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Sample records for transmembrane pore induced

  1. Transmembrane helical interactions in the CFTR channel pore.

    Directory of Open Access Journals (Sweden)

    Jhuma Das

    2017-06-01

    Full Text Available Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF. Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants. Several CFTR homology models have been developed using bacterial ABC transporters as templates but these have low sequence similarity to CFTR and are not ion channels. Here, we refine an earlier model in an outward (OWF and develop an inward (IWF facing model employing an integrated experimental-molecular dynamics simulation (200 ns approach. Our IWF structure agrees well with a recently solved cryo-EM structure of a CFTR IWF state. We utilize cysteine cross-linking to verify positions and orientations of residues within trans-membrane helices (TMHs of the OWF conformation and to reconstruct a physiologically relevant pore structure. Comparison of pore profiles of the two conformations reveal a radius sufficient to permit passage of hydrated Cl- ions in the OWF but not the IWF model. To identify structural determinants that distinguish the two conformations and possible rearrangements of TMHs within them responsible for channel gating, we perform cross-linking by bifunctional reagents of multiple predicted pairs of cysteines in TMH 6 and 12 and 6 and 9. To determine whether the effects of cross-linking on gating observed are the result of switching of the channel from open to close state, we also treat the same residue pairs with monofunctional reagents in separate experiments. Both types of reagents prevent ion currents indicating that pore blockage is primarily responsible.

  2. Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

    Science.gov (United States)

    Notman, Rebecca; Anwar, Jamshed; Briels, W J; Noro, Massimo G; den Otter, Wouter K

    2008-11-15

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening.

  3. Regulation of Exocytotic Fusion Pores by SNARE Protein Transmembrane Domains

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    Zhenyong Wu

    2017-10-01

    Full Text Available Calcium-triggered exocytotic release of neurotransmitters and hormones from neurons and neuroendocrine cells underlies neuronal communication, motor activity and endocrine functions. The core of the neuronal exocytotic machinery is composed of soluble N-ethyl maleimide sensitive factor attachment protein receptors (SNAREs. Formation of complexes between vesicle-attached v- and plasma-membrane anchored t-SNAREs in a highly regulated fashion brings the membranes into close apposition. Small, soluble proteins called Complexins (Cpx and calcium-sensing Synaptotagmins cooperate to block fusion at low resting calcium concentrations, but trigger release upon calcium increase. A growing body of evidence suggests that the transmembrane domains (TMDs of SNARE proteins play important roles in regulating the processes of fusion and release, but the mechanisms involved are only starting to be uncovered. Here we review recent evidence that SNARE TMDs exert influence by regulating the dynamics of the fusion pore, the initial aqueous connection between the vesicular lumen and the extracellular space. Even after the fusion pore is established, hormone release by neuroendocrine cells is tightly controlled, and the same may be true of neurotransmitter release by neurons. The dynamics of the fusion pore can regulate the kinetics of cargo release and the net amount released, and can determine the mode of vesicle recycling. Manipulations of SNARE TMDs were found to affect fusion pore properties profoundly, both during exocytosis and in biochemical reconstitutions. To explain these effects, TMD flexibility, and interactions among TMDs or between TMDs and lipids have been invoked. Exocytosis has provided the best setting in which to unravel the underlying mechanisms, being unique among membrane fusion reactions in that single fusion pores can be probed using high-resolution methods. An important role will likely be played by methods that can probe single fusion pores

  4. Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

    NARCIS (Netherlands)

    Notman, Rebecca; Anwar, Jamshed; Briels, Willem J.; Noro, Massimo G.; den Otter, Wouter K.

    2008-01-01

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO)

  5. Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

    OpenAIRE

    Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.

    2008-01-01

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel pha...

  6. 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.

  7. Functional Architecture of the Cytoplasmic Entrance to the Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel Pore.

    Science.gov (United States)

    El Hiani, Yassine; Linsdell, Paul

    2015-06-19

    As an ion channel, the cystic fibrosis transmembrane conductance regulator must form a continuous pathway for the movement of Cl(-) and other anions between the cytoplasm and the extracellular solution. Both the structure and the function of the membrane-spanning part of this pathway are well defined. In contrast, the structure of the pathway that connects the cytoplasm to the membrane-spanning regions is unknown, and functional roles for different parts of the protein forming this pathway have not been described. We used patch clamp recording and substituted cysteine accessibility mutagenesis to identify positively charged amino acid side chains that attract cytoplasmic Cl(-) ions to the inner mouth of the pore. Our results indicate that the side chains of Lys-190, Arg-248, Arg-303, Lys-370, Lys-1041, and Arg-1048, located in different intracellular loops of the protein, play important roles in the electrostatic attraction of Cl(-) ions. Mutation and covalent modification of these residues have charge-dependent effects on the rate of Cl(-) permeation, demonstrating their functional role in maximization of Cl(-) flux. Other nearby positively charged side chains were not involved in electrostatic interactions with Cl(-). The location of these Cl(-)-attractive residues suggests that cytoplasmic Cl(-) ions enter the pore via a lateral portal located between the cytoplasmic extensions to the fourth and sixth transmembrane helices; a secondary, functionally less relevant portal might exist between the extensions to the 10th and 12th transmembrane helices. These results define the cytoplasmic mouth of the pore and show how it attracts Cl(-) ions from the cytoplasm. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Vitamin A transport and the transmembrane pore in the cell-surface receptor for plasma retinol binding protein.

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    Ming Zhong

    Full Text Available Vitamin A and its derivatives (retinoids play diverse and crucial functions from embryogenesis to adulthood and are used as therapeutic agents in human medicine for eye and skin diseases, infections and cancer. Plasma retinol binding protein (RBP is the principal and specific vitamin A carrier in the blood and binds vitamin A at 1:1 ratio. STRA6 is the high-affinity membrane receptor for RBP and mediates cellular vitamin A uptake. STRA6 null mice have severely depleted vitamin A reserves for vision and consequently have vision loss, even under vitamin A sufficient conditions. STRA6 null humans have a wide range of severe pathological phenotypes in many organs including the eye, brain, heart and lung. Known membrane transport mechanisms involve transmembrane pores that regulate the transport of the substrate (e.g., the gating of ion channels. STRA6 represents a new type of membrane receptor. How this receptor interacts with its transport substrate vitamin A and the functions of its nine transmembrane domains are still completely unknown. These questions are critical to understanding the molecular basis of STRA6's activities and its regulation. We employ acute chemical modification to introduce chemical side chains to STRA6 in a site-specific manner. We found that modifications with specific chemicals at specific positions in or near the transmembrane domains of this receptor can almost completely suppress its vitamin A transport activity. These experiments provide the first evidence for the existence of a transmembrane pore, analogous to the pore of ion channels, for this new type of cell-surface receptor.

  9. Tension-induced vesicle fusion: pathways and pore dynamics

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2008-01-01

    and eventually opens a pore to complete the fusion process. In pathway II, at higher tension, a stalk is formed during the fusion process that is then transformed by transmembrane pore formation into a fusion pore. Whereas the latter pathway II resembles stalk pathways as observed in other simulation studies......, fusion pathway I, which does not involve any stalk formation, has not been described previously to the best of our knowledge. A statistical analysis of the various processes shows that fusion is the dominant pathway for releasing the tension of the vesicles. The functional dependence of the observed...

  10. A simulation of earthquake induced undrained pore pressure ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Plains, Kandla River and Gulf of Kachch, between .... We consider the role of induced pore pressure ... location of the Bhuj earthquake epicentre as estimated by US Geological Survey. .... war R 2001 Changes in Ocean; GIS @ development 5.

  11. Peptidoglycan-associated outer membrane protein Mep45 of rumen anaerobe Selenomonas ruminantium forms a non-specific diffusion pore via its C-terminal transmembrane domain.

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    Kojima, Seiji; Hayashi, Kanako; Tochigi, Saeko; Kusano, Tomonobu; Kaneko, Jun; Kamio, Yoshiyuki

    2016-10-01

    The major outer membrane protein Mep45 of Selenomonas ruminantium, an anaerobic Gram-negative bacterium, comprises two distinct domains: the N-terminal S-layer homologous (SLH) domain that protrudes into the periplasm and binds to peptidoglycan, and the remaining C-terminal transmembrane domain, whose function has been unknown. Here, we solubilized and purified Mep45 and characterized its function using proteoliposomes reconstituted with Mep45. We found that Mep45 forms a nonspecific diffusion channel via its C-terminal region. The channel was permeable to solutes smaller than a molecular weight of roughly 600, and the estimated pore radius was 0.58 nm. Truncation of the SLH domain did not affect the channel property. On the basis of the fact that Mep45 is the most abundant outer membrane protein in S. ruminantium, we conclude that Mep45 serves as a main pathway through which small solutes diffuse across the outer membrane of this bacterium.

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

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    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.

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

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    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

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

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    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.

  15. 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

  16. Ligand Modulation of the Epstein-Barr Virus-induced Seven-transmembrane Receptor EBI2

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Smethurst, Christopher; Holst, Peter Johannes

    2011-01-01

    The Epstein-Barr virus-induced receptor 2 (EBI2) is a constitutively active seven-transmembrane receptor, which was recently shown to orchestrate the positioning of B cells in the follicle. To date, no ligands, endogenously or synthetic, have been identified that modulate EBI2 activity. Here we...... with similar potency. Overexpression of EBI2 profoundly potentiated antibody-stimulated ex vivo proliferation of murine B cells compared with WT cells, whereas this was equivalently reduced for EBI2-deficient B cells. Inhibition of EBI2 constitutive activity suppressed the proliferation in all cases...

  17. Analysis of Light-Induced Transmembrane Ion Gradients and Membrane Potential in Photosystem I Proteoliposomes

    International Nuclear Information System (INIS)

    Pennisi, Cristian P.; Greenbaum, Elias; Yoshida, Ken

    2010-01-01

    Photosystem I (PSI) complexes can support a light-driven electrochemical gradient for protons, which is the driving force for energy-conserving reactions across biological membranes. In this work, a computational model that enables a quantitative description of the light-induced proton gradients across the membrane of PSI proteoliposomes is presented. Using a set of electrodiffusion equations, a compartmental model of a vesicle suspended in aqueous medium was studied. The light-mediated proton movement was modeled as a single proton pumping step with backpressure of the electric potential. The model fits determinations of pH obtained from PSI proteoliposomes illuminated in the presence of mediators of cyclic electron transport. The model also allows analysis of the proton gradients in relation to the transmembrane ion fluxes and electric potential. Sensitivity analysis enabled a determination of the parameters that have greater influence on steady-state levels and onset/decay rates of transmembrane pH and electric potential. This model could be used as a tool for optimizing PSI proteoliposomes for photo-electrochemical applications.

  18. Overexpression of transmembrane protein 168 in the mouse nucleus accumbens induces anxiety and sensorimotor gating deficit.

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    Kequan Fu

    Full Text Available Transmembrane protein 168 (TMEM168 comprises 697 amino acid residues, including some putative transmembrane domains. It is reported that TMEM168 controls methamphetamine (METH dependence in the nucleus accumbens (NAc of mice. Moreover, a strong link between METH dependence-induced adaptive changes in the brain and mood disorders has been evaluated. In the present study, we investigated the effects of accumbal TMEM168 in a battery of behavioral paradigms. The adeno-associated virus (AAV Tmem168 vector was injected into the NAc of C57BL/6J mice (NAc-TMEM mice. Subsequently, the accumbal TMEM168 mRNA was increased approximately by seven-fold when compared with the NAc-Mock mice (controls. The NAc-TMEM mice reported no change in the locomotor activity, cognitive ability, social interaction, and depression-like behaviors; however, TMEM168 overexpression enhanced anxiety in the elevated-plus maze and light/dark box test. The increased anxiety was reversed by pretreatment with the antianxiety drug diazepam (0.3 mg/kg i.p.. Moreover, the NAc-TMEM mice exhibited decreased prepulse inhibition (PPI in the startle response test, and the induced schizophrenia-like behavior was reversed by pretreatment with the antipsychotic drug risperidone (0.01 mg/kg i.p.. Furthermore, accumbal TMEM168 overexpression decreased the basal levels of extracellular GABA in the NAc and the high K+ (100 mM-stimulated GABA elevation; however, the total contents of GABA in the NAc remained unaffected. These results suggest that the TMEM168-regulated GABAergic neuronal system in the NAc might become a novel target while studying the etiology of anxiety and sensorimotor gating deficits.

  19. Wave-induced stresses and pore pressures near a mudline

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    Andrzej Sawicki

    2008-12-01

    Full Text Available Conventional methods for the determination of water-wave induced stresses inseabeds composed of granular soils are based on Biot-type models, in which the soilskeleton is treated as an elastic medium. Such methods predict effective stressesin the soil that are unacceptable from the physical point of view, as they permittensile stresses to occur near the upper surface of the seabed. Therefore, in thispaper the granular soil is assumed to behave as an elastic-ideally plastic material,with the Coulomb-Mohr yield criterion adopted to bound admissible stress states inthe seabed. The governing equations are solved numerically by a~finite differencemethod. The results of simulations, carried out for the case of time-harmonicwater waves, illustrate the depth distributions of the excess pore pressures and theeffective stresses in the seabed, and show the shapes of zones of soil in the plastic state.~In particular, the effects on the seabed behaviour of suchparameters as the degree of pore water saturation, the soil permeability, and theearth pressure coefficient, are illustrated.

  20. 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

  1. 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.

  2. 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.

  3. 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.

    Science.gov (United States)

    Heidebrecht, Hans-Jürgen; Toro-Sierra, José; Kulozik, Ulrich

    2018-06-28

    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 (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.

