closing of the fission pore may be explained by an exponential decrease in pore diameter occurring at a constant rate. PMID:8202480

  4. Pore formation in lipid membrane I: Continuous reversible trajectory from intact bilayer through hydrophobic defect to transversal pore.

    PubMed

    Akimov, Sergey A; Volynsky, Pavel E; Galimzyanov, Timur R; Kuzmin, Peter I; Pavlov, Konstantin V; Batishchev, Oleg V

    2017-09-22

    Lipid membranes serve as effective barriers allowing cells to maintain internal composition differing from that of extracellular medium. Membrane permeation, both natural and artificial, can take place via appearance of transversal pores. The rearrangements of lipids leading to pore formation in the intact membrane are not yet understood in details. We applied continuum elasticity theory to obtain continuous trajectory of pore formation and closure, and analyzed molecular dynamics trajectories of pre-formed pore reseal. We hypothesized that a transversal pore is preceded by a hydrophobic defect: intermediate structure spanning through the membrane, the side walls of which are partially aligned by lipid tails. This prediction was confirmed by our molecular dynamics simulations. Conversion of the hydrophobic defect into the hydrophilic pore required surmounting some energy barrier. A metastable state was found for the hydrophilic pore at the radius of a few nanometers. The dependence of the energy on radius was approximately quadratic for hydrophobic defect and small hydrophilic pore, while for large radii it depended on the radius linearly. The pore energy related to its perimeter, line tension, thus depends of the pore radius. Calculated values of the line tension for large pores were in quantitative agreement with available experimental data.

  5. Thermodynamic and hydrodynamic constraints on overpressure caused by hydrate dissociation: A pore-scale model

    NASA Astrophysics Data System (ADS)

    Holtzman, R.; Juanes, R.

    2011-07-01

    It has been suggested that volume expansion caused by hydrate dissociation in sediment pores can result in large overpressure, which in turn may destabilize the sediment and trigger massive submarine landslides. Here, we investigate the pressure evolution during thermally-induced dissociation, by means of a pore-scale model that couples dissociation kinetics, multiphase flow and geomechanics. Dissociation is controlled by a self-preservation mechanism: increasing pore pressure reduces the driving force for dissociation. Hence, the overpressure is constrained by the phase equilibrium pressure, regardless of the kinetic rate of dissociation, heat supply, and sediment permeability. Furthermore, we find that the timescale for buildup of pressure by dissociation is typically much larger than that for its dissipation by drainage. Consequently, the overpressure is controlled by the capillary entry thresholds, which depend on the mode of gas invasion. In low-permeability systems, fracturing is the preferred mechanism, occurring at capillary pressures lower than the entry thresholds in the undeformed sediment. Our results suggest that while large overpressures cannot be sustained by rapid dissociation in natural systems, dissociation can induce important geomechanical effects. Gas migration by fracturing provides a possible link between dissociation, sediment deformation and methane venting.

  6. Estimates of expansion time scales

    NASA Astrophysics Data System (ADS)

    Jones, E. M.

    Monte Carlo simulations of the expansion of a spacefaring civilization show that descendants of that civilization should be found near virtually every useful star in the Galaxy in a time much less than the current age of the Galaxy. Only extreme assumptions about local population growth rates, emigration rates, or ship ranges can slow or halt an expansion. The apparent absence of extraterrestrials from the solar system suggests that no such civilization has arisen in the Galaxy.

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

    SciTech Connect

    Tomutsa, Liviu; Silin, Dmitriy

    2004-08-19

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

  8. 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.

  9. 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.

  10. Structure and mechanism of peptide-induced membrane pores

    NASA Astrophysics Data System (ADS)

    Qian, Shuo

    This thesis reports the studies of the structure and mechanism of peptide-induced membrane pores by antimicrobial peptide alamethicin and by a peptide named Baxalpha5, which is derived from Bax protein. Alamethicin is one of best known antimicrobial peptides, which are ubiquitous throughout the biological world. Bax-alpha5 peptide is the pore-forming domain of apoptosis regulator protein Bax, which activates pore formation on outer mitochondrial membrane to release cytochrome c to initiate programmed cell death. Both peptides as well as many other pore-forming peptides, induce pores in membrane, however the structure and mechanism of the pore formation were unknown. By utilizing grazing angle x-ray diffraction, I was able to reconstruct the electron density profile of the membrane pores induced by both peptides. The fully hydrated multiple bilayers of peptide-lipid mixture on solid substrate were prepared in the condition that pores were present, as established previously by neutron in-plane scattering and oriented circular dichroism. At dehydrated conditions, the inter bilayer distance of the sample shortened and the interactions between bilayers caused the membrane pores to become long-ranged correlated and formed a periodically ordered lattice of rhombohedral symmetry, so that x-ray diffraction can be applied. To help solving the phase problem of diffraction, a brominated lipid was used and multi-wavelength anomalous diffraction was performed below the bromine K-edge. The reconstructed electron density profiles unambiguously revealed that the alamethicin-induced membrane pore is of barrel-stave type, while the Bax-alpha5 induced pore is of lipidic toroidal (wormhole) type. The underlying mechanism of pore formation was resolved by observing the time-dependent process of pore formation in vesicles exposed to Bax-alpha5 solutions, as well as the membrane thinning experiment. This demonstrated that Bax-alpha5 exhibited the same sigmoidal concentration dependence as

