Self-Assembling Organic Nanopores as Synthetic Transmembrane Channels with Tunable Functions

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Wei, Xiaoxi

A long-standing goal in the area of supramolecular self-assembly involves the development of synthetic ion/water channels capable of mimicking the mass-transport characteristics of biological channels and pores. Few examples of artificial transmembrane channels with large lumen, high conductivity and selectivity are known. A review of pronounced biological transmembrane protein channels and some representative synthetic models have been provided in Chapter 1, followed by our discovery and initial investigation of shape-persistent oligoamide and phenylene ethynylene macrocycles as synthetic ion/water channels. In Chapter 2, the systematic structural modification of oligoamide macrocycles 1, the so-called first-generation of these shape-persistent macrocycles, has led to third-generation macrocycles 3. The third generation was found to exhibit unprecedented, strong intermolecular association in both the solid state and solution via multiple techniques including X-ray diffraction (XRD), SEM, and 1H NMR. Fluorescence spectroscopy paired with dynamic light scattering (DLS) revealed that macrocycles 3 can assemble into a singly dispersed nanotubular structure in solution. The resultant self-assembling pores consisting of 3 were examined by HPTS-LUVs assays and BLM studies (Chapter 3) and found to form cation-selective (PK+/PCl- = 69:1) transmembrane ion channels with large conductance (200 ˜ 2000 pS for alkali cations) and high stability with open times reaching to 103 seconds. Tuning the aggregation state of macrocycles by choosing an appropriate polar solvent mixture (i.e., 3:1, THF:DMF, v/v) and concentration led to the formation of ion channels with well-defined square top behavior. A parallel study using DLS to examine the size of aggregates was used in conjunction with channel activity assays (LUVs/BLM) to reveal the effects of the aggregation state on channel activity. Empirical evidence now clearly indicates that a preassembled state, perhaps that of a

The pore-forming bacterial effector, VopQ, halts autophagic turnover.

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Sreelatha, Anju; Orth, Kim; Starai, Vincent J

2013-12-01

Vibrio parahemolyticus Type III effector VopQ is both necessary and sufficient to induce autophagy within one hour of infection. We demonstrated that VopQ interacts with the Vo domain of the conserved vacuolar H(+)-ATPase. Membrane-associated VopQ subsequently forms pores in the membranes of acidic compartments, resulting in immediate release of protons without concomitant release of lumenal protein contents. These studies show how a bacterial pathogen can compromise host ion potentials using a gated pore-forming effector to equilibrate levels of small molecules found in endolysosomal compartments and disrupt cellular processes such as autophagy.

Radial symmetry in a chimeric glutamate receptor pore

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Wilding, Timothy J.; Lopez, Melany N.; Huettner, James E.

2014-02-01

Ionotropic glutamate receptors comprise two conformationally different A/C and B/D subunit pairs. Closed channels exhibit fourfold radial symmetry in the transmembrane domain (TMD) but transition to twofold dimer-of-dimers symmetry for extracellular ligand binding and N-terminal domains. Here, to evaluate symmetry in open pores we analysed interaction between the Q/R editing site near the pore loop apex and the transmembrane M3 helix of kainate receptor subunit GluK2. Chimeric subunits that combined the GluK2 TMD with extracellular segments from NMDA receptors, which are obligate heteromers, yielded channels made up of A/C and B/D subunit pairs with distinct substitutions along M3 and/or Q/R site editing status, in an otherwise identical homotetrameric TMD. Our results indicate that Q/R site interaction with M3 occurs within individual subunits and is essentially the same for both A/C and B/D subunit conformations, suggesting that fourfold pore symmetry persists in the open state.

Cationic PAMAM dendrimers as pore-blocking binary toxin inhibitors.

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Förstner, Philip; Bayer, Fabienne; Kalu, Nnanya; Felsen, Susanne; Förtsch, Christina; Aloufi, Abrar; Ng, David Y W; Weil, Tanja; Nestorovich, Ekaterina M; Barth, Holger

2014-07-14

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.

Piezo proteins are pore-forming subunits of mechanically activated channels.

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Coste, Bertrand; Xiao, Bailong; Santos, Jose S; Syeda, Ruhma; Grandl, Jörg; Spencer, Kathryn S; Kim, Sung Eun; Schmidt, Manuela; Mathur, Jayanti; Dubin, Adrienne E; Montal, Mauricio; Patapoutian, Ardem

2012-02-19

Mechanotransduction has an important role in physiology. Biological processes including sensing touch and sound waves require as-yet-unidentified cation channels that detect pressure. Mouse Piezo1 (MmPiezo1) and MmPiezo2 (also called Fam38a and Fam38b, respectively) induce mechanically activated cationic currents in cells; however, it is unknown whether Piezo proteins are pore-forming ion channels or modulate ion channels. Here we show that Drosophila melanogaster Piezo (DmPiezo, also called CG8486) also induces mechanically activated currents in cells, but through channels with remarkably distinct pore properties including sensitivity to the pore blocker ruthenium red and single channel conductances. MmPiezo1 assembles as a ∼1.2-million-dalton homo-oligomer, with no evidence of other proteins in this complex. Purified MmPiezo1 reconstituted into asymmetric lipid bilayers and liposomes forms ruthenium-red-sensitive ion channels. These data demonstrate that Piezo proteins are an evolutionarily conserved ion channel family involved in mechanotransduction.

Concentration of Immunoglobulins in Microfiltration Permeates of Skim Milk: Impact of Transmembrane Pressure and Temperature on the IgG Transmission Using Different Ceramic Membrane Types and Pore Sizes

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Hans-Jürgen Heidebrecht

2018-06-01

Full Text Available The use of bioactive bovine milk immunoglobulins (Ig has been found to be an alternative treatment for certain human gastrointestinal diseases. Some methodologies have been developed with bovine colostrum. These are considered in laboratory scale and are bound to high cost and limited availability of the raw material. The main challenge remains in obtaining high amounts of active IgG from an available source as mature cow milk by the means of industrial processes. Microfiltration (MF was chosen as a process variant, which enables a gentle and effective concentration of the Ig fractions (ca. 0.06% in raw milk while reducing casein and lactose at the same time. Different microfiltration membranes (ceramic standard and gradient, pore sizes (0.14–0.8 µm, transmembrane pressures (0.5–2.5 bar, and temperatures (10, 50 °C were investigated. The transmission of immunoglobulin G (IgG and casein during the filtration of raw skim milk (<0.1% fat was evaluated during batch filtration using a single channel pilot plant. The transmission levels of IgG (~160 kDa were measured to be at the same level as the reference major whey protein β-Lg (~18 kDa at all evaluated pore sizes and process parameters despite the large difference in molecular mass of both fractions. Ceramic gradient membranes with a pore sizes of 0.14 µm showed IgG-transmission rates between 45% to 65% while reducing the casein fraction below 1% in the permeates. Contrary to the expectations, a lower pore size of 0.14 µm yielded fluxes up to 35% higher than 0.2 µm MF membranes. It was found that low transmembrane pressures benefit the Ig transmission. Upscaling the presented results to a continuous MF membrane process offers new possibilities for the production of immunoglobulin enriched supplements with well-known processing equipment for large scale milk protein fractionation.

Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses.

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Smith, Kyle C; Weaver, James C

2011-08-19

Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. Copyright © 2011 Elsevier Inc. All rights reserved.

Niobium oxide nanocolumns formed via anodic alumina with modulated pore diameters

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Pligovka, A.; Zakhlebayeva, A.; Lazavenka, A.

2018-03-01

Niobium oxide nanocolumns with modulated diameters were formed for the first time. An Al/Nb bilayer specimen was prepared by successive sputter-deposition of 300 nm niobium layer and 1200 nm aluminum layer onto silicon wafer. Regular anodic alumina matrix with modulated pore diameters was formed by sequential anodization of initial specimen in tartaric acid at 180 V, and in oxalic acid at 37 V. Further potentiodynamic reanodization of the specimen up to 400 V causes the simultaneous growth of 440 nm continuous niobium oxide layer beneath the alumina film and two types of an array of oxide nanocolumns (thick – with 100 nm width and 630 nm high and thin – with 25 nm width and 170 nm high), which are the filling of the alumina pores. The morphology of the formed anodic niobium oxide nanocolumns with modulated diameters was determined by field emission scanning electron microscopy. The formed nanostructures can be used for perspective devices of nano- and optoelectronics such as photonic crystals.

Cordierite containing ceramic membranes from smectetic clay using natural organic wastes as pore-forming agents

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W. Misrar

2017-06-01

Full Text Available Cordierite ceramic membranes were manufactured from natural clay, oxides and organic wastes as pore forming agents. Mixtures aforementioned materials with the pore-forming agents (up to 10 wt.% were investigated in the range 1000–1200 °C using thermal analysis, X-ray diffraction, scanning electron microscopy, mercury porosimetry and filtration tests. Physical properties (density, water absorption and bending strength were correlated to the processing factors (pore-forming agent addition, firing temperature and soaking time. The results showed that cordierite together with spinel, diopside and clinoenstatite neoformed. SEM analysis revealed heterogeneous aspects. The results of the response surface methodology showed that the variations of physical properties versus processing parameters were well described by the used polynomial model. The addition of pore forming agent and temperature were the most influential factors. Filtration tests were performed on the best performing sample. The results allowed to testify that these membranes could be used in waste water treatment.

Rupturing Giant Plasma Membrane Vesicles to Form Micron-sized Supported Cell Plasma Membranes with Native Transmembrane Proteins.

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Chiang, Po-Chieh; Tanady, Kevin; Huang, Ling-Ting; Chao, Ling

2017-11-09

Being able to directly obtain micron-sized cell blebs, giant plasma membrane vesicles (GPMVs), with native membrane proteins and deposit them on a planar support to form supported plasma membranes could allow the membrane proteins to be studied by various surface analytical tools in native-like bilayer environments. However, GPMVs do not easily rupture on conventional supports because of their high protein and cholesterol contents. Here, we demonstrate the possibility of using compression generated by the air-water interface to efficiently rupture GPMVs to form micron-sized supported membranes with native plasma membrane proteins. We demonstrated that not only lipid but also a native transmembrane protein in HeLa cells, Aquaporin 3 (AQP3), is mobile in the supported membrane platform. This convenient method for generating micron-sized supported membrane patches with mobile native transmembrane proteins could not only facilitate the study of membrane proteins by surface analytical tools, but could also enable us to use native membrane proteins for bio-sensing applications.

Development of eco-friendly porous fired clay bricks using pore-forming agents: a review.

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Bories, Cecile; Borredon, Marie-Elisabeth; Vedrenne, Emeline; Vilarem, Gerard

2014-10-01

Today, clay bricks are facing technological challenges and are uncompetitive compared to materials such as concrete. Their performance must be improved if they are to stand up to the competition. Increasing environmental concerns over the accumulation of unmanaged wastes from agricultural or industrial productions have made these good candidates for incorporation into building materials to improve their performance. This process leads to the formation of pores in the bricks, producing lightweight and sustainable building materials. This paper reviews the different pore-forming agents from renewable or mineral resources as described in the literature. It also presents the impact of pore-forming agents on the physical, mechanical and thermal properties of clay bricks. Copyright © 2014 Elsevier Ltd. All rights reserved.

Specific Binding of Adamantane Drugs and Direction of their Polar Amines in the Pore of the Influenza M2 Transmembrane Domain in Lipid Bilayers and Dodecylphosphocholine Micelles Determined by NMR Spectroscopy

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Cady, Sarah D.; Wang, Jun; Wu, Yibing; DeGrado, William F.; Hong, Mei

2011-01-01

The transmembrane domain of the influenza M2 protein (M2TM) forms a tetrameric proton channel important for the virus lifecycle. The proton-channel activity is inhibited by amine-containing adamantyl drugs amantadine and rimantadine, which have been shown to bind specifically to the pore of M2TM near Ser31. However, whether the polar amine points to the N- or C-terminus of the channel has not yet been determined. Elucidating the polar group direction will shed light on the mechanism by which drug binding inhibits this proton channel and will facilitate rational design of new inhibitors. In this study, we determine the polar amine direction using M2TM reconstituted in lipid bilayers as well as DPC micelles. 13C-2H rotational-echo double-resonance NMR experiments of 13C-labeled M2TM and methyl-deuterated rimantadine in lipid bilayers showed that the polar amine pointed to the C-terminus of the channel, with the methyl group close to Gly34. Solution NMR experiments of M2TM in dodecylphosphocholine (DPC) micelles indicate that drug binding causes significant chemical shift perturbations of the protein that are very similar to those seen for M2TM and M2(18–60) bound to lipid bilayers. Specific 2H-labeling of the drugs permitted the assignment of drug-protein cross peaks, which indicate that amantadine and rimantadine bind to the pore in the same fashion as for bilayer-bound M2TM. These results strongly suggest that adamantyl inhibition of M2TM is achieved not only by direct physical occlusion of the pore but also by perturbing the equilibrium constant of the proton-sensing residue His37. The reproduction of the pharmacologically relevant specific pore-binding site in DPC micelles, which was not observed with a different detergent, DHPC, underscores the significant influence of the detergent environment on the functional structure of membrane proteins. PMID:21381693

Conserved allosteric hot spots in the transmembrane domains of cystic fibrosis transmembrane conductance regulator (CFTR) channels and multidrug resistance protein (MRP) pumps.

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Wei, Shipeng; Roessler, Bryan C; Chauvet, Sylvain; Guo, Jingyu; Hartman, John L; Kirk, Kevin L

2014-07-18

ATP-binding cassette (ABC) transporters are an ancient family of transmembrane proteins that utilize ATPase activity to move substrates across cell membranes. The ABCC subfamily of the ABC transporters includes active drug exporters (the multidrug resistance proteins (MRPs)) and a unique ATP-gated ion channel (cystic fibrosis transmembrane conductance regulator (CFTR)). The CFTR channel shares gating principles with conventional ligand-gated ion channels, but the allosteric network that couples ATP binding at its nucleotide binding domains (NBDs) with conformational changes in its transmembrane helices (TMs) is poorly defined. It is also unclear whether the mechanisms that govern CFTR gating are conserved with the thermodynamically distinct MRPs. Here we report a new class of gain of function (GOF) mutation of a conserved proline at the base of the pore-lining TM6. Multiple substitutions of this proline promoted ATP-free CFTR activity and activation by the weak agonist, 5'-adenylyl-β,γ-imidodiphosphate (AMP-PNP). TM6 proline mutations exhibited additive GOF effects when combined with a previously reported GOF mutation located in an outer collar of TMs that surrounds the pore-lining TMs. Each TM substitution allosterically rescued the ATP sensitivity of CFTR gating when introduced into an NBD mutant with defective ATP binding. Both classes of GOF mutations also rescued defective drug export by a yeast MRP (Yor1p) with ATP binding defects in its NBDs. We conclude that the conserved TM6 proline helps set the energy barrier to both CFTR channel opening and MRP-mediated drug efflux and that CFTR channels and MRP pumps utilize similar allosteric mechanisms for coupling conformational changes in their translocation pathways to ATP binding at their NBDs. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Optimization of transdermal delivery using magainin pore-forming peptide

OpenAIRE

Kim, Yeu-Chun; Ludovice, Peter J.; Prausnitz, Mark R.

2008-01-01

The skin's outer layer of stratum corneum, which is a thin tissue containing multilamellar lipid bilayers, is the main barrier to drug delivery to the skin. To increase skin permeability, our previous work has shown large enhancement of transdermal permeation using a pore-forming peptide, magainin, which was formulated with N-lauroyl sarcosine (NLS) in 50% ethanol-in-PBS. Mechanistic analysis suggested that magainin and NLS can increase skin permeability by disrupting stratum corneum lipid st...

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

International Nuclear Information System (INIS)

Onischenko, Evgeny A.; Crafoord, Ellinor; Hallberg, Einar

2007-01-01

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

[Application of Brownian dynamics to the description of transmembrane ion flow as exemplified by the chloride channel of glycine receptor].

Science.gov (United States)

Boronovskiĭ, S E; Nartsissov, Ia R

2009-01-01

Using the Brownian dynamics of the movement of hydrated ion in a viscous water solution, a mathematical model has been built, which describes the transport of charged particles through a single protein pore in a lipid membrane. The dependences of transmembrane ion currents on ion concentrations in solution have been obtained. It was shown that, if the geometry of a membrane pore is identical to that of the inner part of the glycine receptor channel and there is no ion selectivity, then the values of both chloride and sodium currents are not greater than 0.5 pA at the physiological concentrations of these ions. If local charge heterogeneity caused by charged amino acid residues of transmembrane protein segments is included into the model calculations, the chloride current increases to about 3.7 pA, which exceeds more than seven times the value for sodium ions under the conditions of the complex channel geometry in the range of physiological concentrations of ions in the solution. The model takes changes in the density of charge distribution both inside the channel and near the protein surface into account. The alteration of pore geometry can be also considered as a parameter at the researcher's option. Thus, the model appears as an effective tool for the description of transmembrane currents for other types of membrane channels.

SV40 late protein VP4 forms toroidal pores to disrupt membranes for viral release.

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Raghava, Smita; Giorda, Kristina M; Romano, Fabian B; Heuck, Alejandro P; Hebert, Daniel N

2013-06-04

Nonenveloped viruses are generally released from the cell by the timely lysis of host cell membranes. SV40 has been used as a model virus for the study of the lytic nonenveloped virus life cycle. The expression of SV40 VP4 at later times during infection is concomitant with cell lysis. To investigate the role of VP4 in viral release and its mechanism of action, VP4 was expressed and purified from bacteria as a fusion protein for use in membrane disruption assays. Purified VP4 perforated membranes as demonstrated by the release of fluorescent markers encapsulated within large unilamellar vesicles or liposomes. Dynamic light scattering results revealed that VP4 treatment did not cause membrane lysis or change the size of the liposomes. Liposomes encapsulated with 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-3-indacene-labeled streptavidin were used to show that VP4 formed stable pores in membranes. These VP4 pores had an inner diameter of 1-5 nm. Asymmetrical liposomes containing pyrene-labeled lipids in the outer monolayer were employed to monitor transbilayer lipid diffusion. Consistent with VP4 forming toroidal pore structures in membranes, VP4 induced transbilayer lipid diffusion or lipid flip-flop. Altogether, these studies support a central role for VP4 acting as a viroporin in the disruption of cellular membranes to trigger SV40 viral release by forming toroidal pores that unite the outer and inner leaflets of membrane bilayers.

Dependence of cell adhesion on extracellular matrix materials formed on pore bridge boundaries by nanopore opening and closing geometry.

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Kim, Sueon; Han, Dong Yeol; Chen, Zhenzhong; Lee, Won Gu

2018-04-30

In this study, we report experimental results for characterization of the growth and formation of pore bridge materials that modified the adhesion structures of cells cultured on nanomembranes with opening and closing geometry. To perform the proof-of-concept experiments, we fabricated two types of anodized alumina oxide substrates with single-sided opening (i.e., one side open, but closed at the other side) and double-sided opening (i.e., both sides open). In our experiment, we compared the densities of pores formed and of bridge materials which differently act as connective proteins depending on the size of pores. The results show that the pore opening geometry can be used to promote the net contact force between pores, resulting in the growth and formation of pore bridge materials before and after cell culture. The results also imply that the bridge materials can be used to attract the structural protrusion of filopodia that can promote the adhesion of cell-to-cell and cell-to-pore bridge. It is observed that the shape and size of cellular structures of filopodia depend on the presence of pore bridge materials. Overall, this observation brought us a significant clue that cells cultured on nanopore substrates would change the adhesion property depending on not only the formation of nanopores formed on the surface of topological substrates, but also that of pore bridge materials by its morphological growth.

Activation gating kinetics of GIRK channels are mediated by cytoplasmic residues adjacent to transmembrane domains.

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Sadja, Rona; Reuveny, Eitan

2009-01-01

G-protein-coupled inwardly rectifying potassium channels (GIRK/Kir3.x) are involved in neurotransmission-mediated reduction of excitability. The gating mechanism following G protein activation of these channels likely proceeds from movement of inner transmembrane helices to allow K(+) ions movement through the pore of the channel. There is limited understanding of how the binding of G-protein betagamma subunits to cytoplasmic regions of the channel transduces the signal to the transmembrane regions. In this study, we examined the molecular basis that governs the activation kinetics of these channels, using a chimeric approach. We identified two regions as being important in determining the kinetics of activation. One region is the bottom of the outer transmembrane helix (TM1) and the cytoplasmic domain immediately adjacent (the slide helix); and the second region is the bottom of the inner transmembrane helix (TM2) and the cytoplasmic domain immediately adjacent. Interestingly, both of these regions are sufficient in mediating the kinetics of fast activation gating. This result suggests that there is a cooperative movement of either one of these domains to allow fast and efficient activation gating of GIRK channels.

The stability of the three transmembrane and the four transmembrane human vitamin K epoxide reductase models

Science.gov (United States)

Wu, Sangwook

2016-04-01

The three transmembrane and the four transmembrane helix models are suggested for human vitamin K epoxide reductase (VKOR). In this study, we investigate the stability of the human three transmembrane/four transmembrane VKOR models by employing a coarse-grained normal mode analysis and molecular dynamics simulation. Based on the analysis of the mobility of each transmembrane domain, we suggest that the three transmembrane human VKOR model is more stable than the four transmembrane human VKOR model.

Earthworm-Derived Pore-Forming Toxin Lysenin and Screening of Its Inhibitors

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Neelanun Sukumwang

2013-08-01

Full Text Available Lysenin is a pore-forming toxin from the coelomic fluid of earthworm Eisenia foetida. This protein specifically binds to sphingomyelin and induces erythrocyte lysis. Lysenin consists of 297 amino acids with a molecular weight of 41 kDa. We screened for cellular signal transduction inhibitors of low molecular weight from microorganisms and plants. The purpose of the screening was to study the mechanism of diseases using the obtained inhibitors and to develop new chemotherapeutic agents acting in the new mechanism. Therefore, our aim was to screen for inhibitors of Lysenin-induced hemolysis from plant extracts and microbial culture filtrates. As a result, we isolated all-E-lutein from an extract of Dalbergia latifolia leaves. All-E-lutein is likely to inhibit the process of Lysenin-membrane binding and/or oligomer formation rather than pore formation. Additionally, we isolated tyrosylproline anhydride from the culture filtrate of Streptomyces as an inhibitor of Lysenin-induced hemolysis.

Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109.

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Abdali, Narges; Younas, Farhan; Mafakheri, Samaneh; Pothula, Karunakar R; Kleinekathöfer, Ulrich; Tauch, Andreas; Benz, Roland

2018-05-09

Corynebacterium urealyticum, a pathogenic, multidrug resistant member of the mycolata, is known as causative agent of urinary tract infections although it is a bacterium of the skin flora. This pathogenic bacterium shares with the mycolata the property of having an unusual cell envelope composition and architecture, typical for the genus Corynebacterium. The cell wall of members of the mycolata contains channel-forming proteins for the uptake of solutes. In this study, we provide novel information on the identification and characterization of a pore-forming protein in the cell wall of C. urealyticum DSM 7109. Detergent extracts of whole C. urealyticum cultures formed in lipid bilayer membranes slightly cation-selective pores with a single-channel conductance of 1.75 nS in 1 M KCl. Experiments with different salts and non-electrolytes suggested that the cell wall pore of C. urealyticum is wide and water-filled and has a diameter of about 1.8 nm. Molecular modelling and dynamics has been performed to obtain a model of the pore. For the search of the gene coding for the cell wall pore of C. urealyticum we looked in the known genome of C. urealyticum for a similar chromosomal localization of the porin gene to known porH and porA genes of other Corynebacterium strains. Three genes are located between the genes coding for GroEL2 and polyphosphate kinase (PKK2). Two of the genes (cur_1714 and cur_1715) were expressed in different constructs in C. glutamicum ΔporAΔporH and in porin-deficient BL21 DE3 Omp8 E. coli strains. The results suggested that the gene cur_1714 codes alone for the cell wall channel. The cell wall porin of C. urealyticum termed PorACur was purified to homogeneity using different biochemical methods and had an apparent molecular mass of about 4 kDa on tricine-containing sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Biophysical characterization of the purified protein (PorACur) suggested indeed that cur_1714 is the gene

Nanoporous microbead supported bilayers: stability, physical characterization, and incorporation of functional transmembrane proteins.

Energy Technology Data Exchange (ETDEWEB)

Davis, Ryan W. (University of New Mexico, Albuquerque, NM); Brozik, James A. (University of New Mexico, Albuquerque, NM); Brozik, Susan Marie; Cox, Jason M. (University of New Mexico, Albuquerque, NM); Lopez, Gabriel P. (University of New Mexico, Albuquerque, NM); Barrick, Todd A. (University of New Mexico, Albuquerque, NM); Flores, Adrean (University of New Mexico, Albuquerque, NM)

2007-03-01

The introduction of functional transmembrane proteins into supported bilayer-based biomimetic systems presents a significant challenge for biophysics. Among the various methods for producing supported bilayers, liposomal fusion offers a versatile method for the introduction of membrane proteins into supported bilayers on a variety of substrates. In this study, the properties of protein containing unilamellar phosphocholine lipid bilayers on nanoporous silica microspheres are investigated. The effects of the silica substrate, pore structure, and the substrate curvature on the stability of the membrane and the functionality of the membrane protein are determined. Supported bilayers on porous silica microspheres show a significant increase in surface area on surfaces with structures in excess of 10 nm as well as an overall decrease in stability resulting from increasing pore size and curvature. Comparison of the liposomal and detergent-mediated introduction of purified bacteriorhodopsin (bR) and the human type 3 serotonin receptor (5HT3R) are investigated focusing on the resulting protein function, diffusion, orientation, and incorporation efficiency. In both cases, functional proteins are observed; however, the reconstitution efficiency and orientation selectivity are significantly enhanced through detergent-mediated protein reconstitution. The results of these experiments provide a basis for bulk ionic and fluorescent dye-based compartmentalization assays as well as single-molecule optical and single-channel electrochemical interrogation of transmembrane proteins in a biomimetic platform.

Effects of pore forming agents on chitosan-graft-poly(N-vinylpyrrolidone) hydrogel properties for use as a matrix for floating drug delivery

Science.gov (United States)

Budianto, E.; Al-Shidqi, M. F.; Cahyana, A. H.

2017-07-01

Eradicating H. pylori-based infection by using conventional oral dosage form of amoxicillin trihydrate finds difficulties to overcome rapid gastric retention time. Encapsulating amoxicillin trihydrate in floating drug delivery system may solve the problem. In this research, the floating drug delivery system of amoxicillin trihydrate encapsulated in floating chitosan-graft-poly(N-vinyl pyrrolidone) hydrogels containing CaCO3 and NaHCO3 as pore forming agents has been successfully prepared. Pore forming agents used was varied with the ratio of 10 to 25% pore forming agents to total mass of the used materials. The hydrogel were characterizedusing FTIR spectrophotometer and stereo microscope. As pore forming agents compositions increased, the porosity (%) and floating properties increased but followed by decrease in drug entrapment efficiency. Most of the floating hydrogels possessed floating ability longer than 180 min and the highest porosity was found in hydrogel containing 25% NaHCO3. Hydrogel containing CaCO3 showed sustained drug release profile than hydrogel containing NaHCO3. However, the optimum formulation was achieved at composition of 10% NaHCO3 with 57% of drug entrapped within the hydrogel and 43% drug released. The results of these studies show that NaHCO3 is an effective pore forming agents for chitosan-graft-poly(N-vinyl pyrrolidone) hydrogel preparation as compare to CaCO3.

Lah is a transmembrane protein and requires Spa10 for stable positioning of Woronin bodies at the septal pore of Aspergillus fumigatus.

Science.gov (United States)

Leonhardt, Yannik; Kakoschke, Sara Carina; Wagener, Johannes; Ebel, Frank

2017-03-10

Woronin bodies are specialized, fungal-specific organelles that enable an immediate closure of septal pores after injury to protect hyphae from excessive cytoplasmic bleeding. In most Ascomycetes, Woronin bodies are tethered at the septal pore by so-called Lah proteins. Using the pathogenic mold Aspergillus fumigatus as a model organism, we show that the C-terminal 288 amino acids of Lah (LahC 288 ) bind to the rim of the septal pore. LahC 288 essentially consists of a membrane spanning region and a putative extracellular domain, which are both required for the targeting to the septum. In an A. fumigatus rho4 deletion mutant that has a severe defect in septum formation, LahC 288 is recruited to spot-like structures in or at the lateral membrane. This suggests that LahC is recruited before Rho4 starts to govern the septation process. Accordingly, we found that in wild type hyphae Lah is bound before a cross-wall emerges and thus enables a tethering of Woronin bodies at the site of the newly formed septum. Finally, we identified Spa10, a member of a recently described family of septal pore-associated proteins, as a first protein that directly or indirectly interacts with LahC to allow a stable positioning of Woronin bodies at the mature septum.

A localized interaction surface for voltage-sensing domains on the pore domain of a K+ channel.

Science.gov (United States)

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-02-01

Voltage-gated K+ channels contain a central pore domain and four surrounding voltage-sensing domains. How and where changes in the structure of the voltage-sensing domains couple to the pore domain so as to gate ion conduction is not understood. The crystal structure of KcsA, a bacterial K+ channel homologous to the pore domain of voltage-gated K+ channels, provides a starting point for addressing this question. Guided by this structure, we used tryptophan-scanning mutagenesis on the transmembrane shell of the pore domain in the Shaker voltage-gated K+ channel to localize potential protein-protein and protein-lipid interfaces. Some mutants cause only minor changes in gating and when mapped onto the KcsA structure cluster away from the interface between pore domain subunits. In contrast, mutants producing large changes in gating tend to cluster near this interface. These results imply that voltage-sensing domains interact with localized regions near the interface between adjacent pore domain subunits.

Chemotherapy drugs form ion pores in membranes due to physical interactions with lipids.

Science.gov (United States)

Ashrafuzzaman, Mohammad; Tseng, Chih-Yuan; Duszyk, Marek; Tuszynski, Jack A

2012-12-01

We demonstrate the effects on membrane of the tubulin-binding chemotherapy drugs: thiocolchicoside and taxol. Electrophysiology recordings across lipid membranes in aqueous phases containing drugs were used to investigate the drug effects on membrane conductance. Molecular dynamics simulation of the chemotherapy drug-lipid complexes was used to elucidate the mechanism at an atomistic level. Both drugs are observed to induce stable ion-flowing pores across membranes. Discrete pore current-time plots exhibit triangular conductance events in contrast to rectangular ones found for ion channels. Molecular dynamics simulations indicate that drugs and lipids experience electrostatic and van der Waals interactions for short periods of time when found within each other's proximity. The energies from these two interactions are found to be similar to the energies derived theoretically using the screened Coulomb and the van der Waals interactions between peptides and lipids due to mainly their charge properties while forming peptide-induced ion channels in lipid bilayers. Experimental and in silico studies together suggest that the chemotherapy drugs induce ion pores inside lipid membranes due to drug-lipid physical interactions. The findings reveal cytotoxic effects of drugs on the cell membrane, which may aid in novel drug development for treatment of cancer and other diseases. © 2012 John Wiley & Sons A/S.

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

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Jolene Read

2015-06-01

Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

Biological amine transport in chromaffin ghosts. Coupling to the transmembrane proton and potential gradients.

Science.gov (United States)

Johnson, R G; Pfister, D; Carty, S E; Scarpa, A

1979-11-10

The effect of the transmembrane proton gradient (delta pH) and potential gradient (delta psi) upon the rate and extent of amine accumulation was investigated in chromaffin ghosts. The chromaffin ghosts were formed by hypo-osmotic lysis of isolated bovine chromaffin granules and extensive dialysis in order to remove intragranular binding components and dissipate the endogenous electrochemical gradients. Upon ATP addition to suspensions of chromaffin ghosts, a transmembrane proton gradient alone, a transmembrane gradient alone, or both, could be established, depending upon the compositions of the media in which the ghosts were formed and resuspended. When chloride was present in the medium, addition of ATP resulted in the generation of a transmembrane proton gradient, acidic inside of 1 pH unit (measured by [14C]methylamine distribution), and no transmembrane potential (measured by [14C]-thiocyanate distribution). When ATP was added to chromaffin ghosts suspended in a medium in which chloride was substituted by isethionate, a transmembrane potential, inside positive, of 45 mV and no transmembrane proton gradient, was measured. In each medium, the addition of agents known to affect proton or potential gradients, respectively, exerted a predictable mechanism of action. Accumulation of [14C]epinephrine or [14C]5-hydroxytryptamine was over 1 order of magnitude greater in the presence of the transmembrane proton gradient or the transmembrane potential than in the absence of any gradient and, moreover, was related to the magnitude of the proton or potential gradient in a dose-dependent manner. When ghosts were added to a medium containing chloride and isethionate, both a delta pH and delta psi could be generated upon addition of ATP. In this preparation, the maximal rate of amine accumulation was observed. The results indicate that amine accumulation into chromaffin ghosts can occur in the presence of either a transmembrane proton gradient, or a transmembrane potential

Transmembrane Signaling Proteoglycans

DEFF Research Database (Denmark)

Couchman, John R

2010-01-01

Virtually all metazoan cells contain at least one and usually several types of transmembrane proteoglycans. These are varied in protein structure and type of polysaccharide, but the total number of vertebrate genes encoding transmembrane proteoglycan core proteins is less than 10. Some core prote...... proteins, including those of the syndecans, always possess covalently coupled glycosaminoglycans; others do not. Syndecan has a long evolutionary history, as it is present in invertebrates, but many other transmembrane proteoglycans are vertebrate inventions. The variety of proteins...... proteins has been obtained in mouse knockout experiments. Here some of the latest developments in the field are examined in hopes of stimulating further interest in this fascinating group of molecules. Expected final online publication date for the Annual Review of Cell and Developmental Biology Volume 26...

Atomic force microscopy of bacteria reveals the mechanobiology of pore forming peptide action.

Science.gov (United States)

Mularski, Anna; Wilksch, Jonathan J; Hanssen, Eric; Strugnell, Richard A; Separovic, Frances

2016-06-01

Time-resolved AFM images revealed that the antimicrobial peptide (AMP) caerin 1.1 caused localised defects in the cell walls of lysed Klebsiella pneumoniae cells, corroborating a pore-forming mechanism of action. The defects continued to grow during the AFM experiment, in corroboration with large holes that were visualised by scanning electron microscopy. Defects in cytoplasmic membranes were visualised by cryo-EM using the same peptide concentration as in the AFM experiments. At three times the minimum inhibitory concentration of caerin, 'pores' were apparent in the outer membrane. The capsule of K. pneumoniae AJ218 was unchanged by exposure to caerin, indicating that the ionic interaction of the positively charged peptide with the negatively charged capsular polysaccharide is not a critical component of AMP interaction with K. pneumoniae AJ218 cells. Further, the presence of a capsule confers no advantage to wild-type over capsule-deficient cells when exposed to the AMP caerin. Copyright © 2016 Elsevier B.V. All rights reserved.

Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish.

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Rumfelt, Lynn L; Diaz, Marilyn; Lohr, Rebecca L; Mochon, Evonne; Flajnik, Martin F

2004-07-15

In most jawed vertebrates including cartilaginous fish, membrane-bound IgM is expressed as a five Ig superfamily (Igsf)-domain H chain attached to a transmembrane (Tm) region. Heretofore, bony fish IgM was the one exception with IgM mRNA spliced to produce a four-domain Tm H chain. We now demonstrate that the Tm and secretory (Sec) mRNAs of the novel cartilaginous fish Ig isotypes, IgW and IgNAR, are present in multiple forms, most likely generated by alternative splicing. In the nurse shark, Ginglymostoma cirratum, and horn shark, Heterodontus francisci, alternative splicing of Tm exons to the second or the fourth constant (C(H)) exons produces two distinct IgW Tm cDNAs. Although the seven-domain IgW Sec cDNA form contains a canonical secretory tail shared with IgM, IgNAR, and IgA, we report a three-domain cDNA form of shark IgW (IgW(short)) having an unusual Sec tail, which is orthologous to skate IgX(short) cDNA. The IgW and IgW(short) Sec transcripts are restricted in their tissue distribution and expression levels vary among individual sharks, with all forms expressed early in ontogeny. IgNAR mRNA is alternatively spliced to produce a truncated four-domain Tm cDNA and a second Tm cDNA is expressed identical in Igsf domains as the Sec form. PBL is enriched in the Tm cDNA of these Igs. These molecular data suggest that cartilaginous fish have augmented their humoral immune repertoire by diversifying the sizes of their Ig isotypes. Furthermore, these Tm cDNAs are prototypical and the truncated variants may translate as more stable protein at the cell surface.

Measuring kinetic drivers of pneumolysin pore structure.

Science.gov (United States)

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

2016-05-01

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

Pore formation by actinoporins, cytolysins from sea anemones.

Science.gov (United States)

Rojko, Nejc; Dalla Serra, Mauro; Maček, Peter; Anderluh, Gregor

2016-03-01

Actinoporins (APs) from sea anemones are ~20 kDa pore forming toxins with a β-sandwich structure flanked by two α-helices. The molecular mechanism of APs pore formation is composed of several well-defined steps. APs bind to membrane by interfacial binding site composed of several aromatic amino acid residues that allow binding to phosphatidylcholine and specific recognition of sphingomyelin. Subsequently, the N-terminal α-helix from the β-sandwich has to be inserted into the lipid/water interphase in order to form a functional pore. Functional studies and single molecule imaging revealed that only several monomers, 3-4, oligomerise to form a functional pore. In this model the α-helices and surrounding lipid molecules build toroidal pore. In agreement, AP pores are transient and electrically heterogeneous. On the contrary, crystallized oligomers of actinoporin fragaceatoxin C were found to be composed of eight monomers with no lipids present between the adjacent α-helices. This article is part of a Special Issue entitled: Pore-Forming Toxins edited by Maur Dalla Serra and Franco Gambale. Copyright © 2015 Elsevier B.V. All rights reserved.

Kv7.1 ion channels require a lipid to couple voltage sensing to pore opening.

Science.gov (United States)

Zaydman, Mark A; Silva, Jonathan R; Delaloye, Kelli; Li, Yang; Liang, Hongwu; Larsson, H Peter; Shi, Jingyi; Cui, Jianmin

2013-08-06

Voltage-gated ion channels generate dynamic ionic currents that are vital to the physiological functions of many tissues. These proteins contain separate voltage-sensing domains, which detect changes in transmembrane voltage, and pore domains, which conduct ions. Coupling of voltage sensing and pore opening is critical to the channel function and has been modeled as a protein-protein interaction between the two domains. Here, we show that coupling in Kv7.1 channels requires the lipid phosphatidylinositol 4,5-bisphosphate (PIP2). We found that voltage-sensing domain activation failed to open the pore in the absence of PIP2. This result is due to loss of coupling because PIP2 was also required for pore opening to affect voltage-sensing domain activation. We identified a critical site for PIP2-dependent coupling at the interface between the voltage-sensing domain and the pore domain. This site is actually a conserved lipid-binding site among different K(+) channels, suggesting that lipids play an important role in coupling in many ion channels.

Membrane shape modulates transmembrane protein distribution.

Science.gov (United States)

Aimon, Sophie; Callan-Jones, Andrew; Berthaud, Alice; Pinot, Mathieu; Toombes, Gilman E S; Bassereau, Patricia

2014-01-27

Although membrane shape varies greatly throughout the cell, the contribution of membrane curvature to transmembrane protein targeting is unknown because of the numerous sorting mechanisms that take place concurrently in cells. To isolate the effect of membrane shape, we used cell-sized giant unilamellar vesicles (GUVs) containing either the potassium channel KvAP or the water channel AQP0 to form membrane nanotubes with controlled radii. Whereas the AQP0 concentrations in flat and curved membranes were indistinguishable, KvAP was enriched in the tubes, with greater enrichment in more highly curved membranes. Fluorescence recovery after photobleaching measurements showed that both proteins could freely diffuse through the neck between the tube and GUV, and the effect of each protein on membrane shape and stiffness was characterized using a thermodynamic sorting model. This study establishes the importance of membrane shape for targeting transmembrane proteins and provides a method for determining the effective shape and flexibility of membrane proteins. Copyright © 2014 Elsevier Inc. All rights reserved.

A CLOSED-FORM EXPRESSION APPROXIMATING THE MIE SOLUTION FOR THE REAL-IN-LINE TRANSMISSION OF CERAMICS WITH SPHERICAL INCLUSIONS OR PORES

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Pabst W.

2013-06-01

Full Text Available A new closed-form expression is presented for estimating the real-in-line transmission of ceramics consisting of non-absorbing phases in dependence of the inclusion or pore size. The classic approximations to the exact Mie solution of the scattering problem for spheres are recalled (Rayleigh, Fraunhofer, Rayleigh-Gans-Debye/RGD, van de Hulst, and it is recalled that the large-size variant of the RGD approximation is the basis of the Apetz-van-Bruggen approach. All approximations and our closed-form expression are compared mutually and vis-a-vis the exact Mie solution. A parametric study is performed for monochromatic light in the visible range (600 nm for two model systems corresponding to composites of yttrium aluminum garnet (YAG, refractive index 1.832 with spherical alumina inclusions (refractive index 1.767, and to porous YAG ceramics with spherical pores (refractive index 1. It is shown that for the YAG-alumina composites to achieve maximum transmission with inclusion volume fractions of 1 % (and slab thickness 1 mm, inclusion sizes of up to 100 nm can be tolerated, while pore sizes of 100 nm will be completely detrimental for porosities as low as 0.1 %. While the van-de-Hulst approximation is excellent for small phase contrast and low concentration of inclusions, it fails for principal reasons for small inclusion or pore sizes. Our closed-form expression, while less precise in the aforementioned special case, is always the safer choice and performs better in most cases of practical interest, including high phase contrasts and high concentrations of inclusions or pores.

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

Science.gov (United States)

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

2013-01-01

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

Preparation of mesoporous titanium dioxide anode by a film- and pore-forming agent for the dye-sensitized solar cell

Energy Technology Data Exchange (ETDEWEB)

Hou, Wenjing; Xiao, Yaoming, E-mail: ymxiao@sxu.edu.cn; Han, Gaoyi, E-mail: han_gaoyis@sxu.edu.cn; Zhou, Haihan; Chang, Yunzhen; Zhang, Ying

2016-04-15

Highlights: • PVP is used as a film- and pore-forming agent to prepare the mesoporous TiO{sub 2} anode. • The TiO{sub 2} anode supplies high surface area for the dye adsorption. • The DSSC efficiency is strongly dependent on the pore properties of the TiO{sub 2} anode. • The DSSC efficiency with the TiO{sub 2} anode prepared by 20 wt% PVP reaches 8.39%. - Abstract: A novel mean of generating mesoporous titanium dioxide (TiO{sub 2}) anodes by employing polyvinylpyrrolidone (PVP) as the film- and pore-forming agent are proposed for dye-sensitized solar cells (DSSCs). The influences on the morphology and photovoltaic performances of the TiO{sub 2} anodes are investigated by adjusting the PVP content in synthesizing the mesoporous TiO{sub 2} anodes. The photovoltaic conversion efficiency of the DSSC is found to be strongly dependent on the pore properties of the TiO{sub 2} anode. After the sintering process, the removal of the PVP leaves porously interconnected channel structures inside the TiO{sub 2} anode, supplying enhanced specific surface area for the dye adsorption as well as the efficient electron transmission. As a result, the TiO{sub 2} anode prepared by 20 wt% PVP presents the highest performances, based on which the DSSC achieves the highest conversion efficiency of 8.39%, approximately increased by 56.53% than that of the DSSC fabricated without PVP (5.36%).

Identification of MarvelD3 as a tight junction-associated transmembrane protein of the occludin family

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Balda Maria S

2009-12-01

Full Text Available Abstract Background Tight junctions are an intercellular adhesion complex of epithelial and endothelial cells, and form a paracellular barrier that restricts the diffusion of solutes on the basis of size and charge. Tight junctions are formed by multiprotein complexes containing cytosolic and transmembrane proteins. How these components work together to form functional tight junctions is still not well understood and will require a complete understanding of the molecular composition of the junction. Results Here we identify a new transmembrane component of tight junctions: MarvelD3, a four-span transmembrane protein. Its predicted transmembrane helices form a Marvel (MAL and related proteins for vesicle traffic and membrane link domain, a structural motif originally discovered in proteins involved in membrane apposition and fusion events, such as the tight junction proteins occludin and tricellulin. In mammals, MarvelD3 is expressed as two alternatively spliced isoforms. Both isoforms exhibit a broad tissue distribution and are expressed by different types of epithelial as well as endothelial cells. MarvelD3 co-localises with occludin at tight junctions in intestinal and corneal epithelial cells. RNA interference experiments in Caco-2 cells indicate that normal MarvelD3 expression is not required for the formation of functional tight junctions but depletion results in monolayers with increased transepithelial electrical resistance. Conclusions Our data indicate that MarvelD3 is a third member of the tight junction-associated occludin family of transmembrane proteins. Similar to occludin, normal expression of MarvelD3 is not essential for the formation of functional tight junctions. However, MarvelD3 functions as a determinant of epithelial paracellular permeability properties.

X-ray pore optic developments

Science.gov (United States)

Wallace, Kotska; Bavdaz, Marcos; Collon, Maximilien; Beijersbergen, Marco; Kraft, Stefan; Fairbend, Ray; Séguy, Julien; Blanquer, Pascal; Graue, Roland; Kampf, Dirk

2017-11-01

In support of future x-ray telescopes ESA is developing new optics for the x-ray regime. To date, mass and volume have made x-ray imaging technology prohibitive to planetary remote sensing imaging missions. And although highly successful, the mirror technology used on ESA's XMM-Newton is not sufficient for future, large, x-ray observatories, since physical limits on the mirror packing density mean that aperture size becomes prohibitive. To reduce telescope mass and volume the packing density of mirror shells must be reduced, whilst maintaining alignment and rigidity. Structures can also benefit from a modular optic arrangement. Pore optics are shown to meet these requirements. This paper will discuss two pore optic technologies under development, with examples of results from measurement campaigns on samples. One activity has centred on the use of coated, silicon wafers, patterned with ribs, that are integrated onto a mandrel whose form has been polished to the required shape. The wafers follow the shape precisely, forming pore sizes in the sub-mm region. Individual stacks of mirrors can be manufactured without risk to, or dependency on, each other and aligned in a structure from which they can also be removed without hazard. A breadboard is currently being built to demonstrate this technology. A second activity centres on glass pore optics. However an adaptation of micro channel plate technology to form square pores has resulted in a monolithic material that can be slumped into an optic form. Alignment and coating of two such plates produces an x-ray focusing optic. A breadboard 20cm aperture optic is currently being built.

Engineering a pH responsive pore forming protein.

Science.gov (United States)

Kisovec, Matic; Rezelj, Saša; Knap, Primož; Cajnko, Miša Mojca; Caserman, Simon; Flašker, Ajda; Žnidaršič, Nada; Repič, Matej; Mavri, Janez; Ruan, Yi; Scheuring, Simon; Podobnik, Marjetka; Anderluh, Gregor

2017-02-08

Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor. Molecular dynamics simulation further suggested which other amino acid residues may also allosterically influence the pH-sensor. LLO was engineered to the point where it can, in a pH-regulated manner, perforate artificial and cellular membranes. The single mutant Tyr406Ala bound to membranes and oligomerized similarly to the wild-type LLO, however, the final membrane insertion step was pH-affected by the introduced mutation. We show that the mutant toxin can be activated at the surface of artificial membranes or living cells by a single wash with slightly acidic pH buffer. Y406A mutant has a high potential in development of novel nanobiotechnological applications such as controlled release of substances or as a sensor of environmental pH.

Engineering a pH responsive pore forming protein

Science.gov (United States)

Kisovec, Matic; Rezelj, Saša; Knap, Primož; Cajnko, Miša Mojca; Caserman, Simon; Flašker, Ajda; Žnidaršič, Nada; Repič, Matej; Mavri, Janez; Ruan, Yi; Scheuring, Simon; Podobnik, Marjetka; Anderluh, Gregor

2017-02-01

Listeriolysin O (LLO) is a cytolysin capable of forming pores in cholesterol-rich lipid membranes of host cells. It is conveniently suited for engineering a pH-governed responsiveness, due to a pH sensor identified in its structure that was shown before to affect its stability. Here we introduced a new level of control of its hemolytic activity by making a variant with hemolytic activity that was pH-dependent. Based on detailed structural analysis coupled with molecular dynamics and mutational analysis, we found that the bulky side chain of Tyr406 allosterically affects the pH sensor. Molecular dynamics simulation further suggested which other amino acid residues may also allosterically influence the pH-sensor. LLO was engineered to the point where it can, in a pH-regulated manner, perforate artificial and cellular membranes. The single mutant Tyr406Ala bound to membranes and oligomerized similarly to the wild-type LLO, however, the final membrane insertion step was pH-affected by the introduced mutation. We show that the mutant toxin can be activated at the surface of artificial membranes or living cells by a single wash with slightly acidic pH buffer. Y406A mutant has a high potential in development of novel nanobiotechnological applications such as controlled release of substances or as a sensor of environmental pH.

Preparation, characterization and enhanced adsorption performance for Cr(VI) of mesoporous NiFe2O4 by twice pore-forming method

International Nuclear Information System (INIS)

Jia, Zhigang; Peng, Kuankuan; Xu, Lixin

2012-01-01

Magnetic mesoporous NiFe 2 O 4 with higher surface area has been prepared by the twice pore-forming method, including the calcination of the oxalate precursor and leaching of ZnO pore-forming agent. The X-ray diffraction (XRD), Scanning electron microscopy (SEM), Energy dispersive spectroscopy (EDS) and BET surface area measurement are used to evaluate the pore structural parameters and surface chemistry of the adsorbent respectively. The pore-forming mechanism is proposed based on the experimental results. The adsorption behavior of mesoporous NiFe 2 O 4 for Cr(VI) is investigated in detail. The results show that kinetic data follow a pseudo-second-order model and equilibrium data are well fitted by the Langmuir model. The maximum adsorption capacity is 43.68 mg g −1 at pH 2. The removal for Cr(VI) is mainly physisorption process derived from coulombic interaction. The as-prepared TPF-NiFe 2 O 4 is promising as sorbent for Cr(VI) removal because of its higher adsorption capacity, separation convenience and highly efficient reusability. -- Highlights: ► The increase of BET area was realized by leaching of ZnO from mesoporous ZnO/NiFe 2 O 4 . ► TPF-NiFe 2 O 4 demenstrates higher adsorption capacity for Cr(VI) in aqueous solution. ► TPF-NiFe 2 O 4 with magnetic sensitivity is promosing for Cr(VI) removal. ► The used TPF-NiFe 2 O 4 adsorbent can be recycled.

Biophysical and biochemical strategies to understand membrane binding and pore formation by sticholysins, pore-forming proteins from a sea anemone.

Science.gov (United States)

Alvarez, Carlos; Ros, Uris; Valle, Aisel; Pedrera, Lohans; Soto, Carmen; Hervis, Yadira P; Cabezas, Sheila; Valiente, Pedro A; Pazos, Fabiola; Lanio, Maria E

2017-10-01

Actinoporins constitute a unique class of pore-forming toxins found in sea anemones that are able to bind and oligomerize in membranes, leading to cell swelling, impairment of ionic gradients and, eventually, to cell death. In this review we summarize the knowledge generated from the combination of biochemical and biophysical approaches to the study of sticholysins I and II (Sts, StI/II), two actinoporins largely characterized by the Center of Protein Studies at the University of Havana during the last 20 years. These approaches include strategies for understanding the toxin structure-function relationship, the protein-membrane association process leading to pore formation and the interaction of toxin with cells. The rational combination of experimental and theoretical tools have allowed unraveling, at least partially, of the complex mechanisms involved in toxin-membrane interaction and of the molecular pathways triggered upon this interaction. The study of actinoporins is important not only to gain an understanding of their biological roles in anemone venom but also to investigate basic molecular mechanisms of protein insertion into membranes, protein-lipid interactions and the modulation of protein conformation by lipid binding. A deeper knowledge of the basic molecular mechanisms involved in Sts-cell interaction, as described in this review, will support the current investigations conducted by our group which focus on the design of immunotoxins against tumor cells and antigen-releasing systems to cell cytosol as Sts-based vaccine platforms.

Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

Science.gov (United States)

Alavizargar, Azadeh; Berti, Claudio; Ejtehadi, Mohammad Reza; Furini, Simone

2018-04-26

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca 2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca 2+ over Na + . The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

Structure of Voltage-gated Two-pore Channel TPC1 from Arabidopsis thaliana

Science.gov (United States)

Guo, Jiangtao; Zeng, Weizhong; Chen, Qingfeng; Lee, Changkeun; Chen, Liping; Yang, Yi; Cang, Chunlei; Ren, Dejian; Jiang, Youxing

2015-01-01

Two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in both animals and plants as organellar cation channels. Here, we present the first crystal structure of a vacuolar two-pore channel from Arabidopsis thaliana, AtTPC1, which functions as a homodimer. AtTPC1 activation requires both voltage and cytosolic Ca2+. Ca2+ binding to the cytosolic EF-hand domain triggers conformational changes coupled to the pair of pore-lining inner helices (IS6 helices) from the first 6-TM domains, whereas membrane potential only activates the second voltage-sensing domain (VSD2) whose conformational changes are coupled to the pair of inner helices (IIS6 helices) from the second 6-TM domains. Luminal Ca2+ or Ba2+ can modulate voltage activation by stabilizing VSD2 in the resting state and shifts voltage activation towards more positive potentials. Our Ba2+ bound AtTPC1 structure reveals a voltage sensor in the resting state, providing hitherto unseen structural insight into the general voltage-gating mechanism among voltage-gated channels. PMID:26689363

Unusual mechanism of capillary condensation in pores modified with chains forming pillars.

Science.gov (United States)

Borówko, M; Patrykiejew, A; Sokołowski, S

2011-08-07

Density functional approach is applied to study the phase behavior of Lennard-Jones(12,6) fluid in pillared slit-like pores. Our focus is in the evaluation of phase transitions in fluid adsorbed in the pore of a fixed width. If the length of pillars is sufficiently large, we observe additional phase transitions of the first and second order due to the symmetry breaking of the distribution of chain segments and fluid species with respect to the slit-like pore center. Re-entrant symmetry changes and additional critical, critical end points and tricritical points then are observed. The scenario of phase changes is sensitive to the energy of fluid-solid interaction, the amount, and the length of the pillars. Quantitative trends and qualitative changes of the phase diagrams topology are examined depending on the values of these parameters.

Control of phospholipid flip-flop by transmembrane peptides

International Nuclear Information System (INIS)

Kaihara, Masanori; Nakao, Hiroyuki; Yokoyama, Hirokazu; Endo, Hitoshi; Ishihama, Yasushi; Handa, Tetsurou; Nakano, Minoru

2013-01-01

Highlights: ► Phospholipid flip-flop in transmembrane peptide-containing vesicles was investigated. ► Peptides that contained polar residues in the center of the transmembrane region promoted phospholipid flip-flop. ► A bioinformatics approach revealed the presence of polar residues in the transmembrane region of ER membrane proteins. ► Polar residues in ER membrane proteins possibly provide flippase-like activity. - Abstract: We designed three types of transmembrane model peptides whose sequence originates from a frequently used model peptide KALP23, and we investigated their effects on phospholipid flip-flop. Time-resolved small-angle neutron scattering and a dithionite fluorescent quenching assay demonstrated that TMP-L, which has a fully hydrophobic transmembrane region, did not enhance phospholipid flip-flop, whereas TMP-K and TMP-E, which have Lys and Glu, respectively, in the center of their transmembrane regions, enhanced phospholipid flip-flop. Introduction of polar residues in the membrane-spanning helices is considered to produce a locally polar region and enable the lipid head group to interact with the polar side-chain inside the bilayers, thereby reducing the activation energy for the flip-flop. A bioinformatics approach revealed that acidic and basic residues account for 4.5% of the central region of the transmembrane domain in human ER membrane proteins. Therefore, polar residues in ER membrane proteins are considered to provide flippase-like activity

Molecular basis of usher pore gating in Escherichia coli pilus biogenesis.

Science.gov (United States)

Volkan, Ender; Kalas, Vasilios; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Pham, Thieng; Waksman, Gabriel; Delcour, Anne H; Thanassi, David G; Hultgren, Scott J

2013-12-17

Extracellular fibers called chaperone-usher pathway pili are critical virulence factors in a wide range of Gram-negative pathogenic bacteria that facilitate binding and invasion into host tissues and mediate biofilm formation. Chaperone-usher pathway ushers, which catalyze pilus assembly, contain five functional domains: a 24-stranded transmembrane β-barrel translocation domain (TD), a β-sandwich plug domain (PLUG), an N-terminal periplasmic domain, and two C-terminal periplasmic domains (CTD1 and 2). Pore gating occurs by a mechanism whereby the PLUG resides stably within the TD pore when the usher is inactive and then upon activation is translocated into the periplasmic space, where it functions in pilus assembly. Using antibiotic sensitivity and electrophysiology experiments, a single salt bridge was shown to function in maintaining the PLUG in the TD channel of the P pilus usher PapC, and a loop between the 12th and 13th beta strands of the TD (β12-13 loop) was found to facilitate pore opening. Mutation of the β12-13 loop resulted in a closed PapC pore, which was unable to efficiently mediate pilus assembly. Deletion of the PapH terminator/anchor resulted in increased OM permeability, suggesting a role for the proper anchoring of pili in retaining OM integrity. Further, we introduced cysteine residues in the PLUG and N-terminal periplasmic domains that resulted in a FimD usher with a greater propensity to exist in an open conformation, resulting in increased OM permeability but no loss in type 1 pilus assembly. These studies provide insights into the molecular basis of usher pore gating and its roles in pilus biogenesis and OM permeability.

Structure and Mechanism of Proton Transport Through the Transmembrane Tetrameric M2 Protein Bundle of the Influenza A Virus

Energy Technology Data Exchange (ETDEWEB)

R Acharya; V Carnevale; G Fiorin; B Levine; A Polishchuk; V Balannick; I Samish; R Lamb; L Pinto; et al.

2011-12-31

The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Protons are conducted as the total charge of the four His37 side chains passes through 2{sup +} and 3{sup +} with a pK{sub a} near 6. A 1.65 {angstrom} resolution X-ray structure of the transmembrane protein (residues 25-46), crystallized at pH 6.5, reveals a pore that is lined by alternating layers of sidechains and well-ordered water clusters, which offer a pathway for proton conduction. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms at close distance. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters. Thus, the new crystal structure provides a possible unification of the discrete site versus continuum conduction models.

Dissolution at porous interfaces VI: Multiple pore systems.

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Grijseels, H; Crommelin, D J; De Blaey, C J

1984-12-01

With the aid of rapidly dissolving sodium chloride particles, cubic pores were made in the surface of a theophylline tablet. The influence of the pores on the dissolution rate of the surface was investigated in a rotating disk apparatus. Like the drilled pores used in earlier studies, downstream on the surface they caused a turbulent flow regimen with the development of a trough due to enhanced erosion. The phenomenon of a critical pore diameter, discovered with single, drilled pores, seems to be applicable to the cubic pores investigated in this study, although a higher degree of surface coverage with pores caused complications, probably due to particles bordering one another and forming larger pores. The behavior of the porous surfaces at different rotation speeds was studied. Due to the presence of pores the laminar character of the boundary layer flow changes to turbulent, which induces locally an increased dissolution flux in the wake of a pore.

Crystallographic and single-particle analyses of native- and nucleotide-bound forms of the cystic fibrosis transmembrane conductance regulator (CFTR) protein.