  4. Fat storage-inducing transmembrane protein 2 is required for normal fat storage in adipose tissue.

    Science.gov (United States)

    Miranda, Diego A; Kim, Ji-Hyun; Nguyen, Long N; Cheng, Wang; Tan, Bryan C; Goh, Vera J; Tan, Jolene S Y; Yaligar, Jadegoud; Kn, Bhanu Prakash; Velan, S Sendhil; Wang, Hongyan; Silver, David L

    2014-04-04

    Triglycerides within the cytosol of cells are stored in a phylogenetically conserved organelle called the lipid droplet (LD). LDs can be formed at the endoplasmic reticulum, but mechanisms that regulate the formation of LDs are incompletely understood. Adipose tissue has a high capacity to form lipid droplets and store triglycerides. Fat storage-inducing transmembrane protein 2 (FITM2/FIT2) is highly expressed in adipocytes, and data indicate that FIT2 has an important role in the formation of LDs in cells, but whether FIT2 has a physiological role in triglyceride storage in adipose tissue remains unproven. Here we show that adipose-specific deficiency of FIT2 (AF2KO) in mice results in progressive lipodystrophy of white adipose depots and metabolic dysfunction. In contrast, interscapular brown adipose tissue of AF2KO mice accumulated few but large LDs without changes in cellular triglyceride levels. High fat feeding of AF2KO mice or AF2KO mice on the genetically obese ob/ob background accelerated the onset of lipodystrophy. At the cellular level, primary adipocyte precursors of white and brown adipose tissue differentiated in vitro produced fewer but larger LDs without changes in total cellular triglyceride or triglyceride biosynthesis. These data support the conclusion that FIT2 plays an essential, physiological role in fat storage in vivo.

  5. 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.

  6. Human Cytomegalovirus Exploits Interferon-Induced Transmembrane Proteins To Facilitate Morphogenesis of the Virion Assembly Compartment

    Science.gov (United States)

    Xie, Maorong; Xuan, Baoqin; Shan, Jiaoyu; Pan, Deng; Sun, Yamei; Shan, Zhao; Zhang, Jinping; Yu, Dong

    2014-01-01

    ABSTRACT Recently, interferon-induced transmembrane proteins (IFITMs) have been identified to be key effector molecules in the host type I interferon defense system. The invasion of host cells by a large range of RNA viruses is inhibited by IFITMs during the entry step. However, the roles of IFITMs in DNA virus infections have not been studied in detail. In this study, we report that human cytomegalovirus (HCMV), a large human DNA virus, exploits IFITMs to facilitate the formation of the virion assembly compartment (vAC) during infection of human fibroblasts. We found that IFITMs were expressed constitutively in human embryonic lung fibroblasts (MRC5 cells). HCMV infection inhibited IFITM protein accumulation in the later stages of infection. Overexpression of an IFITM protein in MRC5 cells slightly enhanced HCMV production and knockdown of IFITMs by RNA interference reduced the virus titer by about 100-fold on day 8 postinfection, according to the findings of a virus yield assay at a low multiplicity of infection. Virus gene expression and DNA synthesis were not affected, but the typical round structure of the vAC was not formed after the suppression of IFITMs, thereby resulting in defective virion assembly and the production of less infectious virion particles. Interestingly, the replication of herpes simplex virus, a human herpesvirus that is closely related to HCMV, was not affected by the suppression of IFITMs in MRC5 cells. These results indicate that IFITMs are involved in a specific pathway required for HCMV replication. IMPORTANCE HCMV is known to repurpose the interferon-stimulated genes (ISGs) viperin and tetherin to facilitate its replication. Our results expand the range of ISGs that can be exploited by HCMV for its replication. This is also the first report of a proviral function of IFITMs in DNA virus replication. In addition, whereas previous studies showed that IFITMs modulate virus entry, which is a very early stage in the virus life cycle, we

  7. The nectin-1α transmembrane domain, but not the cytoplasmic tail, influences cell fusion induced by HSV-1 glycoproteins

    International Nuclear Information System (INIS)

    Subramanian, Ravi P.; Dunn, Jennifer E.; Geraghty, Robert J.

    2005-01-01

    Nectin-1 is a receptor for herpes simplex virus (HSV), a member of the immunoglobulin superfamily, and a cellular adhesion molecule. To study domains of nectin-1α involved in cell fusion, we measured the ability of nectin-1α/nectin-2α chimeras, nectin-1α/CD4 chimeras, and transmembrane domain and cytoplasmic tail mutants of nectin-1α to promote cell fusion induced by HSV-1 glycoproteins. Our results demonstrate that only chimeras and mutants containing the entire V-like domain and a link to the plasma membrane conferred cell-fusion activity. The transmembrane domain and cytoplasmic tail of nectin-1 were not required for any viral receptor or cell adhesion function tested. Cellular cytoplasmic factors that bind to the nectin-1α cytoplasmic tail, therefore, did not influence virus entry or cell fusion. Interestingly, the efficiency of cell fusion was reduced when membrane-spanning domains of nectin-1α and gD were replaced by glycosylphosphatidylinositol tethers, indicating that transmembrane domains may play a modulatory role in the gD/nectin-1α interaction in fusion

  8. 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

  9. Polarization-induced local pore-wall functionalization for biosensing: from micropore to nanopore.

    Science.gov (United States)

    Liu, Jie; Pham, Pascale; Haguet, Vincent; Sauter-Starace, Fabien; Leroy, Loïc; Roget, André; Descamps, Emeline; Bouchet, Aurélie; Buhot, Arnaud; Mailley, Pascal; Livache, Thierry

    2012-04-03

    The use of biological-probe-modified solid-state pores in biosensing is currently hindered by difficulties in pore-wall functionalization. The surface to be functionalized is small and difficult to target and is usually chemically similar to the bulk membrane. Herein, we demonstrate the contactless electrofunctionalization (CLEF) approach and its mechanism. This technique enables the one-step local functionalization of the single pore wall fabricated in a silica-covered silicon membrane. CLEF is induced by polarization of the pore membrane in an electric field and requires a sandwich-like composition and a conducting or semiconducting core for the pore membrane. The defects in the silica layer of the micropore wall enable the creation of an electric pathway through the silica layer, which allows electrochemical reactions to take place locally on the pore wall. The pore diameter is not a limiting factor for local wall modification using CLEF. Nanopores with a diameter of 200 nm fabricated in a silicon membrane and covered with native silica layer have been successfully functionalized with this method, and localized pore-wall modification was obtained. Furthermore, through proof-of-concept experiments using ODN-modified nanopores, we show that functionalized nanopores are suitable for translocation-based biosensing.

  10. 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

    Science.gov (United States)

    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

  11. Temporal pore pressure induced stress changes during injection and depletion

    Science.gov (United States)

    Müller, Birgit; Heidbach, Oliver; Schilling, Frank; Fuchs, Karl; Röckel, Thomas

    2016-04-01

    Induced seismicity is observed during injection of fluids in oil, gas or geothermal wells as a rather immediate response close to the injection wells due to the often high-rate pressurization. It was recognized even earlier in connection with more moderate rate injection of fluid waste on a longer time frame but higher induced event magnitudes. Today, injection-related induced seismicity significantly increased the number of events with M>3 in the Mid U.S. However, induced seismicity is also observed during production of fluids and gas, even years after the onset of production. E.g. in the Groningen gas field production was required to be reduced due to the increase in felt and damaging seismicity after more than 50 years of exploitation of that field. Thus, injection and production induced seismicity can cause severe impact in terms of hazard but also on economic measures. In order to understand the different onset times of induced seismicity we built a generic model to quantify the role of poro-elasticity processes with special emphasis on the factors time, regional crustal stress conditions and fault parameters for three case studies (injection into a low permeable crystalline rock, hydrothermal circulation and production of fluids). With this approach we consider the spatial and temporal variation of reservoir stress paths, the "early" injection-related induced events during stimulation and the "late" production induced ones. Furthermore, in dependence of the undisturbed in situ stress field conditions the stress tensor can change significantly due to injection and long-term production with changes of the tectonic stress regime in which previously not critically stressed faults could turn to be optimally oriented for fault reactivation.

  12. Induced charge electrophoresis of a conducting cylinder in a nonconducting cylindrical pore and its micromotoring application

    Science.gov (United States)

    Feng, Huicheng; Wong, Teck Neng; Che, Zhizhao

    2016-08-01

    Induced charge electrophoresis of a conducting cylinder suspended in a nonconducting cylindrical pore is theoretically analyzed and a micromotor is proposed that utilizes the cylinder rotation. The cylinder velocities are analytically obtained in the Dirichlet and the Neumann boundary conditions of the electric field on the cylindrical pore. The results show that the cylinder not only translates but also rotates when it is eccentric with respect to the cylindrical pore. The influences of a number of parameters on the cylinder velocities are characterized in detail. The cylinder trajectories show that the cylinder approaches and becomes stationary at certain positions within the cylindrical pore. The proposed micromotor is capable of working under a heavy load with a high rotational velocity when the eccentricity is large and the applied electric field is strong.

  13. Oscillatory phase separation in giant lipid vesicles induced by transmembrane osmotic differentials

    Science.gov (United States)

    Oglęcka, Kamila; Rangamani, Padmini; Liedberg, Bo; Kraut, Rachel S; Parikh, Atul N

    2014-01-01

    Giant lipid vesicles are closed compartments consisting of semi-permeable shells, which isolate femto- to pico-liter quantities of aqueous core from the bulk. Although water permeates readily across vesicular walls, passive permeation of solutes is hindered. In this study, we show that, when subject to a hypotonic bath, giant vesicles consisting of phase separating lipid mixtures undergo osmotic relaxation exhibiting damped oscillations in phase behavior, which is synchronized with swell–burst lytic cycles: in the swelled state, osmotic pressure and elevated membrane tension due to the influx of water promote domain formation. During bursting, solute leakage through transient pores relaxes the pressure and tension, replacing the domain texture by a uniform one. This isothermal phase transition—resulting from a well-coordinated sequence of mechanochemical events—suggests a complex emergent behavior allowing synthetic vesicles produced from simple components, namely, water, osmolytes, and lipids to sense and regulate their micro-environment. DOI: http://dx.doi.org/10.7554/eLife.03695.001 PMID:25318069

  14. Postnatal Deletion of Fat Storage-inducing Transmembrane Protein 2 (FIT2/FITM2) Causes Lethal Enteropathy.

    Science.gov (United States)

    Goh, Vera J; Tan, Jolene S Y; Tan, Bryan C; Seow, Colin; Ong, Wei-Yi; Lim, Yen Ching; Sun, Lei; Ghosh, Sujoy; Silver, David L

    2015-10-16

    Lipid droplets (LDs) are phylogenetically conserved cytoplasmic organelles that store neutral lipids within a phospholipid monolayer. LDs compartmentalize lipids and may help to prevent cellular damage caused by their excess or bioactive forms. FIT2 is a ubiquitously expressed transmembrane endoplasmic reticulum (ER) membrane protein that has previously been implicated in LD formation in mammalian cells and tissue. Recent data indicate that FIT2 plays an essential role in fat storage in an in vivo constitutive adipose FIT2 knock-out mouse model, but the physiological effects of postnatal whole body FIT2 depletion have never been studied. Here, we show that tamoxifen-induced FIT2 deletion using a whole body ROSA26CreER(T2)-driven FIT2 knock-out (iF2KO) mouse model leads to lethal intestinal pathology, including villus blunting and death of intestinal crypts, and loss of lipid absorption. iF2KO mice lose weight and die within 2 weeks after the first tamoxifen dose. At the cellular level, LDs failed to form in iF2KO enterocytes after acute oil challenge and instead accumulated within the ER. Intestinal bile acid transporters were transcriptionally dysregulated in iF2KO mice, leading to the buildup of bile acids within enterocytes. These data support the conclusion that FIT2 plays an essential role in regulating intestinal health and survival postnatally. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. Characterization of the Respiration-Induced Yeast Mitochondrial Permeability Transition Pore

    OpenAIRE

    Bradshaw, Patrick C.; Pfeiffer, Douglas R.

    2013-01-01

    When isolated mitochondria from the yeast Saccharomyces cerevisiae oxidize respiratory substrates in the absence of phosphate and ADP, the yeast mitochondrial unselective channel, also called the yeast permeability transition pore (yPTP), opens in the inner membrane dissipating the electrochemical gradient. ATP also induces yPTP opening. yPTP opening allows mannitol transport into isolated mitochondria of laboratory yeast strains, but mannitol is not readily permeable throug...

  16. Excess pore water pressure induced in the foundation of a tailings dyke at Muskeg River Mine, Fort McMurray

    Energy Technology Data Exchange (ETDEWEB)

    Eshraghian, A.; Martens, S. [Klohn Crippen Berger Ltd., Calgary, AB (Canada)

    2010-07-01

    This paper discussed the effect of staged construction on the generation and dissipation of excess pore water pressure within the foundation clayey units of the External Tailings Facility dyke. Data were compiled from piezometers installed within the dyke foundation and used to estimate the dissipation parameters for the clayey units for a selected area of the foundation. Spatial and temporal variations in the pore water pressure generation parameters were explained. Understanding the process by which excess pore water pressure is generated and dissipates is critical to optimizing dyke design and performance. Piezometric data was shown to be useful in improving estimates of the construction-induced pore water pressure and dissipation rates within the clay layers in the foundation during dyke construction. In staged construction, a controlled rate of load application is used to increase foundation stability. Excess pore water pressure dissipates after each application, so the most critical stability condition happens after each load. Slow loading allows dissipation, whereas previous load pressure remains during fast loading. The dyke design must account for the rate of loading and the rate of pore pressure dissipation. Controlling the rate of loading and the rate of stress-induced excess pore water pressure generation is important to dyke stability during construction. Effective stress-strength parameters for the foundation require predictions of the pore water pressure induced during staged construction. It was found that both direct and indirect loading generates excess pore water pressure in the foundation clays. 2 refs., 2 tabs., 11 figs.