  11. Multiplexing Prisms for Field Expansion.

    PubMed

    Peli, Eli; Jung, Jae-Hyun

    2017-08-01

    Prisms used for field expansion are limited by the optical scotoma at a prism apex (apical scotoma). For a patient with two functioning eyes, fitting prisms unilaterally allows the other eye to compensate for the apical scotoma. A monocular patient's field loss cannot be expanded with a conventional or Fresnel prism because of the apical scotoma. A newly invented optical device, the multiplexing prism (MxP), was developed to overcome the apical scotoma limitation in monocular field expansion. A Fresnel-prism-like device with alternating prism and flat elements superimposes shifted and see-through views, thus creating the (monocular) visual confusion required for field expansion and eliminating the apical scotoma. Several implementations are demonstrated and preliminarily evaluated for different monocular conditions with visual field loss. The field expansion of the MxP is compared with the effect of conventional prisms using calculated and measured perimetry. Field expansion without apical scotomas is shown to be effective for monocular patients with hemianopia or constricted peripheral field. The MxPs are shown to increase the nasal field for a patient with only one eye and for patients with bitemporal hemianopia. The MxPs placed at the far temporal field are shown to expand the normal visual field. The ability to control the contrast ratio between the two images is verified. A novel optical device is demonstrated to have the potential for field expansion technology in a variety of conditions. The devices may be inexpensive and can be constructed in a cosmetically acceptable format.

  12. 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.

  13. High Transmembrane Voltage Raised by Close Contact Initiates Fusion Pore

    PubMed Central

    Bu, Bing; Tian, Zhiqi; Li, Dechang; Ji, Baohua

    2016-01-01

    Membrane fusion lies at the heart of neuronal communication but the detailed mechanism of a critical step, fusion pore initiation, remains poorly understood. Here, through atomistic molecular dynamics simulations, a transient pore formation induced by a close contact of two apposed bilayers is firstly reported. Such a close contact gives rise to a high local transmembrane voltage that induces the transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Of note, this close contact induced fusion pore formation is contrasted with previous reported electroporation under ad hoc applied external electric field or ionic charge in-balance. We show that the transmembrane voltage increases with the decrease of the distance between the bilayers. Below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce the transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. A resealing of the membrane pores resulting from the neutralization of the transmembrane voltage by ions through the pores was then observed. We also found that the membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse. This result provides a possible mechanism for fusion pore formation and regulation of pathway of fusion process. PMID:28018169

  14. 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.

  15. High Transmembrane Voltage Raised by Close Contact Initiates Fusion Pore.

    PubMed

    Bu, Bing; Tian, Zhiqi; Li, Dechang; Ji, Baohua

    2016-01-01

    Membrane fusion lies at the heart of neuronal communication but the detailed mechanism of a critical step, fusion pore initiation, remains poorly understood. Here, through atomistic molecular dynamics simulations, a transient pore formation induced by a close contact of two apposed bilayers is firstly reported. Such a close contact gives rise to a high local transmembrane voltage that induces the transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Of note, this close contact induced fusion pore formation is contrasted with previous reported electroporation under ad hoc applied external electric field or ionic charge in-balance. We show that the transmembrane voltage increases with the decrease of the distance between the bilayers. Below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce the transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. A resealing of the membrane pores resulting from the neutralization of the transmembrane voltage by ions through the pores was then observed. We also found that the membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse. This result provides a possible mechanism for fusion pore formation and regulation of pathway of fusion process.

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

    DOE PAGES

    Lin, Qingqing; Li, Huilin; Wang, Tong; ...

    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

  17. Tiny Pores Observed by Hinode/Solar Optical Telescope

    NASA Astrophysics Data System (ADS)

    Cho, Kyung-Suk; Bong, Su-Chan; Chae, Jongchul; Kim, Yeon-Han; Park, Young-Deuk

    2010-11-01

    The study of pores, small penumbraless sunspots, can give us a chance to understand how strong magnetic fields interact with convective motions in the photosphere. For a better understanding of this interaction, we investigate the temporal variation of several tiny pores smaller than 2''. These pores were observed by the Solar Optical Telescope on board Hinode on 2006 December 29. We have analyzed the high-resolution spectropolarimetric (SP) data and the G-band filtergrams taken during the observation. Magnetic flux density and Doppler velocities of the pores are estimated by applying the center-of-gravity method to the SP data. The horizontal motions in and around the pores are tracked by adopting the nonlinear affine velocity estimator method to the G-band filter images. As a result, we found the following. (1) The darkness of the pores is positively correlated with the magnetic flux density. (2) Downflows always exist inside and around the pores. (3) The speed of downflows inside the pores is negatively correlated with their darkness. (4) The pores are surrounded by strong downflows. (5) Brightness changes of the pores are correlated with the divergence of mass flow (correlation coefficient >0.9). (6) The pores in the growing phase are associated with the converging flow pattern and the pores in the decay phase with the diverging flow pattern. Our results support the idea that a pore grows as the magnetic flux density increases due to the convergence of ambient mass flow and it decays with the decrease of the flux density due to the diverging mass flow.