Science.gov (United States)

Awayn, N H; Rosenberg, M F; Kamis, A B; Aleksandrov, L A; Riordan, J R; Ford, R C

2005-11-01

Cystic fibrosis, one of the major human inherited diseases, is caused by defects in the CFTR (cystic fibrosis transmembrane conductance regulator), a cell-membrane protein. CFTR acts as a chloride channel which can be opened by ATP. Low-resolution structural studies of purified recombinant human CFTR are described in the present paper. Localization of the C-terminal decahistidine tag in CFTR was achieved by Ni2+-nitriloacetate nanogold labelling, followed by electron microscopy and single-particle analysis. The presence of the gold label appears to improve the single-particle-alignment procedure. Projection structures of CFTR from two-dimensional crystals analysed by electron crystallography displayed two alternative conformational states in the presence of nucleotide and nanogold, but only one form of the protein was observed in the quiescent (nucleotide-free) state.

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

Science.gov (United States)

Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

2010-11-01

The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

ATP Release from Human Airway Epithelial Cells Exposed to Staphylococcus aureus Alpha-Toxin

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Romina Baaske

2016-12-01

Full Text Available Airway epithelial cells reduce cytosolic ATP content in response to treatment with S. aureus alpha-toxin (hemolysin A, Hla. This study was undertaken to investigate whether this is due to attenuated ATP generation or to release of ATP from the cytosol and extracellular ATP degradation by ecto-enzymes. Exposure of cells to rHla did result in mitochondrial calcium uptake and a moderate decline in mitochondrial membrane potential, indicating that ATP regeneration may have been attenuated. In addition, ATP may have left the cells through transmembrane pores formed by the toxin or through endogenous release channels (e.g., pannexins activated by cellular stress imposed on the cells by toxin exposure. Exposure of cells to an alpha-toxin mutant (H35L, which attaches to the host cell membrane but does not form transmembrane pores, did not induce ATP release from the cells. The Hla-mediated ATP-release was completely blocked by IB201, a cyclodextrin-inhibitor of the alpha-toxin pore, but was not at all affected by inhibitors of pannexin channels. These results indicate that, while exposure of cells to rHla may somewhat reduce ATP production and cellular ATP content, a portion of the remaining ATP is released to the extracellular space and degraded by ecto-enzymes. The release of ATP from the cells may occur directly through the transmembrane pores formed by alpha-toxin.

Optimization of protein fractionation by skim milk microfiltration: Choice of ceramic membrane pore size and filtration temperature.

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Jørgensen, Camilla Elise; Abrahamsen, Roger K; Rukke, Elling-Olav; Johansen, Anne-Grethe; Schüller, Reidar B; Skeie, Siv B

2016-08-01

The objective of this study was to investigate how ceramic membrane pore size and filtration temperature influence the protein fractionation of skim milk by cross flow microfiltration (MF). Microfiltration was performed at a uniform transmembrane pressure with constant permeate flux to a volume concentration factor of 2.5. Three different membrane pore sizes, 0.05, 0.10, and 0.20µm, were used at a filtration temperature of 50°C. Furthermore, at pore size 0.10µm, 2 different filtration temperatures were investigated: 50 and 60°C. The transmission of proteins increased with increasing pore size, giving the permeate from MF with the 0.20-µm membrane a significantly higher concentration of native whey proteins compared with the permeates from the 0.05- and 0.10-µm membranes (0.50, 0.24, and 0.39%, respectively). Significant amounts of caseins permeated the 0.20-µm membrane (1.4%), giving a permeate with a whitish appearance and a casein distribution (αS2-CN: αS1-CN: κ-CN: β-CN) similar to that of skim milk. The 0.05- and 0.10-µm membranes were able to retain all caseins (only negligible amounts were detected). A permeate free from casein is beneficial in the production of native whey protein concentrates and in applications where transparency is an important functional characteristic. Microfiltration of skim milk at 50°C with the 0.10-µm membrane resulted in a permeate containing significantly more native whey proteins than the permeate from MF at 60°C. The more rapid increase in transmembrane pressure and the significantly lower concentration of caseins in the retentate at 60°C indicated that a higher concentration of caseins deposited on the membrane, and consequently reduced the native whey protein transmission. Optimal protein fractionation of skim milk into a casein-rich retentate and a permeate with native whey proteins were obtained by 0.10-µm MF at 50°C. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All

Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel.

Science.gov (United States)

Schow, Eric V; Freites, J Alfredo; Nizkorodov, Alex; White, Stephen H; Tobias, Douglas J

2012-07-01

Voltage-dependent potassium (Kv), sodium (Nav), and calcium channels open and close in response to changes in transmembrane (TM) potential, thus regulating cell excitability by controlling ion flow across the membrane. An outstanding question concerning voltage gating is how voltage-induced conformational changes of the channel voltage-sensing domains (VSDs) are coupled through the S4-S5 interfacial linking helices to the opening and closing of the pore domain (PD). To investigate the coupling between the VSDs and the PD, we generated a closed Kv channel configuration from Aeropyrum pernix (KvAP) using atomistic simulations with experiment-based restraints on the VSDs. Full closure of the channel required, in addition to the experimentally determined TM displacement, that the VSDs be displaced both inwardly and laterally around the PD. This twisting motion generates a tight hydrophobic interface between the S4-S5 linkers and the C-terminal ends of the pore domain S6 helices in agreement with available experimental evidence.

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

Science.gov (United States)

Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

2016-11-01

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel

Science.gov (United States)

Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepúlveda, Romina V.; Aguayo, Daniel; González-Nilo, Fernando

2015-01-01

Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations. PMID:25548136

Hidden markov model for the prediction of transmembrane proteins using MATLAB.

Science.gov (United States)

Chaturvedi, Navaneet; Shanker, Sudhanshu; Singh, Vinay Kumar; Sinha, Dhiraj; Pandey, Paras Nath

2011-01-01

Since membranous proteins play a key role in drug targeting therefore transmembrane proteins prediction is active and challenging area of biological sciences. Location based prediction of transmembrane proteins are significant for functional annotation of protein sequences. Hidden markov model based method was widely applied for transmembrane topology prediction. Here we have presented a revised and a better understanding model than an existing one for transmembrane protein prediction. Scripting on MATLAB was built and compiled for parameter estimation of model and applied this model on amino acid sequence to know the transmembrane and its adjacent locations. Estimated model of transmembrane topology was based on TMHMM model architecture. Only 7 super states are defined in the given dataset, which were converted to 96 states on the basis of their length in sequence. Accuracy of the prediction of model was observed about 74 %, is a good enough in the area of transmembrane topology prediction. Therefore we have concluded the hidden markov model plays crucial role in transmembrane helices prediction on MATLAB platform and it could also be useful for drug discovery strategy. The database is available for free at bioinfonavneet@gmail.comvinaysingh@bhu.ac.in.

Topology of transmembrane channel-like gene 1 protein.

Science.gov (United States)

Labay, Valentina; Weichert, Rachel M; Makishima, Tomoko; Griffith, Andrew J

2010-10-05

Mutations of transmembrane channel-like gene 1 (TMC1) cause hearing loss in humans and mice. TMC1 is the founding member of a family of genes encoding proteins of unknown function that are predicted to contain multiple transmembrane domains. The goal of our study was to define the topology of mouse TMC1 expressed heterologously in tissue culture cells. TMC1 was retained in the endoplasmic reticulum (ER) membrane of five tissue culture cell lines that we tested. We used anti-TMC1 and anti-HA antibodies to probe the topologic orientation of three native epitopes and seven HA epitope tags along full-length TMC1 after selective or complete permeabilization of transfected cells with digitonin or Triton X-100, respectively. TMC1 was present within the ER as an integral membrane protein containing six transmembrane domains and cytosolic N- and C-termini. There is a large cytoplasmic loop, between the fourth and fifth transmembrane domains, with two highly conserved hydrophobic regions that might associate with or penetrate, but do not span, the plasma membrane. Our study is the first to demonstrate that TMC1 is a transmembrane protein. The topologic organization revealed by this study shares some features with that of the shaker-TRP superfamily of ion channels.

Pore forming polyalkylpyridinium salts from marine sponges versus synthetic lipofection systems: distinct tools for intracellular delivery of cDNA and siRNA.

Science.gov (United States)

McLaggan, Debra; Adjimatera, Noppadon; Sepcić, Kristina; Jaspars, Marcel; MacEwan, David J; Blagbrough, Ian S; Scott, Roderick H

2006-01-16

Haplosclerid marine sponges produce pore forming polyalkylpyridinium salts (poly-APS), which can be used to deliver macromolecules into cells. The aim of this study was to investigate the delivery of DNA, siRNA and lucifer yellow into cells mediated by poly-APS and its potential mechanisms as compared with other lipofection systems (lipofectamine and N4,N9-dioleoylspermine (LipoGen)). DNA condensation was evaluated and HEK 293 and HtTA HeLa cells were used to investigate pore formation and intracellular delivery of cDNA, siRNA and lucifer yellow. Poly-APS and LipoGen were both found to be highly efficient DNA condensing agents. Fura-2 calcium imaging was used to measure calcium transients indicative of cell membrane pore forming activity. Calcium transients were evoked by poly-APS but not LipoGen and lipofectamine. The increases in intracellular calcium produced by poly-APS showed temperature sensitivity with greater responses being observed at 12 degrees C compared to 21 degrees C. Similarly, delivery of lucifer yellow into cells with poly-APS was enhanced at lower temperatures. Transfection with cDNA encoding for the expression enhanced green fluorescent protein was also evaluated at 12 degrees C with poly-APS, lipofectamine and LipoGen. Intracellular delivery of siRNA was achieved with knockdown in beta-actin expression when lipofectamine and LipoGen were used as transfection reagents. However, intracellular delivery of siRNA was not achieved with poly-APS. Poly-APS mediated pore formation is critical to its activity as a transfection reagent, but lipofection systems utilise distinct mechanisms to enable delivery of DNA and siRNA into cells.

Pore forming polyalkylpyridinium salts from marine sponges versus synthetic lipofection systems: distinct tools for intracellular delivery of cDNA and siRNA

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Blagbrough Ian S

2006-01-01

Full Text Available Abstract Background Haplosclerid marine sponges produce pore forming polyalkylpyridinium salts (poly-APS, which can be used to deliver macromolecules into cells. The aim of this study was to investigate the delivery of DNA, siRNA and lucifer yellow into cells mediated by poly-APS and its potential mechanisms as compared with other lipofection systems (lipofectamine and N4,N9-dioleoylspermine (LipoGen. DNA condensation was evaluated and HEK 293 and HtTA HeLa cells were used to investigate pore formation and intracellular delivery of cDNA, siRNA and lucifer yellow. Results Poly-APS and LipoGen were both found to be highly efficient DNA condensing agents. Fura-2 calcium imaging was used to measure calcium transients indicative of cell membrane pore forming activity. Calcium transients were evoked by poly-APS but not LipoGen and lipofectamine. The increases in intracellular calcium produced by poly-APS showed temperature sensitivity with greater responses being observed at 12°C compared to 21°C. Similarly, delivery of lucifer yellow into cells with poly-APS was enhanced at lower temperatures. Transfection with cDNA encoding for the expression enhanced green fluorescent protein was also evaluated at 12°C with poly-APS, lipofectamine and LipoGen. Intracellular delivery of siRNA was achieved with knockdown in beta-actin expression when lipofectamine and LipoGen were used as transfection reagents. However, intracellular delivery of siRNA was not achieved with poly-APS. Conclusion Poly-APS mediated pore formation is critical to its activity as a transfection reagent, but lipofection systems utilise distinct mechanisms to enable delivery of DNA and siRNA into cells.

Energy conversion device with support member having pore channels

Science.gov (United States)

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.

X-ray microtomography application in pore space reservoir rock.

Science.gov (United States)

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. Copyright © 2011 Elsevier Ltd. All rights reserved.

Visualization of enzyme activities inside earthworm pores

Science.gov (United States)

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.

Control of pore size in epoxy systems.

Energy Technology Data Exchange (ETDEWEB)

Sawyer, Patricia Sue; Lenhart, Joseph Ludlow (North Dakota State University, Fargo, ND); Lee, Elizabeth (North Dakota State University, Fargo, ND); Kallam, Alekhya (North Dakota State University, Fargo, ND); Majumdar, Partha (North Dakota State University, Fargo, ND); Dirk, Shawn M.; Gubbins, Nathan; Chisholm, Bret J. (North Dakota State University, Fargo, ND); Celina, Mathias C.; Bahr, James (North Dakota State University, Fargo, ND); 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.

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

Science.gov (United States)

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

2014-05-06

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

Monalysin, a novel ß-pore-forming toxin from the Drosophila pathogen Pseudomonas entomophila, contributes to host intestinal damage and lethality.

Directory of Open Access Journals (Sweden)

Onya Opota

2011-09-01

Full Text Available Pseudomonas entomophila is an entomopathogenic bacterium that infects and kills Drosophila. P. entomophila pathogenicity is linked to its ability to cause irreversible damages to the Drosophila gut, preventing epithelium renewal and repair. Here we report the identification of a novel pore-forming toxin (PFT, Monalysin, which contributes to the virulence of P. entomophila against Drosophila. Our data show that Monalysin requires N-terminal cleavage to become fully active, forms oligomers in vitro, and induces pore-formation in artificial lipid membranes. The prediction of the secondary structure of the membrane-spanning domain indicates that Monalysin is a PFT of the ß-type. The expression of Monalysin is regulated by both the GacS/GacA two-component system and the Pvf regulator, two signaling systems that control P. entomophila pathogenicity. In addition, AprA, a metallo-protease secreted by P. entomophila, can induce the rapid cleavage of pro-Monalysin into its active form. Reduced cell death is observed upon infection with a mutant deficient in Monalysin production showing that Monalysin plays a role in P. entomophila ability to induce intestinal cell damages, which is consistent with its activity as a PFT. Our study together with the well-established action of Bacillus thuringiensis Cry toxins suggests that production of PFTs is a common strategy of entomopathogens to disrupt insect gut homeostasis.

HYDROXYETHYL METHACRYLATE BASED NANOCOMPOSITE HYDROGELS WITH TUNABLE PORE ARCHITECTURE

Directory of Open Access Journals (Sweden)

Erhan Bat

2016-10-01

Full Text Available Hydroxyethyl methacrylate (HEMA based hydrogels have found increasing number of applications in areas such as chromatographic separations, controlled drug release, biosensing, and membrane separations. In all these applications, the pore size and pore interconnectivity are crucial for successful application of these materials as they determine the rate of diffusion through the matrix. 2-Hydroxyethyl methacrylate is a water soluble monomer but its polymer, polyHEMA, is not soluble in water. Therefore, during polymerization of HEMA in aqueous media, a porous structure is obtained as a result of phase separation. Pore size and interconnectivity in these hydrogels is a function of several variables such as monomer concentration, cross-linker concentration, temperature etc. In this study, we investigated the effect of monomer concentration, graphene oxide addition or clay addition on hydrogel pore size, pore interconnectivity, water uptake, and thermal properties. PolyHEMA hydrogels have been prepared by redox initiated free radical polymerization of the monomer using ethylene glycol dimethacrylate as a cross-linker. As a nanofiller, a synthetic hectorite Laponite® XLG and graphene oxide were used. Graphene oxide was prepared by the Tour Method. Pore morphology of the pristine HEMA based hydrogels and nanocomposite hydrogels were studied by scanning electron microscopy. The formed hydrogels were found to be highly elastic and flexible. A dramatic change in the pore structure and size was observed in the range between 22 to 24 wt/vol monomer at 0.5 % of cross-linker. In this range, the hydrogel morphology changes from typical cauliflower architecture to continuous hydrogel with dispersed water droplets forming the pores where the pores are submicron in size and show an interconnected structure. Such controlled pore structure is highly important when these hydrogels are used for solute diffusion or when there’s flow through monolithic hydrogels

Comparison of Polytetrafluoroethylene Flat-Sheet Membranes with Different Pore Sizes in Application to Submerged Membrane Bioreactor

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Manabu Motoori

2012-06-01

Full Text Available This study focused on phase separation of activated sludge mixed liquor by flat-sheet membranes of polytetrafluoroethylene (PTFE. A 20 liter working volume lab-scale MBR incorporating immersed PTFE flat-sheet membrane modules with different pore sizes (0.3, 0.5 and 1.0 μm was operated for 19 days treating a synthetic wastewater. The experiment was interrupted twice at days 5 and 13 when the modules were removed and cleaned physically and chemically in sequence. The pure water permeate flux of each membrane module was measured before and after each cleaning step to calculate membrane resistances. Results showed that fouling of membrane modules with 0.3 μm pore size was more rapid than other membrane modules with different pore sizes (0.5 and 1.0 μm. On the other hand, it was not clear whether fouling of the 0.5 μm membrane module was more severe than that of the 1.0 μm membrane module. This was partly because of the membrane condition after chemical cleaning, which seemed to determine the fouling of those modules over the next period. When irreversible resistance (R_i i.e., differences in membrane resistance before use and after chemical cleaning was high, the transmembrane pressure increased quickly during the next period irrespective of membrane pore size.

Automatic facial pore analysis system using multi-scale pore detection.

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Sun, J Y; Kim, S W; Lee, S H; Choi, J E; Ko, S J

2017-08-01

As facial pore widening and its treatments have become common concerns in the beauty care field, the necessity for an objective pore-analyzing system has been increased. Conventional apparatuses lack in usability requiring strong light sources and a cumbersome photographing process, and they often yield unsatisfactory analysis results. This study was conducted to develop an image processing technique for automatic facial pore analysis. The proposed method detects facial pores using multi-scale detection and optimal scale selection scheme and then extracts pore-related features such as total area, average size, depth, and the number of pores. Facial photographs of 50 subjects were graded by two expert dermatologists, and correlation analyses between the features and clinical grading were conducted. We also compared our analysis result with those of conventional pore-analyzing devices. The number of large pores and the average pore size were highly correlated with the severity of pore enlargement. In comparison with the conventional devices, the proposed analysis system achieved better performance showing stronger correlation with the clinical grading. The proposed system is highly accurate and reliable for measuring the severity of skin pore enlargement. It can be suitably used for objective assessment of the pore tightening treatments. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Molecular Dynamics Simulations of Hydrophilic Pores in Lipid Bilayers

NARCIS (Netherlands)

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

Hydrophilic pores are formed in peptide free lipid bilayers under mechanical stress. It has been proposed that the transport of ionic species across such membranes is largely determined by the existence of such meta-stable hydrophilic pores. To study the properties of these structures and understand

Forming and control of pores by capsule-free hot isostatic pressing in NiTi shape memory alloys

International Nuclear Information System (INIS)

Yuan, B; Zhu, M; Gao, Y; Li, X; Chung, C Y

2008-01-01

In this study, the pore evolution process of porous NiTi shape memory alloys (SMAs) fabricated by capsule-free hot isostatic pressing (CF-HIP) was investigated by adopting different fabricating parameters. It is shown that porous NiTi SMAs with homogeneous pore distribution and nearly spherical pore shape can be prepared by CF-HIP under suitable conditions. In addition, two novel pore structures were produced, one with a sandwich-like structure, and another with controlled gradient of porosity along the radial direction, with pore size increasing from the outside towards the center of the specimen. The former was obtained by balancing the pressure in the HIP chamber and the gas pressure resulting from the gas expansion in the green sample. The latter resulted from the formation of air bubbles in the liquid phase during the sintering

Role of α and β Transmembrane Domains in Integrin Clustering

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Amir Shamloo

2015-11-01

Full Text Available Integrins are transmembrane proteins playing a crucial role in the mechanical signal transduction from the outside to the inside of a cell, and vice versa. Nevertheless, this signal transduction could not be implemented by a single protein. Rather, in order for integrins to be able to participate in signal transduction, they need to be activated and produce clusters first. As integrins consist of α- and β-subunits that are separate in the active state, studying both subunits separately is of a great importance, for, in the active state, the distance between α- and β-subunits is long enough that they do not influence one another significantly. Thus, this study aims to investigate the tendency of transmembrane domains of integrins to form homodimers. We used both Steered and MARTINI Coarse-grained molecular dynamics method to perform our simulations, mainly because of a better resolution and computational feasibility that each of these methods could provide to us. Using the Steered molecular dynamics method for α- and β-subunits, we found that the localized lipid packing prevented them from clustering. Nonetheless, the lipid packing phenomenon was found to be an artifact after investigating this process using a coarse grained (CG model. Exploiting the coarse-grained molecular dynamics simulations, we found that α- and β-subunits tend to form a stable homo-dimer.

Regulation of KV channel voltage-dependent activation by transmembrane β subunits

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Xiaohui eSun

2012-04-01

Full Text Available Voltage-activated K+ (KV channels are important for shaping action potentials and maintaining resting membrane potential in excitable cells. KV channels contain a central pore-gate domain (PGD surrounded by four voltage-sensing domains (VSD. The VSDs will change conformation in response to alterations of the membrane potential thereby inducing the opening of the PGD. Many KV channels are heteromeric protein complexes containing auxiliary β subunits. These β subunits modulate channel expression and activity to increase functional diversity and render tissue specific phenotypes. This review focuses on the KV β subunits that contain transmembrane (TM segments including the KCNE family and the β subunits of large conductance, Ca2+- and voltage-activated K+ (BK channels. These TM β subunits affect the voltage-dependent activation of KV α subunits. Experimental and computational studies have described the structural location of these β subunits in the channel complexes and the biophysical effects on VSD activation, PGD opening and VSD-PGD coupling. These results reveal some common characteristics and mechanistic insights into KV channel modulation by TM β subunits.

The effect of sulfuric acid on pore initiation in anodic alumina formed in oxalic acid

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Behnam Hafezi

2014-07-01

Full Text Available In this work, a tracer study on pore initiation in anodic alumina in oxalic acid was performed. Effects of some experimental parameters such as applied electrical potential, electrolyte composition and heat pretreatment were evaluated. Electrochemical and morphological experiments were performed using potentiostatic anodizing and scanning electron microscopy (SEM techniques, respectively. Effect of electrolyte composition on current density was discussed. In various electrical potentials, electrolyte composition had different effects on current density. Addition of sulfuric acid into oxalic acid increased porosity. Also, distribution of pore size and pore diameter were influenced by presence of sulfuric acid. Effect of electrolyte composition on the morphology of aluminum surface layer depended on the electric potential. Current density and porosity of aluminum surface layer was decreased by heat pretreatment.

Protein crystal nucleation in pores.

Science.gov (United States)

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

2017-01-16

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.

First evidence of the pore-forming properties of a keratin from skin mucus of rainbow trout (Oncorhynchus mykiss, formerly Salmo gairdneri).

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Molle, Virginie; Campagna, Sylvie; Bessin, Yannick; Ebran, Nathalie; Saint, Nathalie; Molle, Gérard

2008-04-01

The epidermis of fish is covered with a layer of mucus, which contributes to the defence of the species against parasites, bacteria and fungi. We have previously extracted glycoproteins from various mucus samples from fish and have shown that they present pore-forming activities well correlated with strong antibacterial properties [Ebran, Julien, Orange, Saglio, Lemaitre and Molle(2000) Biochim. Biophys. Acta 1467, 271-280]. The present study focuses on the 65 kDa glycoprotein, Tr65, from the rainbow trout (Oncorhynchus mykiss, formerly Salmo gairdneri).Enzymatic digestion of Tr65 yielded a fragment pattern with strong homology with that of trout type II cytokeratin. Sequence analysis of the cDNA clone obtained by PCR confirmed this homology. We thus constructed a plasmid to overproduce the recombinant Tr65. We extracted and purified this recombinant Tr65, using it for multichannel and single-channel experiments in azolectin bilayers. Our results with recombinant Tr65 confirmed the pore-forming properties already shown with native antibacterial Tr65. These findings offer new insights into the function of keratin proteins present in various mucosal surfaces of animals and human beings.

Structure-function of proteins interacting with the alpha1 pore-forming subunit of high voltage-activated calcium channel

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Alan eNeely

2014-06-01

Full Text Available Openings of high-voltage-activated calcium channels lead to a transient increase in calcium concentration that in turn activate a plethora of cellular functions, including muscle contraction, secretion and gene transcription. To coordinate all these responses calcium channels form supramolecular assemblies containing effectors and regulatory proteins that couple calcium influx to the downstream signal cascades and to feedback elements. According to the original biochemical characterization of skeletal muscle Dihydropyridine receptors, high-voltage-activated calcium channels are multi-subunit protein complexes consisting of a pore-forming subunit (α1 associated with four additional polypeptide chains β, α2, δ and γ, often referred to as accessory subunits. Twenty-five years after the first purification of a high-voltage calcium channel, the concept of a flexible stoichiometry to expand the repertoire of mechanisms that regulate calcium channel influx has emerged. Several other proteins have been identified that associate directly with the α1-subunit, including calmodulin and multiple members of the small and large GTPase family. Some of these proteins only interact with a subset of α1-subunits and during specific stages of biogenesis. More strikingly, most of the α1-subunit interacting proteins, such as the β-subunit and small GTPases, regulate both gating and trafficking through a variety of mechanisms. Modulation of channel activity covers almost all biophysical properties of the channel. Likewise, regulation of the number of channels in the plasma membrane is performed by altering the release of the α1-subunit from the endoplasmic reticulum, by reducing its degradation or enhancing its recycling back to the cell surface. In this review, we discuss the structural basis, interplay and functional role of selected proteins that interact with the central pore-forming subunit of high-voltage-activated calcium channels.

Structure-function of proteins interacting with the α1 pore-forming subunit of high-voltage-activated calcium channels

Science.gov (United States)

Neely, Alan; Hidalgo, Patricia

2014-01-01

Openings of high-voltage-activated (HVA) calcium channels lead to a transient increase in calcium concentration that in turn activate a plethora of cellular functions, including muscle contraction, secretion and gene transcription. To coordinate all these responses calcium channels form supramolecular assemblies containing effectors and regulatory proteins that couple calcium influx to the downstream signal cascades and to feedback elements. According to the original biochemical characterization of skeletal muscle Dihydropyridine receptors, HVA calcium channels are multi-subunit protein complexes consisting of a pore-forming subunit (α1) associated with four additional polypeptide chains β, α2, δ, and γ, often referred to as accessory subunits. Twenty-five years after the first purification of a high-voltage calcium channel, the concept of a flexible stoichiometry to expand the repertoire of mechanisms that regulate calcium channel influx has emerged. Several other proteins have been identified that associate directly with the α1-subunit, including calmodulin and multiple members of the small and large GTPase family. Some of these proteins only interact with a subset of α1-subunits and during specific stages of biogenesis. More strikingly, most of the α1-subunit interacting proteins, such as the β-subunit and small GTPases, regulate both gating and trafficking through a variety of mechanisms. Modulation of channel activity covers almost all biophysical properties of the channel. Likewise, regulation of the number of channels in the plasma membrane is performed by altering the release of the α1-subunit from the endoplasmic reticulum, by reducing its degradation or enhancing its recycling back to the cell surface. In this review, we discuss the structural basis, interplay and functional role of selected proteins that interact with the central pore-forming subunit of HVA calcium channels. PMID:24917826

Systematic analysis of barrier-forming FG hydrogels from Xenopus nuclear pore complexes

NARCIS (Netherlands)

Labokha, A.A.; Gradmann, S.H.E.; Frey, S.; Hülsmann, B.B.; Urlaub, H.; Baldus, M.; Görlich, D.

2013-01-01

Nuclear pore complexes (NPCs) control the traffic between cell nucleus and cytoplasm. While facilitating translocation of nuclear transport receptors (NTRs) and NTR·cargo complexes, they suppress passive passage of macromolecules ⩾30 kDa. Previously, we reconstituted the NPC barrier as hydrogels

Transmembrane helix M6 in sarco(endo)plasmic reticulum Ca(2+)-ATPase forms a functional interaction site with phospholamban. Evidence for physical interactions at other sites.

Science.gov (United States)

Asahi, M; Kimura, Y; Kurzydlowski, K; Tada, M; MacLennan, D H

1999-11-12

In an earlier study (Kimura, Y., Kurzydlowski, K., Tada, M., and MacLennan, D. H. (1997) J. Biol. Chem. 272, 15061-15064), mutation of amino acids on one face of the phospholamban (PLN) transmembrane helix led to loss of PLN inhibition of sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) molecules. This helical face was proposed to form a site of PLN interaction with a transmembrane helix in SERCA molecules. To determine whether predicted transmembrane helices M4, M5, M6, or M8 in SERCA1a interact with PLN, SERCA1a mutants were co-expressed with wild-type PLN and effects on Ca(2+) dependence of Ca(2+) transport were measured. Wild-type inhibitory interactions shifted apparent Ca(2+) affinity of SERCA1a by an average of -0.34 pCa units, but four of the seven mutations in M4 led to a more inhibitory shift in apparent Ca(2+) affinity, averaging -0.53 pCa units. Seven mutations in M5 led to an average shift of -0.32 pCa units and seven mutations in M8 led to an average shift of -0.30 pCa units. Among 11 mutations in M6, 1, Q791A, increased the inhibitory shift (-0.59 pCa units) and 5, V795A (-0.11), L802A (-0.07), L802V (-0.04), T805A (-0.11), and F809A (-0.12), reduced the inhibitory shift, consistent with the view that Val(795), Leu(802), Thr(805), and Phe(809), located on one face of a predicted M6 helix, form a site in SERCA1a for interaction with PLN. Those mutations in M4, M6, or M8 of SERCA1a that enhanced PLN inhibitory function did not enhance PLN physical association with SERCA1a, but mutants V795A and L802A in M6, which decreased PLN inhibitory function, decreased physical association, as measured by co-immunoprecipitation. In related studies, those PLN mutants that gained inhibitory function also increased levels of co-immunoprecipitation of wild-type SERCA1a and those that lost inhibitory function also reduced association, correlating functional interaction sites with physical interaction sites. Thus, both functional and physical data confirm that PLN

Role of the vaccinia virus O3 protein in cell entry can be fulfilled by its Sequence flexible transmembrane domain

Energy Technology Data Exchange (ETDEWEB)

Satheshkumar, P.S.; Chavre, James; Moss, Bernard, E-mail: bmoss@nih.gov

2013-09-15

The vaccinia virus O3 protein, a component of the entry–fusion complex, is encoded by all chordopoxviruses. We constructed truncation mutants and demonstrated that the transmembrane domain, which comprises two-thirds of this 35 amino acid protein, is necessary and sufficient for interaction with the entry–fusion complex and function in cell entry. Nevertheless, neither single amino acid substitutions nor alanine scanning mutagenesis revealed essential amino acids within the transmembrane domain. Moreover, replication-competent mutant viruses were generated by randomization of 10 amino acids of the transmembrane domain. Of eight unique viruses, two contained only two amino acids in common with wild type and the remainder contained one or none within the randomized sequence. Although these mutant viruses formed normal size plaques, the entry–fusion complex did not co-purify with the mutant O3 proteins suggesting a less stable interaction. Thus, despite low specific sequence requirements, the transmembrane domain is sufficient for function in entry. - Highlights: • The 35 amino acid O3 protein is required for efficient vaccinia virus entry. • The transmembrane domain of O3 is necessary and sufficient for entry. • Mutagenesis demonstrated extreme sequence flexibility compatible with function.

Staphylococcal Bicomponent Pore-Forming Toxins: Targets for Prophylaxis and Immunotherapy

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M. Javad Aman

2014-03-01

Full Text Available Staphylococccus aureus represents one of the most challenging human pathogens as well as a common colonizer of human skin and mucosal surfaces. S. aureus causes a wide range of diseases from skin and soft tissue infection (SSTI to debilitating and life-threatening conditions such as osteomyelitis, endocarditis, and necrotizing pneumonia. The range of diseases reflects the remarkable diversity of the virulence factors produced by this pathogen, including surface antigens involved in the establishment of infection and a large number of toxins that mediate a vast array of cellular responses. The staphylococcal toxins are generally believed to have evolved to disarm the innate immune system, the first line of defense against this pathogen. This review focuses on recent advances on elucidating the biological functions of S. aureus bicomponent pore-forming toxins (BCPFTs and their utility as targets for preventive and therapeutic intervention. These toxins are cytolytic to a variety of immune cells, primarily neutrophils, as well as cells with a critical barrier function. The lytic activity of BCPFTs towards immune cells implies a critical role in immune evasion, and a number of epidemiological studies and animal experiments relate these toxins to clinical disease, particularly SSTI and necrotizing pneumonia. Antibody-mediated neutralization of this lytic activity may provide a strategy for development of toxoid-based vaccines or immunotherapeutics for prevention or mitigation of clinical diseases. However, certain BCPFTs have been proposed to act as danger signals that may alert the immune system through an inflammatory response. The utility of a neutralizing vaccination strategy must be weighed against such immune-activating potential.

Staphylococcal bicomponent pore-forming toxins: targets for prophylaxis and immunotherapy.

Science.gov (United States)

Aman, M Javad; Adhikari, Rajan P

2014-03-04

Staphylococccus aureus represents one of the most challenging human pathogens as well as a common colonizer of human skin and mucosal surfaces. S. aureus causes a wide range of diseases from skin and soft tissue infection (SSTI) to debilitating and life-threatening conditions such as osteomyelitis, endocarditis, and necrotizing pneumonia. The range of diseases reflects the remarkable diversity of the virulence factors produced by this pathogen, including surface antigens involved in the establishment of infection and a large number of toxins that mediate a vast array of cellular responses. The staphylococcal toxins are generally believed to have evolved to disarm the innate immune system, the first line of defense against this pathogen. This review focuses on recent advances on elucidating the biological functions of S. aureus bicomponent pore-forming toxins (BCPFTs) and their utility as targets for preventive and therapeutic intervention. These toxins are cytolytic to a variety of immune cells, primarily neutrophils, as well as cells with a critical barrier function. The lytic activity of BCPFTs towards immune cells implies a critical role in immune evasion, and a number of epidemiological studies and animal experiments relate these toxins to clinical disease, particularly SSTI and necrotizing pneumonia. Antibody-mediated neutralization of this lytic activity may provide a strategy for development of toxoid-based vaccines or immunotherapeutics for prevention or mitigation of clinical diseases. However, certain BCPFTs have been proposed to act as danger signals that may alert the immune system through an inflammatory response. The utility of a neutralizing vaccination strategy must be weighed against such immune-activating potential.

Lennard-Jones fluids in two-dimensional nano-pores. Multi-phase coexistence and fluid structure

Science.gov (United States)

Yatsyshin, Petr; Savva, Nikos; Kalliadasis, Serafim

2014-03-01

We present a number of fundamental findings on the wetting behaviour of nano-pores. A popular model for fluid confinement is a one-dimensional (1D) slit pore formed by two parallel planar walls and it exhibits capillary condensation (CC): a first-order phase transition from vapour to capillary-liquid (Kelvin shift). Capping such a pore at one end by a third orthogonal wall forms a prototypical two-dimensional (2D) pore. We show that 2D pores possess a wetting temperature such that below this temperature CC remains of first order, above it becomes a continuous phase transition manifested by a slab of capillary-liquid filling the pore from the capping wall. Continuous CC exhibits hysteresis and can be preceded by a first-order capillary prewetting transition. Additionally, liquid drops can form in the corners of the 2D pore (remnant of 2D wedge prewetting). The three fluid phases, vapour, capillary-liquid slab and corner drops, can coexist at the pore triple point. Our model is based on the statistical mechanics of fluids in the density functional formulation. The fluid-fluid and fluid-substrate interactions are dispersive. We analyze in detail the microscopic fluid structure, isotherms and full phase diagrams. Our findings also suggest novel ways to control wetting of nano-pores. We are grateful to the European Research Council via Advanced Grant No. 247031 for support.

Functional interactions at the interface between voltage-sensing and pore domains in the Shaker K(v) channel.

Science.gov (United States)

Soler-Llavina, Gilberto J; Chang, Tsg-Hui; Swartz, Kenton J

2006-11-22

Voltage-activated potassium (K(v)) channels contain a central pore domain that is partially surrounded by four voltage-sensing domains. Recent X-ray structures suggest that the two domains lack extensive protein-protein contacts within presumed transmembrane regions, but whether this is the case for functional channels embedded in lipid membranes remains to be tested. We investigated domain interactions in the Shaker K(v) channel by systematically mutating the pore domain and assessing tolerance by examining channel maturation, S4 gating charge movement, and channel opening. When mapped onto the X-ray structure of the K(v)1.2 channel the large number of permissive mutations support the notion of relatively independent domains, consistent with crystallographic studies. Inspection of the maps also identifies portions of the interface where residues are sensitive to mutation, an external cluster where mutations hinder voltage sensor activation, and an internal cluster where domain interactions between S4 and S5 helices from adjacent subunits appear crucial for the concerted opening transition.

Membrane fouling mechanism of biofilm-membrane bioreactor (BF-MBR): Pore blocking model and membrane cleaning.

Science.gov (United States)

Zheng, Yi; Zhang, Wenxiang; Tang, Bing; Ding, Jie; Zheng, Yi; Zhang, Zhien

2018-02-01

Biofilm membrane bioreactor (BF-MBR) is considered as an important wastewater treatment technology that incorporates advantages of both biofilm and MBR process, as well as can alleviate membrane fouling, with respect to the conventional activated sludge MBR. But, to be efficient, it necessitates the establishment of proper methods for the assessment of membrane fouling. Four Hermia membrane blocking models were adopted to quantify and evaluate the membrane fouling of BF-MBR. The experiments were conducted with various operational conditions, including membrane types, agitation speeds and transmembrane pressure (TMP). Good agreement between cake formation model and experimental data was found, confirming the validity of the Hermia models for assessing the membrane fouling of BF-MBR and that cake layer deposits on membrane. Moreover, the influences of membrane types, agitation speeds and transmembrane pressure on the Hermia pore blocking coefficient of cake layer were investigated. In addition, the permeability recovery after membrane cleaning at various operational conditions was studied. This work confirms that, unlike conventional activated sludge MBR, BF-MBR possesses a low degree of membrane fouling and a higher membrane permeability recovery after cleaning. Copyright © 2017 Elsevier Ltd. All rights reserved.

Comparison of the amyloid pore forming properties of rat and human Alzheimer’s beta-amyloid peptide 1-42: Calcium imaging data

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Coralie Di Scala

2016-03-01

Full Text Available The data here consists of calcium imaging of human neuroblastoma SH-SY5Y cells treated with the calcium-sensitive dye Fluo-4AM and then incubated with nanomolar concentrations of either human or rat Alzheimer’s β-amyloid peptide Aβ1-42. These data are both of a qualitative (fluorescence micrographs and semi-quantitative nature (estimation of intracellular calcium concentrations of cells probed by Aβ1-42 peptides vs. control untreated cells. Since rat Aβ1-42 differs from its human counterpart at only three amino acid positions, this comparative study is a good assessment of the specificity of the amyloid pore forming assay. The interpretation of this dataset is presented in the accompanying study “Broad neutralization of calcium-permeable amyloid pore channels with a chimeric Alzheimer/Parkinson peptide targeting brain gangliosides” [1].

Propagation of a plasma streamer in catalyst pores

Science.gov (United States)

Zhang, Quan-Zhi; Bogaerts, Annemie

2018-03-01

Although plasma catalysis is gaining increasing interest for various environmental applications, the underlying mechanisms are still far from understood. For instance, it is not yet clear whether and how plasma streamers can propagate in catalyst pores, and what is the minimum pore size to make this happen. As this is crucial information to ensure good plasma-catalyst interaction, we study here the mechanism of plasma streamer propagation in a catalyst pore, by means of a two-dimensional particle-in-cell/Monte Carlo collision model, for various pore diameters in the nm-range to μm-range. The so-called Debye length is an important criterion for plasma penetration into catalyst pores, i.e. a plasma streamer can penetrate into pores when their diameter is larger than the Debye length. The Debye length is typically in the order of a few 100 nm up to 1 μm at the conditions under study, depending on electron density and temperature in the plasma streamer. For pores in the range of ∼50 nm, plasma can thus only penetrate to some extent and at very short times, i.e. at the beginning of a micro-discharge, before the actual plasma streamer reaches the catalyst surface and a sheath is formed in front of the surface. We can make plasma streamers penetrate into smaller pores (down to ca. 500 nm at the conditions under study) by increasing the applied voltage, which yields a higher plasma density, and thus reduces the Debye length. Our simulations also reveal that the plasma streamers induce surface charging of the catalyst pore sidewalls, causing discharge enhancement inside the pore, depending on pore diameter and depth.

Can membrane-bound carotenoid pigment zeaxanthin carry out a transmembrane proton transfer?

Science.gov (United States)

Kupisz, Kamila; Sujak, Agnieszka; Patyra, Magdalena; Trebacz, Kazimierz; Gruszecki, Wiesław I

2008-10-01

Polar carotenoid pigment zeaxanthin (beta,beta-carotene-3,3'-diol) incorporated into planar lipid membranes formed with diphytanoyl phosphatidylcholine increases the specific electric resistance of the membrane from ca. 4 to 13 x 10(7) Omega cm2 (at 5 mol% zeaxanthin with respect to lipid). Such an observation is consistent with the well known effect of polar carotenoids in decreasing fluidity and structural stabilization of lipid bilayers. Zeaxanthin incorporated into the lipid membrane at 1 mol% has very small effect on the overall membrane resistance but facilitates equilibration of the transmembrane proton gradient, as demonstrated with the application of the H+-sensitive antimony electrodes. Relatively low changes in the electrical potential suggest that the equilibration process may be associated with a symport/antiport activity or with a transmembrane transfer of the molecules of acid. UV-Vis linear dichroism analysis of multibilayer formed with the same lipid-carotenoid system shows that the transition dipole moment of the pigment molecules forms a mean angle of 21 degrees with respect to the axis normal to the plane of the membrane. This means that zeaxanthin spans the membrane and tends to have its two hydroxyl groups anchored in the opposite polar zones of the membrane. Detailed FTIR analysis of beta-carotene and zeaxanthin indicates that the polyene chain of carotenoids is able to form weak hydrogen bonds with water molecules. Possible molecular mechanisms responsible for proton transport by polyenes are discussed, including direct involvement of the polyene chain in proton transfer and indirect effect of the pigment on physical properties of the membrane.

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

Science.gov (United States)

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 pore was also slightly correlated with the number of pores in size of over 0.04 mm(2) (P 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.

X-ray microtomography application in pore space reservoir rock

Energy Technology Data Exchange (ETDEWEB)

Oliveira, M.F.S.; Lima, I. [Nuclear Instrumentation Laboratory, COPPE/UFRJ, P.O. Box 68509, 21.941-972, Rio de Janeiro (Brazil); Borghi, L. [Geology Department, Geosciences Institute, Federal University of Rio de Janeiro, Brazil. (Brazil); Lopes, R.T., E-mail: ricardo@lin.ufrj.br [Nuclear Instrumentation Laboratory, COPPE/UFRJ, P.O. Box 68509, 21.941-972, Rio de Janeiro (Brazil)

2012-07-15

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. - Highlights: Black-Right-Pointing-Pointer This study is about porosity parameter in carbonate rocks by 3D X-Ray Microtomography. Black-Right-Pointing-Pointer This study has become useful as data input for modeling reservoir characterization. Black-Right-Pointing-Pointer This technique was able to provide pores, grains and mineralogical differences among the samples.

Pore-scale investigation of biomass plug development and propagation in porous media.

Science.gov (United States)

Stewart, Terri L; Scott Fogler, H

2002-03-05

Biomass plugging of porous media finds application in enhanced oil recovery and bioremediation. An understanding of biomass plugging of porous media was sought by using a porous glass micromodel through which biomass and nutrient were passed. This study describes the pore-scale physics of biomass plug propagation of Leuconostoc mesenteroides under nutrient-rich conditions. It was found that, as the nutrient flowed through the micromodel, the initial biomass plug occurred at the nutrient-inoculum interface due to growth in the larger pore throats. As growth proceeded, biomass filled and closed these larger pore throats, until only isolated groupings of pore throats with smaller radii remained empty. As nutrient flow continued, a maximum pressure drop was reached. At the maximum pressure drop, the biomass yielded in a manner similar to a Bingham plastic to form a breakthrough channel consisting of a path of interconnected pore throats. The channel incorporated the isolated groupings of empty pore throats that had been present before breakthrough. As the nutrient flow continued, subsequent plugs developed as breakthrough channels refilled with biomass and in situ growth was stimulated in the region just downstream of the previous plug. The downstream plugs had a higher fraction of isolated groupings of empty pore throats, which can be attributed to depletion of nutrient downstream. When the next breakthrough channel formed, it incorporated these isolated groupings, causing the breakthrough channels to be branched. It was observed that the newly formed plug could be less stable with this higher fraction of empty pore throats and that the location of breakthrough channels changed in subsequent plugs. This change in breakthrough channel location could be attributed to the redistribution of nutrient flow and the changes in flowrate in the pore throats. Copyright 2002 John Wiley & Sons, Inc. Biotechnol Bioeng 77: 577-588, 2002; DOI 10.1002/bit.10044

Transmembrane amyloid-related proteins in CSF as potential biomarkers for Alzheimer’s disease

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Inmaculada eLopez-Font

2015-06-01

Full Text Available In the continuing search for new cerebrospinal fluid (CSF biomarkers for Alzheimer’s disease (AD, reasonable candidates are the secretase enzymes involved in the processing of the amyloid precursor protein (APP, as well as the large proteolytic cleavage fragments sAPPα and sAPPβ. The enzymatic activities of some of these secretases, such as BACE1 and TACE, have been investigated as potential AD biomarkers, and it has been assumed that these activities present in human CSF result from the soluble truncated forms of the membrane-bound enzymes. However, we and others recently identified soluble forms of BACE1 and APP in CSF containing the intracellular domains, as well as the multi-pass transmembrane presenilin-1 (PS1 and other subunits of γ-secretase. We also review recent findings that suggest that most of these soluble transmembrane proteins could display self-association properties based on hydrophobic and/or ionic interactions leading to the formation of heteromeric complexes. The oligomerization state of these potential new biomarkers needs to be taken into consideration for assessing their real potential as CSF biomarkers for AD by adequate molecular tools.

Effect of Etching Parameter on Pore Size and Porosity of Electrochemically Formed Nanoporous Silicon

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Pushpendra Kumar

2007-01-01

Full Text Available The most common fabrication technique of porous silicon (PS is electrochemical etching of a crystalline silicon wafer in a hydrofluoric (HF acid-based solution. The electrochemical process allows for precise control of the properties of PS such as thickness of the porous layer, porosity, and average pore diameter. The control of these properties of PS was shown to depend on the HF concentration in the used electrolyte, the applied current density, and the thickness of PS. The change in pore diameter, porosity, and specific surface area of PS was investigated by measuring nitrogen sorption isotherms.

Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT.

Science.gov (United States)

Merkle, Patrick S; Gotfryd, Kamil; Cuendet, Michel A; Leth-Espensen, Katrine Z; Gether, Ulrik; Loland, Claus J; Rand, Kasper D

2018-05-01

LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na + - and K + -dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.

Fusion Pore Diameter Regulation by Cations Modulating Local Membrane Anisotropy

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Doron Kabaso

2012-01-01

Full Text Available The fusion pore is an aqueous channel that is formed upon the fusion of the vesicle membrane with the plasma membrane. Once the pore is open, it may close again (transient fusion or widen completely (full fusion to permit vesicle cargo discharge. While repetitive transient fusion pore openings of the vesicle with the plasma membrane have been observed in the absence of stimulation, their frequency can be further increased using a cAMP-increasing agent that drives the opening of nonspecific cation channels. Our model hypothesis is that the openings and closings of the fusion pore are driven by changes in the local concentration of cations in the connected vesicle. The proposed mechanism of fusion pore dynamics is considered as follows: when the fusion pore is closed or is extremely narrow, the accumulation of cations in the vesicle (increased cation concentration likely leads to lipid demixing at the fusion pore. This process may affect local membrane anisotropy, which reduces the spontaneous curvature and thus leads to the opening of the fusion pore. Based on the theory of membrane elasticity, we used a continuum model to explain the rhythmic opening and closing of the fusion pore.

Surfactant-enhanced control of track-etch pore morphology

International Nuclear Information System (INIS)

Apel', P.Yu.; Blonskaya, I.V.; Didyk, A.Yu.; Dmitriev, S.N.; Orelovich, O.L.; Samojlova, L.I.; Vutsadakis, V.A.; Root, D.

2000-01-01

The influence of surfactants on the process of chemical development of ion tracks in polymers is studied. Based on the experimental data, a mechanism of the surfactant effect on the track-etch pore morphology is proposed. In the beginning of etching the surfactant is adsorbed on the surface and creates a layer that is quasi-solid and partially protects the surface from the etching agent. However, some etchant molecules diffuse through the barrier and react with the polymer surface. This results in the formation of a small hole at the entrance to the ion track. After the hole has attained a few annometers in diameter, the surfactant molecules penetrate into the track and cover its walls. Further diffusion of the surfactant into the growing pore is hindered. The adsorbed surfactant layer is not permeable for large molecules. In contrast, small alkali molecules and water molecules diffuse into the track and provide the etching process enlarging the pore. At this stage the transport of the surfactant into the pore channel can proceed only due to the lateral diffusion in the adsorbed layer. The volume inside the pore is free of surfactant molecules and grows at a higher rate than pore entrance. After a more prolonged etching the bottle-like (or 'cigar-like') pore channels are formed. The bottle-like shape of the pore channels depends on the etching conditions such as alkali and surfactant concentration, temperature, and type of the surfactant. The use of surfactants enables one to produce track-etch membranes with improved flow rate characteristics compared with those having cylindrical pores with the same nominal pore diameters

PrP Knockout Cells Expressing Transmembrane PrP Resist Prion Infection.

Science.gov (United States)

Marshall, Karen E; Hughson, Andrew; Vascellari, Sarah; Priola, Suzette A; Sakudo, Akikazu; Onodera, Takashi; Baron, Gerald S

2017-01-15

) directs it to specific regions of cell membranes called rafts. In order to test the importance of the raft environment on prion propagation, we developed a novel model for prion infection where cells expressing either GPI-anchored PrP C or transmembrane-anchored PrP C , which partitions it to a different location, were treated with infectious, misfolded forms of the prion protein, PrP res We show that only GPI-anchored PrP C was able to convert to PrP res and able to serially propagate. The results strongly suggest that GPI anchoring and the localization of PrP C to rafts are crucial to the ability of PrP C to propagate as a prion. Copyright © 2017 American Society for Microbiology.

PDBTM: Protein Data Bank of transmembrane proteins after 8 years.

Science.gov (United States)

Kozma, Dániel; Simon, István; Tusnády, Gábor E

2013-01-01

The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures. Numerous 'exotic' transmembrane protein structures have been solved since the first release, which has made it necessary to define these new structural elements, such as membrane loops or interfacial helices in the database. This article reports the new features of the PDBTM database that have been added since its first release, and our current efforts to keep the database up-to-date and easy to use so that it may continue to serve as a fundamental resource for the scientific community.

Pore Formation Process of Porous Ti3SiC2 Fabricated by Reactive Sintering

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Huibin Zhang

2017-02-01

Full Text Available Porous Ti3SiC2 was fabricated with high purity, 99.4 vol %, through reactive sintering of titanium hydride (TiH2, silicon (Si and graphite (C elemental powders. The reaction procedures and the pore structure evolution during the sintering process were systematically studied by X-ray diffraction (XRD and scanning electron microscope (SEM. Our results show that the formation of Ti3SiC2 from TiH2/Si/C powders experienced the following steps: firstly, TiH2 decomposed into Ti; secondly, TiC and Ti5Si3 intermediate phases were generated; finally, Ti3SiC2 was produced through the reaction of TiC, Ti5Si3 and Si. The pores formed in the synthesis procedure of porous Ti3SiC2 ceramics are derived from the following aspects: interstitial pores left during the pressing procedure; pores formed because of the TiH2 decomposition; pores formed through the reactions between Ti and Si and Ti and C powders; and the pores produced accompanying the final phase synthesized during the high temperature sintering process.

A Lys-Trp cation-π interaction mediates the dimerization and function of the chloride intracellular channel protein 1 transmembrane domain.

Science.gov (United States)

Peter, Bradley; Polyansky, Anton A; Fanucchi, Sylvia; Dirr, Heini W

2014-01-14

Chloride intracellular channel protein 1 (CLIC1) is a dual-state protein that can exist either as a soluble monomer or in an integral membrane form. The oligomerization of the transmembrane domain (TMD) remains speculative despite it being implicated in pore formation. The extent to which electrostatic and van der Waals interactions drive folding and association of the dimorphic TMD is unknown and is complicated by the requirement of interactions favorable in both aqueous and membrane environments. Here we report a putative Lys37-Trp35 cation-π interaction and show that it stabilizes the dimeric form of the CLIC1 TMD in membranes. A synthetic 30-mer peptide comprising a K37M TMD mutant was examined in 2,2,2-trifluoroethanol, sodium dodecyl sulfate micelles, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine liposomes using far-ultraviolet (UV) circular dichroism, fluorescence, and UV absorbance spectroscopy. Our data suggest that Lys37 is not implicated in the folding, stability, or membrane insertion of the TMD peptide. However, removal of this residue impairs the formation of dimers and higher-order oligomers. This is accompanied by a 30-fold loss of chloride influx activity, suggesting that dimerization modulates the rate of chloride conductance. We propose that, within membranes, individual TMD helices associate via a Lys37-mediated cation-π interaction to form active dimers. The latter findings are also supported by results of modeling a putative TMD dimer conformation in which Lys37 and Trp35 form cation-π pairs at the dimer interface. Dimeric helix bundles may then associate to form fully active ion channels. Thus, within a membrane-like environment, aromatic interactions involving a polar lysine side chain provide a thermodynamic driving force for helix-helix association.

Pore Structure Control of Ordered Mesoporous Silica Film Using Mixed Surfactants

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Tae-Jung Ha

2011-01-01

Full Text Available Materials with nanosized and well-arranged pores have been researched actively in order to be applied to new technology fields. Especially, mesoporous material containing various pore structures is expected to have different pore structure. To form a mixed pore structure, ordered mesoporous silica films were prepared with a mixture of surfactant; Brij-76 and P-123 block copolymer. In mixed surfactant system, mixed pore structure was observed in the region of P-123/(Brij-76 + P-123 with about 50.0 wt.% while a single pore structure was observed in regions which have large difference in ratio between Brij-76 and P-123 through the X-ray diffraction analysis. Regardless of surfactant ratio, porosity was retained almost the same. It is expected that ordered mesoporous silica film with mixed pore structure can be one of the new materials which has distinctive properties.

A structural model of the pore-forming region of the skeletal muscle ryanodine receptor (RyR1.

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Srinivas Ramachandran

2009-04-01

Full Text Available Ryanodine receptors (RyRs are ion channels that regulate muscle contraction by releasing calcium ions from intracellular stores into the cytoplasm. Mutations in skeletal muscle RyR (RyR1 give rise to congenital diseases such as central core disease. The absence of high-resolution structures of RyR1 has limited our understanding of channel function and disease mechanisms at the molecular level. Here, we report a structural model of the pore-forming region of RyR1. Molecular dynamics simulations show high ion binding to putative pore residues D4899, E4900, D4938, and D4945, which are experimentally known to be critical for channel conductance and selectivity. We also observe preferential localization of Ca(2+ over K(+ in the selectivity filter of RyR1. Simulations of RyR1-D4899Q mutant show a loss of preference to Ca(2+ in the selectivity filter as seen experimentally. Electrophysiological experiments on a central core disease mutant, RyR1-G4898R, show constitutively open channels that conduct K(+ but not Ca(2+. Our simulations with G4898R likewise show a decrease in the preference of Ca(2+ over K(+ in the selectivity filter. Together, the computational and experimental results shed light on ion conductance and selectivity of RyR1 at an atomistic level.

Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement

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Gene A Morrill

2016-09-01

Full Text Available ABSTRACT: Globins contain one or more cavities that control or affect such functions as ligand movement and ligand binding. Here we report that the extended globin family [cytoglobin (Cygb; neuroglobin (Ngb; myoglobin (Mb; hemoglobin (Hb subunits Hba(α and Hbb(β] contain either a transmembrane (TM helix or pore-lining region as well as internal cavities. Protein motif/domain analyses indicate that Ngb and Hbb each contain 5 cholesterol-binding (CRAC/CARC domains and 1 caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding motifs. The Hb αβ-tetramer contains 14 cholesterol-binding domains. Computer algorithms indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions, whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba and pore-lining region (Hbb. The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues, 55 of 154 Mb residues and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to 8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities. Erythrocyte Hb αβ-tetramers are largely cytosolic but also bind to a membrane anion exchange protein, band 3, which contains a large internal cavity and 12 TM helices (5 being pore-lining regions. The Hba TM helix may be the erythrocyte membrane band 3 attachment site. Band 3 contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO movement within the large internal cavities and

The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins

Energy Technology Data Exchange (ETDEWEB)

Barta, Michael L.; Dickenson, Nicholas E.; Patil, Mrinalini; Keightley, Andrew; Wyckoff, Gerald J.; Picking, William D.; Picking, Wendy L.; Geisbrecht, Brian V. (UMKC); (OKLU)

2012-03-26

Many pathogenic Gram-negative bacteria utilize type III secretion systems (T3SSs) to alter the normal functions of target cells. Shigella flexneri uses its T3SS to invade human intestinal cells to cause bacillary dysentery (shigellosis) that is responsible for over one million deaths per year. The Shigella type III secretion apparatus is composed of a basal body spanning both bacterial membranes and an exposed oligomeric needle. Host altering effectors are secreted through this energized unidirectional conduit to promote bacterial invasion. The active needle tip complex of S. flexneri is composed of a tip protein, IpaD, and two pore-forming translocators, IpaB and IpaC. While the atomic structure of IpaD has been elucidated and studied, structural data on the hydrophobic translocators from the T3SS family remain elusive. We present here the crystal structures of a protease-stable fragment identified within the N-terminal regions of IpaB from S. flexneri and SipB from Salmonella enterica serovar Typhimurium determined at 2.1 {angstrom} and 2.8 {angstrom} limiting resolution, respectively. These newly identified domains are composed of extended-length (114 {angstrom} in IpaB and 71 {angstrom} in SipB) coiled-coil motifs that display a high degree of structural homology to one another despite the fact that they share only 21% sequence identity. Further structural comparisons also reveal substantial similarity to the coiled-coil regions of pore-forming proteins from other Gram-negative pathogens, notably, colicin Ia. This suggests that these mechanistically separate and functionally distinct membrane-targeting proteins may have diverged from a common ancestor during the course of pathogen-specific evolutionary events.

Neuronal Goα and CAPS regulate behavioral and immune responses to bacterial pore-forming toxins.

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Ferdinand C O Los

Full Text Available Pore-forming toxins (PFTs are abundant bacterial virulence factors that attack host cell plasma membranes. Host defense mechanisms against PFTs described to date all function in the host tissue that is directly attacked by the PFT. Here we characterize a rapid and fully penetrant cessation of feeding of Caenorhabditis elegans in response to PFT attack. We demonstrate via analyses of C. elegans mutants that inhibition of feeding by PFT requires the neuronal G protein Goα subunit goa-1, and that maintenance of this response requires neuronally expressed calcium activator for protein secretion (CAPS homolog unc-31. Independently from their role in feeding cessation, we find that goa-1 and unc-31 are additionally required for immune protection against PFTs. We thus demonstrate that the behavioral and immune responses to bacterial PFT attack involve the cross-talk between the nervous system and the cells directly under attack.

Distinction between Pore Assembly by Staphylococcal α-Toxin versus Leukotoxins

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Olivier Joubert

2007-01-01

Full Text Available The staphylococcal bipartite leukotoxins and the homoheptameric α-toxin belong to the same family of β-barrel pore-forming toxins despite slight differences. In the α-toxin pore, the N-terminal extremity of each protomer interacts as a deployed latch with two consecutive protomers in the vicinity of the pore lumen. N-terminal extremities of leukotoxins as seen in their three-dimensional structures are heterogeneous in length and take part in the β-sandwich core of soluble monomers. Hence, the interaction of these N-terminal extremities within structures of adjacent monomers is questionable. We show here that modifications of their N-termini by two different processes, using fusion with glutathione S-transferase (GST and bridging of the N-terminal extremity to the adjacent β-sheet via disulphide bridges, are not deleterious for biological activity. Therefore, bipartite leukotoxins do not need a large extension of their N-terminal extremities to form functional pores, thus illustrating a microheterogeneity of the structural organizations between bipartite leukotoxins and α-toxin.