  17. 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.

  18. Fat storage-inducing transmembrane (FIT or FITM proteins are related to lipid phosphatase/phosphotransferase enzymes

    Directory of Open Access Journals (Sweden)

    Matthew J Hayes

    2017-12-01

    Full Text Available Fat storage-inducing transmembrane (FIT or FITM proteins have been implicated in the partitioning of triacylglycerol to lipid droplets and the budding of lipid droplets from the ER. At the molecular level, the sole relevant interaction is that FITMs directly bind to triacyglycerol and diacylglycerol, but how they function at the molecular level is not known. Saccharomyces cerevisiae has two FITM homologues: Scs3p and Yft2p. Scs3p was initially identified because deletion leads to inositol auxotrophy, with an unusual sensitivity to addition of choline. This strongly suggests a role for Scs3p in phospholipid biosynthesis. Looking at the FITM family as widely as possible, we found that FITMs are widespread throughout eukaryotes, indicating presence in the last eukaryotic common ancestor. Protein alignments also showed that FITM sequences contain the active site of lipid phosphatase/phosphotransferase (LPT enzymes. This large family transfers phosphate-containing headgroups either between lipids or in exchange for water. We confirmed the prediction that FITMs are related to LPTs by showing that single amino-acid substitutions in the presumptive catalytic site prevented their ability to rescue growth of the mutants on low inositol/high choline media when over-expressed. The substitutions also prevented rescue of other phenotypes associated with loss of FITM in yeast, including mistargeting of Opi1p, defective ER morphology, and aberrant lipid droplet budding. These results suggest that Scs3p, Yft2p and FITMs in general are LPT enzymes involved in an as yet unknown critical step in phospholipid metabolism.

  19. Nanofiltration Membranes with Narrow Pore Size Distribution via Contra-Diffusion-Induced Mussel-Inspired Chemistry.

    Science.gov (United States)

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

    2016-11-02

    Nanofiltration membranes (NFMs) are widely used in saline water desalination, wastewater treatment, and chemical product purification. However, conventional NFMs suffer from broad pore size distribution, which limits their applications for fine separation, especially in complete separation of molecules with slight differences in molecular size. Herein, defect-free composite NFMs with narrow pore size distribution are fabricated using a contra-diffusion method, with dopamine/polyethylenimine solution on the skin side and ammonium persulfate solution on the other side of the ultrafiltration substrate. Persulfate ions can diffuse through the ultrafiltration substrate into the other side and in situ trigger dopamine to form a codeposited coating with polyethylenimine. The codeposition is hindered on those sites completely covered by the polydopamine/polyethylenimine coating, although it is promoted at the defects or highly permeable regions because it is induced by the diffused persulfate ions. Such a "self-completion" process results in NFMs with highly uniform structures and narrow pore size distribution, as determined by their rejection of neutral solutes. These near electrically neutral NFMs show a high rejection of divalent ions with a low rejection of monovalent ions (MgCl 2 rejection = 96%, NaCl rejection = 23%), majorly based on a steric hindrance effect. The as-prepared NFMs can be applied in molecular separation such as isolating cellulose hydrogenation products.

  20. The Water-Induced Linear Reduction Gas Diffusivity Model Extended to Three Pore Regions

    DEFF Research Database (Denmark)

    Chamindu, T. K. K. Deepagoda; de Jonge, Lis Wollesen; Kawamoto, Ken

    2015-01-01

    . Characterization of soil functional pore structure is an essential prerequisite to understand key gas transport processes in variably saturated soils in relation to soil ecosystems, climate, and environmental services. In this study, the water-induced linear reduction (WLR) soil gas diffusivity model originally...... gas diffusivity from moist to dry conditions across differently structured porous media, including narrow soil size fractions, perforated plastic blocks, fractured limestone, peaty soils, aggregated volcanic ash soils, and particulate substrates for Earth- or space-based applications. The new Cip...

  1. What Can We Learn about Cholesterol's Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential?

    DEFF Research Database (Denmark)

    Falkovich, Stanislav G.; Martinez-Seara, Hector; Nesterenko, Alexey M.

    2016-01-01

    Cholesterol is abundant in the plasma membranes of animal cells and is known to regulate a variety of membrane properties. Despite decades of research, the transmembrane distribution of cholesterol is still a matter of debate. Here we consider this outstanding issue through atomistic simulations ...

  2. What Can We Learn about Cholesterol's Transmembrane Distribution Based on Cholesterol-Induced Changes in Membrane Dipole Potential?

    Czech Academy of Sciences Publication Activity Database

    Falkovich, S. G.; Martinez-Seara, Hector; Nesterenko, A. M.; Vattulainen, I.; Gurtovenko, A. A.

    2016-01-01

    Roč. 7, č. 22 (2016), s. 4585-4590 ISSN 1948-7185 Institutional support: RVO:61388963 Keywords : membrane * cholesterol * membrane asymmetry * membrane dipole potential * transmembrane distribution Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 9.353, year: 2016

  3. Resveratrol-Sensitized UVA Induced Apoptosis in Human Keratinocytes through Mitochondrial Oxidative Stress and Pore Opening

    Science.gov (United States)

    Boyer, Jean Z; Jandova, Jana; Janda, Jaroslav; Vleugels, Frank R; Elliott, David; Sligh, James E

    2012-01-01

    Resveratrol (3, 5, 4′-trihydroxy- trans- stilbene), a polyphenol compound, is derived from natural products such as the skin of red grapes, blueberries and cranberries. Resveratrol not only exhibits antioxidant, cardioprotection, and anti-aging properties, but can also inhibit cancer cell growth and induce apoptosis. It has been shown that resveratrol inhibits the activation of Nf-kB and subsequently down regulates the expression of Nf-kB regulated genes such as interleukin-2 and Bcl-2, leading to cell cycle arrest and increased apoptosis in multiple myeloma cells. In the skin, resveratrol has been reported to sensitize keratinocytes to UVA induced apoptosis. However, the effect of resveratrol on opening of the mitochondrial permeability transition pore has not been previously examined. Our data show that UVA (14J/cm2) along with resveratrol causes massive oxidative stress in mitochondria. As a consequence of oxidative stress, the mitochondrial membrane potential decreases which results in opening of the mitochondrial pores ultimately leading to apoptosis in human keratinocytes. These results may have clinical implications for development of future chemotherapeutic treatment for tumors of the skin. PMID:22673012

  4. Propofol and magnesium attenuate isoflurane-induced caspase-3 activation via inhibiting mitochondrial permeability transition pore

    Directory of Open Access Journals (Sweden)

    Zhang Yiying

    2012-08-01

    Full Text Available Abstract Background The inhalation anesthetic isoflurane has been shown to open the mitochondrial permeability transition pore (mPTP and induce caspase activation and apoptosis, which may lead to learning and memory impairment. Cyclosporine A, a blocker of mPTP opening might attenuate the isoflurane-induced mPTP opening, lessening its ripple effects. Magnesium and anesthetic propofol are also mPTP blockers. We therefore set out to determine whether propofol and magnesium can attenuate the isoflurane-induced caspase activation and mPTP opening. Methods We investigated the effects of magnesium sulfate (Mg2+, propofol, and isoflurane on the opening of mPTP and caspase activation in H4 human neuroglioma cells stably transfected to express full-length human amyloid precursor protein (APP (H4 APP cells and in six day-old wild-type mice, employing Western blot analysis and flowcytometry. Results Here we show that Mg2+ and propofol attenuated the isoflurane-induced caspase-3 activation in H4-APP cells and mouse brain tissue. Moreover, Mg2+ and propofol, the blockers of mPTP opening, mitigated the isoflurane-induced mPTP opening in the H4-APP cells. Conclusion These data illustrate that Mg2+ and propofol may ameliorate the isoflurane-induced neurotoxicity by inhibiting its mitochondrial dysfunction. Pending further studies, these findings may suggest the use of Mg2+ and propofol in preventing and treating anesthesia neurotoxicity.

  5. Adsorption-Induced Deformation of Hierarchically Structured Mesoporous Silica-Effect of Pore-Level Anisotropy.

    Science.gov (United States)

    Balzer, Christian; Waag, Anna M; Gehret, Stefan; Reichenauer, Gudrun; Putz, Florian; Hüsing, Nicola; Paris, Oskar; Bernstein, Noam; Gor, Gennady Y; Neimark, Alexander V

    2017-06-06

    The goal of this work is to understand adsorption-induced deformation of hierarchically structured porous silica exhibiting well-defined cylindrical mesopores. For this purpose, we performed an in situ dilatometry measurement on a calcined and sintered monolithic silica sample during the adsorption of N 2 at 77 K. To analyze the experimental data, we extended the adsorption stress model to account for the anisotropy of cylindrical mesopores, i.e., we explicitly derived the adsorption stress tensor components in the axial and radial direction of the pore. For quantitative predictions of stresses and strains, we applied the theoretical framework of Derjaguin, Broekhoff, and de Boer for adsorption in mesopores and two mechanical models of silica rods with axially aligned pore channels: an idealized cylindrical tube model, which can be described analytically, and an ordered hexagonal array of cylindrical mesopores, whose mechanical response to adsorption stress was evaluated by 3D finite element calculations. The adsorption-induced strains predicted by both mechanical models are in good quantitative agreement making the cylindrical tube the preferable model for adsorption-induced strains due to its simple analytical nature. The theoretical results are compared with the in situ dilatometry data on a hierarchically structured silica monolith composed by a network of mesoporous struts of MCM-41 type morphology. Analyzing the experimental adsorption and strain data with the proposed theoretical framework, we find the adsorption-induced deformation of the monolithic sample being reasonably described by a superposition of axial and radial strains calculated on the mesopore level. The structural and mechanical parameters obtained from the model are in good agreement with expectations from independent measurements and literature, respectively.

  6. Characterization of the respiration-induced yeast mitochondrial permeability transition pore.

    Science.gov (United States)

    Bradshaw, Patrick C; Pfeiffer, Douglas R

    2013-12-01

    When isolated mitochondria from the yeast Saccharomyces cerevisiae oxidize respiratory substrates in the absence of phosphate and ADP, the yeast mitochondrial unselective channel, also called the yeast permeability transition pore (yPTP), opens in the inner membrane, dissipating the electrochemical gradient. ATP also induces yPTP opening. yPTP opening allows mannitol transport into isolated mitochondria of laboratory yeast strains, but mannitol is not readily permeable through the yPTP in an industrial yeast strain, Yeast Foam. The presence of oligomycin, an inhibitor of ATP synthase, allowed for respiration-induced mannitol permeability in mitochondria from this strain. Potassium (K+) had varied effects on the respiration-induced yPTP, depending on the concentration of the respiratory substrate added. At low respiratory substrate concentrations K+ inhibited respiration-induced yPTP opening, while at high substrate concentrations this effect diminished. However, at the high respiratory substrate concentrations, the presence of K+ partially prevented phosphate inhibition of yPTP opening. Phosphate was found to inhibit respiration-induced yPTP opening by binding a site on the matrix space side of the inner membrane in addition to its known inhibitory effect of donating protons to the matrix space to prevent the pH change necessary for yPTP opening. The respiration-induced yPTP was also inhibited by NAD, Mg2+, NH4 + or the oxyanion vanadate polymerized to decavanadate. The results demonstrate similar effectors of the respiration-induced yPTP as those previously described for the ATP-induced yPTP and reconcile previous strain-dependent differences in yPTP solute selectivity. Copyright © 2013 John Wiley & Sons, Ltd.

  7. Mitochondrial permeability transition pore inhibitors prevent ethanol-induced neuronal death in mice.

    Science.gov (United States)

    Lamarche, Frederic; Carcenac, Carole; Gonthier, Brigitte; Cottet-Rousselle, Cecile; Chauvin, Christiane; Barret, Luc; Leverve, Xavier; Savasta, Marc; Fontaine, Eric

    2013-01-18

    Ethanol induces brain injury by a mechanism that remains partly unknown. Mitochondria play a key role in cell death processes, notably through the opening of the permeability transition pore (PTP). Here, we tested the effect of ethanol and PTP inhibitors on mitochondrial physiology and cell viability both in vitro and in vivo. Direct addition of ethanol up to 100 mM on isolated mouse brain mitochondria slightly decreased oxygen consumption but did not affect PTP regulation. In comparison, when isolated from ethanol-treated (two doses of 2 g/kg, 2 h apart) 7-day-old mouse pups, brain mitochondria displayed a transient decrease in oxygen consumption but no change in PTP regulation or H2O2 production. Conversely, exposure of primary cultured astrocytes and neurons to 20 mM ethanol for 3 days led to a transient PTP opening in astrocytes without affecting cell viability and to a permanent PTP opening in 10 to 20% neurons with the same percentage of cell death. Ethanol-treated mouse pups displayed a widespread caspase-3 activation in neurons but not in astrocytes and dramatic behavioral alterations. Interestingly, two different PTP inhibitors (namely, cyclosporin A and nortriptyline) prevented both ethanol-induced neuronal death in vivo and ethanol-induced behavioral modifications. We conclude that PTP opening is involved in ethanol-induced neurotoxicity in the mouse.