  18. 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

  19. Development or disease: duality of the mitochondrial permeability transition pore.

    PubMed

    Pérez, María José; Quintanilla, Rodrigo A

    2017-06-01

    Mitochondria is not only a dynamic organelle that produces ATP, but is also an important contributor to cell functions in both development and cell death processes. These paradoxical functions of mitochondria are partially regulated by the mitochondrial permeability transition pore (mPTP), a high-conductance channel that can induce loss of mitochondrial membrane potential, impairment of cellular calcium homeostasis, oxidative stress, and a decrease in ATP production upon pathological activation. Interestingly, despite their different etiologies, several neurodegenerative diseases and heart ischemic injuries share mitochondrial dysfunction as a common element. Generally, mitochondrial impairment is triggered by calcium deregulation that could lead to mPTP opening and cell death. Several studies have shown that opening of the mPTP not only induces mitochondrial damage and cell death, but is also a physiological mechanism involved in different cellular functions. The mPTP participates in regular calcium-release mechanisms that are required for proper metabolic regulation; it is hypothesized that the transient opening of this structure could be the principal mediator of cardiac and brain development. The mPTP also plays a role in protecting against different brain and cardiac disorders in the elderly population. Therefore, the aim of this work was to discuss different studies that show this controversial characteristic of the mPTP; although mPTP is normally associated with several pathological events, new critical findings suggest its importance in mitochondrial function and cell development. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. 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.

  1. 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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2014-06-17

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

  4. 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

  5. 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.

  6. 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. Copyright © 2016 Adams et al.

  7. Rock expansion caused by ultrasound

    NASA Astrophysics Data System (ADS)

    Hedberg, C.; Gray, A.

    2013-12-01

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

  8. Fracture capture of organic pores in shales

    NASA Astrophysics Data System (ADS)

    Daigle, Hugh; Hayman, Nicholas W.; Kelly, Eric D.; Milliken, Kitty L.; Jiang, Han

    2017-03-01

    Shales are heterogeneous media with porosity at many scales and in many microtextural positions, including within organic matter and clay aggregates. Because these materials have contrasting mechanical properties, it remains unclear how induced fractures manage to connect with this porosity whether during hydrocarbon production, wastewater injection, or carbon-capture-and-storage efforts. To explore porosity changes related to fracturing, we experimentally failed shale samples in a triaxial load apparatus and observed changes in microstructure through scanning electron microscopy, low-pressure nitrogen sorption, and nuclear magnetic resonance. We observed a system of microcracks, many of which were likely experimentally induced and localized on grain boundaries. In some cases these fractures propagated into regions of natural porosity in organic matter. In the subsurface this "fracture capture" likely enhances pore connectivity, but only selectively depending upon mechanical conditions. Fracture capture is one possible mechanism by which multiscale compositional heterogeneity in shales may affect rheological heterogeneity.

  9. 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.

  10. 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.

  11. Silicon pore optics for the ATHENA telescope

    NASA Astrophysics Data System (ADS)

    Collon, Maximilien J.; Vacanti, Giuseppe; Günther, Ramses; Yanson, Alex; Barriere, Nicolas; Landgraf, Boris; Vervest, Mark; Chatbi, Abdelhakim; van der Hoeven, Roy; Beijersbergen, Marco W.; Bavdaz, Marcos; Wille, Eric; Shortt, Brian; Haneveld, Jeroen; Koelewijn, Arenda; van Baren, Coen; Eigenraam, Alexander; Müller, Peter; Krumrey, Michael; Burwitz, Vadim; Pareschi, Giovanni; Conconi, Paolo; Massahi, Sonny; Christensen, Finn E.; Valsecchi, Giuseppe

    2016-07-01

    Silicon Pore Optics is a high-energy optics technology, invented to enable the next generation of high-resolution, large area X-ray telescopes such as the ATHENA observatory, a European large (L) class mission with a launch date of 2028. The technology development is carried out by a consortium of industrial and academic partners and focuses on building an optics with a focal length of 12 m that shall achieve an angular resolution better than 5". So far we have built optics with a focal length of 50 m and 20 m. This paper presents details of the work carried out to build silicon stacks for a 12 m optics and to integrate them into mirror modules. It will also present results of x-ray tests taking place at PTB's XPBF with synchrotron radiation and the PANTER test facility.