Influence of corn flour as pore forming agent on porous ceramic material based mullite: Morphology and mechanical properties

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Ayala-Landeros J.G.

2016-01-01

Full Text Available Porous material was processed by the mixing, molding and pressing the ceramic material, afterward burnout and sintering; through the forming porous, using corn flour at different concentration (10, 15 and 20 wt.% as a pore forming agent; in order to determinate the influence of porous on the mechanical, morphological and structural properties. The effect of the volume fraction of corn flour in the mullite matrix, at various sintering temperature from 1100, 1200, 1300 and 1500°C were tested by Diffraction X ray, showing changes in crystalline phases of mullite (3Al2O3-2SiO2, as result of sintered temperatures. Presence of talcum powder in formula, also cause the formation of the cordierite and cristobalite crystalline phases, giving stability and adhesion to the structure of ceramic material. When sintering at temperatures between 1300 to 1500°C, and it was used the concentration of corn flour 15-20 wt.% as forming agent porous, it was found the better mechanical properties. The scanning electron microscopy analysis shows the presence of open porosity and anisotropy.

Methods for controlling pore morphology in aerogels using electric fields and products thereof

Science.gov (United States)

Worsley, Marcus A.; Baumann, Theodore F.; Satcher, Jr., Joe H.; Olson, Tammy Y.; Kuntz, Joshua D.; Rose, Klint A.

2017-12-16

In one embodiment, an aerogel or xerogel includes column structures of a material having minor pores therein and major pores devoid of the material positioned between the column structures, where longitudinal axes of the major pores are substantially parallel to one another. In another embodiment, a method includes heating a sol including aerogel or xerogel precursor materials to cause gelation thereof to form an aerogel or xerogel and exposing the heated sol to an electric field, wherein the electric field causes orientation of a microstructure of the sol during gelation, which is retained by the aerogel or xerogel. In one approach, an aerogel has elongated pores extending between a material arranged in column structures having structural characteristics of being formed from a sol exposed to an electric field that causes orientation of a microstructure of the sol during gelation which is retained by the elongated pores of the aerogel.

A model of lipid rearrangements during pore formation in the DPPC lipid bilayer.

Science.gov (United States)

Wrona, Artur; Kubica, Krystian

2017-07-10

The molecular bases of pore formation in the lipid bilayer remain unclear, as do the exact characteristics of their sizes and distributions. To understand this process, numerous studies have been performed on model lipid membranes including cell-sized giant unilamellar vesicles (GUV). The effect of an electric field on DPPC GUV depends on the lipid membrane state: in the liquid crystalline phase the created pores have a cylinder-like shape, whereas in the gel phase a crack has been observed. The aim of the study was to investigate the geometry of pores created in a lipid bilayer in gel and liquid crystalline phases in reference to literature experimental data. A mathematical model of the pore in a DPPC lipid bilayer developed based on the law of conservation of mass and the assumption of constant volume of lipid molecules, independent of their conformation, allows for analysis of pore shape and accompanying molecular rearrangements. The membrane area occupied by the pore of a cylinder-like shape is greater than the membrane area occupied by lipid molecules creating the pore structure (before pore appearance). Creation of such pores requires more space, which can be achieved by conformational changes of lipid chains toward a more compact state. This process is impossible for a membrane in the most compact, gel phase. We show that the geometry of the pores formed in the lipid bilayer in the gel phase must be different from the cylinder shape formed in the lipid bilayer in a liquid crystalline state, confirming experimental studies. Furthermore, we characterize the occurrence of the 'buffer' zone surrounding pores in the liquid crystalline phase as a mechanism of separation of neighbouring pores.

Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix

DEFF Research Database (Denmark)

Högel, Philipp; Götz, Alexander; Kuhne, Felix

2018-01-01

Flexible transmembrane helices frequently support the conformational transitions between different functional states of membrane proteins. While proline is well known to distort and destabilize transmembrane helices, the role of glycine is still debated. Here, we systematically investigated the e...

TIG Dressing Effects on Weld Pores and Pore Cracking of Titanium Weldments

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Hui-Jun Yi

2016-10-01

Full Text Available Weld pores redistribution, the effectiveness of using tungsten inert gas (TIG dressing to remove weld pores, and changes in the mechanical properties due to the TIG dressing of Ti-3Al-2.5V weldments were studied. Moreover, weld cracks due to pores were investigated. The results show that weld pores less than 300 μm in size are redistributed or removed via remelting due to TIG dressing. Regardless of the temperature condition, TIG dressing welding showed ductility, and there was a loss of 7% tensile strength of the weldments. Additionally, it was considered that porosity redistribution by TIG dressing was due to fluid flow during the remelting of the weld pool. Weld cracks in titanium weldment create branch cracks around pores that propagate via the intragranular fracture, and oxygen is dispersed around the pores. It is suggested that the pore locations around the LBZ (local brittle zone and stress concentration due to the pores have significant effects on crack initiation and propagation.

A new model for pore formation by cholesterol-dependent cytolysins.

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Cyril F Reboul

2014-08-01

Full Text Available Cholesterol Dependent Cytolysins (CDCs are important bacterial virulence factors that form large (200-300 Å membrane embedded pores in target cells. Currently, insights from X-ray crystallography, biophysical and single particle cryo-Electron Microscopy (cryo-EM experiments suggest that soluble monomers first interact with the membrane surface via a C-terminal Immunoglobulin-like domain (Ig; Domain 4. Membrane bound oligomers then assemble into a prepore oligomeric form, following which the prepore assembly collapses towards the membrane surface, with concomitant release and insertion of the membrane spanning subunits. During this rearrangement it is proposed that Domain 2, a region comprising three β-strands that links the pore forming region (Domains 1 and 3 and the Ig domain, must undergo a significant yet currently undetermined, conformational change. Here we address this problem through a systematic molecular modeling and structural bioinformatics approach. Our work shows that simple rigid body rotations may account for the observed collapse of the prepore towards the membrane surface. Support for this idea comes from analysis of published cryo-EM maps of the pneumolysin pore, available crystal structures and molecular dynamics simulations. The latter data in particular reveal that Domains 1, 2 and 4 are able to undergo significant rotational movements with respect to each other. Together, our data provide new and testable insights into the mechanism of pore formation by CDCs.

Molecular cloning and tissue-specific expression analysis of mouse spinesin, a type II transmembrane serine protease 5

International Nuclear Information System (INIS)

Watanabe, Yoshihisa; Okui, Akira; Mitsui, Shinichi; Kawarabuki, Kentaro; Yamaguchi, Tatsuyuki; Uemura, Hidetoshi; Yamaguchi, Nozomi

2004-01-01

We have previously reported novel serine proteases isolated from cDNA libraries of the human and mouse central nervous system (CNS) by PCR using degenerate oligodeoxyribonucleotide primers designed on the basis of the serine protease motifs, AAHC and DSGGP. Here we report a newly isolated serine protease from the mouse CNS. This protease is homologous (77.9% identical) to human spinesin type II transmembrane serine protease 5. Mouse spinesin (m-spinesin) is also composed of (from the N-terminus) a short cytoplasmic domain, a transmembrane domain, a stem region containing a scavenger-receptor-like domain, and a serine protease domain, as is h-spinesin. We also isolated type 1, type 2, and type 3 variant cDNAs of m-spinesin. Full-length spinesin (type 4) and type 3 contain all the domains, whereas type 1 and type 2 variants lack the cytoplasmic, transmembrane, and scavenger-receptor-like domains. Subcellular localization of the variant forms was analyzed using enhanced green fluorescent protein (EGFP) fusion proteins. EGFP-type 4 fusion protein was predominantly localized to the ER, Golgi apparatus, and plasma membrane, whereas EGFP-type 1 was localized to the cytoplasm, reflecting differential classification of m-spinesin variants into transmembrane and cytoplasmic types. We analyzed the distribution of m-spinesin variants in mouse tissues, using RT-PCR with variant-specific primer sets. Interestingly, transmembrane-type spinesin, types 3 and 4, was specifically expressed in the spinal cord, whereas cytoplasmic type, type 1, was expressed in multiple tissues, including the cerebrum and cerebellum. Therefore, m-spinesin variants may have distinct biological functions arising from organ-specific variant expression

Point mutations in the transmembrane region of the clic1 ion channel selectively modify its biophysical properties.

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Stefania Averaimo

Full Text Available Chloride intracellular Channel 1 (CLIC1 is a metamorphic protein that changes from a soluble cytoplasmic protein into a transmembrane protein. Once inserted into membranes, CLIC1 multimerises and is able to form chloride selective ion channels. Whilst CLIC1 behaves as an ion channel both in cells and in artificial lipid bilayers, its structure in the soluble form has led to some uncertainty as to whether it really is an ion channel protein. CLIC1 has a single putative transmembrane region that contains only two charged residues: arginine 29 (Arg29 and lysine 37 (Lys37. As charged residues are likely to have a key role in ion channel function, we hypothesized that mutating them to neutral alanine to generate K37A and R29A CLIC1 would alter the electrophysiological characteristics of CLIC1. By using three different electrophysiological approaches: i single channel Tip-Dip in artificial bilayers using soluble recombinant CLIC1, ii cell-attached and iii whole-cell patch clamp recordings in transiently transfected HEK cells, we determined that the K37A mutation altered the single-channel conductance while the R29A mutation affected the single-channel open probability in response to variation in membrane potential. Our results show that mutation of the two charged amino acids (K37 and R29 in the putative transmembrane region of CLIC1 alters the biophysical properties of the ion channel in both artificial bilayers and cells. Hence these charged residues are directly involved in regulating its ion channel activity. This strongly suggests that, despite its unusual structure, CLIC1 itself is able to form a chloride ion channel.

Pore growth in U-Mo/Al dispersion fuel

Energy Technology Data Exchange (ETDEWEB)

Kim, Yeon Soo, E-mail: yskim@anl.gov [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Jeong, G.Y.; Sohn, D.-S. [Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 689-798 (Korea, Republic of); Jamison, L.M. [Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 (United States)

2016-09-15

U-Mo/Al dispersion fuel is currently under development in the DOE’s Material Management and Minimization program to convert HEU-fueled research reactors to LEU-fueled reactors. In some demanding conditions in high-power and high-performance reactors, large pores form in the interaction layers between the U-Mo fuel particles and the Al matrix, which pose a potential to cause fuel failure. In this study, comprehension of the formation and growth of these pores was explored. As a product, a model to predict pore growth and porosity increase was developed. The model includes three major topics: fission gas release from the U-Mo and the IL to the pores, stress evolution in the fuel meat, and the effect of amorphous IL growth. Well-characterized in-pile data from reduced-size plates were used to fit the model parameters. A data set from full-sized plates, independent and distinctively different from those used to fit the model parameters, was used to examine the accuracy of the model. The model showed fair agreement with the measured data. The model suggested that the growth of the IL has a critical effect on pore growth, as both its material properties and energetics are favorable to pore formation. Therefore, one area of the current effort, focused on suppressing IL growth, appears to be on the right track to improve the performance of this fuel.

Induction of nano pore in Agrobacterial hemoglobin

Directory of Open Access Journals (Sweden)

Mojtaba Tousheh

2014-01-01

Full Text Available Introduction: A variety of oxygen-transport and -binding proteins exist in organisms including bacteria, protozoans, and fungi all have hemoglobin-like proteins. In addition to dealing with transport and sensing of oxygen, they may also deal with NO2, CO2, sulfide compounds, and even O2 scavenging in environments. Also they detoxified chlorinated materials like P450 enzymes and peroxidases and use as a detector of nitrate and hydrogen peroxide. Pore-forming bacterial globins are interested for filtration. Materials and methods: Although there are data for bacterial toxin as a filter, here we used Agrobacterial hem to induce nano pore in the heme structure using point mutation. Results: Investigations showed that three amino acids leucine 76, alanine 83 and histidine 80 are important for pore formation in Agrobacterium hemoglobin. A point mutation on leucine 76 to glycine, histidine 80 to asparagine and alanine 83 to lysine step by step led to create the nano pore 0.7- 0.8 nm in the globin. Discussion and conclusion: These mutations in bacterial hemoglobin increase the stability when mutation is with it’s at pH7. This mutation decreases the aliphatic index however increase the stability index.

Method of forming aluminum oxynitride material and bodies formed by such methods

Science.gov (United States)

Bakas, Michael P [Ammon, ID; Lillo, Thomas M [Idaho Falls, ID; Chu, Henry S [Idaho Falls, ID

2010-11-16

Methods of forming aluminum oxynitride (AlON) materials include sintering green bodies comprising aluminum orthophosphate or another sacrificial material therein. Such green bodies may comprise aluminum, oxygen, and nitrogen in addition to the aluminum orthophosphate. For example, the green bodies may include a mixture of aluminum oxide, aluminum nitride, and aluminum orthophosphate or another sacrificial material. Additional methods of forming aluminum oxynitride (AlON) materials include sintering a green body including a sacrificial material therein, using the sacrificial material to form pores in the green body during sintering, and infiltrating the pores formed in the green body with a liquid infiltrant during sintering. Bodies are formed using such methods.

Transmembrane-sequence-dependent overexpression and secretion of glycoproteins in Saccharomyces cerevisiae.

Science.gov (United States)

Schuster, M; Wasserbauer, E; Aversa, G; Jungbauer, A

2001-02-01

Protein expression using the secretory pathway in Saccharomyces cerevisiae can lead to high amounts of overexpressed and secreted proteins in culture supernatants in a short period of time. These post-translational modified expression products can be purified up to >90% in a single step. The overexpression and secretion of the transmembrane glycoprotein signaling lymphocytic activation molecule (SLAM) was studied. SLAM belongs to the immunoglobulin superfamily and its engagement results in T-cell expansion and INF-gamma production. The molecule is composed of an extracellular, a single-span transmembrane and a cytoplasmatic domain. The extracellular part may be relevant for stimulation studies in vitro since SLAM is a high-affinity self-ligand. Therefore several fragments of this region have been expressed as Flag-fusions in S. cerevisiae: a full-length fragment containing the transmembrane region and the autologous signal sequence, another without the transmembrane region, and two fragments without the autologous signal sequence with and without the transmembrane region. By molecular cloning, the different deletion mutants of the cDNA encoding the full-length construct have been inserted in a yeast episomal plasmid. Upstream of the cDNA, the alpha-leader sequence of a yeast mating pheromone has been cloned to direct the fusion proteins into the secretory protein maturation pathway. All four fragments were expressed but yield, location, and maturation were highly influenced by the transmembrane domain and the autologous signal sequence. Only the fragment without autologous signal sequence and transmembrane domain could be efficiently secreted. High-mannose glycosylation was analyzed by lectin mapping and digestion with specific glycosidases. After enzyme treatment, a single band product with the theoretical size could be detected and identified as SLAM by a specific monoclonal antibody. The fusion protein concentration in the supernatant was 30 microg/ml. The

Design of pore size of macroporous ceramic substrates

International Nuclear Information System (INIS)

Szewald, O.; Kotsis, I.

2000-01-01

A method has been developed for the design of macro-porous ceramic substrates. Based on geometrical and regression models detailed technology was worked out for producing these 100% open porous filters, which were made using quasi homo-disperse fractions of corundum of diameters of several tens and hundreds microns and glassy binding material. Axial pressing was used as a forming process. Pore networks with size distribution that can be defined by a curve having one maximum were provided applying the above technology. Based on geometrical considerations and measurements it was proved that these maximums are at characteristic pore sizes that depend only on characteristic size of the original grain fractions and on the extent of the axial forming pressure. Copyright (2000) AD-TECH - International Foundation for the Advancement of Technology Ltd

Preparation of anode-electrolyte structures using graphite, sodium bicarbonate or citric acid as pore forming agents for application in solid oxide fuel cells

Energy Technology Data Exchange (ETDEWEB)

Paz Fiuza, Raigenis da; Silva, Marcos Aurelio da; Guedes, Bruna C.; Pontes, Luiz A.; Boaventura, Jaime Soares [UFBA, Salvador, Bahia (Brazil). Energy and Materials Science Group

2010-07-01

Cermets based on Ni supported on YSZ or GDC were prepared for use as anode in direct reform SOFCs. NaHCO3 (Na-Ni-YSZ and Na-Ni-GDC) or citric acid (Ac-Ni-YSZ and Ac-Ni-GDC) were used as pore forming agents (PFAs). The SOFC anode was also prepared using graphite (G-Ni-YSZ and G-Ni-GDC) as PFA for the purposes of comparison. The testing unitary SOFC, planar type, was made by pressing the anode-electrolyte assembly, followed by sintering at 1500 C. After this, LSM (lanthanum and strontium manganite) paint was used for the cathode deposition. The powdered cermets were evaluated in ethanol steam reforming at 650 C. The ethanol conversion was 84% and 32% for cermets Na-Ni-YSZ and G-Ni-YSZ, respectively and the selectivity to H{sub 2} was 32 and 20% for the two cermets, respectively. The Na-Ni-YSZ cermet was ten times more resistant to carbon deposition than the G-Ni-YSZ cermet. SEM micrographs of the anode-electrolyte assembly showed that the use of NaHCO{sub 3} as PFA created a well formed interface between layers with homogeneously distributed pores. In contrast, graphite as PFA formed a loose interface between anode and electrolyte. The performance of the unitary SOFC was evaluated using ethanol, hydrogen or methane as fuel. The cell operated well using any of these fuels; however, they exhibited different electrochemical behavior. (orig.)

Different transport behaviors of NH4 (+) and NH3 in transmembrane cyclic peptide nanotubes.

Science.gov (United States)

Zhang, Mingming; Fan, Jianfen; Xu, Jian; Weng, Peipei; Lin, Huifang

2016-10-01

Two water-filled transmembrane cyclic peptide nanotubes (CPNTs) of 8×cyclo-(WL)n=4,5/POPE were chosen to investigate the dependences of the transport properties of the positive NH4 (+) and neutral NH3 on the channel radius. Molecular dynamic simulations revealed that molecular charge, size, ability to form H-bonds and channel radius all significantly influence the behaviors of NH4 (+) and NH3 in a CPNT. Higher electrostatic interactions, more H-bonds, and water-bridges were found in the NH4 (+) system, resulting in NH4 (+) meeting higher energy barriers, while NH3 can enter, exit and permeate the channels effortlessly. This work sheds a first light on the differences between the mechanisms of NH4 (+) and NH3 moving in a CPNT at an atomic level. Graphical Abstract Snapshot of the simulation system of NH4 (+)_octa-CPNT with an NH4 (+) initially positioned at one mouth of the tube, PMF profiles for single NH4 (+) ion and NH3 molecule moving through water-filled transmembrane CPNTs of 8×cyclo-(WL)n=4,5/POPE and sketch graphs of the possible H-bond forms of NH3 and NH4 (+) with the neighboring water.

Lattice density functional theory investigation of pore shape effects. I. Adsorption in single nonperiodic pores.

Science.gov (United States)

Malanoski, A P; van Swol, Frank

2002-10-01

A fully explicit in three dimensions lattice density functional theory is used to investigate adsorption in single nonperiodic pores. The effect of varying pore shape from the slits and cylinders that are normally simulated was our primary interest. A secondary concern was the results for pores with very large diameters. The shapes investigated were square pores with or without surface roughness, cylinders, right triangle pores, and trapezoidal pores. It was found that pores with very similar shape factors gave similar results but that the introduction of acute angled corners or very large side ratio lengths in rectangular pores gave results that were significantly different. Further, a rectangular pore going towards the limit of infinite side ratio does not approach the results of a slit pore. In all of these cases, the importance of features that are present for only a small portion of the pore is demonstrated.

Recombinant expression in E. coli of human FGFR2 with its transmembrane and extracellular domains

Directory of Open Access Journals (Sweden)

Adam Bajinting

2017-06-01

Full Text Available Fibroblast growth factor receptors (FGFRs are a family of receptor tyrosine kinases containing three domains: an extracellular receptor domain, a single transmembrane helix, and an intracellular tyrosine kinase domain. FGFRs are activated by fibroblast growth factors (FGFs as part of complex signal transduction cascades regulating angiogenesis, skeletal formation, cell differentiation, proliferation, cell survival, and cancer. We have developed the first recombinant expression system in E. coli to produce a construct of human FGFR2 containing its transmembrane and extracellular receptor domains. We demonstrate that the expressed construct is functional in binding heparin and dimerizing. Size exclusion chromatography demonstrates that the purified FGFR2 does not form a complex with FGF1 or adopts an inactive dimer conformation. Progress towards the successful recombinant production of intact FGFRs will facilitate further biochemical experiments and structure determination that will provide insight into how extracellular FGF binding activates intracellular kinase activity.

Terbinafine is a novel and selective activator of the two-pore domain potassium channel TASK3.

Science.gov (United States)

Wright, Paul D; Veale, Emma L; McCoull, David; Tickle, David C; Large, Jonathan M; Ococks, Emma; Gothard, Gemma; Kettleborough, Catherine; Mathie, Alistair; Jerman, Jeffrey

2017-11-04

Two-pore domain potassium channels (K2Ps) are characterized by their four transmembrane domain and two-pore topology. They carry background (or leak) potassium current in a variety of cell types. Despite a number of important roles there is currently a lack of pharmacological tools with which to further probe K2P function. We have developed a cell-based thallium flux assay, using baculovirus delivered TASK3 (TWIK-related acid-sensitive K + channel 3, KCNK9, K2P9.1) with the aim of identifying novel, selective TASK3 activators. After screening a library of 1000 compounds, including drug-like and FDA approved molecules, we identified Terbinafine as an activator of TASK3. In a thallium flux assay a pEC50 of 6.2 ( ±0.12) was observed. When Terbinafine was screened against TASK2, TREK2, THIK1, TWIK1 and TRESK no activation was observed in thallium flux assays. Several analogues of Terbinafine were also purchased and structure activity relationships examined. To confirm Terbinafine's activation of TASK3 whole cell patch clamp electrophysiology was carried out and clear potentiation observed in both the wild type channel and the pathophysiological, Birk-Barel syndrome associated, G236R TASK3 mutant. No activity at TASK1 was observed in electrophysiology studies. In conclusion, we have identified the first selective activator of the two-pore domain potassium channel TASK3. Copyright © 2017 Elsevier Inc. All rights reserved.

Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length.

Science.gov (United States)

Portella, Guillem; Pohl, Peter; de Groot, Bert L

2007-06-01

We investigated the structural and energetic determinants underlying water permeation through peptidic nanopores, motivated by recent experimental findings that indicate that water mobility in single-file water channels displays nonlinear length dependence. To address the molecular mechanism determining the observed length dependence, we studied water permeability in a series of designed gramicidin-like channels of different length using atomistic molecular dynamics simulations. We found that within the studied range of length the osmotic water permeability is independent of pore length. This result is at variance with textbook models, where the relationship is assumed to be linear. Energetic analysis shows that loss of solvation rather than specific water binding sites in the pore form the main energetic barrier for water permeation, consistent with our dynamics results. For this situation, we propose a modified expression for osmotic permeability that fully takes into account water motion collectivity and does not depend on the pore length. Different schematic barrier profiles are discussed that explain both experimental and computational interpretations, and we propose a set of experiments aimed at validation of the presented results. Implications of the results for the design of peptidic channels with desired permeation characteristics are discussed.

A portable lipid bilayer system for environmental sensing with a transmembrane protein.

Directory of Open Access Journals (Sweden)

Ryuji Kawano

Full Text Available This paper describes a portable measurement system for current signals of an ion channel that is composed of a planar lipid bilayer. A stable and reproducible lipid bilayer is formed in outdoor environments by using a droplet contact method with a micropipette. Using this system, we demonstrated that the single-channel recording of a transmembrane protein (alpha-hemolysin was achieved in the field at a high-altitude (∼3623 m. This system would be broadly applicable for obtaining environmental measurements using membrane proteins as a highly sensitive sensor.

Pore structure, mechanical properties and polymer characteristics of porous materials impregnated with methylmethacrylate

International Nuclear Information System (INIS)

Hastrup, K.

1976-05-01

The pore structure of porous materials plays a decisive role with regard to many properties of the materials. One therefore expects property improvement due to impregnation to be mostly brought about as a result of pore structure modification. This supposition formed the basis for the project here presented, which had the main aim of investigating polymer impregnation in relation to pore structure. Objectives were: 1) to examine the pore structure of hardened cement paste, beech wood and porous glass before and after gas-phase impregnation with methyl-methacrylate monomer and in situ polymerization, 2) to investigate the influence of the pore structure on the molecular weight of the polymer, 3) to investigate the influence of the degree of pore filling on the elastic modulus, damping coefficient and bending strength. (author)

Pore shape of honeycomb-patterned films: modulation and interfacial behavior.

Science.gov (United States)

Wan, Ling-Shu; Ke, Bei-Bei; Zhang, Jing; Xu, Zhi-Kang

2012-01-12

The control of the pore size of honeycomb-patterned films has been more or less involved in most work on the topic of breath figures. Modulation of the pore shape was largely ignored, although it is important to applications in replica molding, filtration, particle assembly, and cell culture. This article reports a tunable pore shape for patterned films prepared from commercially available polystyrene (PS). We investigated the effects of solvents including tetrahydrofuran (THF) and chloroform (CF) and hydrophilic additives including poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA), poly(ethylene glycol) (PEG), and poly(N-vinyl pyrrolidone) (PVP). Water droplets on/in the polymer solutions were observed and analyzed for simulating the formation and stabilization of breath figures. Interfacial tensions of the studied systems were measured and considered as a main factor to modulate the pore shape. Results indicate that the pores gradually change from near-spherical to ellipsoidal with the increase of additive content when using CF as the solvent; however, only ellipsoidal pores are formed from the THF solution. It is demonstrated that the aggregation of the additives at the water/polymer solution interface is more efficient in the THF solution than that in the CF solution. This aggregation decreases the interfacial tension, stabilizes the condensed water droplets, and shapes the pores of the films. The results may facilitate our understanding of the dynamic breath figure process and provide a new pathway to prepare patterned films with different pore structures.

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

Science.gov (United States)

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.

Optical study of the ultrasonic formation process of noble metal nanoparticles dispersed inside the pores of monolithic mesoporous silica

CERN Document Server

Fu Gan Hua; Kan Cai Xia; Li Cun Cheng; Fang Qi

2003-01-01

Gold nanoparticles dispersed inside the pores of monolithic mesoporous silica were prepared by soaking the silica in a gold (III) ion solution and subsequent ultrasound irradiation. The formation process of gold nanoparticles in the pores of mesoporous silica was investigated based on optical measurements of wrapped and naked soaked silica after ultrasonic irradiation, and the reduction rate effect in solution and pre-soaking effect. It has been shown that acoustic cavitation cannot occur in nano-sized pores. The gold nanoparticles in silica are not formed in situ within the pores but produced mainly by diffusion of the gold clusters formed in the solution during irradiation into the pores. The radicals formed in solution are exhausted before entering the pores of silica. There exists a critical reduction rate in solution, at which the yield of gold nanoparticles in silica reaches a maximum, and above which there is a decrease in the yield. This is attributed to too quick a growth or aggregation of gold clust...

Effects of carbon coating and pore corrugation on capillary condensation of nitrogen in SBA-15 mesoporous silica.

Science.gov (United States)

Morishige, Kunimitsu

2013-09-24

To examine the origin of an ink-bottle-like structure in SBA-15 formed by carbon coating and the effects of pore corrugation on capillary condensation and evaporation of a vapor in the cylindrical pores, we measured the adsorption isotherms of nitrogen at 77 K on 10 kinds of SBA-15 samples before and after a carbon coating process by the exposure to acetylene at 1073 K, as well as desorption scanning curves and subloops on the untreated samples. These SBA-15 samples were synthesized under the different conditions of initial SiO2/P123 ratio and hydrothermal treatment. SBA-15 with relatively large microporosity tends to form easily constrictions inside the main channels by the carbon coating. This strongly suggests that the rough pore walls of SBA-15 may induce the incomplete wetting of carbon layers on the pore walls to form the constrictions inside the cylindrical pores. A comparison of two subloops implies that the pores of SBA-15 synthesized with a SiO2/P123 ratio of 75 consist of an assembly of connecting domains of different diameters; that is, the pores are highly corrugated. For SBA-15 synthesized with a SiO2/P123 ratio of 60, the amplitude of the pore corrugation is significantly decreased by the prolonged hydrothermal treatment at 373 K. On the other hand, for SBA-15 synthesized with a SiO2/P123 ratio of 45, the amplitude of the corrugation is negligibly small, although the cylindrical pores are interconnected through narrow necks with each other. It is found that the smaller the amplitude of the pore corrugation, the smaller the width of the hysteresis loop.

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

Energy Technology Data Exchange (ETDEWEB)

Van Eyndhoven, G., E-mail: geert.vaneyndhoven@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Kurttepeli, M. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Van Oers, C.J.; Cool, P. [Laboratory of Adsorption and Catalysis, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Bals, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Batenburg, K.J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica, Science Park 123, NL-1090 GB Amsterdam (Netherlands); Mathematical Institute, Universiteit Leiden, Niels Bohrweg 1, NL-2333 CA Leiden (Netherlands); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium)

2015-01-15

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. - Highlights: • An electron tomography reconstruction/segmentation method for nanoporous materials. • The method exploits the porous nature of the scanned material. • Validated extensively on both simulation and real data experiments. • Results in increased image resolution and improved porosity quantification.

Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

Directory of Open Access Journals (Sweden)

Tzilhav Shem-Ad

Full Text Available 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.

Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

Science.gov (United States)

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.

Effects of Coke Calcination Level on Pore Structure in Carbon Anodes

Science.gov (United States)

Fang, Ning; Xue, Jilai; Lang, Guanghui; Bao, Chongai; Gao, Shoulei

2016-02-01

Effects of coke calcination levels on pore structure of carbon anodes have been investigated. Bench anodes were prepared by 3 types of cokes with 4 calcination temperatures (800°C, 900°C, 1000°C and 1100°C). The cokes and anodes were characterized using hydrostatic method, air permeability determination, mercury porosimetry, image analysis and confocal microscopy (CSLM). The cokes with different calcination levels are almost the same in LC values (19-20 Å) and real density (1.967-1.985 g/cm3), while the anode containing coke calcined at 900°C has the lowest open porosity and air permeability. Pore size distribution (represented by Anode H sample) can be roughly divided into two ranges: small and medium pores in diameter of 10-400 μm and large pores of 400-580 μm. For the anode containing coke calcined at 800°C, a number of long, narrow pores in the pore size range of 400-580 μm are presented among cokes particles. Formation of these elongated pores may be attributed to coke shrinkages during the anode baking process, which may develop cracking in the anode under cell operations. More small or medium rounded pores with pore size range of 10-400 μm emerge in the anodes with coke calcination temperatures of 900°C, 1000°C and 1100°C, which may be generated due to release of volatiles from the carbon anode during baking. For the anode containing coke calcined at 1100°C, it is found that many rounded pores often closely surround large coke particles, which have potential to form elongated, narrow pores.

Inhibition of the pore-forming protein perforin by a series of aryl-substituted isobenzofuran-1(3H)-ones.

Science.gov (United States)

Spicer, Julie A; Huttunen, Kristiina M; Miller, Christian K; Denny, William A; Ciccone, Annette; Browne, Kylie A; Trapani, Joseph A

2012-02-01

An aryl-substituted isobenzofuran-1(3H)-one lead compound was identified from a high throughput screen designed to find inhibitors of the lymphocyte pore-forming protein perforin. A series of analogs were then designed and prepared, exploring structure-activity relationships through variation of 2-thioxoimidazolidin-4-one and furan subunits on an isobenzofuranone core. The ability of the resulting compounds to inhibit the lytic activity of both isolated perforin protein and perforin delivered in situ by intact KHYG-1 natural killer effector cells was determined. Several compounds showed excellent activity at concentrations that were non-toxic to the killer cells. This series represents a significant improvement on previous classes of compounds, being substantially more potent and largely retaining activity in the presence of serum. Copyright © 2011 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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.

Pore channel surface modification for enhancing anti-fouling membrane distillation

Science.gov (United States)

Qiu, Haoran; Peng, Yuelian; Ge, Lei; Villacorta Hernandez, Byron; Zhu, Zhonghua

2018-06-01

Membrane surface modification by forming a functional layer is an effective way to improve the anti-fouling properties of membranes; however, the additional layer and the potential blockage of bulk pores may increase the mass transfer resistance and reduce the permeability. In this study, we applied a novel method of preparing anti-fouling membranes for membrane distillation by dispersing graphene oxide (GO) on the channel surface of polyvinylidene fluoride membranes. The surface morphology and properties were characterized by scanning electron microscopy, atomic force microscope, and Fourier transform infrared spectrometry. Compared to the membrane surface modification by nanoparticles (e.g. SiO2), GO was mainly located on the pore surface of the membrane bulk, rather than being formed as an individual layer onto the membrane surface. The performance was evaluated via a direct-contact membrane distillation process with anionic and cationic surfactants as the foulants, separately. Compared to the pristine PVDF membrane, the anti-fouling behavior and distillate flux of the GO-modified membranes were improved, especially when using the anionic surfactant as the foulant. The enhanced anti-fouling performance can be attributed to the oxygen containing functional groups in GO and the healing of the membrane pore defects. This method may provide an effective route to manipulate membrane pore surface properties for anti-fouling separation without increasing mass transfer resistance.

Septal Pore Caps in Basidiomycetes, Composition and Ultrastructure

NARCIS (Netherlands)

Driel, K.G.A. van

2007-01-01

Filamentous fungi, including Ascomycota and Basidiomycota, form mycelia that consist of a network of apical growing hyphae. These hyphae are separated into cellular compartments by septa that have pores of about 70 to 500 nm in diameter. The cytoplasm within the mycelium is thus continuous

Weathering Effect on {sup 99}Tc Leachability from Cementitious Waste Form

Energy Technology Data Exchange (ETDEWEB)

Um, Wooyong [Pohang Univ. of Science and Technology, Pohang (Korea, Republic of)

2012-07-01

The mass transfer of contaminants from the solid phase to the waste form pore water, and subsequently out of the solid waste form, is directly related to the number and size distribution of pores as well as the microstructure of the waste form. Because permeability and porosity are controlled by pore aperture size, pore volume, and pore distribution, it is important to have some indication of how these characteristics change in the waste form during weathering. Knowledge of changes in these key parameters can be used to develop predictive models that estimate diffusivity or permeability of radioactive contaminants can be used to develop predictive models that estimate diffusivity or permeability of radioactive contaminants from waste forms for long-term performance assessment. It is known that dissolution or precipitation of amorphous/crystalline phases within waste forms alters their pore structure and controls the transport of contaminants our of waste forms. One very important precipitate is calcite, which is formed as a result of carbonation reactions in cement and other high-alkalinity waste forms. Enhanced oxidation can also increase Tc leachability from the waste form. To account for these changes, weathering experiments were conducted in advance to increase our understating of the long-term Tc leachability, especially out of the cementitious waste form. Pore structure analysis was characterized using both N{sub 2} absorption analysis and XMT techniques, and the results show that cementitious waste form is a relatively highly-porous material compared to other waste forms studied in this task, Detailed characterization of Cast Stone chunks and monolith specimens indicate that carbonation reactions can change the Cast Stone pore structure, which in turn may correlate with Tc leachability. Short carbonation reaction times for the Cast Stone causes pore volume and surface area increases, while the average pore diameter decreases. Based on the changes in pore

The impact of calcium carbonate as pore forming agent and drug entrapment method towards drug dissolution mechanism of amoxicillin trihydrate encapsulated by chitosan-methyl cellulose semi-IPN hydrogel for floating drug delivery system

Science.gov (United States)

Dewantara, Fauzi; Budianto, Emil

2018-04-01

Chitosan-methyl cellulose semi-IPN hydrogel is used as floating drug delivery system, and calcium carbonate also added as pore forming agent. The hydrogel network arranged by not only using biopolymer chitosan and methyl cellulose, but also the crosslink agent that is glutaraldehyde. Amoxicillin trihydrate entrapped into the polymer network with two different method, in situ loading and post loading. Furthermore both method has been tested for drug entrapment efficiency along with drug dissolution test, and the result for drug entrapment efficiency is in situ loading method has highest value of 100%, compared to post loading method which has value only 71%. Moreover, at the final time of drug dissolution test shows in situ loading method has value of 96% for total accumulative of drug dissolution, meanwhile post loading method has 72%. The value of drug dissolution test from both method is used for analyzing drug dissolution mechanism of amoxicillin trihydrate from hydrogel network with four mathematical drug mechanism models as parameter. The polymer network encounter destructive degradation causes by acid solution which used as dissolution medium, and the level of degradation is observed with optical microscope. However the result shows that degradation of the polymer network doesn't affect drug dissolution mechanism directly. Although the pore forming agent causes the pore inside the hydrogel network create interconnection and it was quite influential to drug dissolution mechanism. Interconnected pore is observed with Scanning Electron Microscope (SEM) and shows that the amount and area of interconnected pore inside the hydrogel network is increasing as drug dissolution goes on.

Stochastic generation of explicit pore structures by thresholding Gaussian random fields

Energy Technology Data Exchange (ETDEWEB)

Hyman, Jeffrey D., E-mail: jhyman@lanl.gov [Program in Applied Mathematics, University of Arizona, Tucson, AZ 85721-0089 (United States); Computational Earth Science, Earth and Environmental Sciences (EES-16), and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544 (United States); Winter, C. Larrabee, E-mail: winter@email.arizona.edu [Program in Applied Mathematics, University of Arizona, Tucson, AZ 85721-0089 (United States); Department of Hydrology and Water Resources, University of Arizona, Tucson, AZ 85721-0011 (United States)

2014-11-15

We provide a description and computational investigation of an efficient method to stochastically generate realistic pore structures. Smolarkiewicz and Winter introduced this specific method in pores resolving simulation of Darcy flows (Smolarkiewicz and Winter, 2010 [1]) without giving a complete formal description or analysis of the method, or indicating how to control the parameterization of the ensemble. We address both issues in this paper. The method consists of two steps. First, a realization of a correlated Gaussian field, or topography, is produced by convolving a prescribed kernel with an initial field of independent, identically distributed random variables. The intrinsic length scales of the kernel determine the correlation structure of the topography. Next, a sample pore space is generated by applying a level threshold to the Gaussian field realization: points are assigned to the void phase or the solid phase depending on whether the topography over them is above or below the threshold. Hence, the topology and geometry of the pore space depend on the form of the kernel and the level threshold. Manipulating these two user prescribed quantities allows good control of pore space observables, in particular the Minkowski functionals. Extensions of the method to generate media with multiple pore structures and preferential flow directions are also discussed. To demonstrate its usefulness, the method is used to generate a pore space with physical and hydrological properties similar to a sample of Berea sandstone. -- Graphical abstract: -- Highlights: •An efficient method to stochastically generate realistic pore structures is provided. •Samples are generated by applying a level threshold to a Gaussian field realization. •Two user prescribed quantities determine the topology and geometry of the pore space. •Multiple pore structures and preferential flow directions can be produced. •A pore space based on Berea sandstone is generated.

Adsorption of Carbon Dioxide onto Tetraethylenepentamine Impregnated PMMA Sorbents with Different Pore Structure

Energy Technology Data Exchange (ETDEWEB)

Jo, Dong Hyun; Park, Cheonggi; Jung, Hyunchul; Kim, Sung Hyun [Korea University, Seoul (Korea, Republic of)

2015-02-15

Poly(methyl methacrylate) (PMMA) supports and amine additives were investigated to adsorb CO{sub 2}. PMMA supports were fabricated by using different ratio of pore forming agents (porogen) to control the BET specific surface area, pore volume and distribution. Toluene and xylene are used for porogens. Supported amine sorbents were prepared by wet impregnation of tetraethylenepentamine (TEPA) on PMMA supports. So we could identify the effect of the pore structure of supports and the quantity of impregnated TEPA on the adsorption capacity. The increased amount of toluene as pore foaming agent resulted in the decreased average pore diameter and the increased BET surface area. Polymer supports with huge different pore distribution could be fabricated by controlling the ratio of porogen. After impregnation, the support with micropore structure is supposed the pore blocking and filling effect so that it has low CO{sub 2} capacity and kinetics due to the difficulty of diffusing. Macropore structure indicates fast adsorption capacity and low influence of amine loading. In case of support with mesopore, it has high performance of adsorption capacity and kinetics. So high surface area and meso-/macro- pore structure is suitable for CO{sub 2} capture.

Enterocin P Causes Potassium Ion Efflux from Enterococcus faecium T136 Cells

Science.gov (United States)

Herranz, Carmen; Cintas, Luis M.; Hernández, Pablo E.; Moll, Gert N.; Driessen, Arnold J. M.

2001-01-01

Enterocin P is a bacteriocin produced by Enterococcus faecium P13. We studied the mechanism of its bactericidal action using enterocin-P-sensitive E. faecium T136 cells. The bacteriocin is incapable of dissipating the transmembrane pH gradient. On the other hand, depending on the buffer used, enterocin P dissipates the transmembrane potential. Enterocin P efficiently elicits efflux of potassium ions, but not of intracellularly accumulated anions like phosphate and glutamate. Taken together, these data demonstrate that enterocin P forms specific, potassium ion-conducting pores in the cytoplasmic membrane of target cells. PMID:11181377

Size Control of Porous Silicon-Based Nanoparticles via Pore-Wall Thinning.

Science.gov (United States)

Secret, Emilie; Leonard, Camille; Kelly, Stefan J; Uhl, Amanda; Cozzan, Clayton; Andrew, Jennifer S

2016-02-02

Photoluminescent silicon nanocrystals are very attractive for biomedical and electronic applications. Here a new process is presented to synthesize photoluminescent silicon nanocrystals with diameters smaller than 6 nm from a porous silicon template. These nanoparticles are formed using a pore-wall thinning approach, where the as-etched porous silicon layer is partially oxidized to silica, which is dissolved by a hydrofluoric acid solution, decreasing the pore-wall thickness. This decrease in pore-wall thickness leads to a corresponding decrease in the size of the nanocrystals that make up the pore walls, resulting in the formation of smaller nanoparticles during sonication of the porous silicon. Particle diameters were measured using dynamic light scattering, and these values were compared with the nanocrystallite size within the pore wall as determined from X-ray diffraction. Additionally, an increase in the quantum confinement effect is observed for these particles through an increase in the photoluminescence intensity of the nanoparticles compared with the as-etched nanoparticles, without the need for a further activation step by oxidation after synthesis.

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

Science.gov (United States)

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

2012-12-01

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

Nano-porous anodic aluminium oxide membranes with 6-19 nm pore diameters formed by a low-potential anodizing process

Energy Technology Data Exchange (ETDEWEB)

Zhang Fan; Liu Xiaohua; Pan Caofeng; Zhu Jing [Beijing National Center for Electron Microscopy, Tsinghua University, Beijing 100084 (China); Laboratory of Advanced Materials, Department of Materials Science and Engineering, Tsinghua University, Beijing 100084 (China)

2007-08-29

Self-organized nano-porous anodic aluminium oxide (AAO) membranes with small pore diameters were obtained by applying a low anodizing potential in sulfuric acid solutions. The pore diameters of the as-prepared AAO membranes were in the range of about 6-19 nm and the interpore distances were about 20-58 nm. Low potentials (6-18 V) were applied in anodizing processes to make such small pores. A linear relationship between the anodizing potential (U{sub a}) and the interpore distance (D{sub int}) was also revealed. By carefully monitoring the current density's evolution as a function of time with different U{sub a} (2-18 V) during the anodizing processes, a new formula is proposed to simulate the self-ordering anodizing process.

Conformational Plasticity of the Influenza A M2 Transmembrane Helix in Lipid Bilayers Under Varying pH, Drug Binding and Membrane Thickness

Science.gov (United States)

Hu, Fanghao; Luo, Wenbin; Cady, Sarah D.; Hong, Mei

2010-01-01

Membrane proteins change their conformations to respond to environmental cues, thus conformational plasticity is important for function. The influenza A M2 protein forms an acid-activated proton channel important for the virus lifecycle. Here we have used solid-state NMR spectroscopy to examine the conformational plasticity of membrane-bound transmembrane domain of M2 (M2TM). 13C and 15N chemical shifts indicate coupled conformational changes of several pore-facing residues due to changes in bilayer thickness, drug binding and pH. The structural changes are attributed to the formation of a well-defined helical kink at G34 in the drug-bound state and in thick lipid bilayers, non-ideal backbone conformation of the secondary-gate residue V27 in the presence of drug, and non-ideal conformation of the proton-sensing residue H37 at high pH. The chemical shifts constrained the (ϕ, ψ) torsion angles for three basis states, the equilibrium among which explains the multiple resonances per site in the NMR spectra under different combinations of bilayer thickness, drug binding and pH conditions. Thus, conformational plasticity is important for the proton conduction and inhibition of M2TM. The study illustrates the utility of NMR chemical shifts for probing the structural plasticity and folding of membrane proteins. PMID:20883664

Optimization of hybrid laser arc welding of 42CrMo steel to suppress pore formation

Energy Technology Data Exchange (ETDEWEB)

Zhang, Yan [Hunan University, State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body, Changsha (China); Hunan Institute of Science and Technology, College of Mechanical Engineering, Yueyang (China); Chen, Genyu; Mao, Shuai; Zhou, Cong; Chen, Fei [Hunan University, State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body, Changsha (China)

2017-06-15

The hybrid laser arc welding (HLAW) of 42CrMo quenched and tempered steel was conducted. The effect of the processing parameters, such as the relative positions of the laser and the arc, the shielding gas flow rate, the defocusing distance, the laser power, the wire feed rate and the welding speed, on the pore formation was analyzed, the morphological characteristics of the pores were analyzed using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). The results showed that the majority of the pores were invasive. The pores formed at the leading a laser (LA) welding process were fewer than those at the leading a arc (AL) welding process. Increasing the shielding gas flow rate could also facilitate the reduction of pores. The laser power and the welding speed were two key process parameters to reduce the pores. The flow of the molten pool, the weld cooling rate and the pore escaping rate as a result of different parameters could all affect pore formation. An ideal pore-free weld was obtained for the optimal welding process parameters. (orig.)

Crystallization and preliminary X-ray diffraction analysis of P30, the transmembrane domain of pertactin, an autotransporter from Bordetella pertussis

International Nuclear Information System (INIS)

Zhu, Yanshi; Black, Isobel; Roszak, Aleksander W.; Isaacs, Neil W.

2007-01-01

P30, the transmembrane C-terminal domain of pertactin from B. pertussis has been crystallized after refolding in vitro. Preliminary X-ray crystallographic data are reported. P30, the 32 kDa transmembrane C-terminal domain of pertactin from Bordetella pertussis, is supposed to form a β-barrel inserted into the outer membrane for the translocation of the passenger domain. P30 was cloned and expressed in inclusion bodies in Escherichia coli. After refolding and purification, the protein was crystallized using the sitting-drop vapour-diffusion method at 292 K. The crystals diffract to a resolution limit of 3.5 Å using synchrotron radiation and belong to the hexagonal space group P6 1 22, with unit-cell parameters a = b = 123.27, c = 134.43 Å

Enhanced transdermal delivery with less irritation by magainin pore-forming peptide with a N-lauroylsarcosine and sorbitan monolaurate mixture.

Science.gov (United States)

Lee, Haerin; Park, Juhyun; Kim, Yeu-Chun

2018-02-01

Transdermal drug delivery is advantageous over other conventional drug administration routes. However, it can be inefficient because of the natural barrier of the stratum corneum which is the uppermost layer of the skin. A previous study verified that the treatment of magainin pore-forming peptide with N-lauroylsarcosine (NLS) on human skin can increase skin permeability by 47-fold. However, NLS is well known as a potential skin irritant. The irritation potential of NLS is known to decrease when mixed with sorbitan monolaurate (S20). Encouraged by these results, we combined S20 with magainin-NLS to enhance transdermal drug transport with less skin irritation. In this study, nine groups with magainin and NLS:S20 mixtures at different concentrations and weight fractions were screened to maximize their synergistic effect. To quantify the efficacy to toxicity ratio of each formulation, we defined the ratio as the "enhancement ratio/irritation potential (ER/IP)." The ER was observed by Franz cell diffusion of the target drug fluorescein, and the IP was measured by the cytotoxicity of the NIH/3T3 mouse fibroblast cell line. As a result, the magainin with the NLS:S20 mixture increased the permeability of porcine skin as well as decreased the toxicity. Among the various combinations, a formulation of 2% (w/v) NLS:S20 with a weight fraction of 0.6:0.4 had the largest ER/IP. ATR-FTIR spectroscopy of the formulations and skin was done to analyze the interactions in the formulations themselves and between the formulations and the skin. Both the intercellular lipidic route and transcellular route through the stratum corneum protein were involved in the delivery of fluorescein. This study turned pore-forming peptides into an efficient and safe penetration enhancer by combining them with other chemical penetration enhancers. Moreover, this discovery could be a possible method for enabling the transdermal delivery of macromolecules.

MF/UF rejection and fouling potential of algal organic matter from bloom-forming marine and freshwater algae

KAUST Repository

Villacorte, Loreen O.

2015-07-01

Pretreatment with microfiltration (MF) or ultrafiltration (UF) membranes has been proposed for seawater reverse osmosis (SWRO) plants to address operational issues associated with algal blooms. Here, we investigated the MF/UF rejection and fouling potential of algal organic matter (AOM) released by common species of bloom-forming marine (Alexandrium tamarense and Chaetoceros affinis) and freshwater (Microcystis sp.) algae. Batch culture monitoring of the three algal species illustrated varying growth pattern, cell concentration, AOM released and membrane fouling potential. The high membrane fouling potential of the cultures can be directly associated (R2>0.85) with AOM such as transparent exopolymer particle (TEP) while no apparent relationship with algal cell concentration was observed. The AOM comprised mainly biopolymers (e.g., polysaccharides and proteins) and low molecular weight organic compounds (e.g., humic-like substances). The former were largely rejected by MF/UF membranes while the latter were poorly rejected. MF (0.4μm and 0.1μm pore size) rejected 14%-56% of biopolymers while conventional UF (100kDa) and tight UF (10kDa) rejected up to 83% and 97%, respectively. The retention of AOM resulted in a rapid increase in trans-membrane pressure (δP) over time, characterised by pore blocking followed by cake filtration with enhanced compression as illustrated by an exponential progression of δP. © 2015 Elsevier B.V.

New methodology of preparation support for solid oxide fuel cells using different pore forming agent

Energy Technology Data Exchange (ETDEWEB)

Fiuza, Raigenis da P.; Guedes, Bruna C.F.; Silva, Marcos A. da; Carvalho, Luiz F.V. de; Boaventura, Jaime S. [Universidade Federal da Bahia (IQ/UFBA), Salvador, BA (Brazil). Inst. de Quimica; Pontes, Luiz A.M. [Universidade Federal da Bahia (EP/UFBA), Salvador, BA (Brazil). Escola Politecnica. Programa de Pos-Graduacao em Engenharia Quimica

2008-07-01

The development of environment-friendly energy sources has been of the most important scientific and technological area. Solid oxide fuel cells (SOFC) are very promising alternative for their ability to handle renewable fuels with low emissions and high efficiency. However, this device requires massive improvement before commercial application. This work studies the pore formation in the cell anode and cathode with NaHCO{sub 3} or citric acid, comparing to graphite. The three agents make pore with similar features, but the use of NaHCO{sub 3} and citric acid considerably improves the adhesion of the electrode-electrolyte interface, critical characteristic for good cell efficiency. The prepared anode-electrolyte-cathode structure was studied by SEM technique. The SOFC prepared using citric acid was tested with gaseous ethanol, natural gas and hydrogen. For all these three fuels the SOFC shows virtually no overpotential, indicating the good ionic conductance of the electrodes-electrolyte interface.. (author)

Condensation pressures in small pores: An analytical model based on density functional theory

International Nuclear Information System (INIS)

Nilson, R.H.; Griffiths, S.K.

1999-01-01

Integral methods are used to derive an analytical expression describing fluid condensation pressures in slit pores bounded by parallel plane walls. To obtain this result, the governing equations of density functional theory (DFT) are integrated across the pore width assuming that fluid densities within adsorbed layers are spatially uniform. The thickness, density, and free energy of these layers are expressed as composite functions constructed from asymptotic limits applicable to small and large pores. By equating the total free energy of the adsorbed layers to that of a liquid-full pore, we arrive at a closed-form expression for the condensation pressure in terms of the pore size, surface tension, and Lennard-Jones parameters of the adsorbent and adsorbate molecules. The resulting equation reduces to the Kelvin equation in the large-pore limit. It further reproduces the condensation pressures computed by means of the full DFT equations for all pore sizes in which phase transitions are abrupt. Finally, in the limit of extremely small pores, for which phase transitions may be smooth and continuous, this simple analytical expression provides a good approximation to the apparent condensation pressure indicated by the steepest portion of the adsorption isotherm computed via DFT. copyright 1999 American Institute of Physics

Combined use of rheometry and microscopy to understand pore structure development during coal carbonisation

Energy Technology Data Exchange (ETDEWEB)

John J. Duffy; Miguel Castro Diaz; Colin E. Snape; Merrick R. Mahoney; Karen M. Steel [University of Nottingham, Nottingham (United Kingdom). Nottingham Fuel and Energy Centre

2007-07-01

The viscoelastic behaviour of coal during carbonisation plays a role in the formation, growth and coalescence of pores. While viscosity is considered to govern pore formation and growth, the coalescence of pores or stabilisation of pores is considered to be governed by elasticity, and these two factors need to be considered in tandem when investigating pore network formation. The properties of the pore network, such as the connectivity of the pores, is hypothesised to be a factor controlling the degree of pressure that the carbonising mass exerts on its surrounding walls, called oven wall pressure (OWP). When volatiles are unable to pass out through the newly formed semi-coke due to low permeability, they travel instead to the centre of the charge, possibly condense as it is cooler, and build-up to high levels, causing high OWPs. Possible causes for low permeability on the semi-coke side could include poor connectivity between pores in the resolidifying material due to lack of connections, tortuous flow paths or narrow necks between pores. Low OWPs are thought to be largely due to a reduction in the elasticity of the fluid phase which allows a greater degree of pore coalescence and ultimately pore connectivity. This paper presents viscoelastic measurements for coals exhibiting different OWPs and scanning electron microscopy (SEM) images of the coal, quenched at various temperatures during carbonisation to show the development of their pore networks. 12 refs., 5 figs., 1 tab.

Antera 3D capabilities for pore measurements.

Science.gov (United States)

Messaraa, C; Metois, A; Walsh, M; Flynn, J; Doyle, L; Robertson, N; Mansfield, A; O'Connor, C; Mavon, A

2018-04-29

The cause of enlarged pores remains obscure but still remains of concern for women. To complement subjective methods, bioengineered methods are needed for quantification of pores visibility following treatments. The study objective was to demonstrate the suitability of pore measurements from the Antera 3D. Pore measurements were collected on 22 female volunteers aged 18-65 years with the Antera 3D, the DermaTOP and image analysis on photographs. Additionally, 4 raters graded pore size on photographs on a scale 0-5. Repeatability of Antera 3D parameters was ascertained and the benefit of a pore minimizer product on the cheek was assessed on a sub panel of seven female volunteers. Pore parameters using the Antera were shown to depict pore severity similar to raters on photographs, except for Max Depth. Mean pore volume, mean pore area and count were moderately correlated with DermaTOP parameters (up to r = .50). No relationship was seen between the Antera 3D and pore visibility analysis on photographs. The most repeatable parameters were found to be mean pore volume, mean pore area and max depth, especially for the small and medium filters. The benefits of a pore minimizer product were the most striking for mean pore volume and mean pore area when using the small filter for analysis, rather than the medium/large ones. Pore measurements with the Antera 3D represent a reliable tool for efficacy and field studies, with an emphasis of the small filter for analysis for the mean pore volume/mean pore area parameters. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Pore solution chemistry of simulated low-level liquid waste incorporated in cement grouts

International Nuclear Information System (INIS)

Kruger, A.A.

1995-12-01

Expressed pore solutions from simulated low level liquid waste cement grouts cured at room temperature, 50 degree C and 90 degree C for various duration were analyzed by standard chemical methods and ion chromatography. The solid portions of the grouts were formulated with portland cement, fly ash, slag, and attapulgite clay in the ratios of 3:3:3:1. Two different solutions simulating off-gas condensates expected from vitrification of Hanford low level tank wastes were made. One is highly alkaline and contains the species Na + , P0 4 3- , N0 2 - , NO 3 - and OH - . The other is carbonated and contains the species, Na + , PO 4 3- , NO 2 - , NO 3 - , and CO 3 2- . In both cases phosphate rapidly disappeared from the pore solution, leaving behind sodium in the form of hydroxide. The carbonates were also removed from the pore solution to form calcium carbonate and possibly calcium monocarboaluminate. These reactions resulted in the increase of hydroxide ion concentration in the early period. Subsequently there was a significant reduction OH - and Na + ion concentrations. In contrast high concentration of N0 2 - and N0 3 - were retained in the pore solution indefinitely

Electroosmotic pore transport in human skin.

Science.gov (United States)

Uitto, Olivia D; White, Henry S

2003-04-01

To determine the pathways and origin of electroosmotic flow in human skin. Iontophoretic transport of acetaminophen in full thickness human cadaver skin was visualized and quantified by scanning electrochemical microscopy. Electroosmotic flow in the shunt pathways of full thickness skin was compared to flow in the pores of excised stratum corneum and a synthetic membrane pore. The penetration of rhodamine 6G into pore structures was investigated by laser scanning confocal microscopy. Electroosmotic transport is observed in shunt pathways in full thickness human skin (e.g., hair follicles and sweat glands), but not in pore openings of freestanding stratum corneum. Absolute values of the diffusive and iontophoretic pore fluxes of acetaminophen in full thickness human skin are also reported. Rhodamine 6G is observed to penetrate to significant depths (approximately 200 microm) along pore pathways. Iontophoresis in human cadaver skin induces localized electroosmotic flow along pore shunt paths. Electroosmotic forces arise from the passage of current through negatively charged mesoor nanoscale pores (e.g., gap functions) within cellular regions that define the pore structure beneath the stratum corneum.

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

Science.gov (United States)

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.

Electrical trapping mechanism of single-microparticles in a pore sensor

Directory of Open Access Journals (Sweden)

Akihide Arima

2016-11-01

Full Text Available Nanopore sensing via resistive pulse technique are utilized as a potent tool to characterize physical and chemical property of single –molecules and –particles. In this article, we studied the influence of particle trajectory to the ionic conductance through a pore. We performed the optical/electrical simultaneous sensing of electrophoretic capture dynamics of single-particles at a pore using a microchannel/nanopore system. We detected ionic current drops synchronous to a fluorescently dyed particle being electrophoretically drawn and become immobilized at a pore in the optical imaging. We also identified anomalous trapping events wherein particles were captured at nanoscale pin-holes formed unintentionally in a SiN membrane that gave rise to relatively small current drops. This method is expected to be a useful platform for testing novel nanopore sensor design wherein current behaves in unpredictable manner.

cAMP control of HCN2 channel Mg2+ block reveals loose coupling between the cyclic nucleotide-gating ring and the pore.