  8. Pore former induced porosity in LSM/CGO cathodes for electrochemical cells for flue gas purification

    DEFF Research Database (Denmark)

    Skovgaard, M.; Andersen, Kjeld Bøhm; Kammer Hansen, Kent

    2012-01-01

    In this study the effect of the characteristics of polymethyl methacrylate (PMMA) pore formers on the porosity, pore size distribution and the air flow through the prepared lanthanum strontium manganate/gadolinium-doped cerium oxide (LSM/CGO) cathodes was investigated. Porous cathodes were obtained...... and the highest porosity measured was 46.4% with an average pore diameter of 0.98 μm. The air flow through this cathode was measured to 5.8 ml/(min mm2). Also the effect of exposure time to the solvent was tested for the most promising PMMA pore former and it was found that the average pore diameter decreases...

  9. Loss of mitochondrial transmembrane potential and caspase-9 activation during apoptosis induced by the novel styryl-lactone goniothalamin in HL-60 leukemia cells.

    Science.gov (United States)

    Inayat-Hussain, S H; Annuar, B O; Din, L B; Ali, A M; Ross, D

    2003-08-01

    Styryl-lactones such as goniothalamin represent a new class of compounds with potential anti-cancer properties. In this study, we investigated the mechanisms of goniothalamin (GTN), a plant styryl-lactone induced apoptosis in human promyelocytic leukemia HL-60 cells. This plant extract resulted in apoptosis in HL-60 cells as assessed by the externalisation of phosphatidylserine. Using the mitochondrial membrane dye (DIOC(6)) in conjunction with flow cytometry, we found that GTN treated HL-60 cells demonstrated a loss of mitochondrial transmembrane potential (Deltapsi(m)). Further immunoblotting on these cells showed activation of initiator caspase-9 and the executioner caspases-3 and -7. Pretreatment with the pharmacological caspase inhibitor, benzyloxycarbonyl-Val-Ala-Asp fluoromethyl ketone (Z-VAD.FMK) abrogated apoptosis as assessed by all of the apoptotic features in this study. In summary, our results demonstrate that goniothalamin-induced apoptosis occurs via the mitochondrial pathway in a caspase dependent manner.

  10. Br2 induced oxidative pore modification of a porous coordination network.

    Science.gov (United States)

    Ohtsu, Hiroyoshi; Kawano, Masaki

    2016-01-14

    Iodinated pores of a Zn-based coordination network were modified by Br2 oxidation to produce brominated pores in a polycrystalline-to-polycrystalline manner while maintaining the same network topology. Ab initio X-ray powder diffraction analysis and Raman spectroscopy revealed that the brominated pore can trap Br2 or I2 by strong σ/π-type interactions. A kinetic study in solution revealed that the pore modification by Br2 oxidation is much faster than the Br2 encapsulation process.

  11. Decreased in vitro fertility in male rats exposed to fluoride-induced oxidative stress damage and mitochondrial transmembrane potential loss

    International Nuclear Information System (INIS)

    Izquierdo-Vega, Jeannett A.; Sanchez-Gutierrez, Manuel; Razo, Luz Maria del

    2008-01-01

    Fluorosis, caused by drinking water contamination with inorganic fluoride, is a public health problem in many areas around the world. The aim of the study was to evaluate the effect of environmentally relevant doses of fluoride on in vitro fertilization (IVF) capacity of spermatozoa, and its relationship to spermatozoa mitochondrial transmembrane potential (ΔΨ m ). Male Wistar rats were administered at 5 mg fluoride/kg body mass/24 h, or deionized water orally for 8 weeks. We evaluated several spermatozoa parameters in treated and untreated rats: i) standard quality analysis, ii) superoxide dismutase (SOD) activity, iii) the generation of superoxide anion (O 2 ·- ), iv) lipid peroxidation concentration, v) ultrastructural analyses of spermatozoa using transmission electron microscopy, vi) ΔΨ m , vii) acrosome reaction, and viii) IVF capability. Spermatozoa from fluoride-treated rats exhibited a significant decrease in SOD activity (∼ 33%), accompanied with a significant increase in the generation of O 2 · (∼ 40%), a significant decrease in ΔΨ m (∼ 33%), and a significant increase in lipid peroxidation concentration (∼ 50%), relative to spermatozoa from the control group. Consistent with this finding, spermatozoa from fluoride-treated rats exhibited altered plasmatic membrane. In addition, the percentage of fluoride-treated spermatozoa capable of undergoing the acrosome reaction was decreased relative to control spermatozoa (34 vs. 55%), while the percentage fluoride-treated spermatozoa capable of oocyte fertilization was also significantly lower than the control group (13 vs. 71%). These observations suggest that subchronic exposure to fluoride causes oxidative stress damage and loss of mitochondrial transmembrane potential, resulting in reduced fertility

  12. Outer capsid proteins induce the formation of pores in epithelial cells

    International Nuclear Information System (INIS)

    Ruiz, M; Abad M; Michelangely, F; Charpilienne, A; Cohen, J

    1995-01-01

    Two mechanisms of entrance in cell of the rotavirus, during the infection, were proposed: a direct entrance through the plasmatic membrane or by means of endocytosis. In the two cases, a permeabilization mechanism of the membrane (cellular or of the endocytic vesicle, respectively) should occur. It has been shown that the rotavirus induces permeabilization of liposomes and of membrane vesicles. In this work, are studied the changes of intact cells permeability, measuring the entrance of e tide bromides. Viral particles of double capsid of the RF stump produce an increase of the cells membrane MA104 permeability, while the simple capsid ones don't induce effect. This phenomenon requires the particles trypsinization, and occurs in a means where the concentration of free Ca is lower to 1 micromolar. The temporary course of the fluorescence increase is sigmoid. The latency, the speed and the width depend on the relationship of virus / cell, and it can be observed up to 100% of permeabilization in relation to the effect of digitonin. The pores induced in the membrane by the rotavirus are irreversible. The permeabilizer effect of the rotavirus on the membrane was observed in other cellular lines as Hela and HT29, but not in the L929 ones. These results suggest that one or more proteins of the external capsid are responsible s of the effect. These could be involved in the penetration process of the virus towards the cytoplasm and could be one of the restrictive factor of the cell infection by means of the virus [es

  13. Permeability changes induced by microfissure closure and opening in tectonized materials. Effect on slope pore pressure regime.

    Science.gov (United States)

    De la Fuente, Maria; Vaunat, Jean; Pedone, Giuseppe; Cotecchia, Federica; Sollecito, Francesca; Casini, Francesca

    2015-04-01

    Tectonized clays are complex materials characterized by several levels of structures that may evolve during load and wetting/drying processes. Some microstructural patterns, as microfissures, have a particular influence on the value of permeability which is one of the main factors controlling pore pressure regime in slopes. In this work, the pore pressure regime measured in a real slope of tectonized clay in Southern Italy is analyzed by a numerical model that considers changes in permeability induced by microfissure closure and opening during the wetting and drying processes resulting from climatic actions. Permeability model accounts for the changes in Pore Size Distribution observed by Microscopy Intrusion Porosimetry. MIP tests are performed on representative samples of ground in initial conditions ("in situ" conditions) and final conditions (deformed sample after applying a wetting path that aims to reproduce the saturation of the soil under heavy rains). The resulting measurements allow for the characterization at microstructural level of the soil, identifying the distribution of dominant families pores in the sample and its evolution under external actions. Moreover, comparison of pore size density functions allows defining a microstructural parameter that depends on void ratio and degree of saturation and controls the variation of permeability. Model has been implemented in a thermo-hydro-mechanical code provided with a special boundary condition for climatic actions. Tool is used to analyze pore pressure measurements obtained in the tectonized clay slope. Results are analyzed at the light of the effect that permeability changes during wetting and drying have on the pore pressure regime.

  14. Interferon-inducible transmembrane proteins of the innate immune response act as membrane organizers by influencing clathrin and v-ATPase localization and function.

    Science.gov (United States)

    Wee, Yin Shen; Roundy, Kirstin M; Weis, Janis J; Weis, John H

    2012-12-01

    The innate response interferon-inducible transmembrane (Ifitm) proteins have been characterized as influencing proliferation, signaling complexes and restricting virus infections. Treatment of cells lacking these proteins (IfitmDel) with IFN-β resulted in the loss of clathrin from membrane compartments and the inhibition of clathrin-mediated phagocytosis, suggesting a molecular interaction between clathrin and Ifitm proteins. The pH of endosomes of IfitmDel cells, with or without IFN activation, was neutralized, suggesting the function of the vacular ATPase proton pumps in such cells was compromised. Co-immunoprecipitation of Ifitm3 with Atp6v0b demonstrated a direct interaction between the Ifitm proteins and the v-ATPase. These data suggest that the Ifitm proteins help stabilize v-ATPase complexes in cellular membranes which, in turn, facilitates the appropriate subcellular localization of clathrin.

  15. Transmembrane potential of GlyCl-expressing instructor cells induces a neoplastic-like conversion of melanocytes via a serotonergic pathway

    Directory of Open Access Journals (Sweden)

    Douglas Blackiston

    2011-01-01

    Understanding the mechanisms that coordinate stem cell behavior within the host is a high priority for developmental biology, regenerative medicine and oncology. Endogenous ion currents and voltage gradients function alongside biochemical cues during pattern formation and tumor suppression, but it is not known whether bioelectrical signals are involved in the control of stem cell progeny in vivo. We studied Xenopus laevis neural crest, an embryonic stem cell population that gives rise to many cell types, including melanocytes, and contributes to the morphogenesis of the face, heart and other complex structures. To investigate how depolarization of transmembrane potential of cells in the neural crest’s environment influences its function in vivo, we manipulated the activity of the native glycine receptor chloride channel (GlyCl. Molecular-genetic depolarization of a sparse, widely distributed set of GlyCl-expressing cells non-cell-autonomously induces a neoplastic-like phenotype in melanocytes: they overproliferate, acquire an arborized cell shape and migrate inappropriately, colonizing numerous tissues in a metalloprotease-dependent fashion. A similar effect was observed in human melanocytes in culture. Depolarization of GlyCl-expressing cells induces these drastic changes in melanocyte behavior via a serotonin-transporter-dependent increase of extracellular serotonin (5-HT. These data reveal GlyCl as a molecular marker of a sparse and heretofore unknown cell population with the ability to specifically instruct neural crest derivatives, suggest transmembrane potential as a tractable signaling modality by which somatic cells can control stem cell behavior at considerable distance, identify a new biophysical aspect of the environment that confers a neoplastic-like phenotype upon stem cell progeny, reveal a pre-neural role for serotonin and its transporter, and suggest a novel strategy for manipulating stem cell behavior.

  16. Nucleation in mesoscopic systems under transient conditions: Peptide-induced pore formation in vesicles

    Science.gov (United States)

    Zhdanov, Vladimir P.; Höök, Fredrik

    2013-04-01

    Attachment of lytic peptides to the lipid membrane of virions or bacteria is often accompanied by their aggregation and pore formation, resulting eventually in membrane rupture and pathogen neutralization. The membrane rupture may occur gradually via formation of many pores or abruptly after the formation of the first pore. In academic studies, this process is observed during interaction of peptides with lipid vesicles. We present an analytical model and the corresponding Monte Carlo simulations focused on the pore formation in such situations. Specifically, we calculate the time of the first nucleation-limited pore-formation event and show the distribution of this time in the regime when the fluctuations of the number of peptides attached to a vesicle are appreciable. The results obtained are used to clarify the mechanism of the pore formation and membrane destabilization observed recently during interaction of highly active α-helical peptide with sub-100-nm lipid vesicles that mimic enveloped viruses with nanoscale membrane curvature. The model proposed and the analysis presented are generic and may be applicable to other meso- and nanosystems.

  17. Leptin-induced cardioprotection involves JAK/STAT signaling that may be linked to the mitochondrial permeability transition pore

    OpenAIRE

    Smith, Christopher C. T.; Dixon, Richard A.; Wynne, Abigail M.; Theodorou, Louise; Ong, Sang-Ging; Subrayan, Sapna; Davidson, Sean M.; Hausenloy, Derek J.; Yellon, Derek M.

    2010-01-01

    Leptin-induced protection against myocardial ischemia-reperfusion (I/R) injury involves the activation of the reperfusion injury salvage kinase pathway, incorporating phosphatidylinositol 3-kinase-Akt/protein kinase B and p44/42 MAPK, and the inhibition of the mitochondrial permeability transition pore (MPTP). Recently published data indicate that the JAK/STAT signaling pathway, which mediates the metabolic actions of leptin, also plays a pivotal role in cardioprotection. Consequently, in the...

  18. Galectin-3 Induces Clustering of CD147 and Integrin-β1 Transmembrane Glycoprotein Receptors on the RPE Cell Surface

    Science.gov (United States)

    Priglinger, Claudia S.; Szober, Christoph M.; Priglinger, Siegfried G.; Merl, Juliane; Euler, Kerstin N.; Kernt, Marcus; Gondi, Gabor; Behler, Jennifer; Geerlof, Arie; Kampik, Anselm; Ueffing, Marius; Hauck, Stefanie M.