  12. Silicon pore optics development for ATHENA

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  13. Sumoylation and transcription regulation at nuclear pores.

    PubMed

    Texari, Lorane; Stutz, Françoise

    2015-03-01

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

  14. 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.

  15. Characterization and comparison of pore landscapes in crystalline porous materials.

    PubMed

    Pinheiro, Marielle; Martin, Richard L; Rycroft, Chris H; Jones, Andrew; Iglesia, Enrique; Haranczyk, Maciej

    2013-07-01

    Crystalline porous materials have many applications, including catalysis and separations. Identifying suitable materials for a given application can be achieved by screening material databases. Such a screening requires automated high-throughput analysis tools that characterize and represent pore landscapes with descriptors, which can be compared using similarity measures in order to select, group and classify materials. Here, we discuss algorithms for the calculation of two types of pore landscape descriptors: pore size distributions and stochastic rays. These descriptors provide histogram representations that encode the geometrical properties of pore landscapes. Their calculation involves the Voronoi decomposition as a technique to map and characterize accessible void space inside porous materials. Moreover, we demonstrate pore landscape comparisons for materials from the International Zeolite Association (IZA) database of zeolite frameworks, and illustrate how the choice of pore descriptor and similarity measure affects the perspective of material similarity exhibiting a particular emphasis and sensitivity to certain aspects of structures. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. Singular perturbation analysis of the pore creation transient

    NASA Astrophysics Data System (ADS)

    Neu, John C.; Krassowska, Wanda

    2006-09-01

    Electroporation, in which electric pulses create transient pores in the cell membrane, is an important technique for drug and DNA delivery. Electroporation kinetics is mathematically described by an advection-diffusion boundary value problem. This study uses singular perturbation to derive a reduced description of the pore creation transient in the form of a single integrodifferential equation for the transmembrane voltage V(t) . The number of pores and the distribution of their radii are computed from V(t) . The analysis contains two nonstandard features: the use of the voltage deviation to peel away the strong exponential dependence of pore creation upon the transmembrane potential, and the autonomous approximation of the pore evolution. Comparing the predictions of the reduced equation with the simulations of the original problem demonstrates that this analysis allows one to predict with good accuracy the number and distribution of pores as a function of the electric pulse strength.

  17. Asymptotic Expansions, 1/Z Expansions, and the Critical Nuclear Charge

    NASA Astrophysics Data System (ADS)

    Drake, Gordon

    2014-03-01

    The quantum mechanical three-body problem defies analytic solution, and so computationally intensive approximation methods involving, for example, variational calculations with large correlated basis sets must be used. This talk will review recent work to explore the outer fringes of the quantum mechanical three-body problem for heliumlike atoms. Asymptotic expansions provide a surprisingly simple and accurate account of highly excited Rydberg states with high angular momentum. 1 / Z expansions, where Z is the nuclear charge, provide results for an entire isoelectronic sequence within a single calculation. Its radius of convergence is thought to be related to the critical nuclear charge Zc for a state to be bound. For Z expansions and the critical nuclear charge. Research suppoted by the Natural Sciences and Engineering Research Council of Canada, and by SHARCNET.

  18. Effects of Non-linear Terms and Fault Width on Pore Fluid Pressurization

    NASA Astrophysics Data System (ADS)

    Vredevoogd, M. A.; Oglesby, D. D.; Park, S. K.

    2007-12-01

    Faults generate heat due to friction while slipping in earthquakes. If there are pore fluids along the fault, they will be heated and expand. The pore fluids will have little effect on faults in high permeability settings, as they quickly escape. In a low permeability setting, the expanding pore fluids are not able to escape quickly, and thermal expansion of the fluids will increase the fluid pressure, lowering the effective normal stress (and thus frictional stress) along the fault. To investigate this process, we solve the non-linear equations presented in Mase and Smith (1985). These equations involve several non-linear terms that make it necessary to solve the equations iteratively. We have previously shown some results of this methodology for various permeability structures and slip rates. Here we focus on the importance of individual terms in the equations by running models with individual terms neglected. Among our results, we find that conduction significantly affects the temperature and pressure, while advection has a negligible effect on the solution. The implications may be important for researchers constructing simplified models of the pore fluid pressurization process. We also look at the effect of fault width (the width of the area that is shearing and producing heat). In particular, we are interested in the effects of the fault width on the maximum temperature reached, as well as the total amount of frictional heat generated. While a wider fault will tend to have a lower peak temperature because of the distributed slip, it can also result in a larger overall heat generation, because the average temperature over the fault width can be higher than for a narrow fault with a higher, but narrower temperature peak. In contrast, while the narrow faults initially have the highest pressures, the wider faults eventually surpass them both in maximum pressure, and in the amount of overall pressurization.