Directory of Open Access Journals (Sweden)

Alex K Lyashchenko

Full Text Available Hyperpolarization-activated cyclic nucleotide-regulated HCN channels underlie the Na+-K+ permeable IH pacemaker current. As with other voltage-gated members of the 6-transmembrane KV channel superfamily, opening of HCN channels involves dilation of a helical bundle formed by the intracellular ends of S6 albeit this is promoted by inward, not outward, displacement of S4. Direct agonist binding to a ring of cyclic nucleotide-binding sites, one of which lies immediately distal to each S6 helix, imparts cAMP sensitivity to HCN channel opening. At depolarized potentials, HCN channels are further modulated by intracellular Mg2+ which blocks the open channel pore and blunts the inhibitory effect of outward K+ flux. Here, we show that cAMP binding to the gating ring enhances not only channel opening but also the kinetics of Mg2+ block. A combination of experimental and simulation studies demonstrates that agonist acceleration of block is mediated via acceleration of the blocking reaction itself rather than as a secondary consequence of the cAMP enhancement of channel opening. These results suggest that the activation status of the gating ring and the open state of the pore are not coupled in an obligate manner (as required by the often invoked Monod-Wyman-Changeux allosteric model but couple more loosely (as envisioned in a modular model of protein activation. Importantly, the emergence of second messenger sensitivity of open channel rectification suggests that loose coupling may have an unexpected consequence: it may endow these erstwhile "slow" channels with an ability to exert voltage and ligand-modulated control over cellular excitability on the fastest of physiologically relevant time scales.

Azorhizobium caulinodans Transmembrane Chemoreceptor TlpA1 Involved in Host Colonization and Nodulation on Roots and Stems

Directory of Open Access Journals (Sweden)

Wei Liu

2017-07-01

Full Text Available Azorhizobium caulinodans ORS571 is a motile soil bacterium that interacts symbiotically with legume host Sesbania rostrata, forming nitrogen-fixing root and stem nodules. Bacterial chemotaxis plays an important role in establishing this symbiotic relationship. To determine the contribution of chemotaxis to symbiosis in A. caulinodans ORS571-S. rostrata, we characterized the function of TlpA1 (transducer-like protein in A. caulinodans, a chemoreceptor predicted by SMART (Simple Modular Architecture Research Tool, containing two N-terminal transmembrane regions. The tlpA1 gene is located immediately upstream of the unique che gene cluster and is transcriptionally co-oriented. We found that a ΔtlpA1 mutant is severely impaired for chemotaxis to various organic acids, glycerol and proline. Furthermore, biofilm forming ability of the strain carrying the mutation is reduced under certain growth conditions. Interestingly, competitive colonization ability on S. rostrata root surfaces is impaired in the ΔtlpA1 mutant, suggesting that chemotaxis of the A. caulinodans ORS571 contributes to root colonization. We also found that TlpA1 promotes competitive nodulation not only on roots but also on stems of S. rostrata. Taken together, our data strongly suggest that TlpA1 is a transmembrane chemoreceptor involved in A. caulinodans-S. rostrata symbiosis.

Long n-alkanes isomerization by medium pore zeolites with pore mouth and key lock mechanisms; Isomerisation des paraffines longues par des zeolithes a pores moyens selon les mecanismes ouverture de pore et cle serrure

Energy Technology Data Exchange (ETDEWEB)

Claude, M.

1999-10-01

Skeletal isomerization of long n-alkanes is practiced to improve cold flow properties of diesel and lubricant fractions. In this work, model long n-alkanes (n-C{sub 10} - n-C{sub 24}) were hydro-isomerized in a fixed bed down flow vapour phase reactor loaded with bifunctional Pt/H-ZSM-22 zeolite catalyst. The skeletal isomers were analysed and identified with GC/MS. High isomer yields were obtained. The distribution of positional mono-methyl-branched isomers obtained from n-C{sub 12} to n-C{sub 24} are typically bimodal. This is explained by adsorption and reaction of the alkanes in pore mouths and locks on the external surface of the zeolite crystals. The pore mouth mode favours branching at C{sub 2} and C{sub 3}. The 'key lock' type proceeds by penetration of the two ends of the hydrocarbon chain into a different pore opening and favours more central mono-branching of the chain. The contribution of the key lock mode increases with increasing chain length and with the reaction temperature. The preferentially formed dimethyl-branched isomers have a separation between branchings of three up to fourteen carbon atoms. The formation of the second methyl-branching occurs preferentially from a centrally branched mono-methyl-branched isomer, so that the second branching is generated always more toward the end of the chain. Owing to the differences in adsorption entropy among the locks, at higher temperatures the largest lock is preferred and the distance between the two branching along the carbon chain in the preferred isomers is biggest. Thus the work resulted in the formulation of structure-selectivity relationships. n-C{sub 18} was hydro-isomerized on other zeolites. The nature and distribution of the isomers obtained suggest that the tubular 10-ring zeolites ZSM-23, ZSM-35 and SAPO-11 also operate according to pore mouth and key lock concepts. Zeolites with 12-rings show typical product patterns for catalysis in absence of steric hindrance. (author)

Laboratory characterization of shale pores

Science.gov (United States)

Nur Listiyowati, Lina

2018-02-01

To estimate the potential of shale gas reservoir, one needs to understand the characteristics of pore structures. Characterization of shale gas reservoir microstructure is still a challenge due to ultra-fine grained micro-fabric and micro level heterogeneity of these sedimentary rocks. The sample used in the analysis is a small portion of any reservoir. Thus, each measurement technique has a different result. It raises the question which methods are suitable for characterizing pore shale. The goal of this paper is to summarize some of the microstructure analysis tools of shale rock to get near-real results. The two analyzing pore structure methods are indirect measurement (MIP, He, NMR, LTNA) and direct observation (SEM, TEM, Xray CT). Shale rocks have a high heterogeneity; thus, it needs multiscale quantification techniques to understand their pore structures. To describe the complex pore system of shale, several measurement techniques are needed to characterize the surface area and pore size distribution (LTNA, MIP), shapes, size and distribution of pore (FIB-SEM, TEM, Xray CT), and total porosity (He pycnometer, NMR). The choice of techniques and methods should take into account the purpose of the analysis and also the time and budget.

Using BIB-SEM to determine pore morphology and pore size distributions in coal macerals

Energy Technology Data Exchange (ETDEWEB)

Giffin, S.; Littke, R. [RWTH Aachen Univ. (Germany). Inst. of Geology and Geochemistry of Petroleum and Coal; Klaver, J.; Urai, J.L. [RWTH Aachen Univ. (Germany). Structural Geology, Tectonics and Geomechanics

2013-08-01

The composition of coalbeds is considerably heterogeneous, affecting the transport pathways for fluids within the coal. Transport pathways include cleats and larger pores. However, only a few clues exist as the nature of these pores. This study examines the morphology and distribution of macro- and mesopores in coal samples, using broad ion beam (BIB) milling to prepare relief- and damage-free polished surfaces of coal samples for high-resolution SEM imaging. Broad ion beam milling is advantageous to focused ion beam milling in that a larger surface area can be milled. Combining that with SEM imaging results in a useful tool to study pore morphology and distributions in the size range between 10 nm and 10 {mu}m. Since BIB-sections of a few square millimeters are not large enough to be statistically representative, results cannot be easily interpreted from a coal seam standpoint. Therefore, porosity was investigated as a function of maceral type to characterize pore morphologies. Macerals from the vitrinite and inertinite groups were selected with a known relationship to bedding. BIB-sections were milled parallel to bedding and perpendicular to bedding, and the pores were evaluated in each section. The goal of this study is to (1) qualitatively describe pore morphology with respect to maceral type and (2) quantitatively characterize pore size distributions with respect to maceral and in relationship to bedding. Our results lead to a better understanding of bulk coal porosity due to the visual, spatial representation and quantification of pores in individual macerals. (orig.)

Estimation of adsorption-induced pore pressure and confinement in a nanoscopic slit pore by a density functional theory

Science.gov (United States)

Grégoire, David; Malheiro, Carine; Miqueu, Christelle

2018-03-01

This study aims at characterising the adsorption-induced pore pressure and confinement in nanoscopic pores by molecular non-local density functional theory (DFT). Considering its important potential industrial applications, the adsorption of methane in graphitic slit pores has been selected as the test case. While retaining the accuracy of molecular simulations at pore scale, DFT has a very low computational cost that allows obtaining highly resolved pore pressure maps as a function of both pore width and thermodynamic conditions. The dependency of pore pressure on these parameters (pore width, pressure and temperature) is carefully analysed in order to highlight the effect of each parameter on the confined fluid properties that impact the solid matrix.

Facial Pores: Definition, Causes, and Treatment Options.

Science.gov (United States)

Lee, Sang Ju; Seok, Joon; Jeong, Se Yeong; Park, Kui Young; Li, Kapsok; Seo, Seong Jun

2016-03-01

Enlarged skin pores refer to conditions that present with visible topographic changes of skin surfaces. Although not a medical concern, enlarged pores are a cosmetic concern for a large number of individuals. Moreover, clear definition and possible causes of enlarged pores have not been elucidated. To review the possible causes and treatment options for skin pores. This article is based on a review of the medical literature and the authors' clinical experience in investigating and treating skin pores. There are 3 major clinical causes of enlarged facial pores, namely high sebum excretion, decreased elasticity around pores, and increased hair follicle volume. In addition, chronic recurrent acne, sex hormones, and skin care regimen can affect pore size. Given the different possible causes for enlarged pores, therapeutic modalities must be individualized for each patient. Potential factors that contribute to enlarged skin pores include excessive sebum, decreased elasticity around pores, and increased hair follicle volume. Because various factors cause enlarged facial pores, it might be useful to identify the underlying causes to be able to select the appropriate treatment.

[Bacterial synthesis, purification, and solubilization of transmembrane segments of ErbB family members].

Science.gov (United States)

Goncharuk, M V; Shul'ga, A A; Ermoliuk, Ia S; Tkach, E N; Goncharuk, S A; Pustovalova, Iu E; Mineev, K S; Bocharov, É V; Maslennikov, I V; Arsen'ev, A S; Kirpichnikov, M P

2011-01-01

A family of epidermal growth factor receptors, ErbB, represents an important class of receptor tyrosine kinases, playing a leading role in cellular growth, development and differentiation. Transmembrane domains of these receptors transduce biochemical signals across plasma membrane via lateral homo- and heterodimerization. Relatively small size of complexes of ErbB transmembrane domains with detergents or lipids allows one to study their detailed spatial structure using three-dimensional heteronuclear high-resolution NMR spectroscopy. Here, we describe the effective expression system and purification procedure for preparative-scale production of transmembrane peptides from four representatives of ErbB family, ErbB1, ErbB2, ErbB3, ErbB4, for structural studies. The recombinant peptides were produced in Escherichia coli BL21(DE3)pLysS as C-terminal extensions of thioredoxin A. The fusion protein cleavage was accomplished with the light subunit of human enterokinase. Several (10-30) milligrams of purified isotope-labeled transmembrane peptides were isolated with the use of a simple and convenient procedure, which consists of consecutive steps of immobilized metal affinity chromatography and cation-exchange chromatography. The purified peptides were reconstituted in lipid/detergent environment (micelles or bicelles) and characterized using dynamic light scattering, CD and NMR spectroscopy. The data obtained indicate that the purified ErbB transmembrane peptides are suitable for structural and dynamic studies of their homo- and heterodimer complexes using high resolution NMR spectroscopy.

Crystallization and preliminary X-ray diffraction analysis of P30, the transmembrane domain of pertactin, an autotransporter from Bordetella pertussis

Energy Technology Data Exchange (ETDEWEB)

Zhu, Yanshi; Black, Isobel; Roszak, Aleksander W.; Isaacs, Neil W., E-mail: n.isaacs@chem.gla.ac.uk [Department of Chemistry and WestChem, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow G12 8TA,Scotland (United Kingdom)

2007-07-01

P30, the transmembrane C-terminal domain of pertactin from B. pertussis has been crystallized after refolding in vitro. Preliminary X-ray crystallographic data are reported. P30, the 32 kDa transmembrane C-terminal domain of pertactin from Bordetella pertussis, is supposed to form a β-barrel inserted into the outer membrane for the translocation of the passenger domain. P30 was cloned and expressed in inclusion bodies in Escherichia coli. After refolding and purification, the protein was crystallized using the sitting-drop vapour-diffusion method at 292 K. The crystals diffract to a resolution limit of 3.5 Å using synchrotron radiation and belong to the hexagonal space group P6{sub 1}22, with unit-cell parameters a = b = 123.27, c = 134.43 Å.

Origin of melting point depression for rare gas solids confined in carbon pores

International Nuclear Information System (INIS)

Morishige, Kunimitsu; Kataoka, Takaaki

2015-01-01

To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ∼0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point

Origin of melting point depression for rare gas solids confined in carbon pores

Energy Technology Data Exchange (ETDEWEB)

Morishige, Kunimitsu, E-mail: morishi@chem.ous.ac.jp; Kataoka, Takaaki [Department of Chemistry, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005 (Japan)

2015-07-21

To obtain insights into the mechanism of the melting-point depression of rare gas solids confined in crystalline carbon pores, we examined the freezing and melting behavior of Xe and Ar confined to the crystalline pores of ordered mesoporous carbons as well as compressed exfoliated graphite compared to the amorphous pores of ordered mesoporous silicas, by means of X-ray diffraction. For the Xe and Ar confined to the crystalline carbon pores, there was no appreciable thermal hysteresis between freezing and melting. Furthermore, the position of the main diffraction peak did not change appreciably on freezing and melting. This strongly suggests that the liquids confined in the carbon pores form a multilayered structure parallel to the smooth walls. For the Xe and Ar confined to the amorphous silica pores, on the other hand, the position of the main diffraction peak shifted into higher scattering angle on freezing suggested that the density of the confined solid is distinctly larger than for the confined liquid. Using compressed exfoliated graphite with carbon walls of higher crystallinity, we observed that three-dimensional (3D) microcrystals of Xe confined in the slit-shaped pores melted to leave the unmelted bilayers on the pore walls below the bulk triple point. The lattice spacing of the 3D microcrystals confined is larger by ∼0.7% than that of the bilayer next to the pore walls in the vicinity of the melting point.

Condensation pressures in small pores: An analytical model based on density functional theory

Energy Technology Data Exchange (ETDEWEB)

R. H. Nilson; S. K. Griffiths

1999-02-01

Adsorption and condensation are critical to many applications of porous materials including filtration, separation, and the storage of gases. Integral methods are used to derive an analytical expression describing fluid condensation pressures in slit pores bounded by parallel plane walls. To obtain this result, the governing equations of Density Functional Theory (DFT) are integrated across the pore width assuming that fluid densities within adsorbed layers are spatially uniform. The thickness, density, and energy of these layers are expressed as composite functions constructed from asymptotic limits applicable to small and large pores. By equating the total energy of the adsorbed layers to that of a liquid-full pore, the authors arrive at a closed-form expression for the condensation pressure in terms of the pore size, surface tension, and Lennard-Jones parameters of the adsorbent and adsorbate molecules. The resulting equation reduces to the Kelvin equation in the large-pore limit. It further reproduces the condensation pressures computed by means of the full DFT equations for all pore sizes in which phase transitions are abrupt. Finally, in the limit of extremely small pores, for which phase transitions may be smooth and continuous, this simple analytical expression provides a good approximation to the apparent condensation pressure indicated by the steepest portion of the adsorption isotherm computed via DFT.

The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6.

Directory of Open Access Journals (Sweden)

Lydia Tome-Stangl

Full Text Available Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α-helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein "halves" for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.

Study of shale reservoir nanometer-sized pores in Member 1 of Shahejie Formation in JX area, Liaozhong sag

Science.gov (United States)

Cheng, Yong; Zhang, Yu; Wen, Yiming

2018-02-01

The microscopic pore structure is the key of the shale reservoir study; however, traditional Scanning Electron Microscopy (SEM) methods cannot identify the irregular morphology caused by mechanical polishing. In this work, Scanning Electron Microscopy combined argon ion polishing technology was taken to study the characteristics of shale reservoir pores of Member 1 of Shahejie Formation (E3s1) located in JX1-1 area of Liaozhong Sag. The results show that pores between clay platelets, intraplatelet pores within clay aggregates and organic-matter pores are very rich in the area and with good pore connectivity, so these types of pores are of great significance for oil-gas exporation. Pores between clay platelets are formed by directional or semi-directional contact between edge and surface, edge and edge or surface and surface of laminated clay minerals, whose shapes are linear, mesh, and irregular with the size of 500 nm to 5 μm. The intraplatelet pores within clay aggregates are formed in the process of the transformation and compaction of clay minerals, whose shapes are usually linear with the width of 30 to 500 nm and the length of 2 to 50 μm. The organic-matter pores are from the process of the conversion from organic matters to the hydrocarbon under thermal evolution, whose shapes are gneissic, irregular, pitted and elliptical with the size of 100 nm to 2 μm. This study is of certain guiding significance to selecting target zones, evaluating resource potential and exploring & developing of shale gas in this region.

Tuning the ion selectivity of two-pore channels

Energy Technology Data Exchange (ETDEWEB)

Guo, Jiangtao; Zeng, Weizhong; Jiang, Youxing (UTSMC)

2017-01-17

Organellar two-pore channels (TPCs) contain two copies of a Shaker-like six-transmembrane (6-TM) domain in each subunit and are ubiquitously expressed in plants and animals. Interestingly, plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity. Plant TPC1 functions as a nonselective cation channel on the vacuole membrane, whereas mammalian TPC channels have been shown to be endo/lysosomal Na+-selective or Ca2+-release channels. In this study, we performed systematic characterization of the ion selectivity of TPC1 from Arabidopsis thaliana (AtTPC1) and compared its selectivity with the selectivity of human TPC2 (HsTPC2). We demonstrate that AtTPC1 is selective for Ca2+ over Na+, but nonselective among monovalent cations (Li+, Na+, and K+). Our results also confirm that HsTPC2 is a Na+-selective channel activated by phosphatidylinositol 3,5-bisphosphate. Guided by our recent structure of AtTPC1, we converted AtTPC1 to a Na+-selective channel by mimicking the selectivity filter of HsTPC2 and identified key residues in the TPC filters that differentiate the selectivity between AtTPC1 and HsTPC2. Furthermore, the structure of the Na+-selective AtTPC1 mutant elucidates the structural basis for Na+ selectivity in mammalian TPCs.

Basigin (CD147), a multifunctional transmembrane glycoprotein with various binding partners.

Science.gov (United States)

Muramatsu, Takashi

2016-05-01

Basigin, also called CD147 or EMMPRIN, is a transmembrane glycoprotein that belongs to the immunoglobulin superfamily. Basigin has isoforms; the common form (basigin or basigin-2) has two immunoglobulin domains, and the extended form (basigin-1) has three. Basigin is the receptor for cyclophilins, S100A9 and platelet glycoprotein VI, whereas basigin-1 serves as the receptor for the rod-derived cone viability factor. Basigin tightly associates with monocarboxylate transporters and is essential for their cell surface translocation and activities. In the same membrane plane, basigin also associates with other proteins including GLUT1, CD44 and CD98. The carbohydrate portion of basigin is recognized by lectins, such as galectin-3 and E-selectin. These molecular recognitions form the basis for the role of basigin in the transport of nutrients, migration of inflammatory leukocytes and induction of matrix metalloproteinases. Basigin is important in vision, spermatogenesis and other physiological phenomena, and plays significant roles in the pathogenesis of numerous diseases, including cancer. Basigin is also the receptor for an invasive protein RH5, which is present in malaria parasites. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society.

Peptide microarray analysis of substrate specificity of the transmembrane Ser/Thr kinase KPI-2 reveals reactivity with cystic fibrosis transmembrane conductance regulator and phosphorylase.

Science.gov (United States)

Wang, Hong; Brautigan, David L

2006-11-01

Human lemur (Lmr) kinases are predicted to be Tyr kinases based on sequences and are related to neurotrophin receptor Trk kinases. This study used homogeneous recombinant KPI-2 (Lmr2, LMTK2, Cprk, brain-enriched protein kinase) kinase domain and a library of 1,154 peptides on a microarray to analyze substrate specificity. We found that KPI-2 is strictly a Ser/Thr kinase that reacts with Ser either preceded by or followed by Pro residues but unlike other Pro-directed kinases does not strictly require an adjacent Pro residue. The most reactive peptide in the library corresponds to Ser-737 of cystic fibrosis transmembrane conductance regulator, and the recombinant R domain of cystic fibrosis transmembrane conductance regulator was a preferred substrate. Furthermore the KPI-2 kinase phosphorylated peptides corresponding to the single site in phosphorylase and purified phosphorylase b, making this only the second known phosphorylase b kinase. Phosphorylase was used as a specific substrate to show that KPI-2 is inhibited in living cells by addition of nerve growth factor or serum. The results demonstrate the utility of the peptide library to probe specificity and discover kinase substrates and offer a specific assay that reveals hormonal regulation of the activity of this unusual transmembrane kinase.

Effects of pore forming agents of potassium bicarbonate and drug loading method against dissolution mechanisms of amoxicillin drugs encapsulated in hydrogel full-Ipn chitosan-poly(N-vinylcaprolactam) as a floating drug delivery system

Science.gov (United States)

Aini, Nurul; Rahayu, Dyah Utami Cahyaning; Budianto, Emil

2018-04-01

The limitation of amoxicillin trihydrate in the treatment of H. pylori bacteria is relatively short retention time in the stomach. The FDDS (Floating Drug Delivery System) amoxicillin trihydrate into a chitosan-poly(N-vinylcaprolactam) full-Ipn hydrogel matrix using a pore-forming agent KHCO3 is expected to overcome these limitations. The pore-forming agent to be used is 15% KHCO3 compound. Chemical kinetics approach is performed to determine the dissolution mechanism of amoxicillin trihydrate from K-PNVCL hydrogel in vitro on gastric pH and characterization using SEM performed to confirm the dissolution mechanism. Hydrogels with the addition of pore-forming agents will be loading in situ loading and post loading. Fourier Transform Infra Red (FTIR) spectroscopy was used to characterize K-PNVCL and UV-Vis hydrogels used to calculate the efficiency of encapsulation and drug dissolution rate in K-PNVCL hydrogel. Hydrogel K-PNVCL / KHCO3 that encapsulated by in situ loading method resulted in an encapsulation efficiency of 93.5% and dissolution of 93.4%. While the Hydrogel K-PNVCL / KHCO3 which is drug encapsulation resulted in an encapsulation efficiency of 87.2% with dissolution of 81.5%. Chemical kinetics approach to in situ encapsulation of loading and post loading shows the dissolution mechanism occurring in the K-PNVCL / KHCO3 hydrogel matrix occurs by diffusion. Observation using optical microscope and SEM showed the mechanism of drug dissolution in Hydrogel K-PNVCL occurred by diffusion.

Correlation of Aquaporins and Transmembrane Solute Transporters Revealed by Genome-Wide Analysis in Developing Maize Leaf

Directory of Open Access Journals (Sweden)

Xun Yue

2012-01-01

Full Text Available Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins.

Microporous silica prepared by organic templating: relationship between the molecular template and pore structure

International Nuclear Information System (INIS)

Brinker, C. Jeffrey; Cao, Guozhong; Kale, Rahul P.; Lopez, Gabriel P.; Lu, Yunfeng; Prabakar, S.

1999-01-01

Microporous silica materials with a controlled pore size and a narrow pore size distribution have been prepared by sol-gel processing using an organic-templating approach. Microporous networks were formed by pyrolytic removal of organic ligands (methacryloxypropyl groups) from organic/inorganic hybrid materials synthesized by copolymerization of 3-methacryloxypropylsilane (MPS) and tetraethoxysilane (TEOS). Molecular simulations and experimental measurements were conducted to examine the relationship between the microstructural characteristics of the porous silica (e.g., pore size, total pore volume, and pore connectivity) and the size and amount of organic template ligands added. Adsorption measurements suggest that the final porosity of the microporous silica is due to both primary pores (those present in the hybrid materials prior to pyrolysis) and secondary pores (those created by pyrolytic removal of organic templates). Primary pores were inaccessible to N(sub 2) at 77 K but accessible to CO(sub 2) at 195 K; secondary pores were accessible to both N(sub 2) (at 77 K) and CO(sub 2) (at 195 K) in adsorption measurements. Primary porosity decreases with the amount of organic ligands added because of the enhanced densification of MPS/TEOS hybrid materials as the mole fraction of trifunctional MPS moieties increases. pore volumes measured by nitrogen adsorption experiments at 77 K suggest that the secondary (template-derived) porosity exhibits a percolation behavior as the template concentration is increased. Gas permeation experiments indicate that the secondary pores are approximately 5(angstrom) in diameter, consistent with predictions based on molecular simulations

Pore diameter control of anodic aluminum oxide with ordered array of nanopores

Energy Technology Data Exchange (ETDEWEB)

Bai, Allen; Yang, Yong-Feng [Department of Chemical Engineering, National Tsing Hua University, Hsin-Chu, 30013 (China); Hu, Chi-Chang [Department of Chemical Engineering, National Tsing Hua University, Hsin-Chu 401 (China); Department of Chemical Engineering, National Chung Cheng University, Chia-Yi 621 (China); Lin, Chi-Cheng [Department of Chemical Engineering, National Chung Cheng University, Chia-Yi 621 (China)

2008-01-01

Highly uniform, self-ordered anodic aluminum oxide (AAO) with an ordered nanoporous array can be effectively formed from industrially pure (99.5%) aluminum sheets through an anodizing program in a mixture solution of sulfuric and oxalic acids. The influences of anodizing variables, such as applied voltage, solution temperature, oxalic acid concentration, agitation rate, and sulfuric acid concentration, on the average pore diameter of AAO were systematically investigated using fractional factorial design (FFD). The applied voltage, and sulfuric acid concentration were found to be the key factors affecting the pore diameter of AAO films in the FFD study. The pore diameter of AAO is regularly increased from ca. 50 to 150 nm when the applied voltage and the concentration of sulfuric acid are gradually increased from 53 to 80 V and from 3.5 to 8 M, respectively. Fine tuning of the pore diameter for AAO films with an ordered, nanoporous, arrayed structure from industrially pure aluminum sheets can be achieved. (author)

Formation and decay of rudimentary penumbra around a pore

Energy Technology Data Exchange (ETDEWEB)

Watanabe, Hiroko [Unit of Synergetic Studies for Space, Kyoto University, Yamashina-ku, Kyoto 607-8417 (Japan); Kitai, Reizaburo [Kwasan and Hida Observatories, Kyoto University, Yamashina-ku, Kyoto 607-8417 (Japan); Otsuji, Kenichi, E-mail: watanabe@kwasan.kyoto-u.ac.jp [Solar Observatory, National Astronomical Observatory, Mitaka, Tokyo 181-8588 (Japan)

2014-12-01

We analyze the evolution of a pore in the active region NOAA 10940 using the data obtained by the Hinode satellite on 2007 February 3. The pore we analyzed showed the formation of a rudimentary penumbra structure, succeeded by an abrupt disappearance after about 5 hr. The pore had an approximate radius of 3.5 Mm and a total magnetic flux of 3.0 × 10{sup 19} Mx, which is a little smaller than the necessary magnetic flux for penumbral formation supposed by Rucklidge et al. (1-1.5 × 10{sup 20} Mx). Our observation describes a rare phenomenon which was in the unstable phase between a pore and a sunspot. The area of the dark umbra gradually decreased when the rudimentary penumbral filaments formed the penumbral structure, meaning that the penumbra develops at the expense of the umbral magnetic flux. This statement was confirmed by a rough estimation of the magnetic flux variation observed by the Hinode Fe I magnetogram. Five hours after the formation phase, the decay phase began. In this decaying phase, multiple opposite polarity patches are found to appear in the exterior of the pore (a different location from the penumbra formation site). We interpret these opposite polarities as signatures of the horizontal magnetic field, which preferably appears in the course of the unstable reconfiguration of the magnetic field structure. During the course of the disappearance of the penumbra, the horizontal penumbral field seems to become vertical because of the dark umbral area that recovered by about 10%.

Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K(+ channels.

Directory of Open Access Journals (Sweden)

Seok-Yong Lee

2009-03-01

Full Text Available Voltage-dependent K(+ (Kv channels gate open in response to the membrane voltage. To further our understanding of how cell membrane voltage regulates the opening of a Kv channel, we have studied the protein interfaces that attach the voltage-sensor domains to the pore. In the crystal structure, three physical interfaces exist. Only two of these consist of amino acids that are co-evolved across the interface between voltage sensor and pore according to statistical coupling analysis of 360 Kv channel sequences. A first co-evolved interface is formed by the S4-S5 linkers (one from each of four voltage sensors, which form a cuff surrounding the S6-lined pore opening at the intracellular surface. The crystal structure and published mutational studies support the hypothesis that the S4-S5 linkers convert voltage-sensor motions directly into gate opening and closing. A second co-evolved interface forms a small contact surface between S1 of the voltage sensor and the pore helix near the extracellular surface. We demonstrate through mutagenesis that this interface is necessary for the function and/or structure of two different Kv channels. This second interface is well positioned to act as a second anchor point between the voltage sensor and the pore, thus allowing efficient transmission of conformational changes to the pore's gate.

[A photographic scale for evaluating facial pores and analysis of factors associated with pore widening in Chengdu].

Science.gov (United States)

Wang, Qing; Zhou, Cheng-xia; Meng, Hui-min; Wang, Xi; Li, Li

2010-09-01

To develop a photographic scale for grading widening of pores, and to identify the factors associated with pore widening. People with widened pores were recruited, with photographs taken on their nasal tips, nasal alas and cheeks. A questionnaire survey was undertaken by dermatologists to assess the severity of pore widening. A Cumulative Logit Model was established to identify factors that were associated with pore widening. A total of 115 people participated in the study and 562 photographs were taken. The photographic scale was highly consistent with the clinical judgment. Another 1011 residents aged from 18 to 70 years old in Chengdu were surveyed. The logit model revealed that facial pore widening were associated with gender, age, oily skin, sun protection and anti-aging cosmetic. The photographic scale is reliable and easy to use. Gender, age and oily skin are risk factors, and sun protection and anti-aging cosmetic are protective factors with related to pore widening.

A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes.

Science.gov (United States)

Mimura, Yasuhiro; Takemoto, Satoko; Tachibana, Taro; Ogawa, Yutaka; Nishimura, Masaomi; Yokota, Hideo; Imamoto, Naoko

2017-11-24

Nuclear pore complexes (NPCs) maintain cellular homeostasis by mediating nucleocytoplasmic transport. Although cyclin-dependent kinases (CDKs) regulate NPC assembly in interphase, the location of NPC assembly on the nuclear envelope is not clear. CDKs also regulate the disappearance of pore-free islands, which are nuclear envelope subdomains; this subdomain gradually disappears with increase in homogeneity of the NPC in response to CDK activity. However, a causal relationship between pore-free islands and NPC assembly remains unclear. Here, we elucidated mechanisms underlying NPC assembly from a new perspective by focusing on pore-free islands. We proposed a novel framework for image-based analysis to automatically determine the detailed 'landscape' of pore-free islands from a large quantity of images, leading to the identification of NPC intermediates that appear in pore-free islands with increased frequency in response to CDK activity. Comparison of the spatial distribution between simulated and the observed NPC intermediates within pore-free islands showed that their distribution was spatially biased. These results suggested that the disappearance of pore-free islands is highly related to de novo NPC assembly and indicated the existence of specific regulatory mechanisms for the spatial arrangement of NPC assembly on nuclear envelopes.

Fractal Characteristics of Pores in Taiyuan Formation Shale from Hedong Coal Field, China

Science.gov (United States)

Li, Kunjie; Zeng, Fangui; Cai, Jianchao; Sheng, Guanglong; Xia, Peng; Zhang, Kun

For the purpose of investigating the fractal characteristics of pores in Taiyuan formation shale, a series of qualitative and quantitative experiments were conducted on 17 shale samples from well HD-1 in Hedong coal field of North China. The results of geochemical experiments show that Total organic carbon (TOC) varies from 0.67% to 5.32% and the organic matters are in the high mature or over mature stage. The shale samples consist mainly of clay minerals and quartz with minor pyrite and carbonates. The FE-SEM images indicate that three types of pores, organic-related pores, inorganic-related pores and micro-fractures related pores, are developed well, and a certain number of intragranular pores are found inside quartz and carbonates formed by acid liquid corrosion. The pore size distributions (PSDs) broadly range from several to hundreds nanometers, but most pores are smaller than 10nm. As the result of different adsorption features at relative pressure (0-0.5) and (0.5-1) on the N2 adsorption isotherm, two fractal dimensions D1 and D2 were obtained with the Frenkel-Halsey-Hill (FHH) model. D1 and D2 vary from 2.4227 to 2.6219 and from 2.6049 to 2.7877, respectively. Both TOC and brittle minerals have positive effect on D1 and D2, whereas clay minerals, have a negative influence on them. The fractal dimensions are also influenced by the pore structure parameters, such as the specific surface area, BJH pore volume, etc. Shale samples with higher D1 could provide more adsorption sites leading to a greater methane adsorption capacity, whereas shale samples with higher D2 have little influence on methane adsorption capacity.

Pore-Confined Carriers and Biomolecules in Mesoporous Silica for Biomimetic Separation and Targeting

Science.gov (United States)

Zhou, Shanshan

Selectively permeable biological membranes composed of lipophilic barriers inspire the design of biomimetic carrier-mediated membranes for aqueous solute separation. This work imparts selective permeability to lipid-filled pores of silica thin film composite membranes using carrier molecules that reside in the lipophilic self-assemblies. The lipids confined inside the pores of silica are proven to be a more effective barrier than bilayers formed on the porous surface through vesicle fusion, which is critical for quantifying the function of an immobilized carrier. The ability of a lipophilic carrier embedded in the lipid bilayer to reversibly bind the target solute and transport it through the membrane is demonstrated. Through the functionalization of the silica surface with enzymes, enzymatic catalysis and biomimetic separations can be combined on this nanostructured composite platform. The successful development of biomimetic nanocomposite membrane can provide for efficient dilute aqueous solute upgrading or separations using engineered carrier/catalyst/support systems. While the carrier-mediated biomimetic membranes hold great potential, fully understanding of the transport processes in composite synthetic membranes is essential for improve the membrane performance. Electrochemical impedance spectroscopy (EIS) technique is demonstrated to be a useful tool for characterizing the thin film pore accessibility. Furthermore, the effect of lipid bilayer preparation methods on the silica thin film (in the form of pore enveloping, pore filling) on ion transport is explored, as a lipid bilayer with high electrically insulation is essential for detecting activity of proteins or biomimetic carriers in the bilayer. This study provides insights for making better barriers on mesoporous support for carrier-mediated membrane separation process. Porous silica nanoparticles (pSNPs) with pore sizes appropriate for biomolecule loading are potential for encapsulating dsRNA within the

The membranotropic activity of N-terminal peptides from the pore ...

Indian Academy of Sciences (India)

The membranotropic activity of N-terminal peptides from the pore-forming proteins sticholysin I and II is modulated by hydrophobic and electrostatic interactions ... Center for Protein Studies, Biology Faculty, University of Havana, Havana, Cuba; Department of Applied Physics, Institute of Physics, University of São Paulo, São ...

Functional characterization of mutants in the transmembrane domains of the rat P2X7 receptor that regulate pore conductivity and agonist sensitivity

Czech Academy of Sciences Publication Activity Database

Jindřichová, Marie; Bhattacharya, Anirban; Rupert, Marian; Škopek, Petr; Obšil, T.; Zemková, Hana

2015-01-01

Roč. 133, č. 6 (2015), s. 815-827 ISSN 0022-3042 R&D Projects: GA ČR(CZ) GPP304/12/P371; GA ČR(CZ) GBP304/12/G069; GA MŠk(CZ) EE2.3.30.0025; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:67985823 Keywords : ATP * purinergic receptor channel * P2X7 * pore dilation * YO-PRO-1 uptake Subject RIV: ED - Physiology Impact factor: 3.842, year: 2015

Capillary pressure across a pore throat in the presence of surfactants

KAUST Repository

Jang, Junbong

2016-11-22

Capillarity controls the distribution and transport of multiphase and immiscible fluids in soils and fractured rocks; therefore, capillarity affects the migration of nonaqueous contaminants and remediation strategies for both LNAPLs and DNAPLs, constrains gas and oil recovery, and regulates CO2 injection and geological storage. Surfactants alter interfacial tension and modify the invasion of pores by immiscible fluids. Experiments are conducted to explore the propagation of fluid interfaces along cylindrical capillary tubes and across pore constrictions in the presence of surfactants. Measured pressure signatures reflect the interaction between surface tension, contact angle, and the pore geometry. Various instabilities occur as the interface traverses the pore constriction, consequently, measured pressure signatures differ from theoretical trends predicted from geometry, lower capillary pressures are generated in advancing wetting fronts, and jumps are prone to under-sampling. Contact angle and instabilities are responsible for pronounced differences between pressure signatures recorded during advancing and receding tests. Pressure signatures gathered with surfactant solutions suggest changes in interfacial tension at the constriction; the transient surface tension is significantly lower than the value measured in quasi-static conditions. Interface stiffening is observed during receding fronts for solutions near the critical micelle concentration. Wetting liquids tend to form plugs at pore constrictions after the invasion of a nonwetting fluid; plugs split the nonwetting fluid into isolated globules and add resistance against fluid flow.

Variable pore connectivity model linking gas diffusivity and air-phase tortuosity to soil matric potential

DEFF Research Database (Denmark)

Chamindu, Deepagoda; Møldrup, Per; Schjønning, Per

2012-01-01

information on soil functional pore structure, e.g., pore network tortuosity and connectivity, can also be revealed from Dp/Do–ψ relations. Based on Dp/Do measurements in a wide range of soil types across geographically remote vadose zone profiles, this study analyzed pore connectivity for the development...... of a variable pore connectivity factor, X, as a function of soil matric potential, expressed as pF (=log |−ψ|), for pF values ranging from 1.0 to 3.5. The new model takes the form of X = X* (F/F*)A with F = 1 + pF−1, where X* is the pore network tortuosity at reference F (F*) and A is a model parameter......- and intraaggregate pore regions of aggregated soils. We further suggest that the new model with parameter values of X* = 1.7 and A = 0 may be used for upper limit Dp/Do predictions in risk assessments of, e.g., fluxes of toxic volatile organics from soil to indoor air at polluted soil sites....

Micron-pore-sized metallic filter tube membranes for filtration of particulates and water purification.

Science.gov (United States)

Phelps, T J; Palumbo, A V; Bischoff, B L; Miller, C J; Fagan, L A; McNeilly, M S; Judkins, R R

2008-07-01

Robust filtering techniques capable of efficiently removing particulates and biological agents from water or air suffer from plugging, poor rejuvenation, low permeance, and high backpressure. Operational characteristics of pressure-driven separations are in part controlled by the membrane pore size, charge of particulates, transmembrane pressure and the requirement for sufficient water flux to overcome fouling. With long term use filters decline in permeance due to filter-cake plugging of pores, fouling, or filter deterioration. Though metallic filter tube development at ORNL has focused almost exclusively on gas separations, a small study examined the applicability of these membranes for tangential filtering of aqueous suspensions of bacterial-sized particles. A mixture of fluorescent polystyrene microspheres ranging in size from 0.5 to 6 microm in diameter simulated microorganisms in filtration studies. Compared to a commercial filter, the ORNL 0.6 microm filter averaged approximately 10-fold greater filtration efficiency of the small particles, several-fold greater permeance after considerable use and it returned to approximately 85% of the initial flow upon backflushing versus 30% for the commercial filter. After filtering several liters of the particle-containing suspension, the ORNL composite filter still exhibited greater than 50% of its initial permeance while the commercial filter had decreased to less than 20%. When considering a greater filtration efficiency, greater permeance per unit mass, greater percentage of rejuvenation upon backflushing (up to 3-fold), and likely greater performance with extended use, the ORNL 0.6 microm filters can potentially outperform the commercial filter by factors of 100-1,000 fold.

Expression of genes encoding multi-transmembrane proteins in specific primate taste cell populations.

Directory of Open Access Journals (Sweden)

Bryan D Moyer

Full Text Available BACKGROUND: Using fungiform (FG and circumvallate (CV taste buds isolated by laser capture microdissection and analyzed using gene arrays, we previously constructed a comprehensive database of gene expression in primates, which revealed over 2,300 taste bud-associated genes. Bioinformatics analyses identified hundreds of genes predicted to encode multi-transmembrane domain proteins with no previous association with taste function. A first step in elucidating the roles these gene products play in gustation is to identify the specific taste cell types in which they are expressed. METHODOLOGY/PRINCIPAL FINDINGS: Using double label in situ hybridization analyses, we identified seven new genes expressed in specific taste cell types, including sweet, bitter, and umami cells (TRPM5-positive, sour cells (PKD2L1-positive, as well as other taste cell populations. Transmembrane protein 44 (TMEM44, a protein with seven predicted transmembrane domains with no homology to GPCRs, is expressed in a TRPM5-negative and PKD2L1-negative population that is enriched in the bottom portion of taste buds and may represent developmentally immature taste cells. Calcium homeostasis modulator 1 (CALHM1, a component of a novel calcium channel, along with family members CALHM2 and CALHM3; multiple C2 domains; transmembrane 1 (MCTP1, a calcium-binding transmembrane protein; and anoctamin 7 (ANO7, a member of the recently identified calcium-gated chloride channel family, are all expressed in TRPM5 cells. These proteins may modulate and effect calcium signalling stemming from sweet, bitter, and umami receptor activation. Synaptic vesicle glycoprotein 2B (SV2B, a regulator of synaptic vesicle exocytosis, is expressed in PKD2L1 cells, suggesting that this taste cell population transmits tastant information to gustatory afferent nerve fibers via exocytic neurotransmitter release. CONCLUSIONS/SIGNIFICANCE: Identification of genes encoding multi-transmembrane domain proteins

Phosphate barrier on pore-filled cation-exchange membrane for blocking complexing ions in presence of non-complexing ions

Science.gov (United States)

Chavan, Vivek; Agarwal, Chhavi; Shinde, Rakesh N.

2018-06-01

In present work, an approach has been used to form a phosphate groups bearing surface barrier on a cation-exchange membrane (CEM). Using optimized conditions, the phosphate bearing monomer bis[2-(methacryloyloxy)ethyl] phosphate has been grafted on the surface of the host poly(ethersulfone) membranes using UV light induced polymerization. The detailed characterizations have shown that less than a micron layer of phosphate barrier is formed without disturbing the original microporous structure of the host membrane. The pores of thus formed membrane have been blocked by cationic-gel formed by in situ UV-initiator induced polymerization of 2-acrylamido-2-methyl-1-propane sulphonic acid along with crosslinker ethylene glycol dimethacrylate in the pores of the membrane. UV-initiator is required for pore-filling as UV light would not penetrate the interior matrix of the membrane. The phosphate functionalized barrier membrane has been examined for permselectivity using a mixture of representative complexing Am3+ ions and non-complexing Cs+ ions. This experiment has demonstrated that complex forming Am3+ ions are blocked by phosphate barrier layer while non-complexing Cs+ ions are allowed to pass through the channels formed by the crosslinked cationic gel.

Can ash clog soil pores?

Science.gov (United States)

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

2015-04-01

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

Pore structure and mechanical properties of directionally solidified porous aluminum alloys

Directory of Open Access Journals (Sweden)

Komissarchuk Olga

2014-01-01

Full Text Available Porous aluminum alloys produced by the metal-gas eutectic method or GASAR process need to be performed under a certain pressure of hydrogen, and to carry over melt to a tailor-made apparatus that ensures directional solidification. Hydrogen is driven out of the melt, and then the quasi-cylindrical pores normal to the solidification front are usually formed. In the research, the effects of processing parameters (saturation pressure, solidification pressure, temperature, and holding time on the pore structure and porosity of porous aluminum alloys were analyzed. The mechanical properties of Al-Mg alloys were studied by the compressive tests, and the advantages of the porous structure were indicated. By using the GASAR method, pure aluminum, Al-3wt.%Mg, Al-6wt.%Mg and Al-35wt.%Mg alloys with oriented pores have been successfully produced under processing conditions of varying gas pressure, and the relationship between the final pore structure and the solidification pressure, as well as the influences of Mg quantity on the pore size, porosity and mechanical properties of Al-Mg alloy were investigated. The results show that a higher pressure of solidification tends to yield smaller pores in aluminum and its alloys. In the case of Al-Mg alloys, it was proved that with the increasing of Mg amount, the mechanical properties of the alloys sharply deteriorate. However, since Al-3%Mg and Al-6wt.%Mg alloys are ductile metals, their porous samples have greater compressive strength than that of the dense samples due to the existence of pores. It gives the opportunity to use them in industry at the same conditions as dense alloys with savings in weight and material consumption.

Matrix coatings based on anodic alumina with carbon nanostructures in the pores

Science.gov (United States)

Gorokh, G. G.; Pashechko, M. I.; Borc, J. T.; Lozovenko, A. A.; Kashko, I. A.; Latos, A. I.

2018-03-01

The nanoporous anodic alumina matrixes thickness of 1.5 mm and pore sizes of 45, 90 and 145 nm were formed on Si substrates. The tubular carbon nanostructures were synthesized into the matrixes pores by pyrolysis of fluid hydrocarbon xylene with 1% ferrocene. The structure and composition of the matrix coatings were examined by scanning electron microscopy, Auger analysis and Raman spectroscopy. The carbon nanostructures completely filled the pores of templates and uniformly covered the tops. The structure of carbon nanostructures corresponded to the structure of multiwall carbon nanotubes. Investigations of mechanical and tribological properties of nanostructured oxide-carbon composite performed by scratching and nanoindentation showed nonlinear dependencies of the frictional force, penetration depth of the cantilever, hardness and plane strain modulus on the load. It was found that the microhardness of the samples increases with reduced of alumina pore diameter, and the penetration depth of the cantilever into the film grows with carbon nanostructures size. The results showed the high mechanical strength of nanostructured oxide-carbon composite.

Homologue Structure of the SLAC1 Anion Channel for Closing Stomata in Leaves

Energy Technology Data Exchange (ETDEWEB)

Y Chen; L Hu; M Punta; R Bruni; B Hillerich; B Kloss; B Rost; J Love; S Siegelbaum; W Hendrickson

2011-12-31

The plant SLAC1 anion channel controls turgor pressure in the aperture-defining guard cells of plant stomata, thereby regulating the exchange of water vapour and photosynthetic gases in response to environmental signals such as drought or high levels of carbon dioxide. Here we determine the crystal structure of a bacterial homologue (Haemophilus influenzae) of SLAC1 at 1.20 {angstrom} resolution, and use structure-inspired mutagenesis to analyse the conductance properties of SLAC1 channels. SLAC1 is a symmetrical trimer composed from quasi-symmetrical subunits, each having ten transmembrane helices arranged from helical hairpin pairs to form a central five-helix transmembrane pore that is gated by an extremely conserved phenylalanine residue. Conformational features indicate a mechanism for control of gating by kinase activation, and electrostatic features of the pore coupled with electrophysiological characteristics indicate that selectivity among different anions is largely a function of the energetic cost of ion dehydration.

Dual functions of a small regulatory subunit in the mitochondrial calcium uniporter complex.

Science.gov (United States)

Tsai, Ming-Feng; Phillips, Charles B; Ranaghan, Matthew; Tsai, Chen-Wei; Wu, Yujiao; Willliams, Carole; Miller, Christopher

2016-04-21

Mitochondrial Ca(2+) uptake, a process crucial for bioenergetics and Ca(2+) signaling, is catalyzed by the mitochondrial calcium uniporter. The uniporter is a multi-subunit Ca(2+)-activated Ca(2+) channel, with the Ca(2+) pore formed by the MCU protein and Ca(2+)-dependent activation mediated by MICU subunits. Recently, a mitochondrial inner membrane protein EMRE was identified as a uniporter subunit absolutely required for Ca(2+) permeation. However, the molecular mechanism and regulatory purpose of EMRE remain largely unexplored. Here, we determine the transmembrane orientation of EMRE, and show that its known MCU-activating function is mediated by the interaction of transmembrane helices from both proteins. We also reveal a second function of EMRE: to maintain tight MICU regulation of the MCU pore, a role that requires EMRE to bind MICU1 using its conserved C-terminal polyaspartate tail. This dual functionality of EMRE ensures that all transport-competent uniporters are tightly regulated, responding appropriately to a dynamic intracellular Ca(2+) landscape.

Biophysical characterization of Vpu from HIV-1 suggests a channel-pore dualism.

Science.gov (United States)

Mehnert, T; Routh, A; Judge, P J; Lam, Y H; Fischer, D; Watts, A; Fischer, W B

2008-03-01

Vpu from HIV-1 is an 81 amino acid type I integral membrane protein which consists of a cytoplasmic and a transmembrane (TM) domain. The TM domain is known to alter membrane permeability for ions and substrates when inserted into artificial membranes. Peptides corresponding to the TM domain of Vpu (Vpu(1-32)) and mutant peptides (Vpu(1-32)-W23L, Vpu(1-32)-R31V, Vpu(1-32)-S24L) have been synthesized and reconstituted into artificial lipid bilayers. All peptides show channel activity with a main conductance level of around 20 pS. Vpu(1-32)-W23L has a considerable flickering pattern in the recordings and longer open times than Vpu(1-32). Whilst recordings for Vpu(1-32)-R31V are almost indistinguishable from those of the WT peptide, recordings for Vpu(1-32)-S24L do not exhibit any noticeable channel activity. Recordings of WT peptide and Vpu(1-32)-W23L indicate Michaelis-Menten behavior when the salt concentration is increased. Both peptide channels follow the Eisenman series I, indicative for a weak ion channel with almost pore like characteristics. 2007 Wiley-Liss, Inc.

Emulsification using microporous membranes

Directory of Open Access Journals (Sweden)

Goran T. Vladisavljević

2011-10-01

Full Text Available Membrane emulsification is a process of injecting a pure dispersed phase or pre-emulsion through a microporous membrane into the continuous phase. As a result of the immiscibility of the two phases, droplets of the dispersed phase are formed at the outlets of membrane pores. The droplets formed in the process are removed from the membrane surface by applying cross-flow or stirring of the continuous phase or using a dynamic (rotating or vibrating membrane. The most commonly used membrane for emulsification is the Shirasu Porous Glass (SPG membrane, fabricated through spinodal decomposition in a melt consisting of Japanese volcanic ash (Shirasu, boric acid and calcium carbonate. Microsieve membranes are increasingly popular as an alternative to highly tortuous glass and ceramic membranes. Microsieves are usually fabricated from nickel by photolithography and electroplating or they can be manufactured from silicon nitride via Reactive Ion Etching (RIE. An advantage of microsieves compared to the SPG membrane is in much higher transmembrane fluxes and higher tolerance to fouling by the emulsion ingredients due to the existence of short, straight through pores. Unlike conventional emulsification devices such as high-pressure valve homogenisers and rotor-stator devices, membrane emulsification devices permit a precise control over the mean pore size over a wide range and during the process insignificant amount of energy is dissipated as heat. The drop size is primarily determined by the pore size, but it depends also on other parameters, such as membrane wettability, emulsion formulation, shear stress on the membrane surface, transmembrane pressure, etc.

Cloning and characterization of SCART1, a novel scavenger receptor cysteine-rich type I transmembrane molecule

DEFF Research Database (Denmark)

Holm, Dorte; Fink, Dorte Rosenbek; Grønlund, Jørn

2009-01-01

We have cloned and characterized a novel murine transmembrane molecule, mSCART1 belonging to the scavenger receptor cysteine-rich superfamily. The cDNA encodes a polypeptide chain of 989 amino acids, organized as a type I transmembrane protein that contains eight extracellular SRCR domains followed...

An alternative explanation for evidence that xenon depletion, pore formation, and grain subdivision begin at different local burnups

International Nuclear Information System (INIS)

Rest, J.; Hofman, G.L.

2000-01-01

In order to interpret the recent observation that xenon depletion, pore formation, and grain subdivision occur successively at increasing local burnups, a rate-theory-based model is used to investigate the nucleation and growth of cavities during low-temperature irradiation of UO 2 in the presence of irradiation-induced interstitial-loop formation and growth. Consolidation of the dislocation structure takes into account the generation of forest dislocations and capture of interstitial dislocation loops. The loops accumulate and ultimately evolve into a low-energy cellular dislocation structure. The cell walls have been previously identified as recrystallization nuclei. The calculations indicate that nanometer-size bubbles are associated with this cellular dislocation structure while the observed micron-size bubbles are presumed to be either preexisting pores deformed by adjacent grains and/or new pores formed in the new recrystallized grain-boundary junctions. Subsequent to recrystallization, gas released from the recrystallized grains feeds the preexisting pores and the recrystallized grains may appear to form a preferential concentration of subdivided grains around the growing pores. This picture is illustrated in a sequence of photomicrographs of irradiated U 3 O 8

Fluids in micropores. II. Self-diffusion in a simple classical fluid in a slit pore

International Nuclear Information System (INIS)

Schoen, M.; Cushman, J.H.; Diestler, D.J.; Rhykerd, C.L. Jr.

1988-01-01

Self-diffusion coefficients D are computed for a model slit pore consisting of a rare-gas fluid confined between two parallel face-centered cubic (100) planes (walls) of rigidly fixed rare-gas atoms. By means of an optimally vectorized molecular-dynamics program for the CYBER 205, the dependence of D on the thermodynamic state (specified by the chemical potential μ, temperature T, and the pore width h) of the pore fluid has been explored. Diffusion is governed by Fick's law, even in pores as narrow as 2 or 3 atomic diameters. The diffusion coefficient oscillates as a function of h with fixed μ and T, vanishing at critical values of h, where fluid--solid phase transitions occur. A shift of the pore walls relative to one another in directions parallel with the walls can radically alter the structure of the pore fluid and consequently the magnitude of D. Since the pore fluid forms distinct layers parallel to the walls, a local diffusion coefficient D/sup (//sup i//sup )//sub parallel/ associated with a given layer i can be defined. D/sup (//sup i//sup )//sub parallel/ is least for the contact layer, even for pores as wide as 30 atomic diameters (∼100 A). Moreover, D/sup (//sup i//sup )//sub parallel/ increases with increasing distance of the fluid layer from the wall and, for pore widths between 16 and 30 atomic diameters, D/sup (//sup i//sup )//sub parallel/ is larger in the center of the pore than in the bulk fluid that is in equilibrium with the pore fluid. The opposite behavior is observed in corresponding smooth-wall pores, in which the discrete fluid--wall interactions have been averaged by smearing the wall atoms over the plane of the wall

Tunable pores in mesoporous silica films studied using a pulsed slow positron beam

International Nuclear Information System (INIS)

He Chunqing; Muramatsu, Makoto; Ohdaira, Toshiyuki; Oshima, Nagayasu; Kinomura, Atsushi; Suzuki, Ryoichi; Kobayashi, Yoshinori

2007-01-01

Positron annihilation lifetime spectroscopy (PALS) based on a pulsed slow positron beam was applied to study mesoporous silica films, synthesized using amphiphilic PEO-PPO-PEO triblock copolymers as structure-directing agents. The pore size depends on the loading of different templates. Larger pores were formed in silica films templated by copolymers with higher molecular-weights. Using 2-dimensional PALS, open porosity of silica films was also found to be influenced by the molecular-weight as well as the ratio of hydrophobic PPO moiety of the templates

Sphagnum can 'filter' N deposition, but effects on the plant and pore water depend on the N form.

Science.gov (United States)

Chiwa, Masaaki; Sheppard, Lucy J; Leith, Ian D; Leeson, Sarah R; Tang, Y Sim; Cape, J Neil

2016-07-15

The ability of Sphagnum moss to efficiently intercept atmospheric nitrogen (N) has been assumed to be vulnerable to increased N deposition. However, the proposed critical load (20kgNha(-1)yr(-1)) to exceed the capacity of the Sphagnum N filter has not been confirmed. A long-term (11years) and realistic N manipulation on Whim bog was used to study the N filter function of Sphagnum (Sphagnum capillifolium) in response to increased wet N deposition. On this ombrotrophic peatland where ambient deposition was 8kgNha(-1)yr(-1), an additional 8, 24, and 56kgNha(-1)yr(-1) of either ammonium (NH4(+)) or nitrate (NO3(-)) has been applied for 11years. Nutrient status of Sphagnum and pore water quality from the Sphagnum layer were assessed. The N filter function of Sphagnum was still active up to 32kgNha(-1)yr(-1) even after 11years. N saturation of Sphagnum and subsequent increases in dissolved inorganic N (DIN) concentration in pore water occurred only for 56kgNha(-1)yr(-1) of NH4(+) addition. These results indicate that the Sphagnum N filter is more resilient to wet N deposition than previously inferred. However, functionality will be more compromised when NH4(+) dominates wet deposition for high inputs (56kgNha(-1)yr(-1)). The N filter function in response to NO3(-) uptake increased the concentration of dissolved organic N (DON) and associated organic anions in pore water. NH4(+) uptake increased the concentration of base cations and hydrogen ions in pore water though ion exchange. The resilience of the Sphagnum N filter can explain the reported small magnitude of species change in the Whim bog ecosystem exposed to wet N deposition. However, changes in the leaching substances, arising from the assimilation of NO3(-) and NH4(+), may lead to species change. Copyright © 2016 Elsevier B.V. All rights reserved.

First principles design of a core bioenergetic transmembrane electron-transfer protein

Energy Technology Data Exchange (ETDEWEB)

Goparaju, Geetha; Fry, Bryan A.; Chobot, Sarah E.; Wiedman, Gregory; Moser, Christopher C.; Leslie Dutton, P.; Discher, Bohdana M.

2016-05-01

Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics — the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson.

Revealing Lattice Expansion of Small-Pore Zeolite Catalysts during the Methanol-to-Olefins Process Using Combined Operando X-ray Diffraction and UV–vis Spectroscopy

KAUST Repository

Goetze, Joris; Yarulina, Irina; Gascon, Jorge; Kapteijn, Freek; Weckhuysen, Bert M.

2018-01-01

In small-pore zeolite catalysts, where the size of the pores is limited by eight-ring windows, aromatic hydrocarbon pool molecules that are formed inside the zeolite during the Methanol-to-Olefins (MTO) process cannot exit the pores and are retained

3D Textural and Geochemical Analyses on Carbonado Diamond: Insights from Pores and the Minerals within Them

Science.gov (United States)

Eckley, S. A.; Ketcham, R. A.

2017-12-01

Carbonado is an enigmatic variety of polycrystalline diamond found only in placer deposits and Proterozoic metaconglomerates in Brazil and the Central African Republic with unknown primary origin. These highly porous black nodules possess a narrow range of isotopically light carbon (δ13C -31 to -24 ‰), a primarily crustal inclusion suite unusually enriched in REEs and actinides filling the pore spaces, a crystallization age from 2.6 to 3.8 Ga, and other atypical features which have led to a variety of formation theories from extra-solar to deep mantle. We have completed the first multi-sample 3D textural analysis on nine carbonados using high resolution X-ray CT (XCT), with follow-up geochemical work. We have documented a variety of textures in both pore structure and mineralogy within pores. All pore textures feature a preferred orientation. Spatial coherence in pore fillings in some specimens suggest that secondary minerals formed by in-situ breakdown of primary inclusion phases. This, combined with the presence of pseudomorphs, support the hypothesis that elements comprising the secondary minerals within the pore spaces are actually primary. SEM-EDS analysis of one carbonado's exterior revealed the presence of zircon; XCT analysis of the complete volume indicates zircon is present only on the exterior of that specimen, but may be interior to others. Anticipated follow-up work will include LA-ICP-MS U-Pb dating and REE analysis of the zircon, and step-leaching and ICP analysis of some specimens. Periodic XCT imaging will allow us to trace leaching progress and effectiveness. To provide further context for our observed pore fabrics, we also analyzed a framesite, a less porous polycrystalline diamond found in kimberlites thought to crystallize shortly before eruption. Both diamond varieties have bladed/elongated pores forming a foliation with a moderate lineation. The similarity in fabrics suggests a similar process could have formed both carbonados and

The Immunogenicity of the Tumor-Associated Antigen α-Fetoprotein Is Enhanced by a Fusion with a Transmembrane Domain

Directory of Open Access Journals (Sweden)

Lucile Tran

2012-01-01

Full Text Available Aim. To investigate the ability of recombinant modified vaccinia virus Ankara (rMVA vector to induce an immune response against a well-tolerated self-antigen. Methods. rMVA vectors expressing different form of α-fetoprotein (AFP were produced and characterized. Naïve mice were vaccinated with MVA vectors expressing the AFP antigen in either a secreted, or a membrane-bound, or an intracellular form. The immune response was monitored by an IFNΓ ELISpot assay and antibody detection. Results. Vaccination with the membrane-associated form of AFP induced a stronger CD8+ T-cell response compared to the ones obtained with the MVA encoding the secreted or the intracellular forms of AFP. Moreover, the vaccination with the membrane-bound AFP elicited the production of AFP-specific antibodies. Conclusions. The AFP transmembrane form is more immunogenic. Expressing a membrane-bound form in the context of an MVA vaccination could enhance the immunogenicity of a self-antigen.