    2013-01-01

    Proliferative vitreoretinopathy (PVR) is a blinding disease frequently occurring after retinal detachment surgery. Adhesion, migration and matrix remodeling of dedifferentiated retinal pigment epithelial (RPE) cells characterize the onset of the disease. Treatment options are still restrained and identification of factors responsible for the abnormal behavior of the RPE cells will facilitate the development of novel therapeutics. Galectin-3, a carbohydrate-binding protein, was previously found to inhibit attachment and spreading of retinal pigment epithelial cells, and thus bares the potential to counteract PVR-associated cellular events. However, the identities of the corresponding cell surface glycoprotein receptor proteins on RPE cells are not known. Here we characterize RPE-specific Gal-3 containing glycoprotein complexes using a proteomic approach. Integrin-β1, integrin-α3 and CD147/EMMPRIN, a transmembrane glycoprotein implicated in regulating matrix metalloproteinase induction, were identified as potential Gal-3 interactors on RPE cell surfaces. In reciprocal immunoprecipitation experiments we confirmed that Gal-3 associated with CD147 and integrin-β1, but not with integrin-α3. Additionally, association of Gal-3 with CD147 and integrin-β1 was observed in co-localization analyses, while integrin-α3 only partially co-localized with Gal-3. Blocking of CD147 and integrin-β1 on RPE cell surfaces inhibited binding of Gal-3, whereas blocking of integrin-α3 failed to do so, suggesting that integrin-α3 is rather an indirect interactor. Importantly, Gal-3 binding promoted pronounced clustering and co-localization of CD147 and integrin-β1, with only partial association of integrin-α3. Finally, we show that RPE derived CD147 and integrin-β1, but not integrin-α3, carry predominantly β-1,6-N-actyl-D-glucosamine-branched glycans, which are high-affinity ligands for Gal-3. We conclude from these data that extracellular Gal-3 triggers clustering of CD147 and

  19. Galectin-3 induces clustering of CD147 and integrin-β1 transmembrane glycoprotein receptors on the RPE cell surface.

    Directory of Open Access Journals (Sweden)

    Claudia S Priglinger

    Full Text Available Proliferative vitreoretinopathy (PVR is a blinding disease frequently occurring after retinal detachment surgery. Adhesion, migration and matrix remodeling of dedifferentiated retinal pigment epithelial (RPE cells characterize the onset of the disease. Treatment options are still restrained and identification of factors responsible for the abnormal behavior of the RPE cells will facilitate the development of novel therapeutics. Galectin-3, a carbohydrate-binding protein, was previously found to inhibit attachment and spreading of retinal pigment epithelial cells, and thus bares the potential to counteract PVR-associated cellular events. However, the identities of the corresponding cell surface glycoprotein receptor proteins on RPE cells are not known. Here we characterize RPE-specific Gal-3 containing glycoprotein complexes using a proteomic approach. Integrin-β1, integrin-α3 and CD147/EMMPRIN, a transmembrane glycoprotein implicated in regulating matrix metalloproteinase induction, were identified as potential Gal-3 interactors on RPE cell surfaces. In reciprocal immunoprecipitation experiments we confirmed that Gal-3 associated with CD147 and integrin-β1, but not with integrin-α3. Additionally, association of Gal-3 with CD147 and integrin-β1 was observed in co-localization analyses, while integrin-α3 only partially co-localized with Gal-3. Blocking of CD147 and integrin-β1 on RPE cell surfaces inhibited binding of Gal-3, whereas blocking of integrin-α3 failed to do so, suggesting that integrin-α3 is rather an indirect interactor. Importantly, Gal-3 binding promoted pronounced clustering and co-localization of CD147 and integrin-β1, with only partial association of integrin-α3. Finally, we show that RPE derived CD147 and integrin-β1, but not integrin-α3, carry predominantly β-1,6-N-actyl-D-glucosamine-branched glycans, which are high-affinity ligands for Gal-3. We conclude from these data that extracellular Gal-3 triggers

  20. Ion Transport and Precipitation Kinetics as Key Aspects of Stress Generation on Pore Walls Induced by Salt Crystallization

    Science.gov (United States)

    Naillon, A.; Joseph, P.; Prat, M.

    2018-01-01

    The stress generation on pore walls due to the growth of a sodium chloride crystal in a confined aqueous solution is studied from evaporation experiments in microfluidic channels in conjunction with numerical computations of crystal growth. The study indicates that the stress buildup on the pore walls is a highly transient process taking place over a very short period of time (in less than 1 s in our experiments). The analysis makes clear that what matters for the stress generation is not the maximum supersaturation at the onset of the crystal growth but the supersaturation at the interface between the solution and the crystal when the latter is about to be confined between the pore walls. The stress generation is summarized in a simple stress diagram involving the pore aspect ratio and the Damkhöler number characterizing the competition between the precipitation reaction kinetics and the ion transport towards the growing crystal. This opens up the route for a better understanding of the damage of porous materials induced by salt crystallization, an important issue in Earth sciences, reservoir engineering, and civil engineering.

  1. Transmembrane Tumor Necrosis Factor Controls Myeloid-Derived Suppressor Cell Activity via TNF Receptor 2 and Protects from Excessive Inflammation during BCG-Induced Pleurisy

    Directory of Open Access Journals (Sweden)

    Leslie Chavez-Galan

    2017-08-01

    Full Text Available Pleural tuberculosis (TB is a form of extra-pulmonary TB observed in patients infected with Mycobacterium tuberculosis. Accumulation of myeloid-derived suppressor cells (MDSC has been observed in animal models of TB and in human patients but their role remains to be fully elucidated. In this study, we analyzed the role of transmembrane TNF (tmTNF in the accumulation and function of MDSC in the pleural cavity during an acute mycobacterial infection. Mycobacterium bovis BCG-induced pleurisy was resolved in mice expressing tmTNF, but lethal in the absence of tumor necrosis factor. Pleural infection induced MDSC accumulation in the pleural cavity and functional MDSC required tmTNF to suppress T cells as did pleural wild-type MDSC. Interaction of MDSC expressing tmTNF with CD4 T cells bearing TNF receptor 2 (TNFR2, but not TNFR1, was required for MDSC suppressive activity on CD4 T cells. Expression of tmTNF attenuated Th1 cell-mediated inflammatory responses generated by the acute pleural mycobacterial infection in association with effective MDSC expressing tmTNF and interacting with CD4 T cells expressing TNFR2. In conclusion, this study provides new insights into the crucial role played by the tmTNF/TNFR2 pathway in MDSC suppressive activity required during acute pleural infection to attenuate excessive inflammation generated by the infection.

  2. MELATONIN-INDUCED SUPPRESSION OF PC12 CELL GROWTH IS MEDIATED BY ITS GI COUPLED TRANSMEMBRANE RECEPTORS. (R826248)

    Science.gov (United States)

    The effects of pertussis toxin, an uncoupler of Gi protein from adenylate cyclase, and luzindole, a competitive inhibitor of melatonin receptor binding, were examined for their ability to inhibit melatonin-induced suppression of PC12 cell growth. Both agents inhibited the mela...

  3. 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...

  4. Swine interferon-induced transmembrane protein, sIFITM3, inhibits foot-and-mouth disease virus infection in vitro and in vivo.

    Science.gov (United States)

    Xu, Jinfang; Qian, Ping; Wu, Qunfeng; Liu, Shasha; Fan, Wenchun; Zhang, Keshan; Wang, Rong; Zhang, Huawei; Chen, Huanchun; Li, Xiangmin

    2014-09-01

    The interferon-induced transmembrane protein 3 (IFITM3) is a widely expressed potent antiviral effector of the host innate immune system. It restricts a diverse group of pathogenic, enveloped viruses, by interfering with endosomal fusion. In this report, the swine IFITM3 (sIFITM3) gene was cloned. It shares the functionally conserved CD225 domain and multiple critical amino acid residues (Y19, F74, F77, R86 and Y98) with its human ortholog, which are essential for antiviral activity. Ectopic expression of sIFITM3 significantly inhibited non-enveloped foot-and-mouth disease virus (FMDV) infection in BHK-21 cells. Furthermore, sIFITM3 blocked FMDV infection at early steps in the virus life cycle by disrupting viral attachment to the host cell surface. Importantly, inoculation of 2-day-old suckling mice with a plasmid expressing sIFITM3 conferred protection against lethal challenge with FMDV. These results suggest that sIFITM3 is a promising antiviral agent and that can safeguard the host from infection with FMDV. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Thermal Instability Induced Oriented 2D Pores for Enhanced Sodium Storage.

    Science.gov (United States)

    Kong, Lingjun; Xie, Chen-Chao; Gu, Haichen; Wang, Chao-Peng; Zhou, Xianlong; Liu, Jian; Zhou, Zhen; Li, Zhao-Yang; Zhu, Jian; Bu, Xian-He

    2018-04-19

    Hierarchical porous structures are highly desired for various applications. However, it is still challenging to obtain such materials with tunable architectures. Here, this paper reports hierarchical nanomaterials with oriented 2D pores by taking advantages of thermally instable bonds in vanadium-based metal-organic frameworks (MOFs). High-temperature calcination of these MOFs accompanied by the loss of coordinated water molecules and other components enables the formation of orderly slit-like 2D pores in vanadium oxide/porous carbon nanorods (VO x /PCs). This unique combination leads to an increase of the reactive surface area. In addition, optimized VO x /PCs demonstrate high-rate capability and ultralong cycling life for sodium storage. The assembled full cells also show high capacity and cycling stability. This report provides an effective strategy for producing MOFs-derived composites with hierarchical porous architectures for energy storage. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Microwave-induced synthesis of highly dispersed gold nanoparticles within the pore channels of mesoporous silica

    International Nuclear Information System (INIS)

    Gu Jinlou; Fan Wei; Shimojima, Atsushi; Okubo, Tatsuya

    2008-01-01

    Highly dispersed gold nanoparticles have been incorporated into the pore channels of SBA-15 mesoporous silica through a newly developed strategy assisted by microwave radiation (MR). The sizes of gold are effectively controlled attributed to the rapid and homogeneous nucleation, simultaneous propagation and termination of gold precursor by MR. Diol moieties with high dielectric and dielectric loss constants, and hence a high microwave activation, were firstly introduced to the pore channels of SBA-15 by a simple addition reaction between amino group and glycidiol and subsequently served as the reduction centers for gold nanoparticles. Extraction of the entrapped gold from the nanocomposite resulted in milligram quantities of gold nanoparticles with low dispersity. The successful assembly process of diol groups and formation of gold nanoparticles were monitored and tracked by solid-state NMR and UV-vis measurements. Characterization by small angle X-ray diffraction (XRD) and transmission electron microscopy (TEM) indicated that the incorporation of gold nanoparticles would not breakup the structural integrity and long-range periodicity of SBA-15. The gold nanoparticles had a narrow size distribution with diameters in the size range of 5-10 nm through TEM observation. The average particles size is 7.9 nm via calculation by the Scherrer formula and TEM measurements. Nitrogen adsorption and desorption isotherms gave further evidence that the employed method was efficient and gold nanoparticles were successfully incorporated into the pore channels of SBA-15. - Graphical abstract: A facile and novel strategy has been developed to incorporate gold nanoparticles into the pore channels of mesoporous SBA-15 assisted by microwave radiation (MR) with mild reaction condition and rapid reaction speed. Due to the rapid and homogeneous nucleation, simultaneous propagation and termination by MR, the size of gold nanoparticles are effectively controlled

  7. Breaking the hydrophobicity of the MscL pore: insights into a charge-induced gating mechanism.

    Directory of Open Access Journals (Sweden)

    Balasubramanian Chandramouli

    Full Text Available The mechanosensitive channel of large conductance (MscL is a protein that responds to membrane tension by opening a transient pore during osmotic downshock. Due to its large pore size and functional reconstitution into lipid membranes, MscL has been proposed as a promising artificial nanovalve suitable for biotechnological applications. For example, site-specific mutations and tailored chemical modifications have shown how MscL channel gating can be triggered in the absence of tension by introducing charged residues at the hydrophobic pore level. Recently, engineered MscL proteins responsive to stimuli like pH or light have been reported. Inspired by experiments, we present a thorough computational study aiming at describing, with atomistic detail, the artificial gating mechanism and the molecular transport properties of a light-actuated bacterial MscL channel, in which a charge-induced gating mechanism has been enabled through the selective cleavage of photo-sensitive alkylating agents. Properties such as structural transitions, pore dimension, ion flux and selectivity have been carefully analyzed. Besides, the effects of charge on alternative sites of the channel with respect to those already reported have been addressed. Overall, our results provide useful molecular insights into the structural events accompanying the engineered MscL channel gating and the interplay of electrostatic effects, channel opening and permeation properties. In addition, we describe how the experimentally observed ionic current in a single-subunit charged MscL mutant is obtained through a hydrophobicity breaking mechanism involving an asymmetric inter-subunit motion.

  8. pH controlled gating of toxic protein pores by dendrimers

    Science.gov (United States)

    Mandal, Taraknath; Kanchi, Subbarao; Ayappa, K. G.; Maiti, Prabal K.