  19. Control of pore size and structure of tissue engineering scaffolds produced by supercritical fluid processing.

    PubMed

    Tai, Hongyun; Mather, Melissa L; Howard, Daniel; Wang, Wenxin; White, Lisa J; Crowe, John A; Morgan, Steve P; Chandra, Amit; Williams, David J; Howdle, Steven M; Shakesheff, Kevin M

    2007-12-17

    Tissue engineering scaffolds require a controlled pore size and structure to host tissue formation. Supercritical carbon dioxide (scCO2) processing may be used to form foamed scaffolds in which the escape of CO2 from a plasticized polymer melt generates gas bubbles that shape the developing pores. The process of forming these scaffolds involves a simultaneous change in phase in the CO2 and the polymer, resulting in rapid expansion of a surface area and changes in polymer rheological properties. Hence, the process is difficult to control with respect to the desired final pore size and structure. In this paper, we describe a detailed study of the effect of polymer chemical composition, molecular weight and processing parameters on final scaffold characteristics. The study focuses on poly(DL-lactic acid) (PDLLA) and poly(DL-lactic acid-co-glycolic acid) (PLGA) as polymer classes with potential application as controlled release scaffolds for growth factor delivery. Processing parameters under investigation were temperature (from 5 to 55 degrees C) and pressure (from 60 to 230 bar). A series of amorphous PDLLA and PLGA polymers with various molecular weights (from 13 KD to 96 KD) and/or chemical compositions (the mole percentage of glycolic acid in the polymers was 0, 15, 25, 35 and 50 respectively) were employed. The resulting scaffolds were characterised by optical microscopy, scanning electron microscopy (SEM), and micro X-ray computed tomography (microCT). This is the first detailed study on using these series polymers for scaffold formation by supercritical technique. This study has demonstrated that the pore size and structure of the supercritical PDLLA and PLGA scaffolds can be tailored by careful control of processing conditions.

  20. Aluminium-induced changes of fusion pore properties attenuate prolactin secretion in rat pituitary lactotrophs.

    PubMed

    Calejo, A I; Jorgačevski, J; Silva, V S; Stenovec, M; Kreft, M; Gonçalves, P P; Zorec, R

    2012-01-10

    Hormone secretion is mediated by Ca(2+)-regulated exocytosis. The key step of this process consists of the merger of the vesicle and the plasma membranes, leading to the formation of a fusion pore. This is an aqueous channel through which molecules stored in the vesicle lumen exit into the extracellular space on stimulation. Here we studied the effect of sub-lethal dose of aluminium on prolactin secretion in isolated rat pituitary lactotrophs with an enzyme immunoassay and by monitoring electrophysiologically the interaction of a single vesicle with the plasma membrane in real time, by monitoring membrane capacitance. After 24-h exposure to sub-lethal AlCl(3) (30 μM), the secretion of prolactin was reduced by 14±8% and 46±11% under spontaneous and K(+)-stimulated conditions, respectively. The frequency of unitary exocytotic events, recorded by the high-resolution patch-clamp monitoring of membrane capacitance, a parameter linearly related to the membrane area, under spontaneous and stimulated conditions, was decreased in aluminium-treated cells. Moreover, while the fusion pore dwell-time was increased in the presence of aluminium, the fusion pore conductance, a measure of fusion pore diameter, was reduced, both under spontaneous and stimulated conditions. These results suggest that sub-lethal aluminium concentrations reduce prolactin secretion downstream of the stimulus secretion coupling by decreasing the frequency of unitary exocytotic events and by stabilizing the fusion pore diameter to a value smaller than prolactin molecule, thus preventing its discharge into the extracellular space. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

  1. Structural and Functional Analysis of the Pore-Forming Toxin NetB from Clostridium perfringens

    PubMed Central

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

    2013-01-01

    ABSTRACT Clostridium perfringens is an anaerobic bacterium that causes numerous important human and animal diseases, primarily as a result of its ability to produce many different protein toxins. In chickens, C. perfringens causes necrotic enteritis, a disease of economic importance to the worldwide poultry industry. The secreted pore-forming toxin NetB is a key virulence factor in the pathogenesis of avian necrotic enteritis and is similar to alpha-hemolysin, a β-barrel pore-forming toxin from Staphylococcus aureus. To address the molecular mechanisms underlying NetB-mediated tissue damage, we determined the crystal structure of the monomeric form of NetB to 1.8 Å. Structural comparisons with other members of the alpha-hemolysin family revealed significant differences in the conformation of the membrane binding domain. These data suggested that NetB may recognize different membrane receptors or use a different mechanism for membrane-protein interactions. Consistent with this idea, electrophysiological experiments with planar lipid bilayers revealed that NetB formed pores with much larger single-channel conductance than alpha-hemolysin. Channel conductance varied with phospholipid net charge. Furthermore, NetB differed in its ion selectivity, preferring cations over anions. Using hemolysis as a screen, we carried out a random-mutagenesis study that identified several residues that are critical for NetB-induced cell lysis. Mapping of these residues onto the crystal structure revealed that they were clustered in regions predicted to be required for oligomerization or membrane binding. Together these data provide an insight into the mechanism of NetB-mediated pore formation and will contribute to our understanding of the mode of action of this important toxin. PMID:23386432

  2. 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

  3. 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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  6. Movement of ions through fixed pores in the neural membrane.