Molecular modeling and structural analysis of two-pore domain potassium channels TASK1 interactions with the blocker A1899

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David Mauricio Ramirez

2015-03-01

Full Text Available A1899 is a potent and highly selective blocker of the Two-pore domain potassium (K2P channel TASK-1, it acts as an antagonist blocking the K+ flux and binds to TASK-1 in the inner cavity and shows an activity in nanomolar order. This drug travels through the central cavity and finally binds in the bottom of the selectivity filter with some threonines and waters molecules forming a H-bond network and several hydrophobic interactions. Using alanine mutagenesis screens the binding site was identify involving residues in the P1 and P2 pore loops, the M2 and M4 transmembrane segments, and the halothane response element; mutations were introduced in the human TASK-1 (KCNK3, NM_002246 expressed in Oocytes from anesthetized Xenopus laevis frogs. Based in molecular modeling and structural analysis as such as molecular docking and binding free energy calculations a pose was suggested using a TASK-1 homology models. Recently, various K2P crystal structures have been obtained. We want redefined – from a structural point of view – the binding mode of A1899 in TASK-1 homology models using as a template the K2P crystal structures. By computational structural analysis we describe the molecular basis of the A1899 binding mode, how A1899 travel to its binding site and suggest an interacting pose (Figure 1. after 100 ns of molecular dynamics simulation (MDs we found an intra H-Bond (80% of the total MDs, a H-Bond whit Thr93 (42% of the total MDs, a pi-pi stacking interaction between a ring and Phe125 (88% of the total MDs and several water bridges. Our experimental and computational results allow the molecular understanding of the structural binding mechanism of the selective blocker A1899 to TASK-1 channels. We identified the structural common and divergent features of TASK-1 channel through our theoretical and experimental studies of A1899 drug action.

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation.

Science.gov (United States)

Fu, Yankai; Yan, Tingxuan; Xu, Xia

2017-09-28

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

Numerical modeling of pore-scale phenomena during CO2 sequestration in oceanic sediments

International Nuclear Information System (INIS)

Kang, Qinjun; Tsimpanogiannis, Ioannis N.; Zhang, Dongxiao; Lichtner, Peter C.

2005-01-01

Direct disposal of liquid CO 2 on the ocean floor is one of the approaches considered for sequestering CO 2 in order to reduce its concentration in the atmosphere. At oceanic depths deeper than approximately 3000 m, liquid CO 2 density is higher than the density of seawater and CO 2 is expected to sink and form a pool at the ocean floor. In addition to chemical reactions between CO 2 and seawater to form hydrate, fluid displacement is also expected to occur within the ocean floor sediments. In this work, we consider two different numerical models for hydrate formation at the pore scale. The first model consists of the Lattice Boltzmann (LB) method applied to a single-phase supersaturated solution in a constructed porous medium. The second model is based on the Invasion Percolation (IP) in pore networks, applied to two-phase immiscible displacement of seawater by liquid CO 2 . The pore-scale results are upscaled to obtain constitutive relations for porosity, both transverse and for the entire domain, and for permeability. We examine deposition and displacement patterns, and changes in porosity and permeability due to hydrate formation, and how these properties depend on various parameters including a parametric study of the effect of hydrate formation kinetics. According to the simulations, the depth of CO 2 invasion in the sediments is controlled by changes in the pore-scale porosity close to the hydrate formation front. (author)

Diffusion-controlled growth of hydrogen pores in aluminum-silicon castings: In situ observation and modeling

Energy Technology Data Exchange (ETDEWEB)

Atwood, R.C.; Sridhar, S.; Zhang, W.; Lee, P.D.

2000-01-24

In situ observations were made of the nucleation and growth kinetics of hydrogen porosity during the directional solidification of aluminium-7 wt% silicon (Al7Si) with TiB{sub 2} grain refiner added, using an X-ray temperature gradient stage (XTGS). The effect of altering the solidification velocity on the growth rate and morphology of the porosity formed was characterized by tracking individual pores with digital analysis of the micro-focal video images. It was found that increasing the solidification velocity caused the pore radius to decrease and pore density to increase. Insight gained from the experimental results was used to develop a computational model of the evolution of hydrogen pores during solidification of aluminum-silicon cast alloys. The model solves for the diffusion-limited growth of the pores in spherical coordinates, using a deterministic solution of the grain nucleation and growth as a sub-model to calculate the parameters that depend upon the fraction solid. Sensitivity analysis was carried out to assess the effects of equiaxed grain density, pore density, initial hydrogen content and cooling rate. The model agrees with the experimental results within the resolution limits of the XTGS experiments performed.

Pore-scale modeling of capillary trapping in water-wet porous media: A new cooperative pore-body filling model

Science.gov (United States)

Ruspini, L. C.; Farokhpoor, R.; Øren, P. E.

2017-10-01

We present a pore-network model study of capillary trapping in water-wet porous media. The amount and distribution of trapped non-wetting phase is determined by the competition between two trapping mechanisms - snap-off and cooperative pore-body filling. We develop a new model to describe the pore-body filling mechanism in geologically realistic pore-networks. The model accounts for the geometrical characteristics of the pore, the spatial location of the connecting throats and the local fluid topology at the time of the displacement. We validate the model by comparing computed capillary trapping curves with published data for four different water-wet rocks. Computations are performed on pore-networks extracted from micro-CT images and process-based reconstructions of the actual rocks used in the experiments. Compared with commonly used stochastic models, the new model describes more accurately the experimental measurements, especially for well connected porous systems where trapping is controlled by subtleties of the pore structure. The new model successfully predicts relative permeabilities and residual saturation for Bentheimer sandstone using in-situ measured contact angles as input to the simulations. The simulated trapped cluster size distributions are compared with predictions from percolation theory.

Grafting synthetic transmembrane units to the engineered low-toxicity α-hemolysin to restore its hemolytic activity.

Science.gov (United States)

Ui, Mihoko; Harima, Kousuke; Takei, Toshiaki; Tsumoto, Kouhei; Tabata, Kazuhito V; Noji, Hiroyuki; Endo, Sumire; Akiyama, Kimio; Muraoka, Takahiro; Kinbara, Kazushi

2014-12-01

The chemical modification of proteins to provide desirable functions and/or structures broadens their possibilities for use in various applications. Usually, proteins can acquire new functions and characteristics, in addition to their original ones, via the introduction of synthetic functional moieties. Here, we adopted a more radical approach to protein modification, i.e., the replacement of a functional domain of proteins with alternative chemical compounds to build "cyborg proteins." As a proof of concept model, we chose staphylococcal α-hemolysin (Hla), which is a well-studied, pore-forming toxin. The hemolytic activity of Hla mutants was dramatically decreased by truncation of the stem domain, which forms a β-barrel pore in the membrane. However, the impaired hemolytic activity was significantly restored by attaching a pyrenyl-maleimide unit to the cysteine residue that was introduced in the remaining stem domain. In contrast, negatively charged fluorescein-maleimide completely abolished the remaining activity of the mutants.

FINGERPRINT MATCHING BASED ON PORE CENTROIDS

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S. Malathi

2011-05-01

Full Text Available In recent years there has been exponential growth in the use of bio- metrics for user authentication applications. Automated Fingerprint Identification systems have become popular tool in many security and law enforcement applications. Most of these systems rely on minutiae (ridge ending and bifurcation features. With the advancement in sensor technology, high resolution fingerprint images (1000 dpi pro- vide micro level of features (pores that have proven to be useful fea- tures for identification. In this paper, we propose a new strategy for fingerprint matching based on pores by reliably extracting the pore features The extraction of pores is done by Marker Controlled Wa- tershed segmentation method and the centroids of each pore are con- sidered as feature vectors for matching of two fingerprint images. Experimental results shows that the proposed method has better per- formance with lower false rates and higher accuracy.

A new method for calculating gas content of coal reservoirs with consideration of a micro-pore overpressure environment

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Jinxing Song

2017-05-01

Full Text Available When the gas content of a coal reservoir is calculated, the reservoir pressure measured by well logging and well testing is generally used for inversion calculation instead of gas pressure. However, the calculation result is not accurate because the reservoir pressure is not equal to the gas pressure in overpressure environments. In this paper, coal samples of different ranks in Shanxi and Henan are collected for testing the capillary pressure of coal pores. Based on the formation process of CBM reservoirs and the hydrocarbon generation and expulsion history of coal beds, the forming mechanisms of micro-pore overpressure environments in coal reservoirs were analyzed. Accordingly, a new method for calculating the gas content of coal reservoirs with consideration of a micro-pore overpressure environment was developed. And it was used to calculate the gas content of No. 1 coal bed of the 2nd member of Lower Permian Shanxi Fm in the Zhongmacun Coal Mine in Jiaozuo, Henan. It is indicated that during the formation and evolution of coals, some solid organic matters were converted into gas and water, and gas–water contact is surely formed in pores. In the end, capillary pressure is generated, so the gas pressure in micro-pores is much higher than the hydrostatic column pressure, which results in a micro-pore overpressure environment. Under such an environment, gas pressure is higher than reservoir pressure, so the gas content of coal reservoirs calculated previously based on the conventional reservoir pressure evaluation are usually underestimated. It is also found that the micro-pore overpressure environment exerts a dominating effect on the CBM content calculation of 3–100 nm pores, especially that of 3–10 nm pores, but a little effect on that of pores >100 nm. In conclusion, this new method clarifies the pressure environment of CBM gas reservoirs, thereby ensuring the calculation accuracy of gas content of coal reservoirs.

Cavitation and pore blocking in nanoporous glasses.

Science.gov (United States)

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. © 2011 American Chemical Society

Uncertainties in pore water chemistry of compacted bentonite from Rokle deposit

International Nuclear Information System (INIS)

Cervinka, R.; Vejsadu, J.; Vokal, A.

2012-01-01

Document available in extended abstract form only. The composition of compacted bentonite pore water influences a number of important processes occurring in a deep geological repository (DGR), e.g. corrosion of waste package materials, solubility of radionuclides, or diffusion and sorption of radionuclides. Its determination is not straightforward, because it is difficult to obtain (e.g. squeeze) the pore water from compacted bentonite without changing its properties. It is therefore necessary to combine experimentally obtained parameters and geochemical modelling to approach it compositions. This article describes the results achieved in investigation the composition of pore water of compacted Ca-Mg bentonite from Czech deposits, proposed in Czech DGR concept. Ca-Mg bentonite from the largest operating deposit Rokle (Tertiary neo-volcanic area, NW Bohemia) represents complex mixture of (Ca,Mg)-Fe-rich montmorillonite, micas, kaolinite and other mineral admixtures (mainly Ca, Mg, Fe carbonates, feldspars and iron oxides). For experimental investigations the homogenized and grind raw bentonite material obtained directly from the deposit and commercial product (partly Na-activated) from supplier were used. Geochemical characterization of Rokle bentonite included mineralogical composition analyzed by Xray diffraction, cation exchange capacity determined using Cu-trien method, surface complexation parameters determined by acid-base titrations and 'geochemical' porosity derived from diffusion experiments with tracers ( 3 H and 36 Cl). Soluble salts inventory was calculated on the base of results from aqueous extracts of bentonite in deionized water at different solid to liquid ratios (from 18.6 to 125 g/l) and high pressure squeezing of water saturated bentonite at different solid to liquid ratios (from 1:1 to 4:1 w/w). The geochemical model contained cation exchange in the interlayer space and protonization and de-protonization of surface hydroxyl groups on clay

Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server

DEFF Research Database (Denmark)

Käll, Lukas; Krogh, Anders; Sonnhammer, Erik L L

2007-01-01

. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius. Udgivelsesdato: 2007-Jul......When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all...

The Arabidopsis Nuclear Pore and Nuclear Envelope

OpenAIRE

Meier, Iris; Brkljacic, Jelena

2010-01-01

The nuclear envelope is a double membrane structure that separates the eukaryotic cytoplasm from the nucleoplasm. The nuclear pores embedded in the nuclear envelope are the sole gateways for macromolecular trafficking in and out of the nucleus. The nuclear pore complexes assembled at the nuclear pores are large protein conglomerates composed of multiple units of about 30 different nucleoporins. Proteins and RNAs traffic through the nuclear pore complexes, enabled by the interacting activities...

Synthesis and characterization of thermally stable large-pore mesoporous nanocrystallineanatase

Energy Technology Data Exchange (ETDEWEB)

Ermokhina, Natalia I.; Nevinskiy, Vitaly A.; Manorik, Piotr A.; Ilyin, Vladimir G. [L.V. Pisarzhevskiy Institute of Physical Chemistry, National Academy of Sciences of Ukraine, 31 Prospekt Nauki, Kyiv 03028 (Ukraine); Novichenko, Viktor N.; Shcherbatiuk, Mykola M.; Klymchuk, Dmitro O. [M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, 2Tereshchenkivska St., 01601, Kyiv (Ukraine); Tsyba, Mykola M. [Institute for Sorption and Problems of Endoecology, National Academy of Sciences of Ukraine, 13 Naumov St., Kyiv 03164 (Ukraine); Puziy, Alexander M., E-mail: alexander.puziy@ispe.kiev.ua [Institute for Sorption and Problems of Endoecology, National Academy of Sciences of Ukraine, 13 Naumov St., Kyiv 03164 (Ukraine)

2013-04-15

Thermally stable mesoporous nanocrystalline TiO{sub 2} with a pure anatase structure was obtained by sol–gel synthesis (in combination with hydrothermal treatment) using titanium tetrabutoxide and dibenzo-18-crown-6 as a structure-directing agent in presence of surfactant and/or La{sup 3+} ions additives. Nanocrystalline TiO{sub 2} demonstrates various textures with a well-defined spherical morphology (micro- and nanospheres), a crystallite size of no greater than 10 nm (XRD), and a narrow pore size distribution. Spherical particles of micrometer scale in the presence of La{sup 3+} ions do not form. TiO{sub 2} calcined (at 500 °C) after hydrothermal treatment (at 175 °C) has a significantly more developed porous structure as compared with TiO{sub 2} which was not treated hydrothermally. For example, specific surface area amounts 137 m{sup 2} g{sup −1} and 69 m{sup 2} g{sup −1}, pore volume 0.98 cm{sup 3} g{sup −1} and 0.21 cm{sup 3} g{sup −1}, pore diameter 17.5 nm and 12.5 nm respectively for samples hydrothermally treated and not treated. - Graphical abstract: Large-pore mesoporous nanocristalline anatase. Highlights: ► Large-pore mesoporous nanocrystalline TiO{sub 2} was obtained by sol–gel synthesis. ► Crown ether was used as template in presence of surfactant and/or La{sup 3+} ions. ► Anatase (crystalline size<11 nm) is the only crystalline phase present in TiO{sub 2}. ► TiO{sub 2} shows well-defined homogeneous spherical morphology (micro- and nano-spheres)

Discovery of a new mitochondria permeability transition pore (mPTP) inhibitor based on gallic acid.

Science.gov (United States)

Teixeira, José; Oliveira, Catarina; Cagide, Fernando; Amorim, Ricardo; Garrido, Jorge; Borges, Fernanda; Oliveira, Paulo J

2018-12-01

Pharmacological interventions targeting mitochondria present several barriers for a complete efficacy. Therefore, a new mitochondriotropic antioxidant (AntiOxBEN 3 ) based on the dietary antioxidant gallic acid was developed. AntiOxBEN 3 accumulated several thousand-fold inside isolated rat liver mitochondria, without causing disruption of the oxidative phosphorylation apparatus, as seen by the unchanged respiratory control ratio, phosphorylation efficiency, and transmembrane electric potential. AntiOxBEN 3 showed also limited toxicity on human hepatocarcinoma cells. Moreover, AntiOxBEN 3 presented robust iron-chelation and antioxidant properties in both isolated liver mitochondria and cultured rat and human cell lines. Along with its low toxicity profile and high antioxidant activity, AntiOxBEN 3 strongly inhibited the calcium-dependent mitochondrial permeability transition pore (mPTP) opening. From our data, AntiOxBEN 3 can be considered as a lead compound for the development of a new class of mPTP inhibitors and be used as mPTP de-sensitiser for basic research or clinical applications or emerge as a therapeutic application in mitochondria dysfunction-related disorders.

Pore facies analysis: incorporation of rock properties into pore geometry based classes in a Permo-Triassic carbonate reservoir in the Persian Gulf

International Nuclear Information System (INIS)

Rahimpour-Bonab, H; Aliakbardoust, E

2014-01-01

Pore facies analysis is a useful method for the classification of reservoir rocks according to pore geometry characteristics. The importance of this method is related to the dependence of the dynamic behaviour of the reservoir rock on the pore geometry. In this study, pore facies analysis was performed by the quantification and classification of the mercury injection capillary pressure (MICP) curves applying the multi-resolution graph-based clustering (MRGC) method. Each pore facies includes a limited variety of rock samples with different depositional fabrics and diagenetic histories, which are representative of one type of pore geometry. The present pore geometry is the result of the interaction between the primary rock fabric and its diagenetic overprint. Thus the variations in petrographic properties can be correlated with the pore geometry characteristics. Accordingly, the controlling parameters in the pore geometry characteristics were revealed by detailed petrographic analysis in each pore facies. The reservoir rock samples were then classified using the determined petrographic properties which control the pore system quality. This method is proposed for the classification of reservoir rocks in complicated carbonate reservoirs, in order to reduce the incompatibility of traditional facies analysis with pore system characteristics. The method is applicable where enough capillary pressure data is not available. (papers)

Modeling of Processing-Induced Pore Morphology in an Additively-Manufactured Ti-6Al-4V Alloy.

Science.gov (United States)

Kabir, Mohammad Rizviul; Richter, Henning

2017-02-08

A selective laser melting (SLM)-based, additively-manufactured Ti-6Al-4V alloy is prone to the accumulation of undesirable defects during layer-by-layer material build-up. Defects in the form of complex-shaped pores are one of the critical issues that need to be considered during the processing of this alloy. Depending on the process parameters, pores with concave or convex boundaries may occur. To exploit the full potential of additively-manufactured Ti-6Al-4V, the interdependency between the process parameters, pore morphology, and resultant mechanical properties, needs to be understood. By incorporating morphological details into numerical models for micromechanical analyses, an in-depth understanding of how these pores interact with the Ti-6Al-4V microstructure can be gained. However, available models for pore analysis lack a realistic description of both the Ti-6Al-4V grain microstructure, and the pore geometry. To overcome this, we propose a comprehensive approach for modeling and discretizing pores with complex geometry, situated in a polycrystalline microstructure. In this approach, the polycrystalline microstructure is modeled by means of Voronoi tessellations, and the complex pore geometry is approximated by strategically combining overlapping spheres of varied sizes. The proposed approach provides an elegant way to model the microstructure of SLM-processed Ti-6Al-4V containing pores or crack-like voids, and makes it possible to investigate the relationship between process parameters, pore morphology, and resultant mechanical properties in a finite-element-based simulation framework.

Modeling of Processing-Induced Pore Morphology in an Additively-Manufactured Ti-6Al-4V Alloy

Directory of Open Access Journals (Sweden)

Mohammad Rizviul Kabir

2017-02-01

Full Text Available A selective laser melting (SLM-based, additively-manufactured Ti-6Al-4V alloy is prone to the accumulation of undesirable defects during layer-by-layer material build-up. Defects in the form of complex-shaped pores are one of the critical issues that need to be considered during the processing of this alloy. Depending on the process parameters, pores with concave or convex boundaries may occur. To exploit the full potential of additively-manufactured Ti-6Al-4V, the interdependency between the process parameters, pore morphology, and resultant mechanical properties, needs to be understood. By incorporating morphological details into numerical models for micromechanical analyses, an in-depth understanding of how these pores interact with the Ti-6Al-4V microstructure can be gained. However, available models for pore analysis lack a realistic description of both the Ti-6Al-4V grain microstructure, and the pore geometry. To overcome this, we propose a comprehensive approach for modeling and discretizing pores with complex geometry, situated in a polycrystalline microstructure. In this approach, the polycrystalline microstructure is modeled by means of Voronoi tessellations, and the complex pore geometry is approximated by strategically combining overlapping spheres of varied sizes. The proposed approach provides an elegant way to model the microstructure of SLM-processed Ti-6Al-4V containing pores or crack-like voids, and makes it possible to investigate the relationship between process parameters, pore morphology, and resultant mechanical properties in a finite-element-based simulation framework.

Pore surface engineering in covalent organic frameworks.

Science.gov (United States)

Nagai, Atsushi; Guo, Zhaoqi; Feng, Xiao; Jin, Shangbin; Chen, Xiong; Ding, Xuesong; Jiang, Donglin

2011-11-15

Covalent organic frameworks (COFs) are a class of important porous materials that allow atomically precise integration of building blocks to achieve pre-designable pore size and geometry; however, pore surface engineering in COFs remains challenging. Here we introduce pore surface engineering to COF chemistry, which allows the controlled functionalization of COF pore walls with organic groups. This functionalization is made possible by the use of azide-appended building blocks for the synthesis of COFs with walls to which a designable content of azide units is anchored. The azide units can then undergo a quantitative click reaction with alkynes to produce pore surfaces with desired groups and preferred densities. The diversity of click reactions performed shows that the protocol is compatible with the development of various specific surfaces in COFs. Therefore, this methodology constitutes a step in the pore surface engineering of COFs to realize pre-designed compositions, components and functions.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Alexandra B Wolf

Full Text Available 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.

Effect of Fe- and Si-Enriched Secondary Precipitates and Surface Roughness on Pore Formation on Aluminum Plate Surfaces During Anodizing

Science.gov (United States)

Zhu, Yuanzhi; Wang, Shizhi; Yang, Qingda; Zhou, Feng

2014-09-01

Two twin roll casts (TRCs) and one hot rolled (HR) AA 1235 aluminum alloy plates with different microstructures are prepared. The plates were electrolyzed in a 1.2 wt% HCl solution with a voltage of 21 V and a current of 1.9 mA. The shape, size, and number of pores formed on the surfaces of these plates were analyzed and correlated with the microstructures of the plates. It is found that pores are easier to form on the alloy plates containing subgrains with a lower dislocation density inside the subgrains, rather than along the grain boundaries. Furthermore, Fe- and Si-enriched particles in the AA1235 aluminum alloys lead to the formation of pores on the surface during electrolyzing; the average precipitate sizes of 4, 3.5, and 2 μm in Alloy 1#, Alloy 2# and Alloy 3# result in the average pore sizes of 3.78, 2.76, and 1.9 μm on the surfaces of the three alloys, respectively; The G.P zone in the alloy also facilitates the surface pore formation. High-surface roughness enhances the possibility of entrapping more lubricants into the plate surface, which eventually blocks the formation of the pores on the surface of the aluminum plates in the following electrolyzing process.

Structural Insights into Triglyceride Storage Mediated by Fat Storage-Inducing Transmembrane (FIT) Protein 2

Science.gov (United States)

Gross, David A.; Snapp, Erik L.; Silver, David L.

2010-01-01

Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2) belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9)AAA) in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9)AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation. PMID:20520733

Structural insights into triglyceride storage mediated by fat storage-inducing transmembrane (FIT protein 2.

Directory of Open Access Journals (Sweden)

David A Gross

2010-05-01

Full Text Available Fat storage-Inducing Transmembrane proteins 1 & 2 (FIT1/FITM1 and FIT2/FITM2 belong to a unique family of evolutionarily conserved proteins localized to the endoplasmic reticulum that are involved in triglyceride lipid droplet formation. FIT proteins have been shown to mediate the partitioning of cellular triglyceride into lipid droplets, but not triglyceride biosynthesis. FIT proteins do not share primary sequence homology with known proteins and no structural information is available to inform on the mechanism by which FIT proteins function. Here, we present the experimentally-solved topological models for FIT1 and FIT2 using N-glycosylation site mapping and indirect immunofluorescence techniques. These methods indicate that both proteins have six-transmembrane-domains with both N- and C-termini localized to the cytosol. Utilizing this model for structure-function analysis, we identified and characterized a gain-of-function mutant of FIT2 (FLL(157-9AAA in transmembrane domain 4 that markedly augmented the total number and mean size of lipid droplets. Using limited-trypsin proteolysis we determined that the FLL(157-9AAA mutant has enhanced trypsin cleavage at K86 relative to wild-type FIT2, indicating a conformational change. Taken together, these studies indicate that FIT2 is a 6 transmembrane domain-containing protein whose conformation likely regulates its activity in mediating lipid droplet formation.

Relationship between pore structure and compressive strength

Indian Academy of Sciences (India)

Properties of concrete are strongly dependent on its pore structure features, porosity being an important one among them. This study deals with developing an understanding of the pore structure-compressive strength relationship in concrete. Several concrete mixtures with different pore structures are proportioned and ...

Structure of FGFR3 transmembrane domain dimer: implications for signaling and human pathologies.

Science.gov (United States)

Bocharov, Eduard V; Lesovoy, Dmitry M; Goncharuk, Sergey A; Goncharuk, Marina V; Hristova, Kalina; Arseniev, Alexander S

2013-11-05

Fibroblast growth factor receptor 3 (FGFR3) transduces biochemical signals via lateral dimerization in the plasma membrane, and plays an important role in human development and disease. Eight different pathogenic mutations, implicated in cancers and growth disorders, have been identified in the FGFR3 transmembrane segment. Here, we describe the dimerization of the FGFR3 transmembrane domain in membrane-mimicking DPC/SDS (9/1) micelles. In the solved NMR structure, the two transmembrane helices pack into a symmetric left-handed dimer, with intermolecular stacking interactions occurring in the dimer central region. Some pathogenic mutations fall within the helix-helix interface, whereas others are located within a putative alternative interface. This implies that although the observed dimer structure is important for FGFR3 signaling, the mechanism of FGFR3-mediated transduction across the membrane is complex. We propose an FGFR3 signaling mechanism that is based on the solved structure, available structures of isolated soluble FGFR domains, and published biochemical and biophysical data. Copyright © 2013 Elsevier Ltd. All rights reserved.

Trans-membrane area asymmetry controls the shape of cellular organelles

NARCIS (Netherlands)

Beznoussenko, Galina V; Pilyugin, Sergei S; Geerts, Willie J C; Kozlov, Michael M; Burger, Koert N J; Luini, Alberto; Derganc, Jure; Mironov, Alexander A

2015-01-01

Membrane organelles often have complicated shapes and differ in their volume, surface area and membrane curvature. The ratio between the surface area of the cytosolic and luminal leaflets (trans-membrane area asymmetry (TAA)) determines the membrane curvature within different sites of the organelle.

Modelling of a transmembrane evaporation module for desalination of seawater

NARCIS (Netherlands)

Guijt, C.M.; Racz, I.G.; van Heuven, Jan Willem; Reith, T.; de Haan, A.B.

1999-01-01

Transmembrane evaporation (often called membrane distillation) carried out in a countercurrent flow module, in which incoming cold seawater is heated by the condensing product water flow, is a promising technology for low-cost seawater desalination. This paper presents a model for preliminary design

Revealing Lattice Expansion of Small-Pore Zeolite Catalysts during the Methanol-to-Olefins Process Using Combined Operando X-ray Diffraction and UV-vis Spectroscopy

NARCIS (Netherlands)

Goetze, Joris; Yarulina, I.; Gascon Sabate, J.; Kapteijn, F.; Weckhuysen, Bert M.

2018-01-01

In small-pore zeolite catalysts, where the size of the pores is limited by eight-ring windows, aromatic hydrocarbon pool molecules that are formed inside the zeolite during the Methanol-to-Olefins (MTO) process cannot exit the pores and are retained inside the catalyst. Hydrocarbon species whose

A pore water conductivity sensor

NARCIS (Netherlands)

Hilhorst, M.A.

2001-01-01

The electrical permittivity and conductivity of the bulk soil are a function of the permittivity and conductivity of the pore water. For soil water contents higher than 0.10 both functions are equal, facilitating in situ conductivity measurements of the pore water. A novel method is described, based

Mesoscale Simulations of Pore Migration in a Nuclear Fuel

International Nuclear Information System (INIS)

Radhakrishnan, Balasubramaniam; Gorti, Sarma B.

2010-01-01

The evolution of pore and grain structure in a nuclear fuel environment is strongly influenced by the local temperature, and the temperature gradient. The evolution of pore and grain structure in an externally imposed temperature gradient is simulated for a hypothetical material using a Potts model approach that allows for porosity migration by mechanisms similar to surface, grain boundary and volume diffusion, as well as the interaction of migrating pores with stationary grain boundaries. First, the migration of a single pore in a single crystal in the presence of the temperature gradient is simulated. Next, the interaction of a pore moving in a temperature gradient with a grain boundary that is perpendicular to the pore migration direction is simulated in order to capture the force exerted by the pore on the grain boundary. The simulations reproduce the expected variation of pore velocity with pore size as well as the variation of the grain boundary force with pore size.

Pore-forming virulence factors of Staphylococcus aureus destabilize epithelial barriers-effects of alpha-toxin in the early phases of airway infection

Directory of Open Access Journals (Sweden)

Jan-Peter Hildebrandt

2015-09-01

Full Text Available Staphylococcus aureus (S. aureus is a human commensal and an opportunistic pathogen that may affect the gastrointestinal tract, the heart, bones, skin or the respiratory tract. S. aureus is frequently involved in hospital- or community-acquired lung infections. The pathogenic potential is associated with its ability to secrete highly effective virulence factors. Among these, the pore-forming toxins Panton-Valentine leukocidin (PVL and hemolysin A (Hla are the important virulence factors determining the prognosis of pneumonia cases. This review focuses on the structure and the functions of S. aureus hemolysin A and its sub-lethal effects on airway epithelial cells. The hypothesis is developed that Hla may not just be a tissue-destructive agent providing the bacteria with host-derived nutrients, but may also play complex roles in the very early stages of interactions of bacteria with healthy airways, possibly paving the way for establishing acute infections.

Critical assessment of the pore size distribution in the rim region of high burnup UO_2 fuels

International Nuclear Information System (INIS)

Cappia, F.; Pizzocri, D.; Schubert, A.; Van Uffelen, P.; Paperini, G.; Pellottiero, D.; Macián-Juan, R.; Rondinella, V.V.

2016-01-01

A new methodology is introduced to analyse porosity data in the high burnup structure. Image analysis is coupled with the adaptive kernel density estimator to obtain a detailed characterisation of the pore size distribution, without a-priori assumption on the functional form of the distribution. Subsequently, stereological analysis is carried out. The method shows advantages compared to the classical approach based on the histogram in terms of detail in the description and accuracy within the experimental limits. Results are compared to the approximation of a log-normal distribution. In the investigated local burnup range (80–200 GWd/tHM), the agreement of the two approaches is satisfactory. From the obtained total pore density and mean pore diameter as a function of local burnup, pore coarsening is observed starting from ≈100 GWd/tHM, in agreement with a previous investigation. - Highlights: • A new methodology to analyse porosity is introduced. • The method shows advantages compared to the histogram. • Pore density and mean diameter data vs. burnup are presented. • Pore coarsening is observed starting from ≈100 GWd/tHM.

Influence of pore structure on carbon retention/loss in soil macro-aggregates

Science.gov (United States)

Quigley, Michelle; Kravchenko, Alexandra; Rivers, Mark

2017-04-01

carbon protect were disparate. In intact-structure aggregates, prior to incubation, there was no association between carbon distribution and pores. After incubation, significant correlations (α=0.05) were observed between abundance of 6-40 μm pores and both soil organic carbon (SOC) and δ13C. Sections containing more 6-40 μm pores also had increased amounts of SOC (r2=0.23) with higher presence of C4 carbon (r2=0.27). This indicates preferential preservation of older carbon in the pores of this size range. Prior to incubation, destroyed-structure aggregates had higher amounts of C3 carbon associated with 40-95 μm pores (r2=0.14), pointing to a greater presence of newly added carbon within these pores. However, after incubation there was a significant loss of SOC from these pores (r2=0.22) and, specifically, the loss of C3 carbon (r2=0.16). In the studied soil, pores of 6-40 μm size range appeared to control the preservation of older carbon, while 40-95 μm pores controlled the fate of newly added carbon. Older carbon preservation in 6-40 μm pores was mostly observed in macro-aggregates from the soil with intact structure, while the associations between 40-95 μm pores and gains and losses of newly added carbon were primarily observed in the macro-aggregates that were formed anew in the sieved soil during the plant growing experiment.

Transmembrane adaptor molecules: a new category of lymphoid-cell markers

Czech Academy of Sciences Publication Activity Database

Tedoldi, S.; Paterson, J.C.; Hansmann, M.-L.; Natkunam, Y.; Rüdiger, T.; Angelisová, Pavla; Du, M.Q.; Roberton, H.; Roncador, G.; Sanchez, L.; Pozzobon, M.; Masir, N.; Barry, R.; Pileri, S.; Mason, D.Y.; Marafioti, T.; Hořejší, Václav

2006-01-01

Roč. 107, č. 1 (2006), s. 213-221 ISSN 0006-4971 R&D Projects: GA MŠk(CZ) 1M0506 Institutional research plan: CEZ:AV0Z50520514 Keywords : transmembrane adaptors * PAG * LIME Subject RIV: EC - Immunology Impact factor: 10.370, year: 2006

The one-dimensional compression method for extraction of pore water from unsaturated tuff and effects on pore-water chemistry

Energy Technology Data Exchange (ETDEWEB)

Higgins, J.D.; Burger, P.A. [Colorado School of Mines, Golden, CO (United States); Yang, L.C. [Geological Survey, Denver, CO (United States)

1997-12-31

Study of the hydrologic system at Yucca Mountain, Nevada, requires extraction of pore-water samples from unsaturated tuff bedrock. Two generations of compression cells have been designed and tested for extracting representative, unaltered pore-water samples from unsaturated tuff cores. The one-dimensional compression cell has a maximum compressive stress rating of 552 MPa. Results from 86 tests show that the minimum degree of saturation for successful extraction of pore water was about 14% for non welded tuff and about 61% for densely welded tuff. The high-pressure, one-dimensional compression cell has a maximum compressive stress rating of 827 MPa. Results from 109 tests show that the minimum degree of saturation for successful extraction of pore water was about 7.5% for non welded tuff and about 34% for densely welded tuff. Geochemical analyses show that, in general, there is a decrease in ion concentration of pore waters as extraction pressures increase. Only small changes in pore-water composition occur during the one-dimensional extraction test.

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

NARCIS (Netherlands)

Naylor, R.M.; Jeganathan, K.B.; Cao, X.; Deursen, J.M. van

2016-01-01

The nuclear pore complex protein NUP88 is frequently elevated in aggressive human cancers and correlates with reduced patient survival; however, it is unclear whether and how NUP88 overexpression drives tumorigenesis. Here, we show that mice overexpressing NUP88 are cancer prone and form intestinal

A new mechanism of voltage-dependent gating exposed by KV10.1 channels interrupted between voltage sensor and pore.

Science.gov (United States)

Tomczak, Adam P; Fernández-Trillo, Jorge; Bharill, Shashank; Papp, Ferenc; Panyi, Gyorgy; Stühmer, Walter; Isacoff, Ehud Y; Pardo, Luis A

2017-05-01

Voltage-gated ion channels couple transmembrane potential changes to ion flow. Conformational changes in the voltage-sensing domain (VSD) of the channel are thought to be transmitted to the pore domain (PD) through an α-helical linker between them (S4-S5 linker). However, our recent work on channels disrupted in the S4-S5 linker has challenged this interpretation for the KCNH family. Furthermore, a recent single-particle cryo-electron microscopy structure of K V 10.1 revealed that the S4-S5 linker is a short loop in this KCNH family member, confirming the need for an alternative gating model. Here we use "split" channels made by expression of VSD and PD as separate fragments to investigate the mechanism of gating in K V 10.1. We find that disruption of the covalent connection within the S4 helix compromises the ability of channels to close at negative voltage, whereas disconnecting the S4-S5 linker from S5 slows down activation and deactivation kinetics. Surprisingly, voltage-clamp fluorometry and MTS accessibility assays show that the motion of the S4 voltage sensor is virtually unaffected when VSD and PD are not covalently bound. Finally, experiments using constitutively open PD mutants suggest that the presence of the VSD is structurally important for the conducting conformation of the pore. Collectively, our observations offer partial support to the gating model that assumes that an inward motion of the C-terminal S4 helix, rather than the S4-S5 linker, closes the channel gate, while also suggesting that control of the pore by the voltage sensor involves more than one mechanism. © 2017 Tomczak et al.

A voltage-gated pore for translocation of tRNA

Energy Technology Data Exchange (ETDEWEB)

Koley, Sandip; Adhya, Samit, E-mail: nilugrandson@gmail.com

2013-09-13

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

The charge effect on the hindrance factors for diffusion and convection of a solute in pores: II

Energy Technology Data Exchange (ETDEWEB)

Akinaga, Takeshi; O-tani, Hideyuki; Sugihara-Seki, Masako, E-mail: r091077@kansai-u.ac.jp [Department of Pure and Applied Physics, Kansai University, Yamate-cho, Suita, Osaka 564-8680 (Japan)

2012-10-15

The diffusion and convection of a solute suspended in a fluid across porous membranes are known to be reduced compared to those in a bulk solution, owing to the fluid mechanical interaction between the solute and the pore wall as well as steric restriction. If the solute and the pore wall are electrically charged, the electrostatic interaction between them could affect the hindrance to diffusion and convection. In this study, the transport of charged spherical solutes through charged circular cylindrical pores filled with an electrolyte solution containing small ions was studied numerically by using a fluid mechanical and electrostatic model. Based on a mean field theory, the electrostatic interaction energy between the solute and the pore wall was estimated from the Poisson-Boltzmann equation, and the charge effect on the solute transport was examined for the solute and pore wall of like charge. The results were compared with those obtained from the linearized form of the Poisson-Boltzmann equation, i.e. the Debye-Hueckel equation. (paper)

Facial skin pores: a multiethnic study.

Science.gov (United States)

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

2015-01-01

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

The transmembrane collagen COL-99 guides longitudinally extending axons in C. elegans.

Science.gov (United States)

Taylor, Jesse; Unsoeld, Thomas; Hutter, Harald

2018-06-01

We have identified the transmembrane collagen, COL-99, in a genetic screen for novel genes involved in axon guidance in the nematode C. elegans. COL-99 is similar to transmembrane collagens type XIII, XXIII and XXV in vertebrates. col-99 mutants exhibit guidance defects in axons extending along the major longitudinal axon tracts, most prominently the left ventral nerve cord (VNC). COL-99 is expressed in the hypodermis during the time of axon outgrowth. We provide evidence that a furin cleavage site in COL-99 is essential for function, suggesting that COL-99 is released from the cells producing it. Vertebrate homologs of COL-99 have been shown to be expressed in mammalian nervous systems and linked to various neurological disease but have not been associated with guidance of extending neurons. col-99 acts genetically with the discoidin domain receptors ddr-1 and ddr-2, which are expressed by neurons affected in col-99 mutants. Discoidin domain receptors are activated by collagens in vertebrates. DDR-1 and DDR-2 may function as receptors for COL-99. Our results establish a novel role for a transmembrane collagen in axonal guidance and asymmetry establishment of the VNC. Copyright © 2018 Elsevier Inc. All rights reserved.

Mesoporous ethanesilica materials with bimodal and trimodal pore-size distributions synthesised in the presence of cobalt ions

Directory of Open Access Journals (Sweden)

Alufelwi M. Tshavhungwe

2010-07-01

Full Text Available Mesoporous organosilica materials containing ethane groups in their framework were formed with two and three pore sizes (i.e. bimodal and trimodal pores when synthesised by the sol-gel method in the presence of cobalt ions. The compounds 1,2-bistrimethoxysilylethane and tetraethylorthosilicate were used as silicon sources and the reactions were done in the presence of a surfactant, which served as a template. Diffuse reflectance infrared Fourier transform spectroscopy revealed that organic functional groups were incorporated into the ethanesilica. Powder X-ray diffraction and nitrogen adsorption data indicated that the mesophase and textural properties (surface area, pore volume, pore diameter of the materials were dependent on the ageing temperature, the amount/ratio of silica precursors and cobalt ion incorporation. Secondary mesopores were drastically reduced by changing the ratio of silicon precursors.

Estimating pore-space gas hydrate saturations from well log acoustic data

Science.gov (United States)

Lee, Myung W.; Waite, William F.

2008-07-01

Relating pore-space gas hydrate saturation to sonic velocity data is important for remotely estimating gas hydrate concentration in sediment. In the present study, sonic velocities of gas hydrate-bearing sands are modeled using a three-phase Biot-type theory in which sand, gas hydrate, and pore fluid form three homogeneous, interwoven frameworks. This theory is developed using well log compressional and shear wave velocity data from the Mallik 5L-38 permafrost gas hydrate research well in Canada and applied to well log data from hydrate-bearing sands in the Alaskan permafrost, Gulf of Mexico, and northern Cascadia margin. Velocity-based gas hydrate saturation estimates are in good agreement with Nuclear Magneto Resonance and resistivity log estimates over the complete range of observed gas hydrate saturations.

Real-Time Pore Pressure Detection: Indicators and Improved Methods

Directory of Open Access Journals (Sweden)

Jincai Zhang

2017-01-01

Full Text Available High uncertainties may exist in the predrill pore pressure prediction in new prospects and deepwater subsalt wells; therefore, real-time pore pressure detection is highly needed to reduce drilling risks. The methods for pore pressure detection (the resistivity, sonic, and corrected d-exponent methods are improved using the depth-dependent normal compaction equations to adapt to the requirements of the real-time monitoring. A new method is proposed to calculate pore pressure from the connection gas or elevated background gas, which can be used for real-time pore pressure detection. The pore pressure detection using the logging-while-drilling, measurement-while-drilling, and mud logging data is also implemented and evaluated. Abnormal pore pressure indicators from the well logs, mud logs, and wellbore instability events are identified and analyzed to interpret abnormal pore pressures for guiding real-time drilling decisions. The principles for identifying abnormal pressure indicators are proposed to improve real-time pore pressure monitoring.

A casting based process to fabricate 3D alginate scaffolds and to investigate the influence of heat transfer on pore architecture during fabrication

International Nuclear Information System (INIS)

Parks, W.M.; Guo, Y.B.

2008-01-01

The fabrication of 3-dimensional (3D) tissue scaffolds is a competitive approach to engineered tissues. An ideal tissue scaffold must be highly porous, biocompatible, biodegradable, easily processed and cost-effective, and have adequate mechanical properties. A casting based process has been developed in this study to fabricate 3D alginate tissue scaffolds. The alginate/calcium gluconate hydrogel was quenched in a glass mold and freeze dried to form a highly porous tissue scaffold whose tiny pores retain the shape of the ice crystals during quenching. Knowing that the water in the alginate hydrogel would form ice crystals if frozen and that different cooling conditions may dramatically influence the pore architecture, the speed and direction of the heat transfer in freeze drying hydrogel were examined with regard to pore size and orientation. The pore architecture at the different locations of the fabricated scaffolds was characterized using scanning electron microscopy. The fabricated scaffolds consist of pores that are highly interconnected, with a diameter about 200 μm (average diameter of a capillary) to permit blood vessel penetration. It also has been found that the pore size, orientation, and uniformity are significantly affected by the condition of heat transfer during freeze drying. Tailoring the pore architecture of the scaffolds is feasible by controlling heat transfer. This study provides an insight on pore architecture formation and control by altered process parameters

Precise small-angle X-ray scattering evaluation of the pore structures in track-etched membranes: Comparison with other convenient evaluation methods

Energy Technology Data Exchange (ETDEWEB)

Miyazaki, Tsukasa, E-mail: t_miyazaki@cross.or.jp [Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106 (Japan); Takenaka, Mikihito [Department of Polymer Chemistry, Gradual School of Engineering, Kyoto University, Kyotodaigaku-katsura, Kyoto 615-8510 (Japan)

2017-03-01

Poly(ethylene terephthalate) (PET)-based track-etched membranes (TMs) with pore sizes ranging from few nanometers to approximately 1 μm are used in various applications in the biological field, and their pore structures are determined by small-angle X-ray scattering (SAXS). These TMs with the nanometer-sized cylindrical pores aligned parallel to the film thickness direction are produced by chemical etching of the track in the PET films irradiated by heavy ions with the sodium hydroxide aqueous solution. It is well known that SAXS allows us to precisely and statistically estimate the pore size and the pore size distribution in the TMs by using the form factor of a cylinder with the extremely long pore length relative to the pore diameter. The results obtained were compared with those estimated with scanning electron microscopy and gas permeability measurements. The result showed that the gas permeability measurement is convenient to evaluate the pore size of TMs within a wide length scale, and the SEM observation is also suited to estimate the pore size, although SEM observation is usually limited above approximately 30 nm.

The potential of medium-pore zeolites for improved propene yields from catalytic cracking

Energy Technology Data Exchange (ETDEWEB)

Bager, F.; Salas, N.; Ernst, S. [Technische Univ. Kaiserslautern (Germany). Dept. of Chemistry, Chemical Technology

2011-07-01

The medium-pore zeolites ZSM-5 (MFI), ZSM-22 (TON), ZSM-23 (MTT), and EU-1 (EUO) were synthesized under hydrothermal conditions and modified by ion exchange to obtain the Broensted-acid forms. The activity and selectivity of these catalysts in catalytic cracking of a model compound, viz. n-octane, was studied in a fixed-bed flow-type reactor. The catalytic results clearly reflect the differences in the pore architectures of the tested zeolites on n-octane conversion and on the product selectivities. Over the zeolites with one-dimensional pore systems and without large intracrystalline cavities, a remarkable increase of the contribution of the monomolecular cracking mechanism could be observed as compared to the standard catalyst zeolite ZSM-5. This is indicated by a high selectivity for unsaturated products and, hence, increasing yields of propene. Large cavities in the pore system, viz. in the case of zeolite EU-1, increase the conversion in particular at lower temperatures. However, the large cavities also favor the formation of large transition states required for the classical bimolecular cracking mechanism, resulting in decreased selectivities for unsaturated products, increased selectivities for aromatics formation and faster deactivation. (orig.)

OFF-GAS ANALYSIS RESULTS AND FINE PORE RETROFIT CASE HISTORY FOR HARTFORD, CONNECTICUT

Science.gov (United States)

In the summer of 1982, the Hartford Metropolitan District Commission, Hartford County, Connecticut, Water Pollution Control Facility underwent a retrofit form a spiral roll coarse bubble to a full floor coverage fine pore aeration system. Work performed included all new in-tank ...

Role of protein dynamics in transmembrane receptor signalling

DEFF Research Database (Denmark)

Wang, Yong; Bugge, Katrine Østergaard; Kragelund, Birthe Brandt

2018-01-01

Cells are dependent on transmembrane receptors to communicate and transform chemical and physical signals into intracellular responses. Because receptors transport 'information', conformational changes and protein dynamics play a key mechanistic role. We here review examples where experiment...... to function. Because the receptors function in a heterogeneous environment and need to be able to switch between distinct functional states, they may be particularly sensitive to small perturbations that complicate studies linking dynamics to function....

Multiple Approaches to Characterizing Pore Structure in Natural Rock

Science.gov (United States)

Hu, Q.; Dultz, S.; Hamamoto, S.; Ewing, R. P.

2012-12-01

Microscopic characteristics of porous media - pore shape, pore-size distribution, and pore connectivity - control fluid flow and chemical transport, and are important in hydrogeological studies of rock formations in the context of energy, environmental, and water resources management. This presentation discusses various approaches to investigating pore structure of rock, with a particular focus on the Barnett Shale in north Texas used for natural gas production. Approaches include imbibition, tracer diffusion, porosimetry (MIP, vapor adsorption/desorption isotherms, NMR cyroporometry), and imaging (μ-tomography, Wood's metal impregnation, FIB/SEM). Results show that the Barnett Shale pores are predominantly in the nm size range, with a measured median pore-throat diameter of 6.5 nm. But small pore size is not the major contributor to low gas recovery; rather, the low gas diffusivity appears to be caused by low pore connectivity. Chemical diffusion in sparsely-connected pore spaces is not well described by classical Fickian behavior; anomalous behavior is suggested by percolation theory, and confirmed by results of imbibition tests. Our evolving complementary approaches, with their several advantages and disadvantages, provide a rich toolbox for tackling the pore structure characteristics in the Barnett Shale and other natural rocks.

Effects of pore shape and porosity on the properties of porous LNKN ceramics as bone substitute

International Nuclear Information System (INIS)

Wang Qi; Chen Qiang; Zhu Jianguo; Huang Chunpeng; Darvell, Brian W.; Chen Zhiqing

2008-01-01

A porous lead-free piezoelectric ceramic is investigated as direct bone substitute. Porous lithium sodium potassium niobate (Li 0.06 Na 0.5 K 0.44 )NbO 3 specimens were prepared by pore-forming method. Different volume fraction of ammonium oxalate monohydrate and poly(methyl methacrylate) were used as porogens to obtain different pore shape and porosity. Scanning electron microscopy showed a bicontinuous 3-3 structure of interconnected pores 150-250 μm in size. The piezoelectric constants and electromechanical coupling coefficients may be controlled by both size and shape of the porogens to tune for the best biological response. Such materials show promise for use as a piezoelectric composite bone substitute

Pore structure of natural and regenerated soil aggregates

DEFF Research Database (Denmark)

Naveed, Muhammad; Arthur, Emmanuel; de Jonge, Lis Wollesen

2014-01-01

Quantitative characterization of aggregate pore structure can reveal the evolution of aggregates under different land use and management practices and their effects on soil processes and functions. Advances in X-ray Computed Tomography (CT) provide powerful means to conduct such characterization....... This study examined aggregate pore structure of three differently managed same textured Danish soils (mixed forage cropping, MFC; mixed cash cropping, MCC; cereal cash cropping, CCC) for (i) natural aggregates, and (ii) aggregates regenerated after 20 months of incubation. In total, 27 aggregates (8-16 mm...... pore diameter of 200 and 170 Hm, respectively. Pore shape analysis indicated that CCC and MFC aggregates had an abundance of rounded and elongated pores, respectively, and those of MCC were in-between CCC and MFC. Aggregate pore structure development in the lysimeters was nearly similar irrespective...

Effect of pores formation process and oxygen plasma treatment to hydroxyapatite formation on bioactive PEEK prepared by incorporation of precursor of apatite.

Science.gov (United States)

Yabutsuka, Takeshi; Fukushima, Keito; Hiruta, Tomoko; Takai, Shigeomi; Yao, Takeshi

2017-12-01

When bioinert substrates with fine-sized pores are immersed in a simulated body fluid (SBF) and the pH value or the temperature is increased, fine particles of calcium phosphate, which the authors denoted as 'precursor of apatite' (PrA), are formed in the pores. By this method, hydroxyapatite formation ability can be provided to various kinds of bioinert materials. In this study, the authors studied fabrication methods of bioactive PEEK by using the above-mentioned process. First, the fine-sized pores were formed on the surface of the PEEK substrate by H 2 SO 4 treatment. Next, to provide hydrophilic property to the PEEK, the surfaces of the PEEK were treated with O 2 plasma. Finally, PrA were formed in the pores by the above-mentioned process, which is denoted as 'Alkaline SBF' treatment, and the bioactive PEEK was obtained. By immersing in SBF with the physiological condition, hydroxyapatite formation was induced on the whole surface of the substrate within 1day. The formation of PrA directly contributed to hydroxyapatite formation ability. By applying the O 2 plasma treatment, hydroxyapatite formation was uniformly performed on the whole surface of the substrate. The H 2 SO 4 treatment contributed to a considerable enhancement of adhesive strength of the formed hydroxyapatite layer formed in SBF because of the increase of surface areas of the substrate. As a comparative study, the sandblasting method was applied as the pores formation process instead of the H 2 SO 4 treatment. Although hydroxyapatite formation was provided also in this case, however, the adhesion of the formed hydroxyapatite layer to the substrate was not sufficient even if the O 2 plasma treatment was conducted. This result indicates that the fine-sized pores should be formed on the whole surface of the substrate uniformly to achieve high adhesive strength of the hydroxyapatite layer. Therefore, it is considered that the H 2 SO 4 treatment before the O 2 plasma and the 'Alkaline SBF' treatment

In vivo evidence for a functional role of both tumor necrosis factor (TNF) receptors and transmembrane TNF in experimental hepatitis.

Science.gov (United States)

Küsters, S; Tiegs, G; Alexopoulou, L; Pasparakis, M; Douni, E; Künstle, G; Bluethmann, H; Wendel, A; Pfizenmaier, K; Kollias, G; Grell, M

1997-11-01

The significance of tumor necrosis factor receptor 1 (TNFR1) for TNF function in vivo is well documented, whereas the role of TNFR2 so far remains obscure. In a model of concanavalin A (Con A)-induced, CD4+ T cell-dependent experimental hepatitis in mice, in which TNF is a central mediator of apoptotic and necrotic liver damage, we now provide evidence for an essential in vivo function of TNFR2 in this pathophysiological process. We demonstrate that a cooperation of TNFR1 and TNFR2 is required for hepatotoxicity as mice deficient of either receptor were resistant against Con A. A significant role of TNFR2 for Con A-induced hepatitis is also shown by the enhanced sensitivity of transgenic mice overexpressing the human TNFR2. The ligand for cytotoxic signaling via both TNF receptors is the precursor of soluble TNF, i.e. transmembrane TNF. Indeed, transmembrane TNF is sufficient to mediate hepatic damage, as transgenic mice deficient in wild-type soluble TNF but expressing a mutated nonsecretable form of TNF developed inflammatory liver disease.

Antifungal effect and pore-forming action of lactoferricin B like peptide derived from centipede Scolopendra subspinipes mutilans.

Science.gov (United States)

Choi, Hyemin; Hwang, Jae-Sam; Lee, Dong Gun

2013-11-01

The centipede Scolopendra subspinipes mutilans has been a medically important arthropod species by using it as a traditional medicine for the treatment of various diseases. In this study, we derived a novel lactoferricin B like peptide (LBLP) from the whole bodies of adult centipedes, S. s. mutilans, and investigated the antifungal effect of LBLP. LBLP exerted an antifungal and fungicidal activity without hemolysis. To investigate the antifungal mechanism of LBLP, a membrane study with propidium iodide was first conducted against Candida albicans. The result showed that LBLP caused fungal membrane permeabilization. The assays of the three dimensional flow cytometric contour plot and membrane potential further showed cell shrinkage and membrane depolarization by the membrane damage. Finally, we confirmed the membrane-active mechanism of LBLP by synthesizing model membranes, calcein and FITC-dextran loaded large unilamellar vesicles. These results showed that the antifungal effect of LBLP on membrane was due to the formation of pores with radii between 0.74nm and 1.4nm. In conclusion, this study suggests that LBLP exerts a potent antifungal activity by pore formation in the membrane, eventually leading to fungal cell death. © 2013.

[Research advances in CKLF-like MARVEL transmembrane domain containing member 5].

Science.gov (United States)

Yuan, Ye-qing; Xiao, Yun-bei; Liu, Zhen-hua; Zhang, Xiao-wei; Xu, Tao; Wang, Xiao-feng

2012-12-01

CKLF-like MARVEL transmembrane domain containing member(CMTM)is a novel generic family firstly reported by Peking University Center for Human Disease Genomics. CMTM5 belongs to this family and has exhibited tumor-inhibiting activities. It can encode proteins approaching to the transmembrane 4 superfamily(TM4SF). CMTM5 is broadly expressed in normal adult and fetal human tissues, but is undetectable or down-regulated in most carcinoma cell lines and tissues. Restoration of CMTM5 may inhibit the proliferation, migration, and invasion of carcinoma cells. Although the exact mechanism of its anti-tumor activity remains unclear, CMTM5 may be involved in various signaling pathways governing the occurrence and development of tumors. CMTM5 may be a new target in the gene therapies for tumors, while further studies on CMTM5 and its anti-tumor mechanisms are warranted.

Enhancement of plasma generation in catalyst pores with different shapes

Science.gov (United States)

Zhang, Yu-Ru; Neyts, Erik C.; Bogaerts, Annemie

2018-05-01

Plasma generation inside catalyst pores is of utmost importance for plasma catalysis, as the existence of plasma species inside the pores affects the active surface area of the catalyst available to the plasma species for catalytic reactions. In this paper, the electric field enhancement, and thus the plasma production inside catalyst pores with different pore shapes is studied with a two-dimensional fluid model. The results indicate that the electric field will be significantly enhanced near tip-like structures. In a conical pore with small opening, the strongest electric field appears at the opening and bottom corners of the pore, giving rise to a prominent ionization rate throughout the pore. For a cylindrical pore, the electric field is only enhanced at the bottom corners of the pore, with lower absolute value, and thus the ionization rate inside the pore is only slightly enhanced. Finally, in a conical pore with large opening, the electric field is characterized by a maximum at the bottom of the pore, yielding a similar behavior for the ionization rate. These results demonstrate that the shape of the pore has a significantly influence on the electric field enhancement, and thus modifies the plasma properties.

Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor.

Directory of Open Access Journals (Sweden)

Vanessa Chantreau

Full Text Available The thyrotropin receptor (TSHR is a G protein-coupled receptor (GPCR that is member of the leucine-rich repeat subfamily (LGR. In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors.

Critical assessment of the pore size distribution in the rim region of high burnup UO{sub 2} fuels

Energy Technology Data Exchange (ETDEWEB)

Cappia, F. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, 76125 Karlsruhe (Germany); Department of Nuclear Engineering, Faculty of Mechanical Engineering, Technische Universität München, D-85748 Garching bei München (Germany); Pizzocri, D. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, 76125 Karlsruhe (Germany); Nuclear Engineering Division, Energy Department, Politecnico di Milano, 20156 Milano (Italy); Schubert, A.; Van Uffelen, P.; Paperini, G.; Pellottiero, D. [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, 76125 Karlsruhe (Germany); Macián-Juan, R. [Department of Nuclear Engineering, Faculty of Mechanical Engineering, Technische Universität München, D-85748 Garching bei München (Germany); Rondinella, V.V., E-mail: Vincenzo.RONDINELLA@ec.europa.eu [European Commission, Joint Research Centre, Institute for Transuranium Elements, P.O. Box 2340, 76125 Karlsruhe (Germany)

2016-11-15

A new methodology is introduced to analyse porosity data in the high burnup structure. Image analysis is coupled with the adaptive kernel density estimator to obtain a detailed characterisation of the pore size distribution, without a-priori assumption on the functional form of the distribution. Subsequently, stereological analysis is carried out. The method shows advantages compared to the classical approach based on the histogram in terms of detail in the description and accuracy within the experimental limits. Results are compared to the approximation of a log-normal distribution. In the investigated local burnup range (80–200 GWd/tHM), the agreement of the two approaches is satisfactory. From the obtained total pore density and mean pore diameter as a function of local burnup, pore coarsening is observed starting from ≈100 GWd/tHM, in agreement with a previous investigation. - Highlights: • A new methodology to analyse porosity is introduced. • The method shows advantages compared to the histogram. • Pore density and mean diameter data vs. burnup are presented. • Pore coarsening is observed starting from ≈100 GWd/tHM.