    2016-06-01

    Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent bacterial strains, on a target cell membrane is a challenging and active area of research. Here we demonstrate that PAMAM dendrimers can act as effective pH controlled gating devices once the pore has been formed. We have used fully atomistic molecular dynamics (MD) simulations to characterize the cytolysin A (ClyA) protein pores modified with fifth generation (G5) PAMAM dendrimers. Our results show that the PAMAM dendrimer, in either its protonated (P) or non-protonated (NP) states can spontaneously enter the protein lumen. Protonated dendrimers interact strongly with the negatively charged protein pore lumen. As a consequence, P dendrimers assume a more expanded configuration efficiently blocking the pore when compared with the more compact configuration adopted by the neutral NP dendrimers creating a greater void space for the passage of water and ions. To quantify the effective blockage of the protein pore, we have calculated the pore conductance as well as the residence times by applying a weak force on the ions/water. Ionic currents are reduced by 91% for the P dendrimers and 31% for the NP dendrimers. The preferential binding of Cl- counter ions to the P dendrimer creates a zone of high Cl- concentration in the vicinity of the internalized dendrimer and a high concentration of K+ ions in the transmembrane region of the pore lumen. In addition to steric effects, this induced charge segregation for the P dendrimer effectively blocks ionic transport through the pore. Our investigation shows that the bio-compatible PAMAM dendrimers can potentially be used to develop therapeutic protocols based on the pH sensitive gating of pores formed by pore forming toxins to mitigate bacterial infections.Designing effective nanoscale blockers for membrane inserted pores formed by pore forming toxins, which are expressed by several virulent

  9. Spermine selectively inhibits high-conductance, but not low-conductance calcium-induced permeability transition pore.

    Science.gov (United States)

    Elustondo, Pia A; Negoda, Alexander; Kane, Constance L; Kane, Daniel A; Pavlov, Evgeny V

    2015-02-01

    The permeability transition pore (PTP) is a large channel of the mitochondrial inner membrane, the opening of which is the central event in many types of stress-induced cell death. PTP opening is induced by elevated concentrations of mitochondrial calcium. It has been demonstrated that spermine and other polyamines can delay calcium-induced swelling of isolated mitochondria, suggesting their role as inhibitors of the mitochondrial PTP. Here we further investigated the mechanism by which spermine inhibits the calcium-induced, cyclosporine A (CSA) -sensitive PTP by using three indicators: 1) calcium release from the mitochondria detected with calcium green, 2) mitochondrial membrane depolarization using TMRM, and 3) mitochondrial swelling by measuring light absorbance. We found that despite calcium release and membrane depolarization, indicative of PTP activation, mitochondria underwent only partial swelling in the presence of spermine. This was in striking contrast to the high-amplitude swelling detected in control mitochondria and in mitochondria treated with the PTP inhibitor CSA. We conclude that spermine selectively prevents opening of the high-conductance state, while allowing activation of the lower conductance state of the PTP. We propose that the existence of lower conductance, stress-induced PTP might play an important physiological role, as it is expected to allow the release of toxic levels of calcium, while keeping important molecules (e.g., NAD) within the mitochondrial matrix. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Spectral Induced Polarization of Low-pH Concrete. Influence of the Electrical Double Layer and Pore Size

    Science.gov (United States)

    Leroy, P. G.; Gaboreau, S.; Zimmermann, E.; Hoerdt, A.; Claret, F.; Huisman, J. A.; Tournassat, C.

    2017-12-01

    Low-pH concretes are foreseen to be used in nuclear waste disposal. Understanding their reactivity upon the considered host-rock is a key point. Evolution of mineralogy, porosity, pore size distribution and connectivity can be monitored in situ using geophysical methods such as induced polarization (IP). This electrical method consists of injecting an alternating current and measuring the resulting voltage in the porous medium. Spectral IP (SIP) measurements in the 10 mHz to 10 kHz frequency range were carried out on low-pH concrete and cement paste first in equilibrium and then in contact with a CO2 enriched and diluted water. We observed a very high resistivity of the materials (> 10 kOhm m) and a strong phase shift between injected current and measured voltage (superior to 40 mrad and above 100 mrad for frequencies > 100 Hz). These observations were modelled by considering membrane polarization with ion exclusion in nanopores whose surface electrical properties were computed using a basic Stern model of the cement/water interface. Pore size distribution was deduced from SIP and was compared to the measured ones. In addition, we observed a decrease of the material resistivity due to the dissolution of cement in contact with external water. Our results show that SIP may be a valuable method to monitor the mineralogy and the petrophysical and transport properties of cements.

  11. Neuroglobin overexpression inhibits oxygen-glucose deprivation-induced mitochondrial permeability transition pore opening in primary cultured mouse cortical neurons.

    Science.gov (United States)

    Yu, Zhanyang; Liu, Ning; Li, Yadan; Xu, Jianfeng; Wang, Xiaoying

    2013-08-01

    Neuroglobin (Ngb) is an endogenous neuroprotective molecule against hypoxic/ischemic brain injury, but the underlying mechanisms remain largely undefined. Our recent study revealed that Ngb can bind to voltage-dependent anion channel (VDAC), a regulator of mitochondria permeability transition (MPT). In this study we examined the role of Ngb in MPT pore (mPTP) opening following oxygen-glucose deprivation (OGD) in primary cultured mouse cortical neurons. Co-immunoprecipitation (Co-IP) and immunocytochemistry showed that the binding between Ngb and VDAC was increased after OGD compared to normoxia, indicating the OGD-enhanced Ngb-VDAC interaction. Ngb overexpression protected primary mouse cortical neurons from OGD-induced neuronal death, to an extent comparable to mPTP opening inhibitor, cyclosporine A (CsA) pretreatment. We further measured the role of Ngb in OGD-induced mPTP opening using Ngb overexpression and knockdown approaches in primary cultured neurons, and recombinant Ngb exposure to isolated mitochondria. Same as CsA pretreatment, Ngb overexpression significantly reduced OGD-induced mPTP opening markers including mitochondria swelling, mitochondrial NAD(+) release, and cytochrome c (Cyt c) release in primary cultured neurons. Recombinant Ngb incubation significantly reduced OGD-induced NAD(+) release and Cyt c release from isolated mitochondria. In contrast, Ngb knockdown significantly increased OGD-induced neuron death, and increased OGD-induced mitochondrial NAD(+) release and Cyt c release as well, and these outcomes could be rescued by CsA pretreatment. In summary, our results demonstrated that Ngb overexpression can inhibit OGD-induced mPTP opening in primary cultured mouse cortical neurons, which may be one of the molecular mechanisms of Ngb's neuroprotection. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. Effects of the stress field induced by a running tyre on the soil pore system

    DEFF Research Database (Denmark)

    Berisso, Feto Esimo; Schjønning, Per; Lamandé, Mathieu

    2013-01-01

    state in the soil profile beneath the harvester tyre was calculated using the SoilFlex model. Pore continuity index (N) and blocked air-filled porosity (εb) were estimated from the relationship between ka and air-filled porosity (εa) for a range of matric potentials. Calculated and measured stresses...... repeated wheelings were performed by a forage harvester (wheel load 6100 kg; tyre width 80 cm). Mean normal and horizontal stresses were measured with Bolling probes (at 10, 20 and 40 cm depth) and load cells (at 40, 50, 60 cm lateral distance from the centreline of the wheel rut at 10, 30 and 50 cm depth......), respectively. Intact soil cores of 100 cm3 sampled at 10, 30 and 50 cm depth in a soil transcet running from the centreline of the wheel rut to the unwheeled part of the field were used for measurements of water retention and air permeability (ka) at −30, −100 and −300 hPa matric potential. The complete stress...

  13. The antineoplastic agent α-bisabolol promotes cell death by inducing pores in mitochondria and lysosomes.

    Science.gov (United States)

    Rigo, Antonella; Vinante, Fabrizio

    2016-08-01

    The sesquiterpene α-bisabolol (α-BSB) has been shown to be an effective cytotoxic agent for a variety of human cancer cells in culture and animal models. However, much of its intracellular action remains elusive. We evaluated the cytotoxic action of α-BSB against CML-T1, Jurkat and HeLa cell lines, as preclinical models for myeloid, lymphoid and epithelial neoplasias. The approach included single cell analysis (flow cytometry, immunocytology) combined with cytotoxicity and proliferation assays to characterize organelle damage, autophagy, cytostatic effect, and apoptosis. The study focuses on the relevant steps in the cytotoxic cascade triggered by α-BSB: (1) the lipid rafts through which α-BSB enters the cells, (2) the opening of pores in the mitochondria and lysosomes, (3) the activation of both caspase-dependent and caspase-independent cell death pathways, (4) the induction of autophagy and (5) apoptosis. The effectiveness of α-BSB as an agent against tumor cells is grounded on its capability to act on different layers of cell regulation to elicit different concurrent death signals, thereby neutralizing a variety of aberrant survival mechanisms leading to treatment resistance in neoplastic cell.

  14. Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore.

    Directory of Open Access Journals (Sweden)

    Anusha Panjwani

    2014-08-01

    Full Text Available Non-enveloped viruses must deliver their viral genome across a cell membrane without the advantage of membrane fusion. The mechanisms used to achieve this remain poorly understood. Human rhinovirus, a frequent cause of the common cold, is a non-enveloped virus of the picornavirus family, which includes other significant pathogens such as poliovirus and foot-and-mouth disease virus. During picornavirus cell entry, the small myristoylated capsid protein VP4 is released from the virus, interacts with the cell membrane and is implicated in the delivery of the viral RNA genome into the cytoplasm to initiate replication. In this study, we have produced recombinant C-terminal histidine-tagged human rhinovirus VP4 and shown it can induce membrane permeability in liposome model membranes. Dextran size-exclusion studies, chemical crosslinking and electron microscopy demonstrated that VP4 forms a multimeric membrane pore, with a channel size consistent with transfer of the single-stranded RNA genome. The membrane permeability induced by recombinant VP4 was influenced by pH and was comparable to permeability induced by infectious virions. These findings present a molecular mechanism for the involvement of VP4 in cell entry and provide a model system which will facilitate exploration of VP4 as a novel antiviral target for the picornavirus family.

  15. Pore-network model of evaporation-induced salt precipitation in porous media: The effect of correlations and heterogeneity

    Science.gov (United States)

    Dashtian, Hassan; Shokri, Nima; Sahimi, Muhammad

    2018-02-01

    Salt transport and precipitation in porous media constitute a set of complex and fascinating phenomena that are of considerable interest to several important problems, ranging from storage of CO2 in geological formations, to soil fertility, and protection of pavements and roads, as well as historical monuments. The phenomena occur at the pore scale and are greatly influenced by the heterogeneity of the pore space morphology. We present a pore-network (PN) model to study the phenomena. Vapor diffusion, capillary effect at the brine-vapor interface, flow of brine, and transport of salt and its precipitation in the pores that plug the pores partially or completely are all accounted for. The drying process is modeled by the invasion percolation, while transport of salt in brine is accounted for by the convective-diffusion equation. We demonstrate that the drying patterns, the clustering and connectivity of the pore throats in which salt precipitation occurs, the saturation distribution, and the drying rate are all strongly dependent upon the pore-size distribution, the correlations among the pore sizes, and the anisotropy of the pore space caused by stratification that most natural porous media contain. In particular, if the strata are more or less parallel to the direction of injection of the gas that dries out the pore space (air, for example) and/or causes salt precipitation (CO2, for example), the drying rate increases significantly. Moreover, salt tends to precipitate in clusters of neighboring pores that are parallel to the open surface of the porous medium.

  16. Mutation G805R in the transmembrane domain of the LDL receptor gene causes familial hypercholesterolemia by inducing ectodomain cleavage of the LDL receptor in the endoplasmic reticulum

    Directory of Open Access Journals (Sweden)

    Thea Bismo Strøm

    2014-01-01

    Full Text Available More than 1700 mutations in the low density lipoprotein receptor (LDLR gene have been found to cause familial hypercholesterolemia (FH. These are commonly divided into five classes based upon their effects on the structure and function of the LDLR. However, little is known about the mechanism by which mutations in the transmembrane domain of the LDLR gene cause FH. We have studied how the transmembrane mutation G805R affects the function of the LDLR. Based upon Western blot analyses of transfected HepG2 cells, mutation G805R reduced the amounts of the 120 kDa precursor LDLR in the endoplasmic reticulum. This led to reduced amounts of the mature 160 kDa LDLR at the cell surface. However, significant amounts of a secreted 140 kDa G805R-LDLR ectodomain fragment was observed in the culture media. Treatment of the cells with the metalloproteinase inhibitor batimastat largely restored the amounts of the 120 and 160 kDa forms in cell lysates, and prevented secretion of the 140 kDa ectodomain fragment. Together, these data indicate that a metalloproteinase cleaved the ectodomain of the 120 kDa precursor G805R-LDLR in the endoplasmic reticulum. It was the presence of the polar Arg805 and not the lack of Gly805 which led to ectodomain cleavage. Arg805 also prevented γ-secretase cleavage within the transmembrane domain. It is conceivable that introducing a charged residue within the hydrophobic membrane lipid bilayer, results in less efficient incorporation of the 120 kDa G805R-LDLR in the endoplasmic reticulum membrane and makes it a substrate for metalloproteinase cleavage.

  17. Doxorubicin induced myocardial injury is exacerbated following ischaemic stress via opening of the mitochondrial permeability transition pore

    Energy Technology Data Exchange (ETDEWEB)

    Gharanei, M.; Hussain, A. [Department of Biomolecular and Sport Sciences, Coventry University, Cox Street, Coventry, CV1 5FB (United Kingdom); Janneh, O. [Department of Biomolecular and Sport Sciences, Coventry University, Cox Street, Coventry, CV1 5FB (United Kingdom); Pharmacology Research Laboratories, 70, Pembroke Place, The University of Liverpool, Liverpool. L69 3GF (United Kingdom); Maddock, H.L., E-mail: h.maddock@coventry.ac.uk [Department of Biomolecular and Sport Sciences, Coventry University, Cox Street, Coventry, CV1 5FB (United Kingdom)

    2013-04-15

    Chemotherapeutic agents such as doxorubicin are known to cause or exacerbate cardiovascular cell death when an underlying heart condition is present. However, the mechanism of doxorubicin-induced cardiotoxicity is unclear. Here we assess the cardiotoxic effects of doxorubicin in conditions of myocardial ischaemia reperfusion and the mechanistic basis of protection, in particular the role of the mitochondrial permeability transition pore (mPTP) in such protection. The effects of doxorubicin (1 μM) ± cyclosporine A (CsA, 0.2 μM; inhibits mPTP) were investigated in isolated male Sprague–Dawley rats using Langendorff heart and papillary muscle contraction models subjected to simulated ischaemia and reperfusion injury. Isolated rat cardiac myocytes were used in an oxidative stress model to study the effects of drug treatment on mPTP by confocal microscopy. Western blot analysis evaluated the effects of drug treatment on p-Akt and p-Erk 1/2 levels. Langendorff and the isometric contraction models showed a detrimental effect of doxorubicin throughout reperfusion/reoxygenation as well as increased p-Akt and p-Erk levels. Interestingly, CsA not only reversed the detrimental effects of doxorubicin, but also reduced p-Akt and p-Erk levels. In the sustained oxidative stress assay to study mPTP opening, doxorubicin decreased the time taken to depolarization and hypercontracture, but these effects were delayed in the presence of CsA. Collectively, our data suggest for the first that doxorubicin exacerbates myocardial injury in an ischaemia reperfusion model. If the inhibition of mPTP ameliorates the cardiotoxic effects of doxorubicin, then more selective inhibitors of mPTP should be further investigated for their utility in patients receiving doxorubicin. - Highlights: ► Doxorubicin exacerbates myocardial ischaemia reperfusion injury. ► Co-treatment with CsA protects against doxorubicin induced myocardial injury. ► CsA delays doxorubicin induced mPTP opening in laser

  18. Doxorubicin induced myocardial injury is exacerbated following ischaemic stress via opening of the mitochondrial permeability transition pore

    International Nuclear Information System (INIS)

    Gharanei, M.; Hussain, A.; Janneh, O.; Maddock, H.L.