    PubMed Central

    Wooldridge, D E

    1984-01-01

    A simple configuration is first proposed for the pores used by sodium and potassium ions in moving through the neural membrane. The voltage dependence of the ion current through a system of such pores is then derived from diffusion theory and shown not to agree well with experimental observation. Good agreement is obtained, however, when the end segments of the pores are modified to include constrictions and ion-specific trapping centers. PMID:6089215

  7. 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.

  8. Chemically Mediated Mechanical Expansion of the Pollen Tube Cell Wall

    PubMed Central

    Rojas, Enrique R.; Hotton, Scott; Dumais, Jacques

    2011-01-01

    Morphogenesis of plant cells is tantamount to the shaping of the stiff cell wall that surrounds them. To this end, these cells integrate two concomitant processes: 1), deposition of new material into the existing wall, and 2), mechanical deformation of this material by the turgor pressure. However, due to uncertainty regarding the mechanisms that coordinate these processes, existing models typically adopt a limiting case in which either one or the other dictates morphogenesis. In this report, we formulate a simple mechanism in pollen tubes by which deposition causes turnover of cell wall cross-links, thereby facilitating mechanical deformation. Accordingly, deposition and mechanics are coupled and are both integral aspects of the morphogenetic process. Among the key experimental qualifications of this model are: its ability to precisely reproduce the morphologies of pollen tubes; its prediction of the growth oscillations exhibited by rapidly growing pollen tubes; and its prediction of the observed phase relationships between variables such as wall thickness, cell morphology, and growth rate within oscillatory cells. In short, the model captures the rich phenomenology of pollen tube morphogenesis and has implications for other plant cell types. PMID:22004737

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

    PubMed

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

    2014-05-13

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

  10. Gas permeation in a molecular crystal and space expansion.

    PubMed

    Takasaki, Yuichi; Takamizawa, Satoshi

    2014-05-14

    A novel single-crystal membrane [Cu(II)2(4-F-bza)4(2-mpyz)]n (4-F-bza = 4-fluorobenzoate; 2-mpyz = 2-methylpyrazine) was synthesized and its identical permeability in any crystal direction in the correction for tortuosity proved that gas diffuses inside the channels without detour. H2 permeated by 1.18 × 10(-12) mol m m(-2) s(-1) Pa(-1) with a high selectivity (Fα: 23.5 for H2/CO and 48.0 for H2/CH4) through its 2D-channels having a minimum diameter of 2.6 Å, which is narrower than the Lennard-Jones diameter of H2 (2.827 Å), CO (3.690 Å), and CH4 (3.758 Å). The high rate of permeation was well explained by a modified Knudsen diffusion model based on the space expansion effect, which agrees with the observed permselectivity enhanced for smaller gases in considering the expansion of a channel resulting from the collision of gas molecules or atoms onto the channel wall. An analysis of single-crystal X-ray data showed the expansion order to be H2 > Ar > CH4, which was expected from the permeation analysis. The permselectivity of a porous solid depends on the elasticity of the pores as well as on the diameter of the vacant channel and the size of the target gas.

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

    NASA Astrophysics Data System (ADS)

    Garner, Allen L.; Bogdan Neculaes, V.

    2012-07-01

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

  12. Tight knots in proteins: can they block the mitochondrial pores?

    PubMed

    Szymczak, Piotr

    2013-04-01

    Proteins need to be unfolded when translocated through the pores in mitochondrial and other cellular membranes. Knotted proteins, however, might get stuck during this process since the diameter of the pore is smaller than the size of maximally tightened knot. In the present article, I briefly review the experimental and numerical studies of tight knots in proteins, with a particular emphasis on the estimates of the size of these knots. Next, I discuss the process of protein translocation through the mitochondrial pores and report the results of molecular dynamics simulations of knotted protein translocation, which show how the knot can indeed block the pore.

  13. 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

  14. 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.

  15. 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.

  16. 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.

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

    PubMed

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

    2008-05-15

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

  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. Enzyme screening with synthetic multifunctional pores: focus on biopolymers.

    PubMed

    Sordé, Nathalie; Das, Gopal; Matile, Stefan

    2003-10-14

    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.

  20. Single-Pore Membranes Gated by Microelectromagnetic Traps

    SciTech Connect

    Basore, Joseph; Baker, Lane; Lavrik, Nickolay V

    2010-01-01

    Gating of a single pore with a microelectromagnetic trap consisting of a single-turn gold wire microfabricated on a silicon membrane is described. A single micrometer-sized pore in the center of the microcoil conducts ionic current under the application of an applied transmembrane potential. When energized, the microelectromagnetic trap attracts a droplet of magnetic fluid, bringing the fluid to rest in the center of the trap, blocking the transport of ions through the pore, turning it 'off'. Reversal of the current flow through the trap moves the droplet to the periphery of the trap, turning the pore 'on'.