A method of evaluating facial pores using optical 2D images and analysis of age-dependent changes in facial pores in Koreans.

Science.gov (United States)

Jang, S I; Kim, E J; Lee, H K

2018-05-01

Enlarged facial pores and changes in pore area are of concern for cosmetic reasons. To evaluate pores, measuring tools based on 3D methodology are used. Yet, these methods are limited by their measuring ranges. In this study, we performed pore analysis by measuring the whole face using 2D optical images. We further sought to understand how the pores of Korean women change with age. One hundred sixteen Korean female subjects aged 20-60 years were recruited for this study. Facial images were taken using the VISIA-CR ® adjusted light source. Images were processed using Image-Pro Plus 9.2. Statistical significance was assumed when P pore area, as indicated by pixel count, gradually increased in patients through their 40s, but decreased through their 50s and 60s. Facial pores generally exhibited directionality through the patients' 30s, but this isotropic feature was more prominent in their 50s. Pore elongation increased stepwise. The first increase occurred during the transition from patients' 30s to their 40s and the second increase occurred during the transition from patients' 50s to their 60s. This indicated that the pores deformed from a circular shape to a long elliptic shape over time. A new evaluation method using 2D optical images facilitates the analysis of pore distribution and elongation throughout the entire cheek. This is an improvement over an analysis of pores over a narrow region of interest. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Nuclear Pore-Like Structures in a Compartmentalized Bacterium.

Directory of Open Access Journals (Sweden)

Evgeny Sagulenko

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

The MARVEL transmembrane motif of occludin mediates oligomerization and targeting to the basolateral surface in epithelia.

Science.gov (United States)

Yaffe, Yakey; Shepshelovitch, Jeanne; Nevo-Yassaf, Inbar; Yeheskel, Adva; Shmerling, Hedva; Kwiatek, Joanna M; Gaus, Katharina; Pasmanik-Chor, Metsada; Hirschberg, Koret

2012-08-01

Occludin (Ocln), a MARVEL-motif-containing protein, is found in all tight junctions. MARVEL motifs are comprised of four transmembrane helices associated with the localization to or formation of diverse membrane subdomains by interacting with the proximal lipid environment. The functions of the Ocln MARVEL motif are unknown. Bioinformatics sequence- and structure-based analyses demonstrated that the MARVEL domain of Ocln family proteins has distinct evolutionarily conserved sequence features that are consistent with its basolateral membrane localization. Live-cell microscopy, fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC) were used to analyze the intracellular distribution and self-association of fluorescent-protein-tagged full-length human Ocln or the Ocln MARVEL motif excluding the cytosolic C- and N-termini (amino acids 60-269, FP-MARVEL-Ocln). FP-MARVEL-Ocln efficiently arrived at the plasma membrane (PM) and was sorted to the basolateral PM in filter-grown polarized MDCK cells. A series of conserved aromatic amino acids within the MARVEL domain were found to be associated with Ocln dimerization using BiFC. FP-MARVEL-Ocln inhibited membrane pore growth during Triton-X-100-induced solubilization and was shown to increase the membrane-ordered state using Laurdan, a lipid dye. These data demonstrate that the Ocln MARVEL domain mediates self-association and correct sorting to the basolateral membrane.

Proteomic and Functional Analyses of the Virion Transmembrane Proteome of Cyprinid Herpesvirus 3.

Science.gov (United States)

Vancsok, Catherine; Peñaranda, M Michelle D; Raj, V Stalin; Leroy, Baptiste; Jazowiecka-Rakus, Joanna; Boutier, Maxime; Gao, Yuan; Wilkie, Gavin S; Suárez, Nicolás M; Wattiez, Ruddy; Gillet, Laurent; Davison, Andrew J; Vanderplasschen, Alain F C

2017-11-01

Virion transmembrane proteins (VTPs) mediate key functions in the herpesvirus infectious cycle. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses. The present study was devoted to CyHV-3 VTPs. Using mass spectrometry approaches, we identified 16 VTPs of the CyHV-3 FL strain. Mutagenesis experiments demonstrated that eight of these proteins are essential for viral growth in vitro (open reading frame 32 [ORF32], ORF59, ORF81, ORF83, ORF99, ORF106, ORF115, and ORF131), and eight are nonessential (ORF25, ORF64, ORF65, ORF108, ORF132, ORF136, ORF148, and ORF149). Among the nonessential proteins, deletion of ORF25, ORF132, ORF136, ORF148, or ORF149 affects viral replication in vitro , and deletion of ORF25, ORF64, ORF108, ORF132, or ORF149 impacts plaque size. Lack of ORF148 or ORF25 causes attenuation in vivo to a minor or major extent, respectively. The safety and efficacy of a virus lacking ORF25 were compared to those of a previously described vaccine candidate deleted for ORF56 and ORF57 (Δ56-57). Using quantitative PCR, we demonstrated that the ORF25 deleted virus infects fish through skin infection and then spreads to internal organs as reported previously for the wild-type parental virus and the Δ56-57 virus. However, compared to the parental wild-type virus, the replication of the ORF25-deleted virus was reduced in intensity and duration to levels similar to those observed for the Δ56-57 virus. Vaccination of fish with a virus lacking ORF25 was safe but had low efficacy at the doses tested. This characterization of the virion transmembrane proteome of CyHV-3 provides a firm basis for further research on alloherpesvirus VTPs. IMPORTANCE Virion transmembrane proteins play key roles in the biology of herpesviruses. Cyprinid herpesvirus 3 (CyHV-3) is the archetype of fish alloherpesviruses and the causative agent of major economic losses in common and koi carp worldwide. In this study of the virion transmembrane proteome of CyHV-3, the

Transmembrane protein diffusion in gel-supported dual-leaflet membranes.

Science.gov (United States)

Wang, Chih-Ying; Hill, Reghan J

2014-11-18

Tools to measure transmembrane-protein diffusion in lipid bilayer membranes have advanced in recent decades, providing a need for predictive theoretical models that account for interleaflet leaflet friction on tracer mobility. Here we address the fully three-dimensional flows driven by a (nonprotruding) transmembrane protein embedded in a dual-leaflet membrane that is supported above and below by soft porous supports (e.g., hydrogel or extracellular matrix), each of which has a prescribed permeability and solvent viscosity. For asymmetric configurations, i.e., supports with contrasting permeability, as realized for cells in contact with hydrogel scaffolds or culture media, the diffusion coefficient can reflect interleaflet friction. Reasonable approximations, for sufficiently large tracers on low-permeability supports, are furnished by a recent phenomenological theory from the literature. Interpreting literature data, albeit for hard-supported membranes, provides a theoretical basis for the phenomenological Stokes drag law as well as strengthening assertions that nonhydrodynamic interactions are important in supported bilayer systems, possibly leading to overestimates of the membrane/leaflet viscosity. Our theory provides a theoretical foundation for future experimental studies of tracer diffusion in gel-supported membranes.

Radiative magnetohydrodynamic simulations of solar pores

NARCIS (Netherlands)

Cameron, R.; Schuessler, M.; Vögler, A.; Zakharov, V.

2007-01-01

Context. Solar pores represent a class of magnetic structures intermediate between small-scale magnetic flux concentrations in intergranular lanes and fully developed sunspots with penumbrae. Aims. We study the structure, energetics, and internal dynamics of pore-like magnetic structures by means of

MD simulation of organics adsorption from aqueous solution in carbon slit-like pores. Foundations of the pore blocking effect

International Nuclear Information System (INIS)

Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester; Zieliński, Wojciech; Włoch, Jerzy; Kowalczyk, Piotr

2014-01-01

The results of systematic studies of organics adsorption from aqueous solutions (at the neutral pH level) in a system of slit-like carbon pores having different sizes and oxygen groups located at the pore mouth are reported. Using molecular dynamics simulations (GROMACS package) the properties of adsorbent–adsorbate (benzene, phenol or paracetamol) as well as adsorbent–water systems are discussed. After the introduction of surface oxygen functionalities, adsorption of organic compounds decreases (in accordance with experimental data) and this is caused by the accumulation of water molecules at pore entrances. The pore blocking effect decreases with the diameter of slits and practically vanishes for widths larger than approx. 0.68 nm. We observed the increase in phenol adsorption with the rise in temperature. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents. Among the studied molecules benzene, phenol and paracetamol prefer an almost flat orientation and with the rise in the pore width the number of molecules oriented in parallel decreases. The decrease or increase in temperature (with respect to 298 K) leads to insignificant changes of angular orientation of adsorbed molecules. (paper)

Effect of flow rate and temperature on transmembrane blood pressure drop in an extracorporeal artificial lung.

Science.gov (United States)

Park, M; Costa, E L V; Maciel, A T; Barbosa, E V S; Hirota, A S; Schettino, G de P; Azevedo, L C P

2014-11-01

Transmembrane pressure drop reflects the resistance of an artificial lung system to blood transit. Decreased resistance (low transmembrane pressure drop) enhances blood flow through the oxygenator, thereby, enhancing gas exchange efficiency. This study is part of a previous one where we observed the behaviour and the modulation of blood pressure drop during the passage of blood through artificial lung membranes. Before and after the induction of multi-organ dysfunction, the animals were instrumented and analysed for venous-venous extracorporeal membrane oxygenation, using a pre-defined sequence of blood flows. Blood flow and revolutions per minute (RPM) of the centrifugal pump varied in a linear fashion. At a blood flow of 5.5 L/min, pre- and post-pump blood pressures reached -120 and 450 mmHg, respectively. Transmembrane pressures showed a significant spread, particularly at blood flows above 2 L/min; over the entire range of blood flow rates, there was a positive association of pressure drop with blood flow (0.005 mmHg/mL/minute of blood flow) and a negative association of pressure drop with temperature (-4.828 mmHg/(°Celsius). These associations were similar when blood flows of below and above 2000 mL/minute were examined. During its passage through the extracorporeal system, blood is exposed to pressure variations from -120 to 450 mmHg. At high blood flows (above 2 L/min), the drop in transmembrane pressure becomes unpredictable and highly variable. Over the entire range of blood flows investigated (0-5500 mL/min), the drop in transmembrane pressure was positively associated with blood flow and negatively associated with body temperature. © The Author(s) 2014.

Ostreolysin A/Pleurotolysin B and Equinatoxins: Structure, Function and Pathophysiological Effects of These Pore-Forming Proteins

Directory of Open Access Journals (Sweden)

Robert Frangež

2017-04-01

Full Text Available Acidic ostreolysin A/pleurotolysin B (OlyA/PlyB, formerly known as ostreolysin (Oly, and basic 20 kDa equinatoxins (EqTs are cytolytic proteins isolated from the edible mushroom Pleurotus ostreatus and the sea anemone Actinia equina, respectively. Both toxins, although from different sources, share many similar biological activities: (i colloid-osmotic shock by forming pores in cellular and artificial membranes enriched in cholesterol and sphingomyelin; (ii increased vascular endothelial wall permeability in vivo and perivascular oedema; (iii dose-dependent contraction of coronary vessels; (iv haemolysis with pronounced hyperkalaemia in vivo; (v bradycardia, myocardial ischemia and ventricular extrasystoles accompanied by progressive fall of arterial blood pressure and respiratory arrest in rodents. Both types of toxins are haemolytic within nanomolar range concentrations, and it seems that hyperkalaemia plays an important role in toxin cardiotoxicity. However, it was observed that the haemolytically more active EqT III is less toxic than EqT I, the most toxic and least haemolytic EqT. In mice, EqT II is more than 30 times more toxic than OlyA/PlyB when applied intravenously. These observations imply that haemolysis with hyperkalaemia is not the sole cause of the lethal activity of both toxins. Additional mechanisms responsible for lethal action of the two toxins are direct effects on heart, coronary vasoconstriction and related myocardial hypoxia. In this review, we appraise the pathophysiological mechanisms related to the chemical structure of OlyA/PlyB and EqTs, as well as their toxicity.

Measurements of pore-scale flow through apertures

Energy Technology Data Exchange (ETDEWEB)

Chojnicki, Kirsten [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-09-01

Pore-scale aperture effects on flow in pore networks was studied in the laboratory to provide a parameterization for use in transport models. Four cases were considered: regular and irregular pillar/pore alignment with and without an aperture. The velocity field of each case was measured and simulated, providing quantitatively comparable results. Two aperture effect parameterizations were considered: permeability and transmission. Permeability values varied by an order of magnitude between the cases with and without apertures. However, transmission did not correlate with permeability. Despite having much greater permeability the regular aperture case permitted less transmission than the regular case. Moreover, both irregular cases had greater transmission than the regular cases, a difference not supported by the permeabilities. Overall, these findings suggest that pore-scale aperture effects on flow though a pore-network may not be adequately captured by properties such as permeability for applications that are interested in determining particle transport volume and timing.

Cyclic deformation-induced solute transport in tissue scaffolds with computer designed, interconnected, pore networks: experiments and simulations.

Science.gov (United States)

Den Buijs, Jorn Op; Dragomir-Daescu, Dan; Ritman, Erik L

2009-08-01

Nutrient supply and waste removal in porous tissue engineering scaffolds decrease from the periphery to the center, leading to limited depth of ingrowth of new tissue into the scaffold. However, as many tissues experience cyclic physiological strains, this may provide a mechanism to enhance solute transport in vivo before vascularization of the scaffold. The hypothesis of this study was that pore cross-sectional geometry and interconnectivity are of major importance for the effectiveness of cyclic deformation-induced solute transport. Transparent elastic polyurethane scaffolds, with computer-programmed design of pore networks in the form of interconnected channels, were fabricated using a 3D printing and injection molding technique. The scaffold pores were loaded with a colored tracer for optical contrast, cyclically compressed with deformations of 10 and 15% of the original undeformed height at 1.0 Hz. Digital imaging was used to quantify the spatial distribution of the tracer concentration within the pores. Numerical simulations of a fluid-structure interaction model of deformation-induced solute transport were compared to the experimental data. The results of experiments and modeling agreed well and showed that pore interconnectivity heavily influences deformation-induced solute transport. Pore cross-sectional geometry appears to be of less relative importance in interconnected pore networks. Validated computer models of solute transport can be used to design optimal scaffold pore geometries that will enhance the convective transport of nutrients inside the scaffold and the removal of waste, thus improving the cell survivability deep inside the scaffold.

Role of pore size and morphology in musculo-skeletal tissue regeneration

International Nuclear Information System (INIS)

Perez, Roman A.; Mestres, Gemma

2016-01-01

Biomaterials in the form of scaffolds hold great promise in the regeneration of diseased tissues. The scaffolds stimulate cellular adhesion, proliferation and differentiation. While the scaffold composition will dictate their biocompatibility, their porosity plays a key role in allowing proper cell penetration, nutrient diffusion as well as bone ingrowth. Porous scaffolds are processed with the help of a wide variety of techniques. Designing scaffolds with the appropriate porosity is a complex issue since this may jeopardize other physico-chemical properties. From a macroscopic point of view, parameters such as the overall architecture, pore morphology, interconnectivity and pore size distribution, have unique roles in allowing bone ingrowth to take place. From a microscopic perspective, the adsorption and retention of proteins in the microporosities of the material will dictate the subsequent cell adhesion. Therefore, the microstructure of the substrate can determine cell proliferation as well as the expression of specific osteogenic genes. This review aims at discussing the effect of micro- and macroporosity on the physico-chemical and biological properties of scaffolds for musculo-skeletal tissue regeneration. - Highlights: • Osteoconduction and osteoinduction of a biomaterial relies on its pattern of micro/macroporosity. • Size, morphology, distribution and interconnection of the pores influence both mechanical and biological properties. • Macroporosity (pores > 50 μm) determines cell colonization and therefore growth of vascular and bone tissue. • Micropores (< 50 μm) are crucial for proteins adsorption, which in turn can determine cell fate.

Role of pore size and morphology in musculo-skeletal tissue regeneration

Energy Technology Data Exchange (ETDEWEB)

Perez, Roman A., E-mail: romanp@dankook.ac.kr [Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714 (Korea, Republic of); Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan 330-714 (Korea, Republic of); Mestres, Gemma [Department of Engineering Sciences, Uppsala University, Box 534, 751 21 Uppsala (Sweden)

2016-04-01

Biomaterials in the form of scaffolds hold great promise in the regeneration of diseased tissues. The scaffolds stimulate cellular adhesion, proliferation and differentiation. While the scaffold composition will dictate their biocompatibility, their porosity plays a key role in allowing proper cell penetration, nutrient diffusion as well as bone ingrowth. Porous scaffolds are processed with the help of a wide variety of techniques. Designing scaffolds with the appropriate porosity is a complex issue since this may jeopardize other physico-chemical properties. From a macroscopic point of view, parameters such as the overall architecture, pore morphology, interconnectivity and pore size distribution, have unique roles in allowing bone ingrowth to take place. From a microscopic perspective, the adsorption and retention of proteins in the microporosities of the material will dictate the subsequent cell adhesion. Therefore, the microstructure of the substrate can determine cell proliferation as well as the expression of specific osteogenic genes. This review aims at discussing the effect of micro- and macroporosity on the physico-chemical and biological properties of scaffolds for musculo-skeletal tissue regeneration. - Highlights: • Osteoconduction and osteoinduction of a biomaterial relies on its pattern of micro/macroporosity. • Size, morphology, distribution and interconnection of the pores influence both mechanical and biological properties. • Macroporosity (pores > 50 μm) determines cell colonization and therefore growth of vascular and bone tissue. • Micropores (< 50 μm) are crucial for proteins adsorption, which in turn can determine cell fate.

Pore development in anodic alumina in sulphuric acid and borax electrolytes

International Nuclear Information System (INIS)

Garcia-Vergara, S.J.; Skeldon, P.; Thompson, G.E.; Habakaki, H.

2007-01-01

The formation of porous anodic films on an Al-3.5 at.%W alloy is compared in sulphuric acid and borax electrolytes in order to investigate pore development processes. The findings disclose that for anodizing in sulphuric acid, the pores develop mainly due to the influences of field-induced plasticity of the film and growth stresses; in borax, field-assisted dissolution dominates. The films formed in sulphuric acid are consequently much thicker than the layer of oxidized alloy and tungsten species are retained in the film. In contrast, with borax, the films and oxidized alloy layers are of similar thickness and tungsten species are lost to the electrolyte. Efficiencies of film growth are also significantly different, about 65% in sulphuric acid and about 52% in borax. The retention of tungsten species during anodizing in sulphuric acid is due to the localization of tungsten in the inner regions of the barrier layer and cell walls, with a layer of anodic alumina separating the tungsten-containing regions from the electrolyte. For borax, the tungsten is distributed more uniformly through the film material, enabling loss of tungsten species to the electrolyte from the pore base

Oligomerization is involved in pore formation by Bordetella adenylate cyclase toxin

Czech Academy of Sciences Publication Activity Database

Vojtová, Jana; Basler, Marek; Osička, Radim; Knapp, O.; Maier, E.; Černý, J.; Benada, Oldřich; Benz, R.; Šebo, Peter

2009-01-01

Roč. 23, - (2009), s. 2831-2843 ISSN 0892-6638 R&D Projects: GA AV ČR IAA500200914; GA MŠk 1M0506 Grant - others:-(XE) LSHB-CT-2003-503582 THERAVAC Institutional research plan: CEZ:AV0Z50200510 Keywords : blue native electrophoresis * planar lipid bilayer membranes * pore-forming activity Subject RIV: EE - Microbiology, Virology Impact factor: 6.401, year: 2009

Mn-coatings on the micro-pore formed Ti-29Nb-xHf alloys by RF-magnetron sputtering for dental applications

Science.gov (United States)

Park, Seon-Yeong; Choe, Han-Cheol

2018-02-01

In this study, Mn-coatings on the micro-pore formed Ti-29Nb-xHf alloys by RF-magnetrons sputtering for dental applications were studied using different experimental techniques. Mn coating films were formed on Ti-29Nb-xHf alloys by a radio frequency magnetron sputtering technique for 0, 1, 3, and 5 min at 45 W. The microstructure, composition, and phase structure of the coated alloys were examined by optical microscopy, field emission scanning electron microscopy, X-ray diffraction, and energy-dispersive X-ray spectroscopy. The microstructure of Ti-29Nb alloy showed α" phase in the needle-like structure and Ti-29Nb-15Hf alloy showed β phase in the equiaxed structure. As the sputtering time increased, the circular particles of Mn coatings on the Ti-29Nb alloy increased at inside and outside surfaces. As the sputtering time increased, [Mn + Ca/P] ratio of the plasma electrolytic oxidized films in Ti- 29Nb-xHf alloys increased. The corrosion potential (Ecorr) of Mn coatings on the Ti-29Nb alloy showed higher than that of Mn coatings on the Ti-29Nb-15Hf alloy. The passive current density (Ipass) of the Mn coating on the Ti-29Nb alloy and Mn coatings on the Ti-29Nb-15Hf alloy was less noble than the non-Mn coated Ti-29Nb and Ti-29Nb-15Hf alloys surface.

alpha-helical structural elements within the voltage-sensing domains of a K(+) channel.

Science.gov (United States)

Li-Smerin, Y; Hackos, D H; Swartz, K J

2000-01-01

Voltage-gated K(+) channels are tetramers with each subunit containing six (S1-S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5-S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1-S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K(+) channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of alpha-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting alpha-helical secondary structure. In addition, both the S1-S2 and S3-S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain.

Pore volume and pore size distribution of cement samples measured by a modified mercury intrusion porosimeter

International Nuclear Information System (INIS)

Zamorani, E.; Blanchard, H.

1987-01-01

Important parameters for the characterization of cement specimens are mechanical properties and porosity. This work is carried out at the Ispra Establishment of the Joint Research Centre in the scope of the Radioactive Waste Management programme. A commercial Mercury Intrusion Porosimeter was modified in an attempt to improve the performance of the instrument and to provide fast processing of the recorded values: pressure-volume of pores. The dead volume of the instrument was reduced and the possibility of leakage from the moving parts eliminated. In addition, the modification allows an improvement of data acquisition thus increasing data accuracy and reproducibility. In order to test the improved performance of the modified instrument, physical characterizations of cement forms were carried out. Experimental procedures and results are reported

Evolution of vertebrate interferon inducible transmembrane proteins

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Hickford Danielle

2012-04-01

Full Text Available Abstract Background Interferon inducible transmembrane proteins (IFITMs have diverse roles, including the control of cell proliferation, promotion of homotypic cell adhesion, protection against viral infection, promotion of bone matrix maturation and mineralisation, and mediating germ cell development. Most IFITMs have been well characterised in human and mouse but little published data exists for other animals. This study characterised IFITMs in two distantly related marsupial species, the Australian tammar wallaby and the South American grey short-tailed opossum, and analysed the phylogeny of the IFITM family in vertebrates. Results Five IFITM paralogues were identified in both the tammar and opossum. As in eutherians, most marsupial IFITM genes exist within a cluster, contain two exons and encode proteins with two transmembrane domains. Only two IFITM genes, IFITM5 and IFITM10, have orthologues in both marsupials and eutherians. IFITM5 arose in bony fish and IFITM10 in tetrapods. The bone-specific expression of IFITM5 appears to be restricted to therian mammals, suggesting that its specialised role in bone production is a recent adaptation specific to mammals. IFITM10 is the most highly conserved IFITM, sharing at least 85% amino acid identity between birds, reptiles and mammals and suggesting an important role for this presently uncharacterised protein. Conclusions Like eutherians, marsupials also have multiple IFITM genes that exist in a gene cluster. The differing expression patterns for many of the paralogues, together with poor sequence conservation between species, suggests that IFITM genes have acquired many different roles during vertebrate evolution.

Conformational constraining of inactive and active States of a seven transmembrane receptor by metal ion site engineering in the extracellular end of transmembrane segment V

DEFF Research Database (Denmark)

Rosenkilde, Mette M; David, Ralf; Oerlecke, Ilka

2006-01-01

The extracellular part of transmembrane segment V (TM-V) is expected to be involved in the activation process of 7TM receptors, but its role is far from clear. Here, we study the highly constitutively active CXC-chemokine receptor encoded by human herpesvirus 8 (ORF74-HHV8), in which a metal ion ...

TMFoldWeb: a web server for predicting transmembrane protein fold class.

Science.gov (United States)

Kozma, Dániel; Tusnády, Gábor E

2015-09-17

Here we present TMFoldWeb, the web server implementation of TMFoldRec, a transmembrane protein fold recognition algorithm. TMFoldRec uses statistical potentials and utilizes topology filtering and a gapless threading algorithm. It ranks template structures and selects the most likely candidates and estimates the reliability of the obtained lowest energy model. The statistical potential was developed in a maximum likelihood framework on a representative set of the PDBTM database. According to the benchmark test the performance of TMFoldRec is about 77 % in correctly predicting fold class for a given transmembrane protein sequence. An intuitive web interface has been developed for the recently published TMFoldRec algorithm. The query sequence goes through a pipeline of topology prediction and a systematic sequence to structure alignment (threading). Resulting templates are ordered by energy and reliability values and are colored according to their significance level. Besides the graphical interface, a programmatic access is available as well, via a direct interface for developers or for submitting genome-wide data sets. The TMFoldWeb web server is unique and currently the only web server that is able to predict the fold class of transmembrane proteins while assigning reliability scores for the prediction. This method is prepared for genome-wide analysis with its easy-to-use interface, informative result page and programmatic access. Considering the info-communication evolution in the last few years, the developed web server, as well as the molecule viewer, is responsive and fully compatible with the prevalent tablets and mobile devices.

Capillary pressure-saturation relationships for porous granular materials: Pore morphology method vs. pore unit assembly method

Science.gov (United States)

Sweijen, Thomas; Aslannejad, Hamed; Hassanizadeh, S. Majid

2017-09-01

In studies of two-phase flow in complex porous media it is often desirable to have an estimation of the capillary pressure-saturation curve prior to measurements. Therefore, we compare in this research the capability of three pore-scale approaches in reproducing experimentally measured capillary pressure-saturation curves. To do so, we have generated 12 packings of spheres that are representative of four different glass-bead packings and eight different sand packings, for which we have found experimental data on the capillary pressure-saturation curve in the literature. In generating the packings, we matched the particle size distributions and porosity values of the granular materials. We have used three different pore-scale approaches for generating the capillary pressure-saturation curves of each packing: i) the Pore Unit Assembly (PUA) method in combination with the Mayer and Stowe-Princen (MS-P) approximation for estimating the entry pressures of pore throats, ii) the PUA method in combination with the hemisphere approximation, and iii) the Pore Morphology Method (PMM) in combination with the hemisphere approximation. The three approaches were also used to produce capillary pressure-saturation curves for the coating layer of paper, used in inkjet printing. Curves for such layers are extremely difficult to determine experimentally, due to their very small thickness and the presence of extremely small pores (less than one micrometer in size). Results indicate that the PMM and PUA-hemisphere method give similar capillary pressure-saturation curves, because both methods rely on a hemisphere to represent the air-water interface. The ability of the hemisphere approximation and the MS-P approximation to reproduce correct capillary pressure seems to depend on the type of particle size distribution, with the hemisphere approximation working well for narrowly distributed granular materials.

Pore-Width-Dependent Preferential Interaction of sp2 Carbon Atoms in Cyclohexene with Graphitic Slit Pores by GCMC Simulation

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Natsuko Kojima

2011-01-01

Full Text Available The adsorption of cyclohexene with two sp2 and four sp3 carbon atoms in graphitic slit pores was studied by performing grand canonical Monte Carlo simulation. The molecular arrangement of the cyclohexene on the graphitic carbon wall depends on the pore width. The distribution peak of the sp2 carbon is closer to the pore wall than that of the sp3 carbon except for the pore width of 0.7 nm, even though the Lennard-Jones size of the sp2 carbon is larger than that of the sp3 carbon. Thus, the difference in the interactions of the sp2 and sp3 carbon atoms of cyclohexene with the carbon pore walls is clearly observed in this study. The preferential interaction of sp2 carbon gives rise to a slight tilting of the cyclohexene molecule against the graphitic wall. This is suggestive of a π-π interaction between the sp2 carbon in the cyclohexene molecule and graphitic carbon.

Homogeneous alignment of liquid crystalline dendrimers confined in a slit-pore. A simulation study.

Science.gov (United States)

Workineh, Zerihun G; Vanakaras, Alexandros G

2016-03-23

In this work we present results from isobaric-isothermal (NPT) Monte Carlo simulation studies of model liquid crystalline dendrimer (LCDr) systems confined in a slit-pore made of two parallel flat walls. The dendrimers are modelled as a collection of spherical and ellipsoidal particles corresponding to the junction points of the dendritic core and to the mesogenic units respectively. Assuming planar uniform (unidirectional) soft anchoring of the mesogenic units on the substrates we investigate the conformational and alignment properties of the LCDr system at different thermodynamic state points. Tractable coarse grained force fields have been used from our previous work. At low pressures the interior of the pore is almost empty, since almost all LCDrs are anchored to the substrates forming two-dimensional smectic-like structures with the mesogens aligned along the aligning direction of the substrates. As the pressure grows the LCDrs occupy the whole pore. However, even at low temperatures, the smectic organization does not transmit in the interior of the pore and is preserved for distances of 2-3 mesogenic diameters from the walls. For this reason, the global orientational order decreases with increasing pressure (density). In the vicinity (2-3 mesogenic diameters) of the pore walls, mesogenic units preserve the smectic structure whose layers are separated by layers of spherical beads. In this region individual LCDrs possess a rod like shape.

Homogeneous alignment of liquid crystalline dendrimers confined in a slit-pore. A simulation study

Science.gov (United States)

Workineh, Zerihun G.; Vanakaras, Alexandros G.

2016-03-01

In this work we present results from isobaric-isothermal (NPT) Monte Carlo simulation studies of model liquid crystalline dendrimer (LCDr) systems confined in a slit-pore made of two parallel flat walls. The dendrimers are modelled as a collection of spherical and ellipsoidal particles corresponding to the junction points of the dendritic core and to the mesogenic units respectively. Assuming planar uniform (unidirectional) soft anchoring of the mesogenic units on the substrates we investigate the conformational and alignment properties of the LCDr system at different thermodynamic state points. Tractable coarse grained force fields have been used from our previous work. At low pressures the interior of the pore is almost empty, since almost all LCDrs are anchored to the substrates forming two-dimensional smectic-like structures with the mesogens aligned along the aligning direction of the substrates. As the pressure grows the LCDrs occupy the whole pore. However, even at low temperatures, the smectic organization does not transmit in the interior of the pore and is preserved for distances of 2-3 mesogenic diameters from the walls. For this reason, the global orientational order decreases with increasing pressure (density). In the vicinity (2-3 mesogenic diameters) of the pore walls, mesogenic units preserve the smectic structure whose layers are separated by layers of spherical beads. In this region individual LCDrs possess a rod like shape.

Homogeneous alignment of liquid crystalline dendrimers confined in a slit-pore. A simulation study

International Nuclear Information System (INIS)

Workineh, Zerihun G; Vanakaras, Alexandros G

2016-01-01

In this work we present results from isobaric-isothermal (NPT) Monte Carlo simulation studies of model liquid crystalline dendrimer (LCDr) systems confined in a slit-pore made of two parallel flat walls. The dendrimers are modelled as a collection of spherical and ellipsoidal particles corresponding to the junction points of the dendritic core and to the mesogenic units respectively. Assuming planar uniform (unidirectional) soft anchoring of the mesogenic units on the substrates we investigate the conformational and alignment properties of the LCDr system at different thermodynamic state points. Tractable coarse grained force fields have been used from our previous work. At low pressures the interior of the pore is almost empty, since almost all LCDrs are anchored to the substrates forming two-dimensional smectic-like structures with the mesogens aligned along the aligning direction of the substrates. As the pressure grows the LCDrs occupy the whole pore. However, even at low temperatures, the smectic organization does not transmit in the interior of the pore and is preserved for distances of 2–3 mesogenic diameters from the walls. For this reason, the global orientational order decreases with increasing pressure (density). In the vicinity (2–3 mesogenic diameters) of the pore walls, mesogenic units preserve the smectic structure whose layers are separated by layers of spherical beads. In this region individual LCDrs possess a rod like shape. (paper)

Structure and function of the cystic fibrosis transmembrane conductance regulator

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M.M. Morales

1999-08-01

Full Text Available Cystic fibrosis (CF is a lethal autosomal recessive genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR. Mutations in the CFTR gene may result in a defective processing of its protein and alter the function and regulation of this channel. Mutations are associated with different symptoms, including pancreatic insufficiency, bile duct obstruction, infertility in males, high sweat Cl-, intestinal obstruction, nasal polyp formation, chronic sinusitis, mucus dehydration, and chronic Pseudomonas aeruginosa and Staphylococcus aureus lung infection, responsible for 90% of the mortality of CF patients. The gene responsible for the cellular defect in CF was cloned in 1989 and its protein product CFTR is activated by an increase of intracellular cAMP. The CFTR contains two membrane domains, each with six transmembrane domain segments, two nucleotide-binding domains (NBDs, and a cytoplasmic domain. In this review we discuss the studies that have correlated the role of each CFTR domain in the protein function as a chloride channel and as a regulator of the outwardly rectifying Cl- channels (ORCCs.

The effect of pore diameter in the arrangement of chelating species grafted onto silica surfaces with application to uranium extraction

International Nuclear Information System (INIS)

Charlot, A.; Cuer, F.; Grandjean, A.

2017-01-01

A series of five silica supports with different pore diameters were functionalized in two steps by post-grafting, producing three types of material: (1) initial supports with pores smaller than 4 nm are heterogeneously functionalized because of steric effects; (2) when the pores range from 5 to 20 nm in diameter, a homogeneous organic monolayer is grafted onto the silica skeleton; and (3) when the pores are larger than 30 nm, an organic multilayer covalently linked to the surface is obtained. These hybrid materials were then used to extract uranium from a sulphuric solution. Our results show that the efficiency, capacity and selectivity of the extraction can be controlled through the effect the initial pore size has on the organic structures that form therein. After regeneration moreover, these materials can be reused with the same efficiency. (authors)

Hydrophobic polymers modification of mesoporous silica with large pore size for drug release

Energy Technology Data Exchange (ETDEWEB)

Zhu Shenmin, E-mail: smzhu@sjtu.edu.c [Shanghai Jiao Tong University, State Key Lab of Metal Matrix Composites (China); Zhang Di; Yang Na [Fudan University, Ministry of Education, Key Lab of Molecular Engineering of Polymers (China)

2009-04-15

Mesostructure cellular foam (MCF) materials were modified with hydrophobic polyisoprene (PI) through free radical polymerization in the pores network, and the resulting materials (MCF-PI) were investigated as matrices for drug storage. The successful synthesis of PI inside MCF was characterized by Fourier transform infrared (FT-IR), hydrogen nuclear magnetic resonance ({sup 1}H NMR), X-ray diffraction patterns (XRD) and nitrogen adsorption/desorption measurements. It was interesting to find the resultant system held a relatively large pore size (19.5 nm) and pore volume (1.02 cm{sup 3} g{sup -1}), which would benefit for drug storage. Ibuprofen (IBU) and vancomycin were selected as model drugs and loaded onto unmodified MCF and modified MCF (MCF-PI). The adsorption capacities of these model drugs on MCF-PI were observed increase as compared to that of on pure MCF, due to the trap effects induced by polyisoprene chains inside the pores. The delivery system of MCF-PI was found to be more favorable for the adsorption of IBU (31 wt%, IBU/silica), possibly attributing to the hydrophobic interaction between IBU and PI formed on the internal surface of MCF matrix. The release of drug through the porous network was investigated by measuring uptake and release of IBU.

Synthesis and characterization of nanoparticulate MnS within the pores of mesoporous silica

International Nuclear Information System (INIS)

Barry, Louse; Copley, Mark; Holmes, Justin D.; Otway, David J.; Kazakova, Olga; Morris, Michael A.

2007-01-01

Mesoporous silica was loaded with nanoparticulate MnS via a simple post-synthesis treatment. The mesoporous material that still contained surfactant was passivated to prevent MnS formation at the surface. The surfactant was extracted and a novel manganese ethylxanthate was used to impregnate the pore network. This precursor thermally decomposes to yield MnS particles that are smaller or equal to the pore size. The particles exhibit all three common polymorphs. The passivation treatment is most effective at lower loadings because at the highest loadings (SiO 2 :MnS molar ratio of 6:1) large particles (>50 nm) form at the exterior of the mesoporous particles. The integrity of the mesoporous network is maintained through the preparation and high order is maintained. The MnS particles exhibit unexpected ferromagnetism at low temperatures. Strong luminescence of these samples is observed and this suggests that they may have a range of important application areas. - Graphical abstract: A novel manganese ethylxanthate precursor was used to impregnate the pore network of mesoporous silica and was decomposed to yield MnS particles smaller or equal to the pore size. The particles exhibit all three common polymorphs, demonstrate unexpected ferromagnetism at low temperatures and display a strong luminescence

Characterization of the GXXXG motif in the first transmembrane segment of Japanese encephalitis virus precursor membrane (prM protein

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Wu Suh-Chin

2010-05-01

Full Text Available Abstract The interaction between prM and E proteins in flavivirus-infected cells is a major driving force for the assembly of flavivirus particles. We used site-directed mutagenesis to study the potential role of the transmembrane domains of the prM proteins of Japanese encephalitis virus (JEV in prM-E heterodimerization as well as subviral particle formation. Alanine insertion scanning mutagenesis within the GXXXG motif in the first transmembrane segment of JEV prM protein affected the prM-E heterodimerization; its specificity was confirmed by replacing the two glycines of the GXXXG motif with alanine, leucine and valine. The GXXXG motif was found to be conserved in the JEV serocomplex viruses but not other flavivirus groups. These mutants with alanine inserted in the two prM transmembrane segments all impaired subviral particle formation in cell cultures. The prM transmembrane domains of JEV may play importation roles in prM-E heterodimerization and viral particle assembly.

The equivalent pore aspect ratio as a tool for pore type prediction in carbonate reservoirs

OpenAIRE

FOURNIER , François; Pellerin , Matthieu; Villeneuve , Quentin; Teillet , Thomas; Hong , Fei; Poli , Emmanuelle; Borgomano , Jean; Léonide , Philippe; Hairabian , Alex

2018-01-01

International audience; The equivalent pore aspect ratios (EPAR) provide a tool to detect pore types by combining P-and S-wave velocities, porosity, bulk density and mineralogical composition of carbonate rocks. The integration of laboratory measurements, well log data and petrographic analysis of 468 carbonate samples from various depositional and diagenetic settings (Lower Cretaceous pre-salt non-marine carbonates from offshore Brazil, Lower Cretaceous shallow-water platform carbonates from...

An instrument to measure differential pore pressures in deep ocean sediments: Pop-Up-Pore-Pressure-Instrument (PUPPI)

International Nuclear Information System (INIS)

Schultheiss, P.J.; McPhail, S.D.; Packwood, A.R.; Hart, B.

1985-01-01

A Pop-Up-Pore-Pressure-Instrument (PUPPI) has been developed to measure differential pore pressures in sediments. The differential pressure is the pressure above or below normal hydrostatic pressure at the depth of the measurement. It is designed to operate in water depths up to 6000 metres for periods of weeks or months, if required, and measures differential pore pressures at depths of up to 3 metres into the sediments with a resolution of 0.05 kPa. It is a free-fall device with a lance which penetrates the sediments. This lance and the ballast weight is disposed when the PUPPI is acoustically released from the sea floor. When combined with permeability and porosity values of deep-sea sediments the pore pressure measurements made using the PUPPI suggest advection velocities as low as 8.8 mm/yr. The mechanical, electrical and acoustic systems are described together with data obtained from both shallow and deep water trials. (author)

Impact of pore-pressure cycling on bentonite in constant volume experiments

International Nuclear Information System (INIS)

Graham, C.C.; Harrington, J.F.; Cuss, R.J.; Sellin, P.

2012-01-01

Document available in extended abstract form only. The SKB safety case for a KBS-3 repository highlights the potential importance of future successive glaciation events on repository functions. One particular uncertainty is the likely affect of elevated pore-water pressures on barrier safety functions. Over the repository lifetime such changes in pore-water pressure are likely to be cyclic in nature, as successive glacial episodes lead to loading and unloading of the engineered barrier. For a clay-water system with the pore-water in thermodynamic equilibrium with an external reservoir of water at pressure, p w , the total stress acting on the surrounding vessel can be expressed as: (1) σ = Π + αp w where Π is the swelling pressure and α is a proportionality constant. We present results from a series of laboratory experiments designed to investigate this relationship, in the context of glacial loading. Blocks of pre-compacted Mx80 bentonite were manufactured by Clay Technology AB (Lund, Sweden), by rapidly compacting bentonite granules in a mould under a one dimensionally applied stress (Johannesson et al., 1995). The blocks were then sub-sampled and cylindrical specimens prepared for testing (120 mm in length and 60 mm in diameter). The experiments were conducted using a specially designed constant volume cell, which allows the evolution of the total stresses acting on the surrounding vessel to be monitored during clay swelling (at three radial and two axial locations). A high precision syringe pump was used to maintain a constant applied pore pressure within the bentonite, while the rate of hydraulic inflow, and consequent stress development, were monitored to determine the point at which hydraulic equilibrium was reached. During the tests each sample was subjected to an incremental series of constant pore-pressure steps, with all samples experiencing at least one loading and unloading cycle. The resulting average total stress data yield alpha values in the

System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors

Science.gov (United States)

Trabanino, Rene J; Vaidehi, Nagarajan; Hall, Spencer E; Goddard, William A; Floriano, Wely

2013-02-05

The invention provides computer-implemented methods and apparatus implementing a hierarchical protocol using multiscale molecular dynamics and molecular modeling methods to predict the presence of transmembrane regions in proteins, such as G-Protein Coupled Receptors (GPCR), and protein structural models generated according to the protocol. The protocol features a coarse grain sampling method, such as hydrophobicity analysis, to provide a fast and accurate procedure for predicting transmembrane regions. Methods and apparatus of the invention are useful to screen protein or polynucleotide databases for encoded proteins with transmembrane regions, such as GPCRs.

The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region

DEFF Research Database (Denmark)

Stelzer, Walter; Scharnagl, Christina; Leurs, Ulrike

2016-01-01

The transmembrane helix of the amyloid precursor protein is subject to proteolytic cleavages by γ-secretase at different sites resulting in Aβ peptides of different length and toxicity. A number of point mutations within this transmembrane helix alter the cleavage pattern thus enhancing production...... destabilizes amide hydrogen bonds in the hinge which connects dimerization and cleavage regions. Weaker intrahelical hydrogen bonds at the hinge may enhance helix bending and thereby affect recognition of the transmembrane substrate by the enzyme and/or presentation of its cleavage sites to the catalytic cleft....

Effects of fractal pore on coal devolatilization

Energy Technology Data Exchange (ETDEWEB)

Chen, Yongli; He, Rong [Tsinghua Univ., Beijing (China). Dept. of Thermal Engineering; Wang, Xiaoliang; Cao, Liyong [Dongfang Electric Corporation, Chengdu (China). Centre New Energy Inst.

2013-07-01

Coal devolatilization is numerically investigated by drop tube furnace and a coal pyrolysis model (Fragmentation and Diffusion Model). The fractal characteristics of coal and char pores are investigated. Gas diffusion and secondary reactions in fractal pores are considered in the numerical simulations of coal devolatilization, and the results show that the fractal dimension is increased firstly and then decreased later with increased coal conversions during devolatilization. The mechanisms of effects of fractal pores on coal devolatilization are analyzed.

Nanometer-Scale Pore Characteristics of Lacustrine Shale, Songliao Basin, NE China.

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Min Wang

Full Text Available In shale, liquid hydrocarbons are accumulated mainly in nanometer-scale pores or fractures, so the pore types and PSDs (pore size distributions play a major role in the shale oil occurrence (free or absorbed state, amount of oil, and flow features. The pore types and PSDs of marine shale have been well studied; however, research on lacustrine shale is rare, especially for shale in the oil generation window, although lacustrine shale is deposited widely around the world. To investigate the relationship between nanometer-scale pores and oil occurrence in the lacustrine shale, 10 lacustrine shale core samples from Songliao Basin, NE China were analyzed. Analyses of these samples included geochemical measurements, SEM (scanning electron microscope observations, low pressure CO2 and N2 adsorption, and high-pressure mercury injection experiments. Analysis results indicate that: (1 Pore types in the lacustrine shale include inter-matrix pores, intergranular pores, organic matter pores, and dissolution pores, and these pores are dominated by mesopores and micropores; (2 There is no apparent correlation between pore volumes and clay content, however, a weak negative correlation is present between total pore volume and carbonate content; (3 Pores in lacustrine shale are well developed when the organic matter maturity (Ro is >1.0% and the pore volume is positively correlated with the TOC (total organic carbon content. The statistical results suggest that oil in lacustrine shale mainly occurs in pores with diameters larger than 40 nm. However, more research is needed to determine whether this minimum pore diameter for oil occurrence in lacustrine shale is widely applicable.

Molecular Simulations of Sequence-Specific Association of Transmembrane Proteins in Lipid Bilayers

Science.gov (United States)

Doxastakis, Manolis; Prakash, Anupam; Janosi, Lorant

2011-03-01

Association of membrane proteins is central in material and information flow across the cellular membranes. Amino-acid sequence and the membrane environment are two critical factors controlling association, however, quantitative knowledge on such contributions is limited. In this work, we study the dimerization of helices in lipid bilayers using extensive parallel Monte Carlo simulations with recently developed algorithms. The dimerization of Glycophorin A is examined employing a coarse-grain model that retains a level of amino-acid specificity, in three different phospholipid bilayers. Association is driven by a balance of protein-protein and lipid-induced interactions with the latter playing a major role at short separations. Following a different approach, the effect of amino-acid sequence is studied using the four transmembrane domains of the epidermal growth factor receptor family in identical lipid environments. Detailed characterization of dimer formation and estimates of the free energy of association reveal that these helices present significant affinity to self-associate with certain dimers forming non-specific interfaces.

Pore size determination from charged particle energy loss measurement

International Nuclear Information System (INIS)

Brady, F.P.; Armitage, B.H.

1977-01-01

A new method aimed at measuring porosity and mean pore size in materials has been developed at Harwell. The energy width or variance of a transmitted or backscattered charged particle beam is measured and related to the mean pore size via the assumption that the variance in total path length in the porous material is given by (Δx 2 )=na 2 , where n is the mean number of pores and a the mean pore size. It is shown on the basis of a general and rigorous theory of total path length distribution that this approximation can give rise to large errors in the mean pore size determination particularly in the case of large porosities (epsilon>0.5). In practice it is found that it is not easy to utilize fully the general theory because accurate measurements of the first four moments are required to determine the means and variances of the pore and inter-pore length distributions. Several models for these distributions are proposed. When these are incorporated in the general theory the determinations of mean pore size from experimental measurements on powder samples are in good agreement with values determined by other methods. (Auth.)

Chemical modelling of pore water composition from PFBC residues

International Nuclear Information System (INIS)

Karlsson, L.G.

1991-01-01

The concentration of trace elements varies depending on the source of the coal and also due to the combustion process used. Mercury is one important element among the trace elements in the coal residues, generally recognised as potentially harmful to the biological system. To predict the pore water concentrations of mercury and other important constituents leached from coal combustion residues disposal sites, mechanistic data on chemical reactions are required. The present study is an application of a basially thermodynamical approach using the geochemical code EQ3NR. The presence of discrete solid phases that control the aqueous concentrations of major elements such as aluminium, calcium and silicon are identified. Solid phases are modelled in equilibrium with a hypothetical pore water at a pH range of 7-11. In this study the thermodynamic database of EQ3NR has been complemented with data for cadmium, mercury and lead taken from the OECD/NEA Thermodynamic Database and from a compilation made by Lindsay. Possible solubility limiting phases for the important trace elements arsenic, cadmium, chromium, copper, mercury, nickel and lead have been identified. Concentrations of these trace elements as a function of pH in the hypothetical pore water were calculated using mechanistic thermodynamial data. The thermodynamical approach in this study seems justified because most solid residues that are either present or expected to form during weathering have relatively fast precipitation/dissolution kinetics. (21 refs., 18 figs., 5 tabs.)

Accurate relations between pore size and the pressure of capillary condensation and the evaporation of nitrogen in cylindrical pores.

Science.gov (United States)

Morishige, Kunimitsu; Tateishi, Masayoshi

2006-04-25

To examine the theoretical and semiempirical relations between pore size and the pressure of capillary condensation or evaporation proposed so far, we constructed an accurate relation between the pore radius and the capillary condensation and evaporation pressure of nitrogen at 77 K for the cylindrical pores of the ordered mesoporous MCM-41 and SBA-15 silicas. Here, the pore size was determined from a comparison between the experimental and calculated X-ray diffraction patterns due to X-ray structural modeling recently developed. Among the many theoretical relations that differ from each other in the degree of theoretical improvements, a macroscopic thermodynamic approach based on Broekhoff-de Boer equations was found to be in fair agreement with the experimental relation obtained in the present study.

X-ray CT analysis of pore structure in sand

Science.gov (United States)

Mukunoki, Toshifumi; Miyata, Yoshihisa; Mikami, Kazuaki; Shiota, Erika

2016-06-01

The development of microfocused X-ray computed tomography (CT) devices enables digital imaging analysis at the pore scale. The applications of these devices are diverse in soil mechanics, geotechnical and geoenvironmental engineering, petroleum engineering, and agricultural engineering. In particular, the imaging of the pore space in porous media has contributed to numerical simulations for single-phase and multiphase flows or contaminant transport through the pore structure as three-dimensional image data. These obtained results are affected by the pore diameter; therefore, it is necessary to verify the image preprocessing for the image analysis and to validate the pore diameters obtained from the CT image data. Moreover, it is meaningful to produce the physical parameters in a representative element volume (REV) and significant to define the dimension of the REV. This paper describes the underlying method of image processing and analysis and discusses the physical properties of Toyoura sand for the verification of the image analysis based on the definition of the REV. On the basis of the obtained verification results, a pore-diameter analysis can be conducted and validated by a comparison with the experimental work and image analysis. The pore diameter is deduced from Young-Laplace's law and a water retention test for the drainage process. The results from previous study and perforated-pore diameter originally proposed in this study, called the voxel-percolation method (VPM), are compared in this paper. In addition, the limitations of the REV, the definition of the pore diameter, and the effectiveness of the VPM for an assessment of the pore diameter are discussed.

Design, fabrication, and characterization of silicon pore optics for ATHENA/IXO

DEFF Research Database (Denmark)

Collon, Maximilien J.; Günther, Ramses; Ackermann, Marcelo

2011-01-01

Silicon pore optics is a technology developed to enable future large area X-ray telescopes, such as the International X-ray Observatory (IXO) or the Advanced Telescope for High ENergy Astrophysics (ATHENA), an L-class candidate mission in the ESA Space Science Programme 'Cosmic Visions 2015-2025'...... integrated into petals, and mounted onto the spacecraft to form an X-ray optic. In this paper we will present the silicon pore optics mass manufacturing process and latest X-ray test results.......-2025'. ATHENA/IXO use nested mirrors in Wolter-I configuration to focus grazing incidence X-ray photons on a detector plane. The x-ray optics will have to meet stringent performance requirements including an effective area of a few m2 at 1.25 keV and angular resolution between 5(IXO) and 9(ATHENA) arc seconds...

Combined effect of cortical cytoskeleton and transmembrane proteins on domain formation in biomembranes

DEFF Research Database (Denmark)

Sikder, K. U.; Stone, K. A.; Kumar, P. B. S.

2014-01-01

We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find that mic......We investigate the combined effects of transmembrane proteins and the subjacent cytoskeleton on the dynamics of phase separation in multicomponent lipid bilayers using computer simulations of a particle-based implicit solvent model for lipid membranes with soft-core interactions. We find...... that microphase separation can be achieved by the protein confinement by the cytoskeleton. Our results have relevance to the finite size of lipid rafts in the plasma membrane of mammalian cells. (C) 2014 AIP Publishing LLC....

Modeling the Structure of SARS 3a Transmembrane Protein Using a ...

Indian Academy of Sciences (India)

Modeling the structure of SARS 3a Transmembrane protein using a ... for the implicit membrane molecular dynamics (MD) simulations. ... The coordinates during the simulation were saved every 500 steps, and were used for analysis. ... the pair list for calculation of nonbonded interactions being updated after every 10 steps.

Gas transport and subsoil pore characteristics

DEFF Research Database (Denmark)

Berisso, Feto Esimo; Schjønning, Per; Keller, Thomas

2013-01-01

Arrangements of elementary soil particles during soil deposition and subsequent biological and physical processes in long-term pedogenesis are expected to lead to anisotropy of the non-tilled subsoil pore system. Soil compaction by agricultural machinery is known to affect soil pore characteristics...... were sampled in vertical and horizontal directions from 0.3, 0.5, 0.7 and 0.9 m depth (the two lower depths only in Sweden). In the laboratory, water retention, air permeability (ka) and gas diffusivity (Ds/D0) were determined. For the sandy clay loam, morphological characteristics of pores (effective......). In the sandy clay loam soil, dB and nB displayed significant anisotropy (FAcharacteristics because of its origin...

Toxicity of sediments and pore water from Brunswick Estuary, Georgia

Science.gov (United States)

Winger, Parley V.; Lasier, Peter J.; Geitner, Harvey

1993-01-01

A chlor-alkali plant in Brunswick, Georgia, USA, discharged >2 kg mercury/d into a tributary of the Turtle River-Brunswick Estuary from 1966 to 1971. Mercury concentrations in sediments collected in 1989 along the tributary near the chlor-alkali plant ranged from 1 to 27 μg/g (dry weight), with the highest concentrations found in surface (0–8 cm) sediments of subtidal zones in the vicinity of the discharge site. Toxicity screening in 1990 using Microtox® bioassays on pore water extracted on site from sediments collected at six stations distributed along the tributary indicated that pore water was highly toxic near the plant discharge. Ten-day toxicity tests on pore water from subsequent sediment samples collected near the plant discharge confirmed high toxicity to Hyalella azteca, and feeding activity was significantly reduced in whole-sediment tests. In addition to mercury in the sediments, other metals (chromium, lead, and zinc) exceeded 50 μg/g, and polychlorobiphenyl (PCB) concentrations ranged from 67 to 95 μg/g. On a molar basis, acid-volatile sulfide concentrations (20–45 μmol/g) in the sediments exceeded the metal concentrations. Because acid-volatile sulfides bind with cationic metals and form metal sulfides, which are generally not bioavailable, toxicities shown by these sediments were attributed to the high concentrations of PCBs and possibly methylmercury.

Enlarged facial pores: an update on treatments.

Science.gov (United States)

Dong, Joanna; Lanoue, Julien; Goldenberg, Gary

2016-07-01

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

Method for forming H2-permselective oxide membranes

Science.gov (United States)

Gavalas, G.R.; Nam, S.W.; Tsapatsis, M.; Kim, S.

1995-09-26

Methods are disclosed for forming permselective oxide membranes that are highly selective to permeation of hydrogen by chemical deposition of reactants in the pore of porous tubes, such as Vycor{trademark} glass or Al{sub 2}O{sub 3} tubes. The porous tubes have pores extending through the tube wall. The process involves forming a stream containing a first reactant of the formula RX{sub n}, wherein R is silicon, titanium, boron or aluminum, X is chlorine, bromine or iodine, and n is a number which is equal to the valence of R; and forming another stream containing water vapor as the second reactant. Both of the reactant streams are passed along either the outside or the inside surface of a porous tube and the streams react in the pores of the porous tube to form a nonporous layer of R-oxide in the pores. The membranes are formed by the hydrolysis of the respective halides. In another embodiment, the first reactant stream contains a first reactant having the formula SiH{sub n}Cl{sub 4{minus}n} where n is 1, 2 or 3; and the second reactant stream contains water vapor and oxygen. In still another embodiment the first reactant stream containing a first reactant selected from the group consisting of Cl{sub 3}SiOSiCl{sub 3}, Cl{sub 3}SiOSiCl{sub 2}OSiCl{sub 3}, and mixtures thereof and the second reactant stream contains water vapor. In still another embodiment, membrane formation is carried out by an alternating flow deposition method. This involves a sequence of cycles, each cycle comprising introduction of the halide-containing stream and allowance of a specific time for reaction followed by purge and flow of the water vapor containing stream for a specific length of time. In all embodiments the nonporous layers formed are selectively permeable to hydrogen. 11 figs.

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

Science.gov (United States)

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.

Porous and mesh alumina formed by anodization of high purity aluminum films at low anodizing voltage

International Nuclear Information System (INIS)

Abd-Elnaiem, Alaa M.; Mebed, A.M.; El-Said, Waleed Ahmed; Abdel-Rahim, M.A.

2014-01-01

Electrochemical oxidation of high-purity aluminum (Al) films under low anodizing voltages (1–10) V has been conducted to obtain anodic aluminum oxide (AAO) with ultra-small pore size and inter-pore distance. Different structures of AAO have been obtained e.g. nanoporous and mesh structures. Highly regular pore arrays with small pore size and inter-pore distance have been formed in oxalic or sulfuric acids at different temperatures (22–50 °C). It is found that the pore diameter, inter-pore distance and the barrier layer thickness are independent of the anodizing parameters, which is very different from the rules of general AAO fabrication. The brand formation mechanism has been revealed by the scanning electron microscope study. Regular nanopores are formed under 10 V at the beginning of the anodization and then serve as a template layer dominating the formation of ultra-small nanopores. Anodization that is performed at voltages less than 5 V leads to mesh structured alumina. In addition, we have introduced a simple one-pot synthesis method to develop thin walls of oxide containing lithium (Li) ions that could be used for battery application based on anodization of Al films in a supersaturated mixture of lithium phosphate and phosphoric acid as matrix for Li-composite electrolyte. - Highlights: • We develop anodic aluminum oxide (AAO) with small pore size and inter-pore distance. • Applying low anodizing voltages onto aluminum film leads to form mesh structures. • The value of anodizing voltage (1–10 V) has no effect on pore size or inter-pore distance. • Applying anodizing voltage less than 5 V leads to mesh structured AAO. • AAO can be used as a matrix for Li-composite electrolytes

Porous and mesh alumina formed by anodization of high purity aluminum films at low anodizing voltage

Energy Technology Data Exchange (ETDEWEB)

Abd-Elnaiem, Alaa M., E-mail: alaa.abd-elnaiem@science.au.edu.eg [KACST-Intel Consortium Center of Excellence in Nano-manufacturing Applications (CENA), Riyadh (Saudi Arabia); Physics Department, Faculty of Science, Assiut University, Assiut 71516 (Egypt); Mebed, A.M. [Physics Department, Faculty of Science, Assiut University, Assiut 71516 (Egypt); Department of Physics, Faculty of Science, Al-Jouf University, Sakaka 2014 (Saudi Arabia); El-Said, Waleed Ahmed [Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516 (Egypt); Abdel-Rahim, M.A. [Physics Department, Faculty of Science, Assiut University, Assiut 71516 (Egypt)

2014-11-03

Electrochemical oxidation of high-purity aluminum (Al) films under low anodizing voltages (1–10) V has been conducted to obtain anodic aluminum oxide (AAO) with ultra-small pore size and inter-pore distance. Different structures of AAO have been obtained e.g. nanoporous and mesh structures. Highly regular pore arrays with small pore size and inter-pore distance have been formed in oxalic or sulfuric acids at different temperatures (22–50 °C). It is found that the pore diameter, inter-pore distance and the barrier layer thickness are independent of the anodizing parameters, which is very different from the rules of general AAO fabrication. The brand formation mechanism has been revealed by the scanning electron microscope study. Regular nanopores are formed under 10 V at the beginning of the anodization and then serve as a template layer dominating the formation of ultra-small nanopores. Anodization that is performed at voltages less than 5 V leads to mesh structured alumina. In addition, we have introduced a simple one-pot synthesis method to develop thin walls of oxide containing lithium (Li) ions that could be used for battery application based on anodization of Al films in a supersaturated mixture of lithium phosphate and phosphoric acid as matrix for Li-composite electrolyte. - Highlights: • We develop anodic aluminum oxide (AAO) with small pore size and inter-pore distance. • Applying low anodizing voltages onto aluminum film leads to form mesh structures. • The value of anodizing voltage (1–10 V) has no effect on pore size or inter-pore distance. • Applying anodizing voltage less than 5 V leads to mesh structured AAO. • AAO can be used as a matrix for Li-composite electrolytes.