    2013-01-01

    Chemotherapeutic agents such as doxorubicin are known to cause or exacerbate cardiovascular cell death when an underlying heart condition is present. However, the mechanism of doxorubicin-induced cardiotoxicity is unclear. Here we assess the cardiotoxic effects of doxorubicin in conditions of myocardial ischaemia reperfusion and the mechanistic basis of protection, in particular the role of the mitochondrial permeability transition pore (mPTP) in such protection. The effects of doxorubicin (1 μM) ± cyclosporine A (CsA, 0.2 μM; inhibits mPTP) were investigated in isolated male Sprague–Dawley rats using Langendorff heart and papillary muscle contraction models subjected to simulated ischaemia and reperfusion injury. Isolated rat cardiac myocytes were used in an oxidative stress model to study the effects of drug treatment on mPTP by confocal microscopy. Western blot analysis evaluated the effects of drug treatment on p-Akt and p-Erk 1/2 levels. Langendorff and the isometric contraction models showed a detrimental effect of doxorubicin throughout reperfusion/reoxygenation as well as increased p-Akt and p-Erk levels. Interestingly, CsA not only reversed the detrimental effects of doxorubicin, but also reduced p-Akt and p-Erk levels. In the sustained oxidative stress assay to study mPTP opening, doxorubicin decreased the time taken to depolarization and hypercontracture, but these effects were delayed in the presence of CsA. Collectively, our data suggest for the first that doxorubicin exacerbates myocardial injury in an ischaemia reperfusion model. If the inhibition of mPTP ameliorates the cardiotoxic effects of doxorubicin, then more selective inhibitors of mPTP should be further investigated for their utility in patients receiving doxorubicin. - Highlights: ► Doxorubicin exacerbates myocardial ischaemia reperfusion injury. ► Co-treatment with CsA protects against doxorubicin induced myocardial injury. ► CsA delays doxorubicin induced mPTP opening in laser

  19. 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.

  20. 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.

  1. Familial CJD Associated PrP Mutants within Transmembrane Region Induced Ctm-PrP Retention in ER and Triggered Apoptosis by ER Stress in SH-SY5Y Cells

    Science.gov (United States)

    Wang, Xin; Shi, Qi; Xu, Kun; Gao, Chen; Chen, Cao; Li, Xiao-Li; Wang, Gui-Rong; Tian, Chan; Han, Jun; Dong, Xiao-Ping

    2011-01-01

    Background Genetic prion diseases are linked to point and inserted mutations in the prion protein (PrP) gene that are presumed to favor conversion of the cellular isoform of PrP (PrPC) to the pathogenic one (PrPSc). The pathogenic mechanisms and the subcellular sites of the conversion are not completely understood. Here we introduce several PRNP gene mutations (such as, PrP-KDEL, PrP-3AV, PrP-A117V, PrP-G114V, PrP-P102L and PrP-E200K) into the cultured cells in order to explore the pathogenic mechanism of familial prion disease. Methodology/Principal Findings To address the roles of aberrant retention of PrP in endoplasmic reticulum (ER), the recombinant plasmids expressing full-length human PrP tailed with an ER signal peptide at the COOH-terminal (PrP-KDEL) and PrP with three amino acids exchange in transmembrane region (PrP-3AV) were constructed. In the preparations of transient transfections, 18-kD COOH-terminal proteolytic resistant fragments (Ctm-PrP) were detected in the cells expressing PrP-KDEL and PrP-3AV. Analyses of the cell viabilities in the presences of tunicamycin and brefeldin A revealed that expressions of PrP-KDEL and PrP-3AV sensitized the transfected cells to ER stress stimuli. Western blots and RT-PCR identified the clear alternations of ER stress associated events in the cells expressing PrP-KDEL and PrP-3AV that induced ER mediated apoptosis by CHOP and capase-12 apoptosis pathway. Moreover, several familial CJD related PrP mutants were transiently introduced into the cultured cells. Only the mutants within the transmembrane region (G114V and A117V) induced the formation of Ctm-PrP and caused the ER stress, while the mutants outside the transmembrane region (P102L and E200K) failed. Conclusions/Significance The data indicate that the retention of PrP in ER through formation of Ctm-PrP results in ER stress and cell apoptosis. The cytopathic activities caused by different familial CJD associated PrP mutants may vary, among them the mutants

  2. Familial CJD associated PrP mutants within transmembrane region induced Ctm-PrP retention in ER and triggered apoptosis by ER stress in SH-SY5Y cells.

    Directory of Open Access Journals (Sweden)

    Xin Wang

    Full Text Available BACKGROUND: Genetic prion diseases are linked to point and inserted mutations in the prion protein (PrP gene that are presumed to favor conversion of the cellular isoform of PrP (PrP(C to the pathogenic one (PrP(Sc. The pathogenic mechanisms and the subcellular sites of the conversion are not completely understood. Here we introduce several PRNP gene mutations (such as, PrP-KDEL, PrP-3AV, PrP-A117V, PrP-G114V, PrP-P102L and PrP-E200K into the cultured cells in order to explore the pathogenic mechanism of familial prion disease. METHODOLOGY/PRINCIPAL FINDINGS: To address the roles of aberrant retention of PrP in endoplasmic reticulum (ER, the recombinant plasmids expressing full-length human PrP tailed with an ER signal peptide at the COOH-terminal (PrP-KDEL and PrP with three amino acids exchange in transmembrane region (PrP-3AV were constructed. In the preparations of transient transfections, 18-kD COOH-terminal proteolytic resistant fragments (Ctm-PrP were detected in the cells expressing PrP-KDEL and PrP-3AV. Analyses of the cell viabilities in the presences of tunicamycin and brefeldin A revealed that expressions of PrP-KDEL and PrP-3AV sensitized the transfected cells to ER stress stimuli. Western blots and RT-PCR identified the clear alternations of ER stress associated events in the cells expressing PrP-KDEL and PrP-3AV that induced ER mediated apoptosis by CHOP and caspase-12 apoptosis pathway. Moreover, several familial CJD related PrP mutants were transiently introduced into the cultured cells. Only the mutants within the transmembrane region (G114V and A117V induced the formation of Ctm-PrP and caused the ER stress, while the mutants outside the transmembrane region (P102L and E200K failed. CONCLUSIONS/SIGNIFICANCE: The data indicate that the retention of PrP in ER through formation of Ctm-PrP results in ER stress and cell apoptosis. The cytopathic activities caused by different familial CJD associated PrP mutants may vary, among them

  3. 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.

  4. The first transmembrane domain (TM1) of β2-subunit binds to the transmembrane domain S1 of α-subunit in BK potassium channels

    Science.gov (United States)

    Morera, Francisco J.; Alioua, Abderrahmane; Kundu, Pallob; Salazar, Marcelo; Gonzalez, Carlos; Martinez, Agustin D.; Stefani, Enrico; Toro, Ligia; Latorre, Ramon

    2012-01-01

    The BK channel is one of the most broadly expressed ion channels in mammals. In many tissues, the BK channel pore-forming α-subunit is associated to an auxiliary β-subunit that modulates the voltage- and Ca2+-dependent activation of the channel. Structural components present in β-subunits that are important for the physical association with the α-subunit are yet unknown. Here, we show through co-immunoprecipitation that the intracellular C-terminus, the second transmembrane domain (TM2) and the extracellular loop of the β2-subunit are dispensable for association with the α-subunit pointing transmembrane domain 1 (TM1) as responsible for the interaction. Indeed, the TOXCAT assay for transmembrane protein–protein interactions demonstrated for the first time that TM1 of the β2-subunit physically binds to the transmembrane S1 domain of the α-subunit. PMID:22710124

  5. Observations of wave-induced pore pressure gradients and bed level response on a surf zone sandbar

    Science.gov (United States)

    Anderson, Dylan; Cox, Dan; Mieras, Ryan; Puleo, Jack A.; Hsu, Tian-Jian

    2017-06-01

    Horizontal and vertical pressure gradients may be important physical mechanisms contributing to onshore sediment transport beneath steep, near-breaking waves in the surf zone. A barred beach was constructed in a large-scale laboratory wave flume with a fixed profile containing a mobile sediment layer on the crest of the sandbar. Horizontal and vertical pore pressure gradients were obtained by finite differences of measurements from an array of pressure transducers buried within the upper several centimeters of the bed. Colocated observations of erosion depth were made during asymmetric wave trials with wave heights between 0.10 and 0.98 m, consistently resulting in onshore sheet flow sediment transport. The pore pressure gradient vector within the bed exhibited temporal rotations during each wave cycle, directed predominantly upward under the trough and then rapidly rotating onshore and downward as the wavefront passed. The magnitude of the pore pressure gradient during each phase of rotation was correlated with local wave steepness and relative depth. Momentary bed failures as deep as 20 grain diameters were coincident with sharp increases in the onshore-directed pore pressure gradients, but occurred at horizontal pressure gradients less than theoretical critical values for initiation of the motion for compact beds. An expression combining the effects of both horizontal and vertical pore pressure gradients with bed shear stress and soil stability is used to determine that failure of the bed is initiated at nonnegligible values of both forces.type="synopsis">type="main">Plain Language SummaryThe pressure gradient present within the seabed beneath breaking waves may be an important physical mechanism transporting sediment. A large-scale laboratory was used to replicate realistic surfzone conditions in controlled tests, allowing for horizontal and vertical pressure gradient magnitudes and the resulting sediment bed response to be observed with precise instruments

  6. Differential equations governing slip-induced pore-pressure fluctuations in a water-saturated granular medium

    Science.gov (United States)

    Iverson, R.M.

    1993-01-01

    Macroscopic frictional slip in water-saturated granular media occurs commonly during landsliding, surface faulting, and intense bedload transport. A mathematical model of dynamic pore-pressure fluctuations that accompany and influence such sliding is derived here by both inductive and deductive methods. The inductive derivation shows how the governing differential equations represent the physics of the steadily sliding array of cylindrical fiberglass rods investigated experimentally by Iverson and LaHusen (1989). The deductive derivation shows how the same equations result from a novel application of Biot's (1956) dynamic mixture theory to macroscopic deformation. The model consists of two linear differential equations and five initial and boundary conditions that govern solid displacements and pore-water pressures. Solid displacements and water pressures are strongly coupled, in part through a boundary condition that ensures mass conservation during irreversible pore deformation that occurs along the bumpy slip surface. Feedback between this deformation and the pore-pressure field may yield complex system responses. The dual derivations of the model help explicate key assumptions. For example, the model requires that the dimensionless parameter B, defined here through normalization of Biot's equations, is much larger than one. This indicates that solid-fluid coupling forces are dominated by viscous rather than inertial effects. A tabulation of physical and kinematic variables for the rod-array experiments of Iverson and LaHusen and for various geologic phenomena shows that the model assumptions commonly are satisfied. A subsequent paper will describe model tests against experimental data. ?? 1993 International Association for Mathematical Geology.

  7. Synthetic peptides corresponding to human follicle-stimulating hormone (hFSH)-beta-(1-15) and hFSH-beta-(51-65) induce uptake of 45Ca++ by liposomes: evidence for calcium-conducting transmembrane channel formation

    Energy Technology Data Exchange (ETDEWEB)

    Grasso, P.; Santa-Coloma, T.A.; Reichert, L.E. Jr. (Department of Biochemistry, Albany Medical College, New York, NY (USA))

    1991-06-01

    We have previously described FSH receptor-mediated influx of 45Ca++ in cultured Sertoli cells from immature rats and receptor-enriched proteoliposomes via activation of voltage-sensitive and voltage-independent calcium channels. We have further shown that this effect of FSH does not require cholera toxin- or pertussis toxin-sensitive guanine nucleotide binding protein or activation of adenylate cyclase. In the present study, we have identified regions of human FSH-beta-subunit which appear to be involved in mediating calcium influx. We screened 11 overlapping peptide amides representing the entire primary structure of hFSH-beta-subunit for their effects on 45Ca++ flux in FSH receptor-enriched proteoliposomes. hFSH-beta-(1-15) and hFSH-beta-(51-65) induced uptake of 45Ca++ in a concentration-related manner. This effect of hFSH-beta-(1-15) and hFSH-beta-(51-65) was also observed in liposomes lacking incorporated FSH receptor. Reducing membrane fluidity by incubating liposomes (containing no receptor) with hFSH-beta-(1-15) or hFSH-beta-(51-65) at temperatures lower than the transition temperatures of their constituent phospholipids resulted in no significant (P greater than 0.05) difference in 45Ca++ uptake. The effectiveness of the calcium ionophore A23187, however, was abolished. Ruthenium red, a voltage-independent calcium channel antagonist, was able to completely block uptake of 45Ca++ induced by hFSH-beta-(1-15) and hFSH-beta-(51-65) whereas nifedipine, a calcium channel blocker specific for L-type voltage-sensitive calcium channels, was without effect. These results suggest that in addition to its effect on voltage-sensitive calcium channel activity, interaction of FSH with its receptor may induce formation of transmembrane aqueous channels which also facilitate influx of extracellular calcium.