  1. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. 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.

  3. 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.

  4. Mechanical waves during tissue expansion

    NASA Astrophysics Data System (ADS)

    Serra-Picamal, Xavier; Conte, Vito; Vincent, Romaric; Anon, Ester; Tambe, Dhananjay T.; Bazellieres, Elsa; Butler, James P.; Fredberg, Jeffrey J.; Trepat, Xavier

    2012-08-01

    The processes by which an organism develops its shape and heals wounds involve expansion of a monolayer sheet of cells. The mechanism underpinning this epithelial expansion remains obscure, despite the fact that its failure is known to contribute to several diseases, including carcinomas, which account for about 90% of all human cancers. Here, using the micropatterned epithelial monolayer as a model system, we report the discovery of a mechanical wave that propagates slowly to span the monolayer, traverses intercellular junctions in a cooperative manner and builds up differentials of mechanical stress. Essential features of this wave generation and propagation are captured by a minimal model based on sequential fronts of cytoskeletal reinforcement and fluidization. These findings establish a mechanism of long-range cell guidance, symmetry breaking and pattern formation during monolayer expansion.

  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. The total and the differential mean pore anisotropy in porous solids and the ranking of pores according to Zipf's law.

    PubMed

    Margellou, Antigoni; Pomonis, Philippos

    2017-01-04

    In this work the property of total pore anisotropy in porous solids is introduced. Its calculation is based on a combination of the specific surface area Sp and the specific pore volume Vp estimated via typical nitrogen porosimetry data and tested in two kinds of porous materials: a group of spinels CoAl2O4 with differentiated random porosities and a second group of silicas SiO2 with ordered porosity modulated by the addition of LaFeO3 nanoparticles. Two basic complementary expressions of total pore anisotropy were estimated: (i) the specific total mean pore anisotropy bmean,total = (N·b) ≈ [Sp(3)]/[Vp(2)] corresponding to the total anisotropy value of all N hypothetical similar pores in one gram of a solid with mean size Dmean = 4Vp/Sp and anisotropy b = Ltotal/Dmean. The bmean,total takes a unique value for each particular porous material. (ii) The specific differential mean pore anisotropies bmean,diff = (Ni·bi) ≈ [Spi(3)]/[Vpi(2)] corresponding to the spectrum of partial anisotropy values bmean,diff = Li/Di of Ni pores with similar size Di = 4Vi/Si possessing differential pore volume Vpi and differential specific surface area Spi. The bmean diff takes different values at each particular partial pressure and exhibits a distribution as a function of pore radius bmean,diff = f(ri). It is shown that plots of log(bmean,diff) = f(log(ri)) lead to the ranking of pores according to the Zipf's law log(Ni) = A - B log(Vpi). This ranking is not obeyed by the pores exhibiting appreciable local pore anisotropy.

  7. 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.

  8. 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.

  9. Slow Desorption of Phenanthrene from Silica Particles: Influence of Pore Size, Pore Water, and Aging Time

    SciTech Connect

    Huesemann, Michael H.; Fortman, Timothy J.; Riley, Robert G.; Thompson, Christopher J.; Wang, Zheming; Truex, Michael J.; Peyton, Brent M.

    2006-01-16

    When micro-porous and meso-porous silica particles were exposed to aqueous phenanthrene solutions for various durations it was observed that sorbed-phase phenanthrene concentrations increased with aging time only for meso-porous but not micro-porous silicas. Desorption equilibrium was reached almost instantaneously for the micro-porous particles while both the rate and extent of desorption decreased with increasing aging time for the meso-porous silicas. These findings indicate that phenanthrene can be sequestered within the internal pore-space of meso-porous silicas while the internal surfaces of micro-porous silicas are not accessible to phenanthrene sorption, possibly due to the presence of physi- or chemi-sorbed water that may sterically hinder the diffusion of phenanthrene inside water-filled micro-pores. By contrast, the internal surfaces of these micro-porous silicas are accessible to phenanthrene when aging methods are employed which assure that pores are devoid of physi-sorbed water. Consequently, when phenanthrene was incorporated into these particles using either supercritical CO2 or via solvent soaking, the aqueous desorption kinetics were extremely slow indicating effective sequestration of phenanthrene inside micro-porous particles. Finally, a two-compartment conceptual model is used to interpret the experimental findings.

  10. Bearing-Mounting Concept Accommodates Thermal Expansion

    NASA Technical Reports Server (NTRS)

    Nespodzany, Robert; Davis, Toren S.

    1995-01-01

    Pins or splines allow radial expansion without slippage. Design concept for mounting rotary bearing accommodates differential thermal expansion between bearing and any structure(s) to which bearing connected. Prevents buildup of thermal stresses by allowing thermal expansion to occur freely but accommodating expansion in such way not to introduce looseness. Pin-in-slot configuration also maintains concentricity.

  11. 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 the...

  12. 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 the...