Characterization of bentonite pore structure by combining chloride porosity and SAXS measurements

International Nuclear Information System (INIS)

Muurinen, A.

2010-01-01

Document available in extended abstract form only. The total water porosity, chloride porosity and the microstructure were studied in compacted samples prepared from MX-80 and Deponit bentonites equilibrated through filter plates with 0.1 M NaCl solution for 12.5 months. The dry densities of the samples varied approximately from 0.7 to 1.55 g/cm 3 . XRD and SAXS (Small Angle X-ray Scattering) were used to study the microstructure of the bentonites. It was obvious that the chloride porosity was lower than the water porosity in both clays, which indicates the exclusion caused by the negatively charged montmorillonite surfaces. In the XRD and SAXS measurements the measured basal spaces represented by the diffraction peaks were smaller than the theoretical ones assuming a homogenous microstructure. This indicates that there was a substantial amount of water also in the pores, which were not represented by the peaks. This could explain the difference between the measured chloride porosity and the modelling curve obtained with the Donnan model. By combining the information from the SAXS measurements and the chloride exclusion measurements, it was possible to evaluate the volumes of the soft and dense fractions and the pore sizes in each fraction for MX-80. The chloride porosity was mostly caused by the pores in the soft clay where the pore size is larger. The volume of the soft fraction decreased and its density increased with increasing density of the sample. (authors)

Pore Scale Analysis of Oil Shale/Sands Pyrolysis

Energy Technology Data Exchange (ETDEWEB)

Lin, Chen-Luh [Univ. of Utah, Salt Lake City, UT (United States); Miller, Jan [Univ. of Utah, Salt Lake City, UT (United States)

2011-03-01

There are important questions concerning the quality and volume of pore space that is created when oil shale is pyrolyzed for the purpose of producing shale oil. In this report, 1.9 cm diameter cores of Mahogany oil shale were pyrolyzed at different temperatures and heating rates. Detailed 3D imaging of core samples was done using multiscale X-ray computed tomography (CT) before and after pyrolysis to establish the pore structure. The pore structure of the unreacted material was not clear. Selected images of a core pyrolyzed at 400oC were obtained at voxel resolutions from 39 microns (Οm) to 60 nanometers (nm). Some of the pore space created during pyrolysis was clearly visible at these resolutions and it was possible to distinguish between the reaction products and the host shale rock. The pore structure deduced from the images was used in Lattice Boltzmann simulations to calculate the permeability in the pore space. The permeabilities of the pyrolyzed samples of the silicate-rich zone were on the order of millidarcies, while the permeabilities of the kerogen-rich zone after pyrolysis were very anisotropic and about four orders of magnitude higher.

Evaluation of Colloid Retention Site Dominance in Variably Saturated Porous Media: An All Pores Pore-Scale Analysis

Science.gov (United States)

Morales, Veronica; Perez-Reche, Francisco; Holzner, Markus; Kinzelbach, Wolfgang

2016-04-01

It is well accepted that colloid and nanoparticle transport processes in porous media differ substantially between water saturated and unsaturated conditions. Differences are frequently ascribed to particle immobilization by association with interfaces with the gas, as well as to restrictions of the liquid medium through which colloids are transported. Yet, the current understanding of the importance of particle retention at gas interfaces is based on observations of single pores or two-dimensional pore network representations, leaving open the question of their statistical significance when all pores in the medium are considered. In order to address this question, column experiments were performed using a model porous medium of glass beads through which Silver particles were transported for conditions of varying water content and water chemistry. X-ray microtomography was subsequently employed as a non-destructive imaging technique to obtain pore-scale information of the entire column regarding: i) the presence and distribution of the main locations where colloids can become retained (interfaces with the water-solid, air-water, air-solid, and air-water-solid, grain-grain contacts, and the bulk liquid), ii) deposition profiles of colloids along the column classified by the available retention location, and iii) channel widths of 3-dimensional pore-water network representations. The results presented provide a direct statistical evaluation on the significance of colloid retention by attachment to interfaces or by strainig at contact points where multiple interfaces meet.

Transmembrane Inhibitor of RICTOR/mTORC2 in Hematopoietic Progenitors

Directory of Open Access Journals (Sweden)

Dongjun Lee

2014-11-01

Full Text Available Central to cellular proliferative, survival, and metabolic responses is the serine/threonine kinase mTOR, which is activated in many human cancers. mTOR is present in distinct complexes that are either modulated by AKT (mTORC1 or are upstream and regulatory of it (mTORC2. Governance of mTORC2 activity is poorly understood. Here, we report a transmembrane molecule in hematopoietic progenitor cells that physically interacts with and inhibits RICTOR, an essential component of mTORC2. Upstream of mTORC2 (UT2 negatively regulates mTORC2 enzymatic activity, reducing AKTS473, PKCα, and NDRG1 phosphorylation and increasing FOXO transcriptional activity in an mTORC2-dependent manner. Modulating UT2 levels altered animal survival in a T cell acute lymphoid leukemia (T-ALL model that is known to be mTORC2 sensitive. These studies identify an inhibitory component upstream of mTORC2 in hematopoietic cells that can reduce mortality from NOTCH-induced T-ALL. A transmembrane inhibitor of mTORC2 may provide an attractive target to affect this critical cell regulatory pathway.

Pore Pressure Distribution and Flank Instability in Hydrothermally Altered Stratovolcanoes

Science.gov (United States)

Ball, J. L.; Taron, J.; Hurwitz, S.; Reid, M. E.

2015-12-01

Field and geophysical investigations of stratovolcanoes with long-lived hydrothermal systems commonly reveal that initially permeable regions (such as brecciated layers of pyroclastic material) can become both altered and water-bearing. Hydrothermal alteration in these regions, including clay formation, can turn them into low-permeability barriers to fluid flow, which could increase pore fluid pressures resulting in flank slope instability. We examined elevated pore pressure conditions using numerical models of hydrothermal flow in stratovolcanoes, informed by geophysical data about internal structures and deposits. Idealized radially symmetric meshes were developed based on cross-sectional profiles and alteration/permeability structures of Cascade Range stratovolcanoes. We used the OpenGeoSys model to simulate variably saturated conditions in volcanoes heated only by regional heat fluxes, as well as 650°C intrusions at two km depth below the surface. Meteoric recharge was estimated from precipitation rates in the Cascade Range. Preliminary results indicate zones of elevated pore pressures form: 1) where slopes are underlain by continuous low-permeability altered layers, or 2) when the edifice has an altered core with saturated, less permeable limbs. The first scenario might control shallow collapses on the slopes above the altered layers. The second could promote deeper flank collapses that are initially limited to the summit and upper slopes, but could progress to the core of an edifice. In both scenarios, pore pressures can be further elevated by shallow intrusions, or evolve over longer time scales under forcing from regional heat flux. Geometries without confining low-permeability layers do not show these pressure effects. Our initial scenarios use radially symmetric models, but we are also simulating hydrothermal flow under real 3D geometries with asymmetric subsurface structures (Mount Adams). Simulation results will be used to inform 3D slope

Understanding the mechanisms behind coking pressure: Relationship to pore structure

Energy Technology Data Exchange (ETDEWEB)

John J. Duffy; M. Castro Diaz; Colin E. Snape; Karen M. Steel; Merrick R. Mahoney [University of Nottingham, Nottingham (United Kingdom). Nottingham Fuel and Energy Centre, School of Chemical, Environmental and Mining Engineering

2007-09-15

Three low volatile coals A, B and C with oven wall pressures of 100 kPa, 60 kPa and 20 kPa respectively were investigated using high-temperature rheometry, {sup 1}H NMR, thermogravimetric analysis and SEM, with the primary aim to better understand the mechanisms behind the coking pressure phenomenon. Rheometer plate displacement measurements ({Delta}L) have shown differences in the expansion and contraction behaviour of the three coals, which seem to correlate with changes in rheological properties; while SEM images have shown that the expansion process coincides with development of pore structure. It is considered that the point of maximum plate height ({Delta}L{sub max}) prior to contraction may be indicative of a cell opening or pore network forming process, based on analogies with other foam systems. Such a process may be considered important for coking pressure since it provides a potential mechanism for volatile escape, relieving internal gas pressure and inducing charge contraction. For coal C, which has the highest fluidity {delta}L{sub max} occurs quite early in the softening process and consequently a large degree of contraction is observed; while for the lower fluidity coal B, the process is delayed since pore development and consequently wall thinning progress at a slower rate. When {Delta}L{sub max} is attained, a lower degree of contraction is observed because the event occurs closer to resolidification where the increasing viscosity/elasticity can stabilise the expanded pore structure. For coal A which is relatively high fluidity, but also high coking pressure, a greater degree of swelling is observed prior to cell rupture, which may be due to greater fluid elasticity during the expansion process. This excessive expansion is considered to be a potential reason for its high coking pressure. 58 refs., 15 figs., 1 tab.

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

Science.gov (United States)

Cao, Han; Ng, Marcus C. K.; Jusoh, Siti Azma; Tai, Hio Kuan; Siu, Shirley W. I.

2017-09-01

α-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577-585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD PHP, MySQL and Apache, with all major browsers supported.

Dynamic Pore-Scale Imaging of Reactive Transport in Heterogeneous Carbonates at Reservoir Conditions Across Multiple Dissolution Regimes

Science.gov (United States)

Menke, H. P.; Bijeljic, B.; Andrew, M. G.; Blunt, M. J.

2014-12-01

Sequestering carbon in deep geologic formations is one way of reducing anthropogenic CO2 emissions. When supercritical CO2 mixes with brine in a reservoir, the acid generated has the potential to dissolve the surrounding pore structure. However, the magnitude and type of dissolution are condition dependent. Understanding how small changes in the pore structure, chemistry, and flow properties affect dissolution is paramount for successful predictive modelling. Both 'Pink Beam' synchrotron radiation and a Micro-CT lab source are used in dynamic X-ray microtomography to investigate the pore structure changes during supercritical CO2 injection in carbonate rocks of varying heterogeneity at high temperatures and pressures and various flow-rates. Three carbonate rock types were studied, one with a homogeneous pore structure and two heterogeneous carbonates. All samples are practically pure calcium carbonate, but have widely varying rock structures. Flow-rate was varied in three successive experiments by over an order of magnitude whlie keeping all other experimental conditions constant. A 4-mm carbonate core was injected with CO2-saturated brine at 10 MPa and 50oC. Tomographic images were taken at 30-second to 20-minute time-resolutions during a 2 to 4-hour injection period. A pore network was extracted using a topological analysis of the pore space and pore-scale flow modelling was performed directly on the binarized images with connected pathways and used to track the altering velocity distributions. Significant differences in dissolution type and magnitude were found for each rock type and flowrate. At the highest flow-rates, the homogeneous carbonate was seen to have predominately uniform dissolution with minor dissolution rate differences between the pores and pore throats. Alternatively, the heterogeneous carbonates which formed wormholes at high flow rates. At low flow rates the homogeneous rock developed wormholes, while the heterogeneous samples showed evidence

Three-dimensionally networked graphene hydroxide with giant pores and its application in supercapacitors

Science.gov (United States)

Lee, Dongwook; Seo, Jiwon

2014-12-01

The three-dimensionally networked and layered structure of graphene hydroxide (GH) was investigated. After lengthy immersion in a NaOH solution, most of the epoxy groups in the graphene oxide were destroyed, and more hydroxyl groups were generated, transforming the graphene oxide into graphene hydroxide. Additionally, benzoic acid groups were formed, and the ether groups link the neighboring layers, creating a near-3D structure in the GH. To utilize these unique structural features, electrodes with large pores for use in supercapacitors were fabricated using thermal reduction in vacuum. The reduced GH maintained its layered structure and developed a lot of large of pores between/inside the layers. The GH electrodes exhibited high gravimetric as well as high volumetric capacitance.

Biophysical Aspects of Transmembrane Signaling

CERN Document Server

Damjanovich, Sandor

2005-01-01

Transmembrane signaling is one of the most significant cell biological events in the life and death of cells in general and lymphocytes in particular. Until recently biochemists and biophysicists were not accustomed to thinking of these processes from the side of a high number of complex biochemical events and an equally high number of physical changes at molecular and cellular levels at the same time. Both types of researchers were convinced that their findings are the most decisive, having higher importance than the findings of the other scientist population. Both casts were wrong. Life, even at cellular level, has a number of interacting physical and biochemical mechanisms, which finally build up the creation of an "excited" cell that will respond to particular signals from the outer or inner world. This book handles both aspects of the signalling events, and in some cases tries to unify our concepts and help understand the signals that govern the life and death of our cells. Not only the understanding, bu...

Ordering transitions of weakly anisotropic hard rods in narrow slitlike pores.

Science.gov (United States)

Aliabadi, Roohollah; Gurin, Péter; Velasco, Enrique; Varga, Szabolcs

2018-01-01

The effect of strong confinement on the positional and orientational ordering is examined in a system of hard rectangular rods with length L and diameter D (L>D) using the Parsons-Lee modification of the second virial density-functional theory. The rods are nonmesogenic (L/Dlayers is allowed to form in the pore. In the extreme confinement limit of H≤2D, where only one-layer structures appear, we observe a structural transition from a planar to a homeotropic fluid layer with increasing density, which becomes sharper as L→H. In wider pores (2Dlayers, homeotropic order, and even combined bilayer structures (one layer is homeotropic, while the other is planar) can be stabilized at high densities. Moreover, first-order phase transitions can be seen between different structures. One of them emerges between a monolayer and a bilayer with planar orders at relatively low packing fractions.

Cancer Research Advance in CKLF-like MARVEL Transmembrane Domain Containing Member Family (Review).

Science.gov (United States)

Lu, Jia; Wu, Qian-Qian; Zhou, Ya-Bo; Zhang, Kai-Hua; Pang, Bing-Xin; Li, Liang; Sun, Nan; Wang, Heng-Shu; Zhang, Song; Li, Wen-Jian; Zheng, Wei; Liu, Wei

2016-01-01

CKLF-like MARVEL transmembrane domain-containing family (CMTM) is a novel family of genes first reported at international level by Peking University Human Disease Gene Research Center. The gene products are between chemokines and the transmembrane-4 superfamily. Loaceted in several human chromosomes, CMTMs, which are unregulated in kinds of tumors, are potential tumor suppressor genes consisting of CKLF and CMTM1 to CMTM8. CMTMs play important roles in immune, male reproductive and hematopoietic systems. Also, it has been approved that CMTM family has strong connection with diseases of autoimmunity, haematopoietic system and haematopoietic system. The in-depth study in recent years found the close relation between CMTMs and umorigenesis, tumor development and metastasis. CMTM family has a significant clinical value in diagnosis and treatment to the diseases linking to tumor and immune system.

A universal model for nanoporous carbon supercapacitors applicable to diverse pore regimes, carbon materials, and electrolytes.

Science.gov (United States)

Huang, Jingsong; Sumpter, Bobby G; Meunier, Vincent

2008-01-01

Supercapacitors, commonly called electric double-layer capacitors (EDLCs), are emerging as a novel type of energy-storage device with the potential to substitute batteries in applications that require high power densities. In response to the latest experimental breakthrough in nanoporous carbon supercapacitors, we propose a heuristic theoretical model that takes pore curvature into account as a replacement for the EDLC model, which is based on a traditional parallel-plate capacitor. When the pore size is in the mesopore regime (2-50 nm), counterions enter mesoporous carbon materials and approach the pore wall to form an electric double-cylinder capacitor (EDCC); in the micropore regime (electric wire-in-cylinder capacitor (EWCC). In the macropore regime (>50 nm) at which pores are large enough so that pore curvature is no longer significant, the EDCC model can be reduced naturally to the EDLC model. We present density functional theory calculations and detailed analyses of available experimental data in various pore regimes, which show the significant effects of pore curvature on the supercapacitor properties of nanoporous carbon materials. It is shown that the EDCC/EWCC model is universal for carbon supercapacitors with diverse carbon materials, including activated carbon materials, template carbon materials, and novel carbide-derived carbon materials, and with diverse electrolytes, including organic electrolytes, such as tetraethylammonium tetrafluoroborate (TEABF(4)) and tetraethylammonium methylsulfonate (TEAMS) in acetonitrile, aqueous H(2)SO(4) and KOH electrolytes, and even an ionic liquid electrolyte, such as 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (EMI-TFSI). The EDCC/EWCC model allows the supercapacitor properties to be correlated with pore size, specific surface area, Debye length, electrolyte concentration and dielectric constant, and solute ion size It may lend support for the systematic optimization of the properties of carbon

Bordetella adenylate cyclase toxin: a unique combination of a pore-forming moiety with a cell-invading adenylate cyclase enzyme

Czech Academy of Sciences Publication Activity Database

Mašín, Jiří; Osička, Radim; Bumba, Ladislav; Šebo, Peter

2015-01-01

Roč. 73, č. 8 (2015) ISSN 2049-632X R&D Projects: GA ČR GAP302/12/0460; GA ČR GA15-09157S; GA ČR(CZ) GA15-11851S Institutional support: RVO:61388971 Keywords : adenylate cyclase toxin * membrane penetration * pore-formation Subject RIV: EE - Microbiology, Virology Impact factor: 2.483, year: 2015

The pore space scramble

Science.gov (United States)

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

Preparation of micro-pored silicone elastomer through radiation crosslinking

International Nuclear Information System (INIS)

Gao Xiaoling; Gu Mei; Xie Xubing; Huang Wei

2013-01-01

The radiation crosslinking was adopted to prepare the micro-pored silicone elastomer, which was performed by vulcanization and foaming respectively. Radiation crosslinking is a new method to prepare micro-pored material with high performance by use of radiation technology. Silicon dioxide was used as filler, and silicone elastomer was vulcanized by electron beams, then the micro-pored material was made by heating method at a high temperature. The effects of absorbed dose and filler content on the performance and morphology were investigated. The structure and distribution of pores were observed by SEM. The results show that the micro-pored silicon elastomer can be prepared successfully by controlling the absorbed dose and filler content. It has a smooth surface similar to a rubber meanwhile the pores are round and unconnected to each other with the minimum size of 14 μm. And the good mechanical performance can be suitable for further uses. (authors)

Multiscale pore networks and their effect on deformation and transport property alteration associated with hydraulic fracturing

Science.gov (United States)

Daigle, Hugh; Hayman, Nicholas; Jiang, Han; Tian, Xiao; Jiang, Chunbi

2017-04-01

clusters of organic-hosted pores prevents the overpressure from dissipating, resulting in localized overpressure at the micron scale. When the rock is subjected to a hydraulic fracture stimulation, the rock surrounding the main induced fracture experiences shear deformation. Those parts of the rock that contain overpressured fluids in the organic-hosted pores will be more likely to experience dilatancy in the form of brittle deformation; the portions of the rock lacking in organic-hosted pores will tend to experience compactive shear failure since the effective normal stresses are larger. The microcrack networks that propagate into the regions of organic-hosted porosity allow the hydrocarbons resident in those pores to migrate to the main induced tensile fractures. The disconnected nature of the microcrack networks causes only a slight increase in permeability, which is consistent with other observations. Our work illustrates how multiscale pore networks in shale interact with in situ stresses to affect the bulk shale rheology.

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

NARCIS (Netherlands)

Wolf, A.B.; Vos, de M.; Boer, de W.; Kowalchuk, G.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

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

NARCIS (Netherlands)

Wolf, A.B.; Vos, M.; De Boer, W.; Kowalchuk, G.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

Relative transmembrane segment rearrangements during BK channel activation resolved by structurally assigned fluorophore–quencher pairing

Science.gov (United States)

Pantazis, Antonios

2012-01-01

Voltage-activated proteins can sense, and respond to, changes in the electric field pervading the cell membrane by virtue of a transmembrane helix bundle, the voltage-sensing domain (VSD). Canonical VSDs consist of four transmembrane helices (S1–S4) of which S4 is considered a principal component because it possesses charged residues immersed in the electric field. Membrane depolarization compels the charges, and by extension S4, to rearrange with respect to the field. The VSD of large-conductance voltage- and Ca-activated K+ (BK) channels exhibits two salient inconsistencies from the canonical VSD model: (1) the BK channel VSD possesses an additional nonconserved transmembrane helix (S0); and (2) it exhibits a “decentralized” distribution of voltage-sensing charges, in helices S2 and S3, in addition to S4. Considering these unique features, the voltage-dependent rearrangements of the BK VSD could differ significantly from the standard model of VSD operation. To understand the mode of operation of this unique VSD, we have optically tracked the relative motions of the BK VSD transmembrane helices during activation, by manipulating the quenching environment of site-directed fluorescent labels with native and introduced Trp residues. Having previously reported that S0 and S4 diverge during activation, in this work we demonstrate that S4 also diverges from S1 and S2, whereas S2, compelled by its voltage-sensing charged residues, moves closer to S1. This information contributes spatial constraints for understanding the BK channel voltage-sensing process, revealing the structural rearrangements in a non-canonical VSD. PMID:22802360

Novel Techniques to Characterize Pore Size of Porous Materials

KAUST Repository

Alabdulghani, Ali J.

2016-01-01

Porous materials are implemented in several industrial applications such as water desalination, gas separation and pharmaceutical care which they are mainly governed by the pore size and the PSD. Analyzing shale reservoirs are not excluded from these applications and numerous advantages can be gained by evaluating the PSD of a given shale reservoir. Because of the limitations of the conventional characterization techniques, novel methods for characterizing the PSD have to be proposed in order to obtain better characterization results for the porous materials, in general, and shale rocks in particular. Thus, permporosimetry and evapoporometry (EP) technologies were introduced, designed and utilized for evaluating the two key parameters, pore size and pore size distribution. The pore size and PSD profiles of different shale samples from Norway and Argentina were analyzed using these technologies and then confirmed by mercury intrusion porosimeter (MIP). Norway samples showed an average pore diameter of 12.94 nm and 19.22 nm with an average diameter of 13.77 nm and 23.23 nm for Argentina samples using permporosimetry and EP respectively. Both techniques are therefore indicative of the heterogeneity of the shales. The results from permporosimetry are in good agreement with those obtained from MIP technique, but EP for most part over-estimates the average pore size. The divergence of EP results compared to permporosimetry results is referred to the fact that the latter technique measures only the active pores which is not the case with the former technique. Overall, both techniques are complementary to each other which the results from both techniques seem reasonable and reliable and provide two simple techniques to estimate the pore size and pore size distributions for shale rocks.

Novel Techniques to Characterize Pore Size of Porous Materials

KAUST Repository

Alabdulghani, Ali J.

2016-04-24

Porous materials are implemented in several industrial applications such as water desalination, gas separation and pharmaceutical care which they are mainly governed by the pore size and the PSD. Analyzing shale reservoirs are not excluded from these applications and numerous advantages can be gained by evaluating the PSD of a given shale reservoir. Because of the limitations of the conventional characterization techniques, novel methods for characterizing the PSD have to be proposed in order to obtain better characterization results for the porous materials, in general, and shale rocks in particular. Thus, permporosimetry and evapoporometry (EP) technologies were introduced, designed and utilized for evaluating the two key parameters, pore size and pore size distribution. The pore size and PSD profiles of different shale samples from Norway and Argentina were analyzed using these technologies and then confirmed by mercury intrusion porosimeter (MIP). Norway samples showed an average pore diameter of 12.94 nm and 19.22 nm with an average diameter of 13.77 nm and 23.23 nm for Argentina samples using permporosimetry and EP respectively. Both techniques are therefore indicative of the heterogeneity of the shales. The results from permporosimetry are in good agreement with those obtained from MIP technique, but EP for most part over-estimates the average pore size. The divergence of EP results compared to permporosimetry results is referred to the fact that the latter technique measures only the active pores which is not the case with the former technique. Overall, both techniques are complementary to each other which the results from both techniques seem reasonable and reliable and provide two simple techniques to estimate the pore size and pore size distributions for shale rocks.

Nonlinear electro-mechanobiological behavior of cell membrane during electroporation

KAUST Repository

Deng, Peigang

2012-01-01

A nonlinear electroporation (EP) model is proposed to study the electro-mechanobiological behavior of cell membrane during EP, by taking the nonlinear large deformation of the membrane into account. The proposed model predicts the critical transmembrane potential and the activation energy for EP, the equilibrium pore size, and the resealing process of the pore. Single-cell EP experiments using a micro EP chip were conducted on chicken red blood cells at different temperatures to determine the activation energy and the critical transmembrane potential for EP. The experimental results are in good agreement with the theoretical predictions. © 2012 American Institute of Physics.

OBSERVATIONS OF SAUSAGE MODES IN MAGNETIC PORES

International Nuclear Information System (INIS)

Morton, R. J.; Erdelyi, R.; Jess, D. B.; Mathioudakis, M.

2011-01-01

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.

Estimation of pore pressure from seismic velocities

International Nuclear Information System (INIS)

Perez, Zayra; Ojeda, German Y; Mateus, Darwin

2009-01-01

On pore pressure calculations it is common to obtain a profile in a well bore, which is then extrapolated toward offset wells. This practice might generate mistakes on pore pressure measurements, since geological conditions may change from a well bore to another, even into the same basin. Therefore, it is important to use other tools which allow engineers not only to detect and estimate in an indirect way overpressure zones, but also to keep a lateral tracking of possible changes that may affect those values in the different formations. Taking into account this situation, we applied a methodology that estimates formation pressure from 3D seismic velocities by using the Eaton method. First, we estimated formation pore pressure; then, we identified possible overpressure zones. Finally, those results obtained from seismic information were analyzed involving well logs and pore pressure tests, in order to compare real data with prediction based on seismic information from the Colombian foothill.

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

Science.gov (United States)

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

2014-03-07

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

Micro-CT scan reveals an unexpected high-volume and interconnected pore network in a Cretaceous Sanagasta dinosaur eggshell.

Science.gov (United States)

Hechenleitner, E Martín; Grellet-Tinner, Gerald; Foley, Matthew; Fiorelli, Lucas E; Thompson, Michael B

2016-03-01

The Cretaceous Sanagasta neosauropod nesting site (La Rioja, Argentina) was the first confirmed instance of extinct dinosaurs using geothermal-generated heat to incubate their eggs. The nesting strategy and hydrothermal activities at this site led to the conclusion that the surprisingly 7 mm thick-shelled eggs were adapted to harsh hydrothermal microenvironments. We used micro-CT scans in this study to obtain the first three-dimensional microcharacterization of these eggshells. Micro-CT-based analyses provide a robust assessment of gas conductance in fossil dinosaur eggshells with complex pore canal systems, allowing calculation, for the first time, of the shell conductance through its thickness. This novel approach suggests that the shell conductance could have risen during incubation to seven times more than previously estimated as the eggshell erodes. In addition, micro-CT observations reveal that the constant widening and branching of pore canals form a complex funnel-like pore canal system. Furthermore, the high density of pore canals and the presence of a lateral canal network in the shell reduce the risks of pore obstruction during the extended incubation of these eggs in a relatively highly humid and muddy nesting environment. © 2016 The Author(s).

A mathematical study of the influence of pore geometry on diffusion

International Nuclear Information System (INIS)

Melnyk, T.W.; Skeet, A.M.M.

1987-01-01

Diffusion into the pore space of plutonic rock matrices is an important phenomenon that can affect the migration of radionuclides and other contaminants in groundwater systems. The effects of irregular pore geometry on rates of diffusive transport are examined in this report. Approximate equations describing steady-state diffusive transport in pores of variable geometry are presented and indicate a strong dependence of the diffusion rates on the geometry of the pore space. Finite-element diffusion calculations were carried out for a series of pores containing storage spaces with rectangular cross-sections. The calculations showed the time taken to reach steady-state is affected by the pore geometry. The results of these calculations were used to simulate typical laboratory diffusion experiments and to evaluate the interpretation of effective diffusion parameters obtained from analysis of the simulated experiments using both capillary and dead-end pore models of the pore space. A capillary model of the pore space requires two independent parameters to characterize the pore space, and is shown, in general, to be inadequate to describe the pre-steady-state regime. The diffusion of radionuclides in groundwater systems lies in this non-steady-state regime. More complex mathematical descriptions of the pore space, using more variables and parameters, can accurately describe the non-steady-state transport. The capillary model, with effective parameter values, gives reasonable results when the size of the dead-end pore space is small relative to the overall diffusion distance under consideration

Micro/Nano-pore Network Analysis of Gas Flow in Shale Matrix.

Science.gov (United States)

Zhang, Pengwei; Hu, Liming; Meegoda, Jay N; Gao, Shengyan

2015-08-27

The gas flow in shale matrix is of great research interests for optimized shale gas extraction. The gas flow in the nano-scale pore may fall in flow regimes such as viscous flow, slip flow and Knudsen diffusion. A 3-dimensional nano-scale pore network model was developed to simulate dynamic gas flow, and to describe the transient properties of flow regimes. The proposed pore network model accounts for the various size distributions and low connectivity of shale pores. The pore size, pore throat size and coordination number obey normal distribution, and the average values can be obtained from shale reservoir data. The gas flow regimes were simulated using an extracted pore network backbone. The numerical results show that apparent permeability is strongly dependent on pore pressure in the reservoir and pore throat size, which is overestimated by low-pressure laboratory tests. With the decrease of reservoir pressure, viscous flow is weakening, then slip flow and Knudsen diffusion are gradually becoming dominant flow regimes. The fingering phenomenon can be predicted by micro/nano-pore network for gas flow, which provides an effective way to capture heterogeneity of shale gas reservoir.

Ligand-mediated negative regulation of a chimeric transmembrane receptor tyrosine phosphatase

DEFF Research Database (Denmark)

Desai, D M; Sap, J; Schlessinger, J

1993-01-01

CD45, a transmembrane protein tyrosine phosphatase (PTPase), is required for TCR signaling. Multiple CD45 isoforms, differing in the extracellular domain, are expressed in a tissue- and activation-specific manner, suggesting an important function for this domain. We report that a chimeric protein...... that ligand-mediated regulation of receptor-PTPases may have mechanistic similarities with receptor tyrosine kinases....

Electrochemical platform for the detection of transmembrane proteins reconstituted into liposomes

Czech Academy of Sciences Publication Activity Database

Vacek, J.; Zatloukalová, M.; Geletičová, J.; Kubala, M.; Modriansky, M.; Fekete, Ladislav; Mašek, J.; Hubatka, F.; Turánek, J.

2016-01-01

Roč. 88, č. 8 (2016), s. 4548-4556 ISSN 0003-2700 R&D Projects: GA MŠk LO1409; GA MŠk LM2015088 Institutional support: RVO:68378271 Keywords : detection * transmembrane proteins * liposomes * electrochemistry Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 6.320, year: 2016

Electrokinetic flows in cylindrical and slit capillaries in clays: from pore scale to sample scale

International Nuclear Information System (INIS)

Obliger, Amael; Jardat, Marie; Rotenberg, Benjamin; Duvail, Magali; Bekri, Samir; Coelho, Daniel

2012-01-01

Document available in extended abstract form only. Full text of publication follows: Transport on the nanometer scale of clay interlayers and on the macroscopic sample scale can be well characterized experimentally, using either X-ray or neutron diffraction and diffusion on the one hand, and solute diffusion experiments on the other hand. Current imaging techniques do not allow to provide a direct picture of the pore network on the scale of several nanometers to several micrometers. The lack of knowledge of the pore network structure on intermediate scales requires to use numerical models of analog porous media. We attempt to describe the ionic transport in meso (diam. ∼ 10-50 nm) and macro-porosity (diam. > 50 nm) (due to the organization of clays particles) with a multi-scale approach provided by the Pore Network Model (PNM) that takes into consideration the topology of the media. Such an approach requires to know the transport coefficients of solvent and solutes in a throat connecting two pores, modelled as a capillary. The challenge in the case of clays, compared to the usual PNM methods, is to capture the effect of the surface charge of clay minerals on the transport of ions and water, under the effect of macroscopic pressure, salt concentration and electric potential gradients. Solvent and ionic transports are governed by the Stokes, the Nernst-Planck and the Poisson- Boltzmann equations. This set of equations can be solved analytically using the linearized form of the latter in order to get an approximation of the electro-osmotic speed and the ionic density profile. At variant with most previous works, we consider the case of a fixed surface charge instead of fixed surface potential. In addition to the Nernst-Einstein and chemical flows of solute, we calculated analytically the Poiseuille flow of solutes and the electro-osmotic flow of solvent and solutes. When the linearization is not possible, one must use numerical results for transport coefficients

α-Helical Structural Elements within the Voltage-Sensing Domains of a K+ Channel

Science.gov (United States)

Li-Smerin, Yingying; Hackos, David H.; Swartz, Kenton J.

2000-01-01

Voltage-gated K+ channels are tetramers with each subunit containing six (S1–S6) putative membrane spanning segments. The fifth through sixth transmembrane segments (S5–S6) from each of four subunits assemble to form a central pore domain. A growing body of evidence suggests that the first four segments (S1–S4) comprise a domain-like voltage-sensing structure. While the topology of this region is reasonably well defined, the secondary and tertiary structures of these transmembrane segments are not. To explore the secondary structure of the voltage-sensing domains, we used alanine-scanning mutagenesis through the region encompassing the first four transmembrane segments in the drk1 voltage-gated K+ channel. We examined the mutation-induced perturbation in gating free energy for periodicity characteristic of α-helices. Our results are consistent with at least portions of S1, S2, S3, and S4 adopting α-helical secondary structure. In addition, both the S1–S2 and S3–S4 linkers exhibited substantial helical character. The distribution of gating perturbations for S1 and S2 suggest that these two helices interact primarily with two environments. In contrast, the distribution of perturbations for S3 and S4 were more complex, suggesting that the latter two helices make more extensive protein contacts, possibly interfacing directly with the shell of the pore domain. PMID:10613917

Ionic Liquid Confined in Mesoporous Polymer Membrane with Improved Stability for CO2/N2 Separation

Directory of Open Access Journals (Sweden)

Ming Tan

2017-09-01

Full Text Available Supported ionic liquid membranes (SILMs have a promising prospect of application in flue gas separation, owing to its high permeability and selectivity of CO2. However, existing SILMs have the disadvantage of poor stability due to the loss of ionic liquid from the large pores of the macroporous support. In this study, a novel SILM with high stability was developed by confining ionic liquid in a mesoporous polymer membrane. First, a mesoporous polymer membrane derived from a soluble, low-molecular-weight phenolic resin precursor was deposited on a porous Al2O3 support, and then 1-ethyl-3-methylimidazolium tetrafluoroborate ([emim][BF4] was immobilized inside mesopores of phenolic resin, forming the SILM under vacuum. Effects of trans-membrane pressure difference on the SILM separation performance were investigated by measuring the permeances of CO2 and N2. The SILM exhibits a high ideal CO2/N2 selectivity of 40, and an actual selectivity of approximately 25 in a mixed gas (50% CO2 and 50% N2 at a trans-membrane pressure difference of 2.5 bar. Compared to [emim][BF4] supported by polyethersulfone membrane with a pore size of around 0.45 μm, the [emim][BF4] confined in a mesoporous polymer membrane exhibits an improved stability, and its separation performance remained stable for 40 h under a trans-membrane pressure difference of 1.5 bar in a mixed gas before the measurement was intentionally stopped.

Silver Nanoparticle Transport Through Soil: Illuminating the Pore-Scale Processes

Science.gov (United States)

Molnar, I. L.; Willson, C. S.; Gerhard, J.; O'Carroll, D. M.

2015-12-01

For nanoparticle transport through soil, the pore-scale (i.e., tens to hundreds of grains and pores) is a crucial intermediate scale which links nanoparticle-surface interactions with field-scale transport behaviour. However, very little information exists on how nanoparticles behave within real three-dimensional pore spaces. As a result, pore-scale processes are poorly characterized for nanoparticle systems and, subsequently, continuum-scale transport models struggle to describe commonly observed 'anomalous' behaviour such as extended tailing. This knowledge gap is due to two primary factors: an inability to experimentally observe nanoparticles within real pore spaces, and the computationally expensive models required to simulate nanoparticle movement. However, due to recent advances in Synchrotron X-Ray Computed Microtomography (SXCMT), it is now possible to quantify in-situ pore-scale nanoparticle concentrations during transport through real 3-dimensional porous media [1]. Employing this SXCMT quantification method to examine real nanoparticle/soil transport experiments has yielded new insights into the pore-scale processes governing nanoparticle transport. By coupling SXCMT nanoparticle quantification method with Computational Fluid Dynamics (CFD) simulations we are able to construct a better picture of how nanoparticles flow through real pore spaces. This talk presents SXCMT/CFD analyses of three silver nanoparticle transport experiments. Silver nanoparticles were flushed through three different sands to characterize the influence of grain distribution and retention rates on pore-scale flow and transport processes. These CFD/SXCMT analyses illuminate how processes such as temporary hydraulic retention govern nanoparticle transport. In addition, the observed distributions of pore water velocities and nanoparticle mass flow rates challenge the standard conceptual model of nanoparticle transport, suggesting that pore-scale processes require explicit consideration

Cystic Fibrosis Transmembrane Conductance Regulator Potentiation as a Therapeutic Strategy for Pulmonary Edema: A Proof-of-Concept Study in Pigs.

Science.gov (United States)

Li, Xiaopeng; Vargas Buonfiglio, Luis G; Adam, Ryan J; Stoltz, David A; Zabner, Joseph; Comellas, Alejandro P

2017-12-01

To determine the feasibility of using a cystic fibrosis transmembrane conductance regulator potentiator, ivacaftor (VX-770/Kalydeco, Vertex Pharmaceuticals, Boston, MA), as a therapeutic strategy for treating pulmonary edema. Prospective laboratory animal investigation. Animal research laboratory. Newborn and 3 days to 1 week old pigs. Hydrostatic pulmonary edema was induced in pigs by acute volume overload. Ivacaftor was nebulized into the lung immediately after volume overload. Grams of water per grams of dry lung tissue were determined in the lungs harvested 1 hour after volume overload. Ivacaftor significantly improved alveolar liquid clearance in isolated pig lung lobes ex vivo and reduced edema in a volume overload in vivo pig model of hydrostatic pulmonary edema. To model hydrostatic pressure-induced edema in vitro, we developed a method of applied pressure to the basolateral surface of alveolar epithelia. Elevated hydrostatic pressure resulted in decreased cystic fibrosis transmembrane conductance regulator activity and liquid absorption, an effect which was partially reversed by cystic fibrosis transmembrane conductance regulator potentiation with ivacaftor. Cystic fibrosis transmembrane conductance regulator potentiation by ivacaftor is a novel therapeutic approach for pulmonary edema.

Atomistic Insight on the Charging Energetics in Sub-nanometer Pore Supercacitors

Energy Technology Data Exchange (ETDEWEB)

Qiao, Rui [ORNL; Huang, Jingsong [ORNL; Sumpter, Bobby G [ORNL; Meunier, Vincent [ORNL; Feng, Guang [Clemson University

2010-01-01

Electrodes featuring sub-nanometer pores can significantly enhance the capacitance and energy density of supercapacitors. However, ions must pay an energy penalty to enter sub-nanometer pores as they have to shed part of their solvation shell. The magnitude of such energy penalty plays a key role in determining the accessibility and charging/discharging of these sub-nanometer pores. Here we report on the atomistic simulation of Na+ and Cl ions entering a polarizable slit pore with a width of 0.82 nm. We show that the free energy penalty for these ions to enter the pore is less than 14 kJ/mol for both Na+ and Cl ions. The surprisingly small energy penalty is caused by the van der Waals attractions between ion and pore walls, the image charge effects, the moderate (19-26%) de-hydration of the ions inside the pore, and the strengthened interactions between ions and their hydration water molecules in the sub-nanometer pore. The results provide strong impetus for further developing nanoporous electrodes featuring sub- nanometer pores.

Direct observations of the 3D pore network of a Callovo-Oxfordian clay-stone

International Nuclear Information System (INIS)

Robinet, J.C.; Talandier, J.; Davy, C.A.; Ghayaza, M.; Skoczylas, F.; Troadec, D.; Sardini, P.

2012-01-01

Document available in extended abstract form only. Long term deep underground storage of radioactive nuclear waste is planned in the East of France within an argillaceous rock layer (the host rock), also called argillite, situated at ca. 450-500 m depth. Andra, the French national agency for nuclear waste management, is in charge of assessing the feasibility, the safety and the performance of this underground disposal. The drilling of storage tunnels generates an Excavated Damaged Zone (EDZ), where argillite is macro-cracked in various locations. This requires strengthening by different means, e.g. shotcrete or pre-fabricated concrete arches. It is also expected that underground water seepage will contribute to argillite sealing: mainly self-sealing, and sealing at the interface with concrete. Sealing phenomena include crystalline swelling of smectitic clay components of argillite and inter-particle swelling of clay minerals due to osmosis mechanisms. Small scale pores and mineral organisation of the COx clay-stone are widely acknowledged to control transfer properties of water, gas and varied solutes. In order to assess these properties, the COx small-scale structure has been imaged down to micrometric resolution by various means, including classical Scanning Electron Microscopy (SEM), X-ray computed microtomography and autoradiography. To go further into pore and mineral characterisation of COx clay-stone, the following investigations are currently under way: (i) acquiring/quantifying the 3D geometry of the pore network of undisturbed COx with a nano-metric resolution and (ii) imaging/quantifying the small-scale (mm-nm) structure of self-sealed volumes. The FIB (Focused Ion Beam) /SEM technique allows performing 3D observations of solid volumes of ca. a few microns, with a resolution of about ten nanometers, by acquiring and computing regularly spaced 2D SEM images. This technique provides quantification of the 3D spatial distribution mainly of macro- and meso-pores

Pore opening dynamics in the exocytosis of serotonin

Science.gov (United States)

Ramirez-Santiago, Guillermo; Cercos, Montserrat G.; Martinez-Valencia, Alejandro; Salinas Hernandez, Israel; Rodríguez-Sosa, Leonardo; de-Miguel, Francisco F.

2015-03-01

The current view of the exocytosis of transmitter molecules is that it starts with the formation of a fusion pore that connects the intravesicular and the extracellular spaces, and is completed by the release of the rest of the transmitter contained in the vesicle upon the full fusion and collapse of the vesicle with the plasma membrane. However, under certain circumstances, a rapid closure of the pore before the full vesicle fusion produces only a partial release of the transmitter. Here we show that whole release of the transmitter occurs through fusion pores that remain opened for tens of milliseconds without vesicle collapse. This was demonstrated through amperometric measurements of serotonin release from electrodense vesicles in the axon of leech Retzius neurons and mathematical modelling. By modeling transmitter release with a diffusion equation subjected to boundary conditions that are defined by the experiment, we showed that those pores with a fast half rise time constant remained opened and allowed the full quantum release without vesicle collapse, whereas pores with a slow rise time constant closed rapidly, thus producing partial release. We conclude that a full transmitter release may occur through the fusion pore in the absence of vesicle collapse. This work was founded by a DGAPA-UNAM grants IN200914 and IN118410 CONACYT GRANT 130031, and CONACyT doctoral fellowships.

Moving Magnetic Features Around a Pore

Energy Technology Data Exchange (ETDEWEB)

Kaithakkal, A. J.; Riethmüller, T. L.; Solanki, S. K.; Lagg, A.; Barthol, P.; Gandorfer, A.; Gizon, L.; Hirzberger, J.; VanNoort, M. [Max Planck Institute for Solar System Research, Justus-von-Liebig-Weg 3, Göttingen D-37077 (Germany); Rodríguez, J. Blanco [Grupo de Astronomía y Ciencias del Espacio, Universidad de Valencia, E-46980 Paterna, Valencia (Spain); Iniesta, J. C. Del Toro; Suárez, D. Orozco [Instituto de Astrofísica de Andalucía (CSIC), Apartado de Correos 3004, E-18080 Granada (Spain); Schmidt, W. [Kiepenheuer-Institut für Sonnenphysik, Schöneckstr. 6, D-79104 Freiburg (Germany); Pillet, V. Martínez [National Solar Observatory, 3665 Discovery Drive, Boulder, CO 80303 (United States); Knölker, M., E-mail: anjali@mps.mpg.de [High Altitude Observatory, National Center for Atmospheric Research, P.O. Box 3000, Boulder, CO 80307-3000 (United States)

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{sup −1} and 1.2 km s{sup −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 × 10{sup 17} Mx.

An evaluation of factors influencing pore pressure in accretionary complexes: Implications for taper angle and wedge mechanics

Science.gov (United States)

Saffer, D.M.; Bekins, B.A.

2006-01-01

At many subduction zones, accretionary complexes form as sediment is off-scraped from the subducting plate. Mechanical models that treat accretionary complexes as critically tapered wedges of sediment demonstrate that pore pressure controls their taper angle by modifying basal and internal shear strength. Here, we combine a numerical model of groundwater flow with critical taper theory to quantify the effects of sediment and de??collement permeability, sediment thickness, sediment partitioning between accretion and underthrusting, and plate convergence rate on steady state pore pressure. Our results show that pore pressure in accretionary wedges can be viewed as a dynamically maintained response to factors which drive pore pressure (source terms) and those that limit flow (permeability and drainage path length). We find that sediment permeability and incoming sediment thickness are the most important factors, whereas fault permeability and the partitioning of sediment have a small effect. For our base case model scenario, as sediment permeability is increased, pore pressure decreases from near-lithostatic to hydrostatic values and allows stable taper angles to increase from ??? 2.5?? to 8??-12.5??. With increased sediment thickness in our models (from 100 to 8000 m), increased pore pressure drives a decrease in stable taper angle from 8.4??-12.5?? to 15?? to <4??) with increased sediment thickness (from <1 to 7 km). One key implication is that hydrologic properties may strongly influence the strength of the crust in a wide range of geologic settings. Copyright 2006 by the American Geophysical Union.

Pore water pressure response to small and large openings in argillaceous rocks

International Nuclear Information System (INIS)

Garitte, B.; Gens, A.; Vaunat, J.; Armand, G.; Conil, N.

2012-01-01

Document available in extended abstract form only. In the last decade an important amount of piezometers have been installed in the Bure Underground Rock Laboratory (URL) in the vicinity of ongoing works involving gallery excavations and drilling of boreholes and alveoles both in the major and minor stress directions. Relatively far field piezometers (placed one to four diameters from the excavation wall) showed a qualitatively consistent response at different scales. Here, we investigate whether the pore water pressure response around openings of different scales may be up-scaled. An attempt is made to find a common set of parameters that explains quantitatively the rock response at the different scales. The mechanisms underlying the pore water pressure response around an underground opening are twofold. The first class of mechanisms is usually associated with nearly undrained behaviour and the related pore water pressure changes are induced by the stress redistribution triggered by the creation of the tunnel opening causing a reorientation of the principal stresses and influenced by the initial stress anisotropy. These pore water pressure changes are closely linked to the mechanical constitutive law of the rock and to the damage zone around the opening. The second class of mechanisms is related to the drainage of excess pore water pressure relative to a state governed by the atmospheric water pressure condition prescribed at gallery wall and the water flow law, usually Darcy's. Strong anisotropy effects on the hydraulic response of Callovo-Oxfordian Clay can be observed with reference to Figure 1 that shows the pore pressure response to the drilling of a 150 mm-diameter borehole performed to install a heater for the TER thermal experiment. The borehole is aligned with the major horizontal principal stress. Therefore, in principle, the stress state should be approximately isotropic in a cross section of the borehole. As a matter of fact, however, a degree of

Microtomography and pore-scale modeling of two-phase Fluid Distribution

Energy Technology Data Exchange (ETDEWEB)

Silin, D.; Tomutsa, L.; Benson, S.; Patzek, T.

2010-10-19

Synchrotron-based X-ray microtomography (micro CT) at the Advanced Light Source (ALS) line 8.3.2 at the Lawrence Berkeley National Laboratory produces three-dimensional micron-scale-resolution digital images of the pore space of the reservoir rock along with the spacial distribution of the fluids. Pore-scale visualization of carbon dioxide flooding experiments performed at a reservoir pressure demonstrates that the injected gas fills some pores and pore clusters, and entirely bypasses the others. Using 3D digital images of the pore space as input data, the method of maximal inscribed spheres (MIS) predicts two-phase fluid distribution in capillary equilibrium. Verification against the tomography images shows a good agreement between the computed fluid distribution in the pores and the experimental data. The model-predicted capillary pressure curves and tomography-based porosimetry distributions compared favorably with the mercury injection data. Thus, micro CT in combination with modeling based on the MIS is a viable approach to study the pore-scale mechanisms of CO{sub 2} injection into an aquifer, as well as more general multi-phase flows.

Synthesis, characterization, and evaluation of a superficially porous particle with unique, elongated pore channels normal to the surface.

Science.gov (United States)

Wei, Ta-Chen; Mack, Anne; Chen, Wu; Liu, Jia; Dittmann, Monika; Wang, Xiaoli; Barber, William E

2016-04-01

In recent years, superficially porous particles (SPPs) have drawn great interest because of their special particle characteristics and improvement in separation efficiency. Superficially porous particles are currently manufactured by adding silica nanoparticles onto solid cores using either a multistep multilayer process or one-step coacervation process. The pore size is mainly controlled by the size of the silica nanoparticles and the tortuous pore channel geometry is determined by how those nanoparticles randomly aggregate. Such tortuous pore structure is also similar to that of all totally porous particles used in HPLC today. In this article, we report on the development of a next generation superficially porous particle with a unique pore structure that includes a thinner shell thickness and ordered pore channels oriented normal to the particle surface. The method of making the new superficially porous particles is a process called pseudomorphic transformation (PMT), which is a form of micelle templating. Porosity is no longer controlled by randomly aggregated nanoparticles but rather by micelles that have an ordered liquid crystal structure. The new particle possesses many advantages such as a narrower particle size distribution, thinner porous layer with high surface area and, most importantly, highly ordered, non-tortuous pore channels oriented normal to the particle surface. This PMT process has been applied to make 1.8-5.1μm SPPs with pore size controlled around 75Å and surface area around 100m(2)/g. All particles with different sizes show the same unique pore structure with tunable pore size and shell thickness. The impact of the novel pore structure on the performance of these particles is characterized by measuring van Deemter curves and constructing kinetic plots. Reduced plate heights as low as 1.0 have been achieved on conventional LC instruments. This indicates higher efficiency of such particles compared to conventional totally porous and

The Production of Nickel-Chromium-Molybdenum Alloy with Open Pore Structure as an Implant and the Investigation of Its Biocompatibility In Vivo

Directory of Open Access Journals (Sweden)

Yusuf Er

2013-01-01

Full Text Available A dental crown material, Nickel-Chrome-Molybdenum alloy, is manufactured using precision casting method from a polyurethane foam model in a regular and open-pore form, as a hard tissue implant for orthopedic applications. The samples produced have 10, 20, and 30 (±3 pores per inch of pore densities and 0.0008, 0.0017, and 0.0027 g/mm3 densities, respectively. Samples were implanted in six dogs and observed for a period of two, four, and six months for the histopathological examinations. The dogs were examined radiologically in 15-day intervals and clinically in certain intervals. The implants were taken out with surrounding tissue at the end of these periods. Implants and surrounding tissues were examined histopathologically in terms of biocompatibility. As a result, it is seen that new bone tissue was formed, in pores of the porous implant at the head of the tibia in dogs implanted. Any pathology, inflammation, and reaction in old and new tissues were not observed. It was concluded that a dental alloy (Ni-Cr-Mo alloy could also be used as a biocompatible hard tissue implant material for orthopedics.

Pore-Fractal Structure in Porous Carbons Made from Corn and Wheat

Science.gov (United States)

Kapoor, Y. M.; Schmidt, P. W.; Rice, Randall D.; Shulse, Laural; Voss, D. J.; Venkatraman, A.; Fan, L. T.; Walawender, W. P.; Rieker, T. P.

1998-03-01

Small-angle X-ray scattering has been used in a study of the pore structure of some porous and activated carbons on length scales between about 5 and 10^4 ÅThe carbons were obtained by pyrolysis and activation of wheat and American corn (maize). The scattering data showed that in each carbon there are at least two of the following four types of pores: (1) pores with diameters of at least 10^4 Åpores with smooth or fractal surfaces and diameters of at least 5 x 10^3 Åpore-fractals with diameters of no more than about 10^3 Åand (4) pores with diameters no larger than 100 ÅThe relation between the pore structure and the procedure used to obtain the carbon and will be discussed.

Identification of an Arabidopsis transmembrane bZIP transcription factor involved in the endoplasmic reticulum stress response

International Nuclear Information System (INIS)

Tajima, Hiromi; Iwata, Yuji; Iwano, Megumi; Takayama, Seiji; Koizumi, Nozomu

2008-01-01

Among 75 bZIP transcription factors identified in Arabidopsis, 3 (AtbZIP17, AtbZIP28, and AtbZIP49) possess a putative transmembrane domain (TMD) in addition to AtbZIP60, which was characterized previously. In the present study, cDNAs of AtbZIP17 and AtbZIP28 were isolated. Truncated forms of AtbZIP17 and AtbZIP28 lacking the C-terminal domain including TMD were examined as putative active forms. One of them, AtbZIP28ΔC, activated BiP1 and BiP3 promoters through the cis-elements P-UPRE and ERSE responsible for the ER stress response. Subsequently, a fusion protein of green fluorescent protein (GFP) and AtbZIP28 was expressed in Arabidopsis cultured cells. Under non-stress conditions, GFP fluorescence localization almost overlapped with an ER marker; however, tunicamycin and dithiothreitol treatment clearly increased GFP fluorescence in the nucleus suggesting that the N-terminal fragment of AtbZIP28 translocates to the nucleus in response to ER stress

Pore Structure and Fluoride Ion Adsorption Characteristics of Zr (IV) Surface-Immobilized Resin Prepared Using Polystyrene as a Porogen

Science.gov (United States)

Mizuki, Hidenobu; Ito, Yudai; Harada, Hisashi; Uezu, Kazuya

Zr(IV) surface-immobilized resins for removal of fluoride ion were prepared by surface template polymerization using polystyrene as a porogen. At polymerization, polystyrene was added in order to increase mesopores (2-50 nm) and macropore (>50 nm) with large macropores (around 300 nm) formed with internal aqueous phase of W⁄O emulsion. The pore structure of Zr(IV) surface-immobilized resins was evaluated by measuring specific surface area, pore volume, and pore size distribution with volumetric adsorption measurement instrument and mercury porosimeter. The adsorption isotherms were well fitted by Langmuir equation. The removal of fluoride was also carried out with column method. Zr(IV) surface-immobilized resins, using 10 g⁄L polystyrene in toluene at polymerization, possessed higher volume of not only mesopores and macropores but also large macropores. Furethermore, by adding the polystyrene with smaller molecular size, the pore volume of mesopores, macropores and large macropores was significantly increased, and the fluoride ion adsorption capacity and the column utilization also increased.

Early vertebrate origin and diversification of small transmembrane regulators of cellular ion transport.

Science.gov (United States)

Pirkmajer, Sergej; Kirchner, Henriette; Lundell, Leonidas S; Zelenin, Pavel V; Zierath, Juleen R; Makarova, Kira S; Wolf, Yuri I; Chibalin, Alexander V

2017-07-15

Small transmembrane proteins such as FXYDs, which interact with Na + ,K + -ATPase, and the micropeptides that interact with sarco/endoplasmic reticulum Ca 2+ -ATPase play fundamental roles in regulation of ion transport in vertebrates. Uncertain evolutionary origins and phylogenetic relationships among these regulators of ion transport have led to inconsistencies in their classification across vertebrate species, thus hampering comparative studies of their functions. We discovered the first FXYD homologue in sea lamprey, a basal jawless vertebrate, which suggests small transmembrane regulators of ion transport emerged early in the vertebrate lineage. We also identified 13 gene subfamilies of FXYDs and propose a revised, phylogeny-based FXYD classification that is consistent across vertebrate species. These findings provide an improved framework for investigating physiological and pathophysiological functions of small transmembrane regulators of ion transport. Small transmembrane proteins are important for regulation of cellular ion transport. The most prominent among these are members of the FXYD family (FXYD1-12), which regulate Na + ,K + -ATPase, and phospholamban, sarcolipin, myoregulin and DWORF, which regulate the sarco/endoplasmic reticulum Ca 2+ -ATPase (SERCA). FXYDs and regulators of SERCA are present in fishes, as well as terrestrial vertebrates; however, their evolutionary origins and phylogenetic relationships are obscure, thus hampering comparative physiological studies. Here we discovered that sea lamprey (Petromyzon marinus), a representative of extant jawless vertebrates (Cyclostomata), expresses an FXYD homologue, which strongly suggests that FXYDs predate the emergence of fishes and other jawed vertebrates (Gnathostomata). Using a combination of sequence-based phylogenetic analysis and conservation of local chromosome context, we determined that FXYDs markedly diversified in the lineages leading to cartilaginous fishes (Chondrichthyes) and bony

Monte-Carlo simulation of crystallographical pore growth in III-V-semiconductors

International Nuclear Information System (INIS)

Leisner, Malte; Carstensen, Juergen; Foell, Helmut

2011-01-01

The growth of crystallographical pores in III-V-semiconductors can be understood in the framework of a simple model, which is based on the assumption that the branching of pores is proportional to the current density at the pore tips. The stochastic nature of this model allows its implementation into a three-dimensional Monte-Carlo-simulation of pore growth. The simulation is able to reproduce the experimentally observed crysto pore structures in III-V-semiconductors in full quantitative detail. The different branching probabilities for different semiconductors, as well as doping levels, can be deduced from the specific passivation behavior of the semiconductor-electrolyte-interface at the pore tips.

The effect of pore size on tissue ingrowth and neovascularization in porous bioceramics of controlled architecture in vivo

Energy Technology Data Exchange (ETDEWEB)

Bai Feng; Zhang Jinkang; Wang Zhen; Liu Jian; Meng Guolin; Dong Xin [Institute of Orthopedic Surgery, Xijing Hospital, Fourth Military Medical University, Xi' an 710032 (China); Lu Jianxi; Chang Jiang, E-mail: baifeng_fmmu@126.com [Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China)

2011-02-15

The purpose of this study was to investigate the role of pore size on tissue ingrowth and neovascularization in porous bioceramics under the accurate control of the pore parameters. For that purpose, {beta}-tricalcium phosphate ({beta}-TCP) cylinders with four different macropore sizes (300-400, 400-500, 500-600 and 600-700 {mu}m) but the same interconnection size (120 {mu}m) and unchangeable porosity were implanted into fascia lumbodorsalis in rabbits. The fibrous tissues and blood vessels formed in scaffolds were observed histologically and histomorphometrically. The vascularization of the porous bioceramics was analyzed by single-photon emission computed tomography (SPECT). It is found that pore size as an important parameter of a porous structure plays an important role in tissue infiltration into porous biomaterial scaffolds. The amount of fibrous tissue ingrowth increases with the decrease of the pore size. In four kinds of scaffolds with different macropore sizes (300-400, 400-500, 500-600 and 600-700 {mu}m) and a constant interconnection size of 120 {mu}m, the areas of fibrous tissue (%) were 60.5%, 52.2%, 41.3% and 37.3%, respectively, representing a significant decrease at 4 weeks (P < 0.01). The pore size of a scaffold is closely related to neovascularization of macroporous biomaterials implanted in vivo. A large pore size is beneficial for the growth of blood vessels, and the diameter of a pore smaller than 400 {mu}m limits the growth of blood vessels and results in a smaller blood vessel diameter.