  13. 48 CFR 570.403 - Expansion requests.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

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

  14. 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 expansion...

  15. 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 expansion...

  16. 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, the...

  17. 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 expansion...

  18. 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, the...

  19. 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 expansion...

  20. 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, determine...

  1. 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, the...

  2. 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 the...

  3. 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 the...

  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 expansion...

  5. 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 the...

  6. 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.

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

    PubMed Central

    Hu, Yuan; Sinha, Sudipta Kumar

    2015-01-01

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

  8. Effects of supersaturation on pore shape in solid

    NASA Astrophysics Data System (ADS)

    Wei, P. S.; Hsiao, S. Y.

    2017-02-01

    The shape of a pore resulting from a bubble entrapped by a solidification front with different supersaturation ratios is predicted in this work. Supersaturation ratio, representing the ratio between solute concentration and saturation solute concentration, determines nucleation of a bubble and development of the pore shape in the early stage. Pore formation and its shape in solid influence contemporary issues of biology, engineering, foods, geophysics and climate change, etc. This work extends and combines previous models accounting for realistic mass and momentum transport, and physico-chemical equilibrium of solute gas across the bubble cap to self-consistently determine shape of the bubble cap beyond the solidification front and the pore shape in solid. The study also deal with that pore formation can be resulted from three different mechanisms, depending on the directions and magnitude of solute gas transport across the bubble cap. Case 1 is subject to solute transport from the pore across the cap into the surrounding liquid in the early stage. Cases 2a and 2b indicate opposite direction of solute transport. In contrast to Case 2b, the effect of solute transport on solute gas pressure in the pore in Case 2a is stronger than that of pore volume expansionin the last stage. The results find that an increase in supersaturation ratio decreases pore radius and time for bubble entrapment in Case 1. The bubble cannot be entrapped in Case 2. The predicted pore shape in solid agrees with experimental data. Understanding, prediction and control of the growth of the pore shape have therefore been obtained.

  9. 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.

  10. 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

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

    PubMed

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

    2016-01-25

    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.

  12. 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

  13. Mediation Analysis

    PubMed Central

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

    2010-01-01

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

  14. 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.

  15. Void and pore formation inside the hair cortex by a denaturation and super-contraction process occurring during hair setting with hot irons.

    PubMed

    Gamez-Garcia, Manuel

    2011-01-01

    An analysis of hair fibers from donors that frequently use hot irons for hair straightening showed the presence of multiple pores and voids (φ approximately 0.1-1.5 μm) that extend from the cuticle sheath to regions inside the hair cortex. Pore formation in the cortex was found to be confined at its periphery and could be reproduced in the laboratory with virgin hair fibers after the application of various hot-iron straightening cycles. The appearance of pores and voids in the cortex was found to be associated to the production of hot water vapor while the fiber is undergoing mechanical elongation or contraction. The number of pores was seen to rapidly increase with temperature in the range from 190 to 220°C and also with the number of straightening cycles. Larger hair voids (φ approximately 2-5 μm) were also detected in the cortex. The small pores found at the cortex periphery appear to occur by the simultaneous occurrence of rearrangement of hair proteins, fiber mechanical contraction/expansion, and the flow of super-heated steam. Hot irons create, thus, the conditions for the onset of pore formation as the high temperatures produce superheated steam and soften the native state of hair proteins by a process involving denaturation and changes in the crystalline regions.

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

    SciTech Connect

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

    2009-11-06

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

  17. A jumbo problem: mapping the structure and functions of the nuclear pore complex

    PubMed Central

    Fernandez-Martinez, Javier; Rout, Michael P

    2012-01-01

    Macromolecular assemblies can be intrinsically refractive to classical structural analysis, due to their size, complexity, plasticity and dynamic nature. One such assembly is the nuclear pore complex (NPC). The NPC is formed from ~450 copies of 30 different proteins, called nucleoporins, and is the sole mediator of exchange between the nucleus and the cytoplasm in eukaryotic cells. Despite significant progress, it has become increasingly clear that new approaches, integrating different sources of structural and functional data, will be needed to understand the functional biology of the NPC. Here, we discuss the latest approaches trying to address this challenge. PMID:22321828

  18. Reforming naphtha with boron-containing large-pore zeolites

    SciTech Connect

    Zones, S.I.; Holtermann, D.L.; Rainis, A.

    1992-05-19

    This patent describes a catalytic reforming process. It comprises contacting a hydrocarbonaceous feedstream under catalytic reforming conditions with a composition comprising larger-pore borosilicate zeolites having a pore size greater than 6 and less than 8 angstroms containing less that 1000 parts per million aluminum.

  19. Reversible Self-Actuated Thermo-Responsive Pore Membrane.

    PubMed

    Park, Younggeun; Gutierrez, Maria Paz; Lee, Luke P

    2016-12-19

    Smart membranes, which can selectively control the transfer of light, air, humidity and temperature, are important to achieve indoor climate regulation. Even though reversible self-actuation of smart