Development of pore interconnectivity/morphology in porous silica films investigated by cyclic voltammetry and slow positron annihilation spectroscopy

International Nuclear Information System (INIS)

Tang, Xiuqin; Xiong, Bangyun; Li, Qichao; Mao, Wenfeng; Xiao, Wei; Fang, Pengfei; He, Chunqing

2015-01-01

Highlights: •Porous silica films were studied by cyclic voltammetry and positron annihilation. •Highly interconnected pores were formed in the film fabricated with more CTAB. •Aligned nanochannels were observed in the porous flim prepared with 25 wt.% CTAB. •I − and Ps diffusion in the films was governed by pore interconnectivity/morphology. •Cyclic voltammetry is feasible to explore pore interconnectivity/morphology. -- Abstract: Cyclic voltammetry and positronium (Ps) 3γ-annihilation spectroscopy were applied to investigate pore interconnectivity/morphology of porous silica films fabricated with various loading of cetyltrimethyl ammonium bromide (CTAB). With increasing the ratio of CTAB up to 15 wt.%, the total charge Q, resulted from I − diffusion across the silica films, increased remarkably, indicative of formation of highly interconnected pores in the films prepared with more porogen. However, it decreased dramatically with further loading CTAB of 25 wt.%. Interestingly, 3γ-annihilation fraction I 3γ due to a triplet-state Ps (ortho-positronium, o-Ps) emission from the silica films showed a similar behavior as a function of CTAB loading. The abnormal decrement in Q and I 3γ in the film fabricated with 25 wt.% CTAB was well explained by formation of long nanochannels aligning parallel to the film surface. The results indicated that the total charge Q and Ps 3γ-annihilation fraction were closely associated with I − and Ps diffusion governed by the pore interconnectivity/morphology of the silica films, which made cyclic voltammetry possible to be a feasible tool to characterize pore interconnectivity/morphology of porous thin films

Long-pore Electrostatics in Inward-rectifier Potassium Channels

Science.gov (United States)

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

2008-01-01

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

Impact of Pore-Scale Wettability on Rhizosphere Rewetting

Directory of Open Access Journals (Sweden)

Pascal Benard

2018-04-01

Full Text Available Vast amounts of water flow through a thin layer of soil around the roots, the rhizosphere, where high microbial activity takes place—an important hydrological and biological hotspot. The rhizosphere was shown to turn water repellent upon drying, which has been interpreted as the effect of mucilage secreted by roots. The effects of such rhizosphere water dynamics on plant and microbial activity are unclear. Furthermore, our understanding of the biophysical mechanisms controlling the rhizosphere water repellency remains largely speculative. Our hypothesis is that the key to describe the emergence of water repellency lies within the microscopic distribution of wettability on the pore-scale. At a critical mucilage content, a sufficient fraction of pores is blocked and the rhizosphere turns water repellent. Here we tested whether a percolation approach is capable to predict the flow behavior near the critical mucilage content. The wettability of glass beads and sand mixed with chia seed mucilage was quantified by measuring the infiltration rate of water drops. Drop infiltration was simulated using a simple pore-network model in which mucilage was distributed heterogeneously throughout the pore space with a preference for small pores. The model approach proved capable to capture the percolation nature of the process, the sudden transition from wettable to water repellent and the high variability in infiltration rates near the percolation threshold. Our study highlights the importance of pore-scale distribution of mucilage in the emergent flow behavior across the rhizosphere.

Software Image J to study soil pore distribution

Directory of Open Access Journals (Sweden)

Sabrina Passoni

2014-04-01

Full Text Available In the soil science, a direct method that allows the study of soil pore distribution is the bi-dimensional (2D digital image analysis. Such technique provides quantitative results of soil pore shape, number and size. The use of specific softwares for the treatment and processing of images allows a fast and efficient method to quantify the soil porous system. However, due to the high cost of commercial softwares, public ones can be an interesting alternative for soil structure analysis. The objective of this work was to evaluate the quality of data provided by the Image J software (public domain used to characterize the voids of two soils, characterized as Geric Ferralsol and Rhodic Ferralsol, from the southeast region of Brazil. The pore distribution analysis technique from impregnated soil blocks was utilized for this purpose. The 2D image acquisition was carried out by using a CCD camera coupled to a conventional optical microscope. After acquisition and treatment of images, they were processed and analyzed by the software Noesis Visilog 5.4® (chosen as the reference program and ImageJ. The parameters chosen to characterize the soil voids were: shape, number and pore size distribution. For both soils, the results obtained for the image total porosity (%, the total number of pores and the pore size distribution showed that the Image J is a suitable software to be applied in the characterization of the soil sample voids impregnated with resin.

MutHTP: Mutations in Human Transmembrane Proteins.

Science.gov (United States)

A, Kulandaisamy; S, Binny Priya; R, Sakthivel; Tarnovskaya, Svetlana; Bizin, Ilya; Hönigschmid, Peter; Frishman, Dmitrij; Gromiha, M Michael

2018-02-01

We have developed a novel database, MutHTP, which contains information on 183395 disease-associated and 17827 neutral mutations in human transmembrane proteins. For each mutation site MutHTP provides a description of its location with respect to the membrane protein topology, structural environment (if available) and functional features. Comprehensive visualization, search, display and download options are available. The database is publicly available at http://www.iitm.ac.in/bioinfo/MutHTP/. The website is implemented using HTML, PHP and javascript and supports recent versions of all major browsers, such as Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2018). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

The effect of scaffold pore size in cartilage tissue engineering.

Science.gov (United States)

Nava, Michele M; Draghi, Lorenza; Giordano, Carmen; Pietrabissa, Riccardo

2016-07-26

The effect of scaffold pore size and interconnectivity is undoubtedly a crucial factor for most tissue engineering applications. The aim of this study was to examine the effect of pore size and porosity on cartilage construct development in different scaffolds seeded with articular chondrocytes. We fabricated poly-L-lactide-co-trimethylene carbonate scaffolds with different pore sizes, using a solvent-casting/particulate-leaching technique. We seeded primary bovine articular chondrocytes on these scaffolds, cultured the constructs for 2 weeks and examined cell proliferation, viability and cell-specific production of cartilaginous extracellular matrix proteins, including GAG and collagen. Cell density significantly increased up to 50% with scaffold pore size and porosity, likely facilitated by cell spreading on the internal surface of bigger pores, and by increased mass transport of gases and nutrients to cells, and catabolite removal from cells, allowed by lower diffusion barriers in scaffolds with a higher porosity. However, both the cell metabolic activity and the synthesis of cartilaginous matrix proteins significantly decreased by up to 40% with pore size. We propose that the association of smaller pore diameters, causing 3-dimensional cell aggregation, to a lower oxygenation caused by a lower porosity, could have been the condition that increased the cell-specific synthesis of cartilaginous matrix proteins in the scaffold with the smallest pores and the lowest porosity among those tested. In the initial steps of in vitro cartilage engineering, the combination of small scaffold pores and low porosity is an effective strategy with regard to the promotion of chondrogenesis.

15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

Science.gov (United States)

Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

2005-04-01

This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

Evaporation of J13 and UZ pore waters at Yucca Mountain

International Nuclear Information System (INIS)

Rosenberg, N D; Gdowski, G E; Knauss, K G

2000-01-01

This work is motivated by a need to characterize the chemistry of aqueous films that might form at elevated temperatures on engineered components at the potential high-level, nuclear-waste repository at Yucca Mountain, Nevada. Such aqueous films might form through evaporation of water that seeps into the drifts, or by water vapor absorption by hydroscopic salts directly deposited on these components (possibly from previous evaporation events or possibly from air-blown particles drawn into the drifts through a drift ventilation system). There is no consensus at this time on the chemical composition of water that might come in contact with engineered components at Yucca Mountain. Two possibilities have received the most attention: well J13 water and pore waters from the unsaturated zone (UZ) above the repository horizon. These waters represent the two major types of natural waters at Yucca Mountain. Well J13 water is a dilute Na-HCO 3 -CO 3 water, representative of regional perched water and groundwater. The UZ pore waters are Ca-Cl-SO 4 -rich waters with a higher dissolved ion content. These waters are less well-characterized. We have studied the evaporative evolution of these two major types of waters through a series of open system laboratory experiments, with and without crushed repository-horizon tuff present, conducted at sub-boiling temperatures (75 C-85 C)

Kinetic models of controllable pore growth of anodic aluminum oxide membrane

Science.gov (United States)

Huang, Yan; Zeng, Hong-yan; Zhao, Ce; Qu, Ye-qing; Zhang, Pin

2012-06-01

An anodized Al2O3 (AAO) membrane with apertures about 72 nm in diameter was prepared by two-step anodic oxidation. The appearance and pore arrangement of the AAO membrane were characterized by energy dispersive x-ray spectroscopy and scanning electron microscopy. It was confirmed that the pores with high pore aspect ratio were parallel, well-ordered, and uniform. The kinetics of pores growth in the AAO membrane was derived, and the kinetic models showed that pores stopped developing when the pressure ( σ) trended to equal the surface tension at the end of anodic oxidation. During pore expansion, the effects of the oxalic acid concentration and expansion time on the pore size were investigated, and the kinetic behaviors were explained with two kinetic models derived in this study. They showed that the pore size increased with extended time ( r= G· t+ G'), but decreased with increased concentration ( r = - K·ln c- K') through the derived mathematic formula. Also, the values of G, G', K, and K' were derived from our experimental data.

Visualization of soil structure and pore structure modifications by pioneering ground beetles (Cicindelidae) in surface sediments of an artificial catchment

Science.gov (United States)

Badorreck, Annika; Gerke, Horst H.; Weller, Ulrich; Vontobel, Peter

2010-05-01

An artificial catchment was constructed to study initial soil and ecosystem development. As a key process, the pore structure dynamics in the soil at the surface strongly influences erosion, infiltration, matter dynamics, and vegetation establishment. Little is known, however, about the first macropore formation in the very early stage. This presentation focuses on observations of soil pore geometry and its effect on water flow at the surface comparing samples from three sites in the catchment and in an adjacent "younger" site composed of comparable sediments. The surface soil was sampled in cylindrical plastic rings (10 cm³) down to 2 cm depth in three replicates each site and six where caves from pioneering ground-dwelling beetles Cicindelidae were found. The samples were scanned with micro-X-ray computed tomography (at UFZ-Halle, Germany) with a resolution of 0.084 mm. The infiltration dynamics were visualized with neutronradiography (at Paul-Scherer-Institute, Switzerland) on slab-type soil samples in 2D. The micro-tomographies exhibit formation of surface sealing whose thickness and intensity vary with silt and clay content. The CT images show several coarser- and finer-textured micro-layers at the sample surfaces that were formed as a consequence of repeated washing in of finer particles in underlying coarser sediment. In micro-depressions, the uppermost layers consist of sorted fine sand and silt due to wind erosion. Similar as for desert pavements, a vesicular pore structure developed in these sediments on top, but also scattered in fine sand- and silt-enriched micro-layers. The ground-dwelling activity of Cicindelidae beetles greatly modifies the soil structure through forming caves in the first centimetres of the soil. Older collapsed caves, which form isolated pores within mixed zones, were also found. The infiltration rates were severely affected both, by surface crusts and activity of ground-dwelling beetles. The observations demonstrate relatively

Promiscuous Seven Transmembrane Receptors Sensing L-α-amino Acids

DEFF Research Database (Denmark)

Smajilovic, Sanela; Wellendorph, Petrine; Bräuner-Osborne, Hans

2014-01-01

A number of nutrient sensing seven trans-membrane (7TM) receptors have been identified and characterized over the past few years. While the sensing mechanisms to carbohydrates and free fatty acids are well understood, the molecular basis of amino acid sensing has recently come to the limelight....... The present review describes the current status of promiscuous L-α-amino acid sensors, the calcium sensing receptor (CaSR), the GPRC6A receptor, the T1R1/T1R3 receptor and also their molecular pharmacology, expression pattern and physiological significance....

Effect of Pore Size and Pore Connectivity on Unidirectional Capillary Penetration Kinetics in 3-D Porous Media using Direct Numerical Simulation

Science.gov (United States)

Fu, An; Palakurthi, Nikhil; Konangi, Santosh; Comer, Ken; Jog, Milind

2017-11-01

The physics of capillary flow is used widely in multiple fields. Lucas-Washburn equation is developed by using a single pore-sized capillary tube with continuous pore connection. Although this equation has been extended to describe the penetration kinetics into porous medium, multiple studies have indicated L-W does not accurately predict flow patterns in real porous media. In this study, the penetration kinetics including the effect of pore size and pore connectivity will be closely examined since they are expected to be the key factors effecting the penetration process. The Liquid wicking process is studied from a converging and diverging capillary tube to the complex virtual 3-D porous structures with Direct Numerical Simulation (DNS) using the Volume-Of-Fluid (VOF) method within the OpenFOAM CFD Solver. Additionally Porous Medium properties such as Permeability (k) , Tortuosity (τ) will be also analyzed.

Characteristics of Pore Structure and Fractal Dimension of Isometamorphic Anthracite

Directory of Open Access Journals (Sweden)

Di Gao

2017-11-01

Full Text Available The geologic conditions of No. 3 coal seams are similar to Sihe and Zhaozhuang Collieries, however, the gas production is significantly different. To better understand the effect of pores, by means of experimental measurements and quantitative analysis, the pore properties of high-rank isometamorphic anthracite were thoroughly studied. Our study showed that the pore structures were predominantly adsorptive, accounting for more than 88% of the specific surface area. The coal pores showed typical three-stage fractal characteristics at boundary points of 1 nm and 9 nm (7 nm of coal samples from Zhaozhuang Colliery, and the fractal dimension with 1–9 nm (or 1–7 nm, as being significantly larger than those measured outside the given ranges. Pores in samples from Sihe Colliery were mainly open spherical or ellipsoidal pores in shape; conversely, those from Zhaozhuang Colliery were mainly Y-shaped, V-shaped, or ‘ink-bottle’ type.

Diffusion in the pore water of compacted crushed salt

Energy Technology Data Exchange (ETDEWEB)

Fluegge, Judith; Herr, Sebastian; Lauke, Thomas; Meleshyn, Artur; Miehe, Ruediger; Ruebel, Andre

2016-07-15

Diffusion of dissolved radionuclides in the pore water of compacted crushed salt in the long-term is the most relevant process for the release of radionuclides from a dedicated repository for high-level waste in a salt formation as has been shown in latest safety assessments and research projects /BUH 16/. So far, diffusion coefficients for free water have been applied for the diffusion in pore water in models for long-term safety assessments. This conservative assumption was used, because data on the diffusion coefficient of dissolved substances in crushed salt have been missing. Furthermore, the diffusion coefficient in the pore water was assumed to be constant and independent from the degree of compaction of the crushed salt. The work presented in this report was intended to contribute to fill this gap of knowledge about how the diffusion of radionuclides takes place in the compacted backfill of a repository in salt. For the first time, the pore diffusion coefficient as well as its dependence on the porosity of the crushed salt was determined experimentally by means of through-diffusion experiments using caesium as tracer. The results achieved in this project suggest that the diffusion in compacted crushed salt is not fully comparable to that in a homogeneous, temporally stable porous medium like sand or clay. The results obtained from four diffusion experiments show a remarkably different behaviour and all yield unique concentration versus time plots which includes highly temporal variable tracer fluxes with even full interruptions of the flux for longer periods of time. This effect cannot be explained by assuming a tracer transport by diffusion in a temporarily invariant pore space and / or under temporally invariant experimental conditions. From our point of view, a restructuring of the pore space seems to lead to closed areas of pore water in the sample which may open up again after some time, leading to a variable pore space and hence variable diffusive

Hexadecane trapped in nano-pores of silica-aerogel

International Nuclear Information System (INIS)

Slavikova, B.; Jesenak, K.; Iskrova, M.; Majernik, V.; Sausa, O.; Kristiak, J.

2009-01-01

Ways of filling of the high-porous silica-aerogel with hydrocarbon C 16 H 34 and its efficient removal from the pores by physical method of the Positron Annihilation Spectroscopy were studied. As the most effective way to fill the SiO 2 aerogel appears through the implementation of a liquid phase, while the most appropriate way of removing of hexadecane is firing at an elevated temperature. Molecular system of hexadecane closed in nano-pores of silica-aerogel behaves otherwise than volume system of the same molecules. In the case of pure hexadecane phase transition was observed at 291 K, while solidification process is gradual with decrease of temperature in cetane trapped in pores of silica-aerogel. The results of the periods of life of o-Ps indicate greater turbidity in the pores of the molecular system compared to the volume sample of hexadecane.

Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation

KAUST Repository

Yu, H.

2016-09-14

Membranes with a hierarchical porous structure could be manufactured from a block copolymer blend by pure solvent evaporation. Uniform pores in a 30 nm thin skin layer supported by a macroporous structure were formed. This new process is attractive for membrane production because of its simplicity and the lack of liquid waste.

Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation

KAUST Repository

Yu, H.; Qiu, Xiaoyan; Behzad, Ali Reza; Musteata, Valentina-Elena; Smilgies, D.-M.; Nunes, Suzana Pereira; Peinemann, Klaus-Viktor

2016-01-01

Membranes with a hierarchical porous structure could be manufactured from a block copolymer blend by pure solvent evaporation. Uniform pores in a 30 nm thin skin layer supported by a macroporous structure were formed. This new process is attractive for membrane production because of its simplicity and the lack of liquid waste.

Nuclear pores and perinuclear expression sites of var and ribosomal DNA genes correspond to physically distinct regions in Plasmodium falciparum.

Science.gov (United States)

Guizetti, Julien; Martins, Rafael Miyazawa; Guadagnini, Stéphanie; Claes, Aurélie; Scherf, Artur

2013-05-01

The human malaria parasite Plasmodium falciparum modifies the erythrocyte it infects by exporting variant proteins to the host cell surface. The var gene family that codes for a large, variant adhesive surface protein called P. falciparum erythrocyte membrane protein 1 (PfEMP1) plays a particular role in this process, which is linked to pathogenesis and immune evasion. A single member of this gene family is highly transcribed while the other 59 members remain silenced. Importantly, var gene transcription occurs at a spatially restricted, but yet undefined, perinuclear site that is distinct from repressed var gene clusters. To advance our understanding of monoallelic expression, we investigated whether nuclear pores associate with the var gene expression site. To this end, we studied the nuclear pore organization during the asexual blood stage using a specific antibody directed against a subunit of the nuclear pore, P. falciparum Nup116 (PfNup116). Ring and schizont stage parasites showed highly polarized nuclear pore foci, whereas in trophozoite stage nuclear pores redistributed over the entire nuclear surface. Colocalization studies of var transcripts and anti-PfNup116 antibodies showed clear dissociation between nuclear pores and the var gene expression site in ring stage. Similar results were obtained for another differentially transcribed perinuclear gene family, the ribosomal DNA units. Furthermore, we show that in the poised state, the var gene locus is not physically linked to nuclear pores. Our results indicate that P. falciparum does form compartments of high transcriptional activity at the nuclear periphery which are, unlike the case in yeast, devoid of nuclear pores.

Position-Dependent Dynamics Explain Pore-Averaged Diffusion in Strongly Attractive Adsorptive Systems.

Science.gov (United States)

Krekelberg, William P; Siderius, Daniel W; Shen, Vincent K; Truskett, Thomas M; Errington, Jeffrey R

2017-12-12

Using molecular simulations, we investigate the relationship between the pore-averaged and position-dependent self-diffusivity of a fluid adsorbed in a strongly attractive pore as a function of loading. Previous work (Krekelberg, W. P.; Siderius, D. W.; Shen, V. K.; Truskett, T. M.; Errington, J. R. Connection between thermodynamics and dynamics of simple fluids in highly attractive pores. Langmuir 2013, 29, 14527-14535, doi: 10.1021/la4037327) established that pore-averaged self-diffusivity in the multilayer adsorption regime, where the fluid exhibits a dense film at the pore surface and a lower density interior pore region, is nearly constant as a function of loading. Here we show that this puzzling behavior can be understood in terms of how loading affects the fraction of particles that reside in the film and interior pore regions as well as their distinct dynamics. Specifically, the insensitivity of pore-averaged diffusivity to loading arises from the approximate cancellation of two factors: an increase in the fraction of particles in the higher diffusivity interior pore region with loading and a corresponding decrease in the particle diffusivity in that region. We also find that the position-dependent self-diffusivities scale with the position-dependent density. We present a model for predicting the pore-average self-diffusivity based on the position-dependent self-diffusivity, which captures the unusual characteristics of pore-averaged self-diffusivity in strongly attractive pores over several orders of magnitude.

Sebum output as a factor contributing to the size of facial pores.

Science.gov (United States)

Roh, M; Han, M; Kim, D; Chung, K

2006-11-01

Many endogenous and exogenous factors are known to cause enlarged pilosebaceous pores. Such factors include sex, genetic predisposition, ageing, chronic ultraviolet light exposure, comedogenic xenobiotics, acne and seborrhoea. This study was an attempt to determine the factors related to enlarged pores. To assess the relationship of sebum output, age, sex, hormonal factors and severity of acne with pore size. A prospective, randomized, controlled study was designed. A total of 60 volunteers, 30 males and 30 females, were recruited for this study. Magnified images of pores were taken using a dermoscopic video camera and measured using an image analysis program. The sebum output level was measured with a Sebumeter. Using multiple linear regression analysis, increased pore size was significantly associated with increased sebum output level, sex and age. Among the variables, sebum output level correlated most with the pore size followed by male sex. In comparing male and female participants, males had higher correlation between the sebum output level and the pore size (male: r = 0.47, female: r = 0.38). Thus, additional factors seem to influence pore size in females. Pore size was significantly increased during the ovulation phase (P = 0.008), but severity of acne was not significantly associated with the pore size. Enlarged pore sizes are associated with increased sebum output level, age and male sex. In female patients, additional hormonal factors, such as those of the menstrual cycle, affect the pore size.

Scanning electron microscope investigations of nuclear pore filters in polyester foils

International Nuclear Information System (INIS)

Hopfe, J.

1980-01-01

In order to understand and characterize the action of nuclear pore filters it is necessary to know their surface, as well as their bulk, structure. In the present work, investigations of the surface structure (pore size, pore density, pore distribution) and of the pore geometry, especially in the bulk of the filters, are carried out by scanning electron microscopic (SEM) studies. The preparation technique needed is liquid-nitrogen freeze-fracturing followed by a conductive-coating step. Nuclear pore filters studied in this paper were produced by a track etching technique. Laboratory specimens were obtained by bombarding 10 μm thick polyester foils with Xe-ions and a subsequent etching with 20% NaOH. The SEM results are shown and discussed. (author)

Interactions between charged residues in the transmembrane segments of the voltage-sensing domain in the hERG channel.

Science.gov (United States)

Zhang, M; Liu, J; Jiang, M; Wu, D-M; Sonawane, K; Guy, H R; Tseng, G-N

2005-10-01

Studies on voltage-gated K channels such as Shaker have shown that positive charges in the voltage-sensor (S4) can form salt bridges with negative charges in the surrounding transmembrane segments in a state-dependent manner, and different charge pairings can stabilize the channels in closed or open states. The goal of this study is to identify such charge interactions in the hERG channel. This knowledge can provide constraints on the spatial relationship among transmembrane segments in the channel's voltage-sensing domain, which are necessary for modeling its structure. We first study the effects of reversing S4's positive charges on channel activation. Reversing positive charges at the outer (K525D) and inner (K538D) ends of S4 markedly accelerates hERG activation, whereas reversing the 4 positive charges in between either has no effect or slows activation. We then use the 'mutant cycle analysis' to test whether D456 (outer end of S2) and D411 (inner end of S1) can pair with K525 and K538, respectively. Other positive charges predicted to be able, or unable, to interact with D456 or D411 are also included in the analysis. The results are consistent with predictions based on the distribution of these charged residues, and confirm that there is functional coupling between D456 and K525 and between D411 and K538.

Radial distribution of ions in pores with a surface charge

NARCIS (Netherlands)

Stegen, J.H.G. van der; Görtzen, J.; Kuipers, J.A.M.; Hogendoorn, J.A.; Versteeg, G.F.

2001-01-01

A sorption model applicable to calculate the radial equilibrium concentrations of ions in the pores of ion-selective membranes with a pore structure is developed. The model is called the radial uptake model. Because the model is applied to a Nafion sulfonic layer with very small pores and the radial

The human dopamine transporter forms a tetramer in the plasma membrane: cross-linking of a cysteine in the fourth transmembrane segment is sensitive to cocaine analogs.

Science.gov (United States)

Hastrup, Hanne; Sen, Namita; Javitch, Jonathan A

2003-11-14

Using cysteine cross-linking, we demonstrated previously that the dopamine transporter (DAT) is at least a homodimer, with the extracellular end of transmembrane segment (TM) 6 at a symmetrical dimer interface. We have now explored the possibility that DAT exists as a higher order oligomer in the plasma membrane. Cysteine cross-linking of wild type DAT resulted in bands on SDS-PAGE consistent with dimer, trimer, and tetramer, suggesting that DAT forms a tetramer in the plasma membrane. A cysteine-depleted DAT (CD-DAT) into which only Cys243 or Cys306 was reintroduced was cross-linked to dimer, suggesting that these endogenous cysteines in TM4 and TM6, respectively, were cross-linked at a symmetrical dimer interface. Reintroduction of both Cys243 and Cys306 into CD-DAT led to a pattern of cross-linking indistinguishable from that of wild type, with dimer, trimer, and tetramer bands. This indicated that the TM4 interface and the TM6 interface are distinct and further suggested that DAT may exist in the plasma membrane as a dimer of dimers, with two symmetrical homodimer interfaces. The cocaine analog MFZ 2-12 and other DAT inhibitors, including benztropine and mazindol, protected Cys243 against cross-linking. In contrast, two substrates of DAT, dopamine and tyramine, did not significantly impact cross-linking. We propose that the impairment of cross-linking produced by the inhibitors results from a conformational change at the TM4 interface, further demonstrating that these compounds are not neutral blockers but by themselves have effects on the structure of the transporter.

Effect drug loading process on dissolution mechanism of encapsulated amoxicillin trihydrate in hydrogel semi-IPN chitosan methyl cellulose with pore forming agent KHCO3 as a floating drug delivery system

Science.gov (United States)

Fithawati, Garnis; Budianto, Emil

2018-04-01

Common treatment for Helicobacter pylori by repeated oral consumption of amoxicillin trihydrate is not effective. Amoxicillin trihydrate has a very short residence time in stomach which leads into its ineffectiveness. Residence time of amoxicillin trihydrate can be improved by encapsulating amoxicillin trihydrate into a floating drug delivery system. In this study, amoxicillin trihydrate is encapsulated into hydrogel semi-IPN chitosan methyl cellulose matrix as a floating drug delivery system and then treated with 20% KHCO3 as pore forming agent. Drug loading process used are in-situ loading and post loading. In-situ loading process has higher efficiency percentage and dissolution percentage than post loading process. In-situ loading process resulted 100% efficiency with 92,70% dissolution percentage. Post loading process resulted 98,7% efficiency with 90,42% dissolution percentage. Mechanism of drug dissolution study by kinetics approach showed both in-situ loading process and post loading process are diffusion and degradation process (n=0,4913) and (n=0,4602) respectively. These results are supported by characterization data from optical microscope and scanning electron microscopy (SEM). Data from optical microscope showed both loading process resulted in coarser hydrogel surface. Characterization using SEM showed elongated pores in both loading process after dissolution test.

Generation and Nuclear Translocation of Sumoylated Transmembrane Fragment of Cell Adhesion Molecule L1

Science.gov (United States)

Lutz, David; Wolters-Eisfeld, Gerrit; Joshi, Gunjan; Djogo, Nevena; Jakovcevski, Igor; Schachner, Melitta; Kleene, Ralf

2012-01-01

The functions of the cell adhesion molecule L1 in the developing and adult nervous system are triggered by homophilic and heterophilic interactions that stimulate signal transductions that activate cellular responses. Here, we show that stimulation of signaling by function-triggering L1 antibodies or L1-Fc leads to serine protease-dependent cleavage of full-length L1 at the plasma membrane and generation of a sumoylated transmembrane 70-kDa fragment comprising the intracellular and transmembrane domains and part of the extracellular domain. The 70-kDa transmembrane fragment is transported from the plasma membrane to a late endosomal compartment, released from endosomal membranes into the cytoplasm, and transferred from there into the nucleus by a pathway that depends on importin and chromatin-modifying protein 1. Mutation of the sumoylation site at Lys1172 or of the nuclear localization signal at Lys1147 abolished L1-stimulated generation or nuclear import of the 70-kDa fragment, respectively. Nuclear import of the 70-kDa fragment may activate cellular responses in parallel or in association with phosphorylation-dependent signaling pathways. Alterations in the levels of the 70-kDa fragment during development and in the adult after spinal cord injury or in a mouse model of Alzheimer disease suggest that this fragment is functionally implicated in development, regeneration, neurodegeneration, tumorigenesis, and possibly synaptic plasticity in the mature nervous system. PMID:22431726

Phe783, Thr797, and Asp804 in transmembrane hairpin M5-M6 of Na+,K+-ATPase play a key role in ouabain binding.

Science.gov (United States)

Qiu, Li Yan; Koenderink, Jan B; Swarts, Herman G P; Willems, Peter H G M; De Pont, Jan Joep H H M

2003-11-21

Ouabain is a glycoside that binds to and inhibits the action of Na+,K+-ATPase. Little is known, however, about the specific requirements of the protein surface for glycoside binding. Using chimeras of gastric H+,K+-ATPase and Na+,K+-ATPase, we demonstrated previously that the combined presence of transmembrane hairpins M3-M4 and M5-M6 of Na+,K+-ATPase in a backbone of H+,K+-ATPase (HN34/56) is both required and sufficient for high affinity ouabain binding. Since replacement of transmembrane hairpin M3-M4 by the N terminus up to transmembrane segment 3 (HNN3/56) resulted in a low affinity ouabain binding, hairpin M5-M6 seems to be essential for ouabain binding. To assess which residues of M5-M6 are required for ouabain action, we divided this transmembrane hairpin in seven parts and individually replaced these parts by the corresponding sequences of H+,K+-ATPase in chimera HN34/56. Three of these chimeras failed to bind ouabain following expression in Xenopus laevis oocytes. Altogether, these three chimeras contained 7 amino acids that were specific for Na+,K+-ATPase. Individual replacement of these 7 amino acids by the corresponding amino acids in H+,K+-ATPase revealed a dramatic loss of ouabain binding for F783Y, T797C, and D804E. As a proof of principle, the Na+,K+-ATPase equivalents of these 3 amino acids were introduced in different combinations in chimera HN34. The presence of all 3 amino acids appeared to be required for ouabain action. Docking of ouabain onto a three-dimensional-model of Na+,K+-ATPase suggests that Asp804, in contrast to Phe783 and Thr797, does not actually form part of the ouabain-binding pocket. Most likely, the presence of this amino acid is required for adopting of the proper conformation for ouabain binding.

Study of pore pressure reaction on hydraulic fracturing

Science.gov (United States)

Trimonova, Mariia; Baryshnikov, Nikolay; Turuntaev, Sergey; Zenchenko, Evgeniy; Zenchenko, Petr

2017-04-01

We represent the results of the experimental study of the hydraulic fracture propagation influence on the fluid pore pressure. Initial pore pressure was induced by injection and production wells. The experiments were carried out according to scaling analysis based on the radial model of the fracture. All required geomechanical and hydrodynamical properties of a sample were derived from the scaling laws. So, gypsum was chosen as a sample material and vacuum oil as a fracturing fluid. The laboratory setup allows us to investigate the samples of cylindrical shape. It can be considered as an advantage in comparison with standard cubic samples, because we shouldn't consider the stress field inhomogeneity induced by the corners. Moreover, we can set 3D-loading by this setting. Also the sample diameter is big enough (43cm) for placing several wells: the fracturing well in the center and injection and production wells on two opposite sides of the central well. The experiment consisted of several stages: a) applying the horizontal pressure; b) applying the vertical pressure; c) water solution injection in the injection well with a constant pressure; d) the steady state obtaining; e) the oil injection in the central well with a constant rate. The pore pressure was recorded in the 15 points along bottom side of the sample during the whole experiment. We observe the pore pressure change during all the time of the experiment. First, the pore pressure changed due to water injection. Then we began to inject oil in the central well. We compared the obtained experimental data on the pore pressure changes with the solution of the 2D single-phase equation of pore-elasticity, and we found significant difference. The variation of the equation parameters couldn't help to resolve the discrepancy. After the experiment, we found that oil penetrated into the sample before and after the fracture initiation. This fact encouraged us to consider another physical process - the oil

Role of the synaptobrevin C terminus in fusion pore formation

DEFF Research Database (Denmark)

Ngatchou, Annita N; Kisler, Kassandra; Fang, Qinghua

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...... 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...

Extraction of pores from microtomographic reconstructions of intact soil aggregates

Energy Technology Data Exchange (ETDEWEB)

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.

Specificity of transmembrane protein palmitoylation in yeast.

Directory of Open Access Journals (Sweden)

Ayelén González Montoro

Full Text Available Many proteins are modified after their synthesis, by the addition of a lipid molecule to one or more cysteine residues, through a thioester bond. This modification is called S-acylation, and more commonly palmitoylation. This reaction is carried out by a family of enzymes, called palmitoyltransferases (PATs, characterized by the presence of a conserved 50- aminoacids domain called "Asp-His-His-Cys- Cysteine Rich Domain" (DHHC-CRD. There are 7 members of this family in the yeast Saccharomyces cerevisiae, and each of these proteins is thought to be responsible for the palmitoylation of a subset of substrates. Substrate specificity of PATs, however, is not yet fully understood. Several yeast PATs seem to have overlapping specificity, and it has been proposed that the machinery responsible for palmitoylating peripheral membrane proteins in mammalian cells, lacks specificity altogether.Here we investigate the specificity of transmembrane protein palmitoylation in S. cerevisiae, which is carried out predominantly by two PATs, Swf1 and Pfa4. We show that palmitoylation of transmembrane substrates requires dedicated PATs, since other yeast PATs are mostly unable to perform Swf1 or Pfa4 functions, even when overexpressed. Furthermore, we find that Swf1 is highly specific for its substrates, as it is unable to substitute for other PATs. To identify where Swf1 specificity lies, we carried out a bioinformatics survey to identify amino acids responsible for the determination of specificity or Specificity Determination Positions (SDPs and showed experimentally, that mutation of the two best SDP candidates, A145 and K148, results in complete and partial loss of function, respectively. These residues are located within the conserved catalytic DHHC domain suggesting that it could also be involved in the determination of specificity. Finally, we show that modifying the position of the cysteines in Tlg1, a Swf1 substrate, results in lack of palmitoylation, as

Superplastically foaming method to make closed pores inclusive porous ceramics

International Nuclear Information System (INIS)

Kishimoto, Akira; Hayashi, Hidetaka

2011-01-01

Porous ceramics incorporates pores to improve several properties including thermal insulation maintaining inherenet ceramic properties such as corrosion resistance and large mechanical strength. Conventional porous ceramics is usually fabricated through an insufficient sintering. Since the sintering accompanies the exclusion of pores, it must be terminated at the early stage to maintain the high porosity, leading to degraded strength and durability. Contrary to this, we have innovated superplastically foaming method to make ceramic foams only in the solid state. In this method, the previously inserted foam agent evaporates after the full densification of matrix at around the sintering temperature. Closed pores expand utilizing the superplastic deformation driven by the evolved gas pressure. The typical features of this superplastically foaming method are listed as follows, 1. The pores are introduced after sintering the solid polycrystal. 2. Only closed pores are introduced, improving the insulation of gas and sound in addition to heat. 3. The pore walls are fully densified expecting a large mechanical strength. 4. Compared with the melt foaming method, this method is practical because the fabrication temperature is far below the melting point and it does not need molds. 5. The size and the location pores can be controlled by the amount and position of the foam agent.

METHODS FOR PORE WATER EXTRACTION FROM UNSATURATED ZONE TUFF, YUCCA MOUNTAIN, NEVADA

International Nuclear Information System (INIS)

K.M. SCOFIELD

2006-01-01

Assessing the performance of the proposed high-level radioactive waste repository at Yucca Mountain, Nevada, requires an understanding of the chemistry of the water that moves through the host rock. The uniaxial compression method used to extract pore water from samples of tuffaceous borehole core was successful only for nonwelded tuff. An ultracentrifugation method was adopted to extract pore water from samples of the densely welded tuff of the proposed repository horizon. Tests were performed using both methods to determine the efficiency of pore water extraction and the potential effects on pore water chemistry. Test results indicate that uniaxial compression is most efficient for extracting pore water from nonwelded tuff, while ultracentrifugation is more successful in extracting pore water from densely welded tuff. Pore water splits taken from a single nonwelded tuff core during uniaxial compression tests have shown changes in pore water chemistry with increasing pressure for calcium, chloride, sulfate, and nitrate, while the chemistry of pore water splits from welded and nonwelded tuffs using ultracentrifugation indicates that there is no significant fractionation of solutes

Unstable Pore-Water Flow in Intertidal Wetlands

Science.gov (United States)

Barry, D. A.; Shen, C.; Li, L.

2014-12-01

Salt marshes are important intertidal wetlands strongly influenced by interactions between surface water and groundwater. Bordered by coastal water, the marsh system undergoes cycles of inundation and exposure driven by the tide. This leads to dynamic, complex pore-water flow and solute transport in the marsh soil. Pore-water circulations occur over vastly different spatial and temporal scales with strong link to the marsh topography. These circulations control solute transport between the marsh soil and the tidal creek, and ultimately affect the overall nutrient exchange between the marsh and coastal water. The pore-water flows also dictate the soil condition, particularly aeration, which influences the marsh plant growth. Numerous studies have been carried out to examine the pore-water flow process in the marsh soil driven by tides, focusing on stable flow with the assumption of homogeneity in soil and fluid properties. This assumption, however, is questionable given the actual inhomogeneous conditions in the field. For example, the salinity of surface water in the tidal creek varies temporally and spatially due to the influence of rainfall and evapotranspiration as well as the freshwater input from upland areas to the estuary, creating density gradients across the marsh surface and within the marsh soil. Many marshes possess soil stratigraphy with low-permeability mud typically overlying high-permeability sandy deposits. Macropores such as crab burrows are commonly distributed in salt marsh sediments. All these conditions are prone to the development of non-uniform, unstable preferential pore-water flow in the marsh soil, for example, funnelling and fingering. Here we present results from laboratory experiments and numerical simulations to explore such unstable flow. In particular, the analysis aims to address how the unstable flow modifies patterns of local pore-water movement and solute transport, as well as the overall exchange between the marsh soil and

Material science studies on the formation and growth of pores in the production and creep of single-crystal nickel-based superalloys; Werkstoffwissenschaftliche Untersuchungen zur Bildung und zum Wachstum von Poren bei der Herstellung und beim Kriechen einkristalliner Nickelbasis-Superlegierungen

Energy Technology Data Exchange (ETDEWEB)

Buck, Heinrich Joergen

2015-02-20

Single crystal Ni-base superalloys (SX) are used for blades in fossil fuel fired power plants and aero engines. Here they have to withstand high mechanical stresses at temperatures close to their melting point. The blades are manufactured by a Bridgman type of directional solidification, followed by a multiple step heat treatment. During the dendritic solidification, pores can form due to undissolved gas, macroshrinkage by inadequate gating and microshrinkage caused by poor feeding between dendrites. Additional pores can form in the interdendritic regions during the multiple step heat treatment which follows solidification. It is believed, that these pores form on the basis of a Kirkendall effect which accounts for the fast diffusion of Al atoms away from microstructural regions with non-equilibrium γ/γ' eutectic. During creep, pores can grow and change their shapes. It has been shown, that during creep in the high temperature / low stress regime new pores form, which are smaller than those pores that can be found in the undeformed material. In the present work, the evolution of porosity in the single crystal Ni-base superalloy ERBO/1 during processing and creep is investigated. Quantitative microstructural analyses were performed on metallographic cross sections. Sampling fields of 4500 x 1000 μm{sup 2} were investigated by using a combination of scanning electron microscopy with quantitative image analysis. Interrupted creep tests with a miniature tensile creep specimen were performed with load direction parallel to left angle 100 right angle and left angle 110 right angle direction, respectively. Pore parameters (area, perimeter, Feret's diameter) for individual pores were obtained and two form factors were introduced. The evolution of the compiled statistical distributions of pore parameters and shape factors are discussed. The results are compared to recent findings by Link et al., 2006 and Maelzer et al., 2007. In the present study it was shown

Pore-scale uncertainty quantification with multilevel Monte Carlo

KAUST Repository

Icardi, Matteo

2014-01-06

Computational fluid dynamics (CFD) simulations of pore-scale transport processes in porous media have recently gained large popularity. However the geometrical details of the pore structures can be known only in a very low number of samples and the detailed flow computations can be carried out only on a limited number of cases. The explicit introduction of randomness in the geometry and in other setup parameters can be crucial for the optimization of pore-scale investigations for random homogenization. Since there are no generic ways to parametrize the randomness in the porescale structures, Monte Carlo techniques are the most accessible to compute statistics. We propose a multilevel Monte Carlo (MLMC) technique to reduce the computational cost of estimating quantities of interest within a prescribed accuracy constraint. Random samples of pore geometries with a hierarchy of geometrical complexities and grid refinements, are synthetically generated and used to propagate the uncertainties in the flow simulations and compute statistics of macro-scale effective parameters.

Effects of Wood Pollution on Pore-Water Sulfide Levels and Eelgrass Germination

Science.gov (United States)

Ekelem, C.

2016-02-01

Historically, sawmills released wood waste onto coastal shorelines throughout the Pacific Northwest of the USA, enriching marine sediments with organic material. The increase in organic carbon boosts the bacterial reduction of sulfate and results in the production of a toxic metabolite, hydrogen sulfide. Hydrogen sulfide is a phytotoxin and can decrease the growth and survival of eelgrass. This is a critical issue since eelgrass, Zostera marina, forms habitat for many species, stabilizes sediment, and plays a role in nutrient cycling and sediment chemistry. The objective of our study was to determine the effects of wood debris on sediment pore-water hydrogen sulfide concentrations and eelgrass germination. To test the impact of wood inputs on sulfide production and seed germination, we conducted a laboratory mesocosm experiment, adding sawdust to marine sediments and measuring the sulfide levels weekly. We subsequently planted seeds in the mesocosms and measured germination rates. Higher concentrations of sawdust led to higher levels of pore-water hydrogen sulfide and drastically slower eelgrass germination rates. Treatments with greater than 10% wood enrichment developed free sulfide concentrations of 0.815 (± 0.427) mM after 118 days, suggesting sediments with greater than 10% wood pollution may have threateningly high pore-water hydrogen sulfide levels. These results can be used to set thresholds for remediation efforts and guide seed distribution in wood polluted areas.

Identification and validation of a linear protective neutralizing epitope in the β-pore domain of alpha toxin.

Science.gov (United States)

Oscherwitz, Jon; Cease, Kemp B

2015-01-01

The plethora of virulence factors associated with Staphylococcus aureus make this bacterium an attractive candidate for a molecularly-designed epitope-focused vaccine. This approach, which necessitates the identification of neutralizing epitopes for incorporation into a vaccine construct, is being evaluated for pathogens where conventional approaches have failed to elicit protective humoral responses, like HIV-1 and malaria, but may also hold promise for pathogens like S. aureus, where the elicitation of humoral immunity against multiple virulence factors may be required for development of an effective vaccine. Among the virulence factors employed by S. aureus, animal model and epidemiological data suggest that alpha toxin, a multimeric β-pore forming toxin like protective antigen from Bacillus anthracis, is particularly critical, yet no candidate neutralizing epitopes have been delineated in alpha toxin to date. We have previously shown that a linear determinant in the 2β2-2β3 loop of the pore forming domain of B. anthracis protective antigen is a linear neutralizing epitope. Antibody against this site is highly potent for neutralizing anthrax lethal toxin in vitro and for protection of rabbits in vivo from virulent B. anthracis. We hypothesized that sequences in the β-pore of S. aureus alpha toxin that share structural and functional homology to β-pore sequences in protective antigen would contain a similarly critical neutralizing epitope. Using an in vivo mapping strategy employing peptide immunogens, an optimized in vitro toxin neutralization assay, and an in vivo dermonecrosis model, we have now confirmed the presence of this epitope in alpha toxin, termed the pore neutralizing determinant. Antibody specific for this determinant neutralizes alpha toxin in vitro, and is highly effective for mitigating dermonecrosis and bacterial growth in a mouse model of S. aureus USA300 skin infection. The delineation of this linear neutralizing determinant in alpha

Identification and validation of a linear protective neutralizing epitope in the β-pore domain of alpha toxin.

Directory of Open Access Journals (Sweden)

Jon Oscherwitz

Full Text Available The plethora of virulence factors associated with Staphylococcus aureus make this bacterium an attractive candidate for a molecularly-designed epitope-focused vaccine. This approach, which necessitates the identification of neutralizing epitopes for incorporation into a vaccine construct, is being evaluated for pathogens where conventional approaches have failed to elicit protective humoral responses, like HIV-1 and malaria, but may also hold promise for pathogens like S. aureus, where the elicitation of humoral immunity against multiple virulence factors may be required for development of an effective vaccine. Among the virulence factors employed by S. aureus, animal model and epidemiological data suggest that alpha toxin, a multimeric β-pore forming toxin like protective antigen from Bacillus anthracis, is particularly critical, yet no candidate neutralizing epitopes have been delineated in alpha toxin to date. We have previously shown that a linear determinant in the 2β2-2β3 loop of the pore forming domain of B. anthracis protective antigen is a linear neutralizing epitope. Antibody against this site is highly potent for neutralizing anthrax lethal toxin in vitro and for protection of rabbits in vivo from virulent B. anthracis. We hypothesized that sequences in the β-pore of S. aureus alpha toxin that share structural and functional homology to β-pore sequences in protective antigen would contain a similarly critical neutralizing epitope. Using an in vivo mapping strategy employing peptide immunogens, an optimized in vitro toxin neutralization assay, and an in vivo dermonecrosis model, we have now confirmed the presence of this epitope in alpha toxin, termed the pore neutralizing determinant. Antibody specific for this determinant neutralizes alpha toxin in vitro, and is highly effective for mitigating dermonecrosis and bacterial growth in a mouse model of S. aureus USA300 skin infection. The delineation of this linear neutralizing

Nuclear Track-Etched Pore Membrane Production Using OAEP's Research Reactor

International Nuclear Information System (INIS)

Chittrakarn, Thawat; Bhongsuwan, Tripob; Wanichapichart, Pikul; Nuanuin, Paiboon; Chongkum, Somporn; Khonduangkaew, Areerat; Bordeepong, Sunaree

2003-10-01

Result of this study shows that the OAEP's nuclear research reactor is a good source of both fast and thermal neutrons for pore piercing process on polycarbonate thin film. With our experimental design, the fast neutron provides better results in pore piercing comparing with thermal neutron bombardment. This can be explained that most of the latent tracks that occur by thermal neutron bombardment do not piercing through the thin film. Chemical etching process using NaOH solution with an appropriated time, concentration and temperature was employed to enlarge the latent tracks in the bombarded film by fast neutrons. Fast neutron bombardment with 5, 10 and 20 minutes bombarding time successfully produces the nuclear track membrane. Pore size and pore density of the produced membranes examined by SEM were 0.24-1.01 μm and 4.67 - 245 x 10 6 pore/cm 2 , respectively. Bubble point test showed the maximum pore diameter of the produced membrane ranged between 1.18 - 3.25 μm. Water permeability was studied and compared between the produced and commercial membranes

Modeling and Simulating Asymmetrical Conductance Changes in Gramicidin Pores

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Xu Shixin

2014-01-01

Full Text Available Gramicidin A is a small and well characterized peptide that forms an ion channel in lipid membranes. An important feature of gramicidin A (gA pore is that its conductance is affected by the electric charges near the its entrance. This property has led to the application of gramicidin A as a biochemical sensor for monitoring and quantifying a number of chemical and enzymatic reactions. Here, a mathematical model of conductance changes of gramicidin A pores in response to the presence of electrical charges near its entrance, either on membrane surface or attached to gramicidin A itself, is presented. In this numerical simulation, a two dimensional computational domain is set to mimic the structure of a gramicidin A channel in the bilayer surrounded by electrolyte. The transport of ions through the channel is modeled by the Poisson-Nernst-Planck (PNP equations that are solved by Finite Element Method (FEM. Preliminary numerical simulations of this mathematical model are in qualitative agreement with the experimental results in the literature. In addition to the model and simulations, we also present the analysis of the stability of the solution to the boundary conditions and the convergence of FEM method for the two dimensional PNP equations in our model.

NTAL (non-T cell activation linker):a transmembrane adaptor protein involved in immunoreceptor signaling

Czech Academy of Sciences Publication Activity Database

Brdička, Tomáš; Imrich, Martin; Angelisová, Pavla; Brdičková, Naděžda; Horváth, Ondřej; Špička, Jiří; Hilgert, Ivan; Lusková, Petra; Dráber, Petr; Novák, P.; Engels, N.; Wienands, J.; Simeoni, L.; Osterreicher, J.; Aguado, E.; Malissen, M.; Schraven, B.; Hořejší, Václav

2002-01-01

Roč. 196, č. 12 (2002), s. 16180-16185 ISSN 0022-1007 R&D Projects: GA MŠk LN00A026 Keywords : NTAL * transmembrane adaptor * immunoreceptor signaling Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 15.838, year: 2002

Comparative characteristic of transmembrane currents and caffeine-induced responses of intact and irradiated small intestine smooth muscle cells

International Nuclear Information System (INIS)

Stepanov, Yu.V.; Gordienko, D.V.; Preobrazhenskaya, T.D.; Stepanova, L.I.; Vojtsitskij, V.M.

1994-01-01

A comparative investigation of transmembrane ion currents and caffeine-induced responses of single smooth muscle cells isolated from the circular layer of rat small intestine was curried out by the method of 'patch-clamp'. No reliable difference in potential-dependent and amplitude-kinetic characteristics of transmembrane ion currents in cells of intact and irradiated with dose of 3 Gy rats was revealed. In cells of irradiated animals external application of caffeine (4 mM) was not accompanied by strong quick-inactivated transient Ca 2+ -dependent potassium current as in control

When a transmembrane channel isn't, or how biophysics and biochemistry (mis)communicate.

Science.gov (United States)

Reviakine, Ilya

2018-02-12

Annexins are a family of soluble proteins that bind to acidic phospholipids such as phosphatidylserine in a calcium-dependent manner. The archetypical member of the annexin family is annexin A5. For many years, its function remained unknown despite the availability of a high-resolution structure. This, combined with the observations of specific ion conductance in annexin-bound membranes, fueled speculations about the possible membrane-spanning forms of annexins that functioned as ion channels. The channel hypothesis remained controversial and did not gather sufficient evidence to become accepted. Yet, it continues to draw attention as a framework for interpreting indirect (e.g., biochemical) data. The goal of the mini-review is to examine the data on annexin-lipid interactions from the last ~30 years from the point of view of the controversy between the two lines of inquiry: the well-characterized peripheral assembly of the annexins at membranes vs. their putative transmembrane insertion. In particular, the potential role of lipid rearrangements induced by annexin binding is highlighted. Copyright © 2018 Elsevier B.V. All rights reserved.

Transmembrane carbonic anhydrase isozymes IX and XII in the female mouse reproductive organs

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Tomas Eija

2004-10-01

Full Text Available Abstract Background Carbonic anhydrase (CA classically catalyses the reversible hydration of dissolved CO2 to form bicarbonate ions and protons. The twelve active CA isozymes are thought to regulate a variety of cellular functions including several processes in the reproductive systems. Methods The present study was designed to investigate the expression of transmembrane CAs, CA IX and XII, in the mouse uterus, ovary and placenta. The expression of CA IX and XII was examined by immunoperoxidase staining method and western blotting. CA II and XIII served as positive controls since they are known to be present in the mouse reproductive tract. Results The data of our study indicated that CA XII is expressed in the mouse endometrium. Only very faint signal was observed in the corpus luteum of the ovary and the placenta remained mainly negative. CA IX showed weak reaction in the endometrial epithelium, while it was completely absent in the ovary and placenta. Conclusion The conservation of CA XII expression in both mouse and human endometrium suggests a role for this isozyme in reproductive physiology.

Controlled synthesis of ordered mesoporous TiO{sub 2}-supported on activated carbon and pore-pore synergistic photocatalytic performance

Energy Technology Data Exchange (ETDEWEB)

Liu, Chen; Li, Youji, E-mail: bcclyj@163.com; Xu, Peng; Li, Ming; Zeng, Mengxiong

2015-01-15

Ordered mesoporous titania/activated carbon (OMTAC) were prepared by the template technique with the aid of an ultrasonic method. To explore the relationship between the structure and properties of OMTAC, the ultrasonic-sol-gel technique was applied to synthesize titania dioxide/activated carbon (USTAC). The obtained material structure was characterized by X-ray diffraction (XRD), nitrogen adsorption – desorption, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), UV diffuse reflectance (DRS) and Photoluminescence (PL) emission spectra. OMTAC photocatalytic performance was evaluated by means of acid red B (ARB) degradation. The pore-pore synergistic amplification mechanism of photocatalysis was proposed and the effects of catalytic conditions on synergistic amplification were explored. The results show that compared to OMT, OMTAC has a small particle size, low electron-hole recombination rate and high surface areas, due to the hindering effect of activated carbon on crystalline grain growth and an ordered mesoporous structure of titania. OMTAC has higher catalytic activity than USTAC, OMT and P25, due to pore-pore synergistic amplification effect of photocatalysis. The OMT content is strongly affected OMTAC photocatalytic activity, and OMTAC-3 (loading 3 times of OMT on AC) has the highest photocatalytic activity due to high hydroxyl concentration, surface area and low electron-hole recombination rate. When ARB is degraded by OMTAC-3, the optimum catalytic conditions are a catalyst concentration of 1 g/L, an ARB concentration of 15 mg/L and a pH of 5. - Graphical abstract: We investigate the influence of mesoporous titania content upon the photocatalytic performance of OMTAC in acid red B degradation. - Highlights: • OMTAC were fabricated by a template technique with the aid of an ultrasonic method. • OMTAC show high photoactivity for acid red B (ARB) degradation. • OMTAC also show pore-pore synergistic photocatalytic

Investigating the effects of stress on the pore structures of nuclear grade graphites

Energy Technology Data Exchange (ETDEWEB)

Taylor, Joshua E.L., E-mail: joshua.taylor@postgrad.manchester.ac.uk; Hall, Graham N., E-mail: graham.n.hall@manchester.ac.uk; Mummery, Paul M., E-mail: paul.m.mummery@manchester.ac.uk

2016-03-15

Graphite is used as a moderating material and as a structural component in a number of current generation nuclear reactors. During reactor operation stresses develop in the graphite components, causing them to deform. It is important to understand how the microstructure of graphite affects the material's response to these stresses. A series of experiments were performed to investigate how the pore structures of Pile Grade A and Gilsocarbon graphites respond to loading stresses. A compression rig was used to simulate the build-up of operational stresses in graphite components, and a confocal laser microscope was used to study variation of a number of important pore properties. Values of elastic modulus and Poisson's ratio were calculated and compared to existing literature to confirm the validity of the experimental techniques. Mean pore areas were observed to decrease linearly with increasing applied load, mean pore eccentricity increased linearly, and a small amount of clockwise pore rotation was observed. The response to build-up of stresses was dependent on the orientation of the pores and basal planes and the shapes of the pores with respect to the loading axis. It was proposed that pore closure and pore reorientation were competing processes. Pore separation was quantified using ‘nearest neighbour’ and Voronoi techniques, and non-pore regions were found to shrink linearly with increasing applied load. - Highlights: • Effects of stress on pore structures of Gilsocarbon and PGA graphites were studied. • Application of a compressive load was used to generate stresses in graphite. • Inverse linear relationship between stress and pore area was observed. • Mean pore eccentricity increased, clockwise pore rotation observed. • Separation of pores quantified using Voronoi and ‘nearest-neighbour’ methods.

Obif, a Transmembrane Protein, Is Required for Bone Mineralization and Spermatogenesis in Mice.

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Koji Mizuhashi

Full Text Available Various kinds of transmembrane and secreted proteins play pivotal roles in development through cell-cell communication. We previously reported that Obif (Osteoblast induction factor, Tmem119, encoding a single transmembrane protein, is expressed in differentiating osteoblasts, and that Obif-/- mice exhibit significantly reduced bone volume in the femur. In the current study, we characterized the Obif protein and further investigated the biological phenotypes of a variety of tissues in Obif-/- mice.First, we found that O-glycosylation of the Obif protein occurs at serine residue 36 in the Obif extracellular domain. Next, we observed that Obif-/- mice exhibit bone dysplasia in association with significantly increased osteoid volume per osteoid surface (OV/OS and osteoid maturation time (Omt, and significantly decreased mineral apposition rate (MAR and bone formation rate per bone surface (BFR/BS. In addition, we observed that Obif-/- mice show a significant decrease in testis weight as well as in sperm number. By histological analysis, we found that Obif is expressed in spermatocytes and spermatids in the developing testis and that spermatogenesis is halted at the round spermatid stage in the Obif-/- testis that lacks sperm. However, the number of litters fathered by male mice was slightly reduced in Obif-/- mice compared with wild-type mice, although this was not statistically significant.Our results, taken together with previous observations, indicate that Obif is a type Ia transmembrane protein whose N-terminal region is O-glycosylated. In addition, we found that Obif is required for normal bone mineralization and late testicular differentiation in vivo. These findings suggest that Obif plays essential roles in the development of multiple tissues.

Obif, a Transmembrane Protein, Is Required for Bone Mineralization and Spermatogenesis in Mice.

Science.gov (United States)

Mizuhashi, Koji; Chaya, Taro; Kanamoto, Takashi; Omori, Yoshihiro; Furukawa, Takahisa

2015-01-01

Various kinds of transmembrane and secreted proteins play pivotal roles in development through cell-cell communication. We previously reported that Obif (Osteoblast induction factor, Tmem119), encoding a single transmembrane protein, is expressed in differentiating osteoblasts, and that Obif-/- mice exhibit significantly reduced bone volume in the femur. In the current study, we characterized the Obif protein and further investigated the biological phenotypes of a variety of tissues in Obif-/- mice. First, we found that O-glycosylation of the Obif protein occurs at serine residue 36 in the Obif extracellular domain. Next, we observed that Obif-/- mice exhibit bone dysplasia in association with significantly increased osteoid volume per osteoid surface (OV/OS) and osteoid maturation time (Omt), and significantly decreased mineral apposition rate (MAR) and bone formation rate per bone surface (BFR/BS). In addition, we observed that Obif-/- mice show a significant decrease in testis weight as well as in sperm number. By histological analysis, we found that Obif is expressed in spermatocytes and spermatids in the developing testis and that spermatogenesis is halted at the round spermatid stage in the Obif-/- testis that lacks sperm. However, the number of litters fathered by male mice was slightly reduced in Obif-/- mice compared with wild-type mice, although this was not statistically significant. Our results, taken together with previous observations, indicate that Obif is a type Ia transmembrane protein whose N-terminal region is O-glycosylated. In addition, we found that Obif is required for normal bone mineralization and late testicular differentiation in vivo. These findings suggest that Obif plays essential roles in the development of multiple tissues.

Effect of porosity and pore morphology on the low-frequency ...

Indian Academy of Sciences (India)

Effect of porosity and pore size distribution on the low-frequency dielectric response, in the range 0.01-100 kHz, in sintered ZrO2-8 mol% Y2O3 ceramic compacts have been investigated. Small-angle neutron scattering (SANS) technique has been employed to obtain the pore characteristics like pore size distribution, ...

Pore Structure and Fractal Characteristics of Niutitang Shale from China