  8. Mutagenesis of Dengue Virus Protein NS2A Revealed a Novel Domain Responsible for Virus-Induced Cytopathic Effect and Interactions between NS2A and NS2B Transmembrane Segments.

    Science.gov (United States)

    Wu, Ren-Huang; Tsai, Ming-Han; Tsai, Kuen-Nan; Tian, Jia Ni; Wu, Jian-Sung; Wu, Su-Ying; Chern, Jyh-Haur; Chen, Chun-Hong; Yueh, Andrew

    2017-06-15

    The NS2A protein of dengue virus (DENV) has eight predicted transmembrane segments (pTMS1 to -8) and participates in RNA replication, virion assembly, and host antiviral response. However, the roles of specific amino acid residues within the pTMS regions of NS2A during the viral life cycle are not clear. Here, we explore the function of DENV NS2A by introducing a series of alanine substitutions into the N-terminal half (pTMS1 to -4) of the protein in the context of a DENV infectious clone or subgenomic replicon. Six NS2A mutants (NM5, -7, -9, and -17 to -19) around pTMS1 and -2 displayed a novel phenotype showing a >1,000-fold reduction in virus yield, an absence of plaque formation despite wild-type-like replicon activity, and infectious-virus-like particle yields. HEK-293 cells infected with the six NS2A mutant viruses failed to cause a virus-induced cytopathic effect (CPE) by MitoCapture staining, cell proliferation, and lactate dehydrogenase release assays. Sequencing analyses of pseudorevertant viruses derived from lethal-mutant viruses revealed two consensus reversion mutations, leucine to phenylalanine at codon 181 (L181F) within pTMS7 of NS2A and isoleucine to threonine at codon 114 (I114T) within NS2B. The introduction of an NS2A-L181F mutation into the lethal (NM15, -16, -25, and -33) and CPE-defective (NM7, -9, and -19) mutants substantially rescued virus infectivity and virus-induced CPE, respectively, whereas the NS2B-L114T mutation rescued the NM16, -25, and -33 mutants. In conclusion, the results revealed the essential roles of the N-terminal half of NS2A in RNA replication and virus-induced CPE. Intramolecular interactions between pTMSs of NS2A and intermolecular interactions between the NS2A and NS2B proteins were also implicated. IMPORTANCE The characterization of the N-terminal (current study) and C-terminal halves of DENV NS2A is the most comprehensive mutagenesis study to date to investigate the function of NS2A during the flaviviral life cycle

  9. Nuclear receptor CAR specifically activates the two-pore K+ channel Kcnk1 gene in male mouse livers, which attenuates phenobarbital-induced hepatic hyperplasia.

    Science.gov (United States)

    Saito, Kosuke; Moore, Rick; Negishi, Masahiko

    2013-03-01

    KCNK1, a member of the family of two-pore K(+) ion channels, is specifically induced in the livers of male mice after phenobarbital treatment. Here, we have determined the molecular mechanism of this male-specific activation of the Kcnk1 gene and characterized KCNK1 as a phenobarbital-inducible antihyperplasia factor. Upon activation by phenobarbital, nuclear receptor CAR binds the 97-bp response element (-2441/-2345) within the Kcnk1 promoter. This binding is observed in the livers of male mice, but not in the livers of female mice and requires the pituitary gland, because hypophysectomy abrogates it. Hyperplasia further progressed in the livers of Kcnk1 ( -/- ) male mice compared with those of Kcnk1 ( +/+ ) males after phenobarbital treatment. Thus, KCNK1 suppresses phenobarbital-induced hyperplasia. These results indicate that phenobarbital treatment induces KCNK1 to elicit a male-specific and growth-suppressing signal. Thus, KCNK1 and Kcnk1 ( -/- ) mice provide an experimental tool for further investigation into the molecular mechanism of CAR-mediated promotion of the development of hepatocellular carcinoma in mice.

  10. Bithermal and isothermal experimental test design and resulting influence on the pore formation during high-temperature-induced fatigue of the alloy 800 H

    International Nuclear Information System (INIS)

    Hurta, S.

    1991-01-01

    For investigating the damaging mechanism, bithermal TMF tests have been carried out with the alloy 800H, applying fast pressure half-cycles at low temperature (e.g. 300 C) and slow tensile phases at high temperature (e.g. 700 C). The experimental data thus obtained have been compared with the results of isothermal tests performed at 700 C. Most of the experiments have been performed stress-controlled and with a constant range of plastic strain. Under this regime, deformation is induced in the case of asymmetric test design within the tensile load phase, at various constant tensile stresses each, wheras in the compressive load phase, the stress is constantly increased for compressive stress-governed testing. The results obtained from both test types show that the type of compressive load phase is the factor governing the efficiency of pore formation. (orig.) [de

  11. Transmembrane voltage: Potential to induce lateral microdomains.

    Czech Academy of Sciences Publication Activity Database

    Malínský, Jan; Tanner, W.; Opekarová, Miroslava

    2016-01-01

    Roč. 1861, č. 8 (2016), s. 806-811 ISSN 1388-1981 R&D Projects: GA ČR(CZ) GA15-10641S Institutional support: RVO:68378041 Keywords : membrane microdomain * membrane potential * fluorescence spectroscopy * membrane structure * fluorescence microscopy Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.547, year: 2016

  12. Dissolution at porous interfaces VI: Multiple pore systems.

    Science.gov (United States)

    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.

  13. 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...

  14. High Level Antibody Response to Pandemic Influenza H1N1/09 Virus Is Associated With Interferon-Induced Transmembrane Protein-3 rs12252-CC in Young Adults

    Directory of Open Access Journals (Sweden)

    Ling Qin

    2018-05-01

    Full Text Available Background: The C allele of the interferon-induced transmembrane protein-3 (IFITM3 SNP rs12252, a common allele in South East Asia and China, is strongly associated with severe influenza infection. However, despite the high occurrence of rs12252-CC genotype in Chinese population (~25%, severe influenza infection is rare. The aim of study is to determine whether rs12252-CC individuals have pre-existing antibody responses to previous seasonal influenza infections.Cohort and Method: A total 99 young healthy volunteers (18–20 years were recruited and received an influenza seasonal Vaccination [A/Switzerland/9715293/2013(H3N2, A/California/7/2009 (pdm09H1N1 and B/Jeep/3073/2013-like virus (Flu-B]. Plasma and gDNA was isolated from each volunteer before, and 14, 28, 180, 360, and 540 days after vaccination. Additionally, 68 elderlies (>65 years were also recruited as a control group to compare the levels of antibodies at baseline between the young adults and the elderly. For each sample IFITM3 rs12252 genotype was determined and antibody levels in response to pdmH1N1, H3N2 and Influenza B infection were measured for each time point.Results: We found a significantly higher level of pre-existing antibodies to pandemic influenza H1N1/09 virus (pdm09H1N1 but not to H3N2 or FluB in CC donors in comparison with CT/TT donors prior to vaccination. No impact of IFITM3 genotype in boosting influenza specific antibodies in young adults within 1 year after receiving seasonal influenza vaccination was observed. In addition, there was no difference in pdm09H1N1 specific antibody levels observed in the elderly cohort between volunteers carrying different IFITM3 genotypes. Higher levels of antibodies to pdmH1N1 were observed in elderly CC carriers when compared to the young CC carriers, but this trend was not replicated in TT carriers.Conclusion:IFITM3-rs12252 CC carriers exhibit a high level of pre-existing immunity to pdm09H1N1 compared to TT carriers in the

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. Astragaloside IV Inhibits Oxidative Stress-Induced Mitochondrial Permeability Transition Pore Opening by Inactivating GSK-3β via Nitric Oxide in H9c2 Cardiac Cells

    Directory of Open Access Journals (Sweden)

    Yonggui He

    2012-01-01

    Full Text Available Objective. This study aimed to investigate whether astragaloside IV modulates the mitochondrial permeability transition pore (mPTP opening through glycogen synthase kinase 3β (GSK-3β in H9c2 cells. Methods. H9c2 cells were exposed to astragaloside IV for 20 min. GSK-3β (Ser9, Akt (Ser473, and VASP (Ser239 activities were determined with western blot. The mPTP opening was evaluated by measuring mitochondrial membrane potential (ΔΨm. Nitric oxide (NO generation was measured by 4-amino-5-methylamino-2′, 7′-difluorofluorescein (DAF-FM diacetate. Fluorescence images were obtained with confocal microscopy. Results. Astragaloside IV significantly enhanced GSK-3β phosphorylation and prevented H2O2-induced loss of ΔΨm. These effects of astragaloside IV were reversed by the phosphatidylinositol 3-kinase (PI3K inhibitor LY294002, the NO sensitive guanylyl cyclase selective inhibitor ODQ, and the PKG inhibitor KT5823. Astragaloside IV activated Akt and PKG. Astragaloside IV was also shown to increase NO production, an effect that was reversed by L-NAME and LY294002. Astragaloside IV applied at reperfusion reduced cell death caused by simulated ischemia/reperfusion, indicating that astragaloside IV can prevent reperfusion injury. Conclusions. These data suggest that astragaloside IV prevents the mPTP opening and reperfusion injury by inactivating GSK-3β through the NO/cGMP/PKG signaling pathway. NOS is responsible for NO generation and is activated by the PI3K/Akt pathway.

  1. 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

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

    Science.gov (United States)

    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.

  3. Three-dimensional image analysis of plugging at the septal pore by Woronin body during hypotonic shock inducing hyphal tip bursting in the filamentous fungus Aspergillus oryzae

    International Nuclear Information System (INIS)

    Maruyama, Jun-ichi; Juvvadi, Praveen Rao; Ishi, Kazutomo; Kitamoto, Katsuhiko

    2005-01-01

    We observed that the filamentous fungus, Aspergillus oryzae, grown on agar media burst out cytoplasmic constituents from the hyphal tip soon after flooding with water. Woronin body is a specialized organelle known to plug the septal pore adjacent to the lysed compartment to prevent extensive loss of cytoplasm. A. oryzae Aohex1 gene homologous to Neurospora crassa HEX1 gene encoding a major protein in Woronin body was expressed as a fusion with DsRed2, resulting in visualization of Woronin body. Confocal microscopy and three-dimensional reconstruction of images visualized the septal pore as a dark region surrounded by green fluorescence of EGFP-fused secretory protein, RNase T1, on the septum. Dual fluorescent labeling revealed the plugging of the septal pores adjacent to the lysed apical compartments by Woronin bodies during hypotonic shock. Disruption of Aohex1 gene caused disappearance of Woronin bodies and the defect to prevent extensive loss of cytoplasm during hypotonic shock

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2010-01-01

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

  6. Temperature-induced phase transformations of the small-pore zirconosilicate Na2ZrSi2O7 center dot H2O

    Czech Academy of Sciences Publication Activity Database

    Petrova, N.R.; Noriaki, N.; Bakardjieva, Snejana; Bezdička, Petr; Vladislav, K.K.

    2011-01-01

    Roč. 13, č. 5 (2011), s. 1187-1190 ISSN 1293-2558 Institutional research plan: CEZ:AV0Z40320502 Keywords : Sodium zirconosilicate * Small-pore material * Topotactic dehydration * Phase transition Subject RIV: CA - Inorganic Chemistry Impact factor: 1.856, year: 2011

  7. Periodically ordered meso – and macroporous SiO2 thin films and their induced electrochemical activity as a function of pore hierarchy

    Czech Academy of Sciences Publication Activity Database

    Sel, O.; Sallard, S.; Brezesinski, T.; Rathouský, Jiří; Dunphy, D. R.; Collord, A.; Smarsly, B. M.

    2007-01-01

    Roč. 17, č. 16 (2007), s. 3241-3250 ISSN 1616-301X Institutional research plan: CEZ:AV0Z40400503 Keywords : SiO2 * thin films * pore hierarchy * electrochemistry Subject RIV: CG - Electrochemistry Impact factor: 7.496, year: 2007

  8. 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.

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

    Science.gov (United States)

    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.

  10. Modulating the skin barrier function by DMSO: molecular dynamics simulations of hydrophilic and hydrophobic transmembrane pores

    NARCIS (Netherlands)

    den Otter, Wouter K.; Notman, R.; Anwar, J.; Noro, M.G.; Briels, Willem J.

    2008-01-01

    The dense lipid bilayers at the outer surface of the skin represent the primary barrier to molecules penetrating the human skin. One approach to overcome this barrier, with promising applications in administering medicinal drugs to the body, is to employ chemical permeability enhancers. How these

  11. Functions of phenylalanine residues within the beta-barrel stem of the anthrax toxin pore.

    Directory of Open Access Journals (Sweden)

    Jie Wang

    2009-07-01

    Full Text Available A key step of anthrax toxin action involves the formation of a protein-translocating pore within the endosomal membrane by the Protective Antigen (PA moiety. Formation of this transmembrane pore by PA involves interaction of the seven 2beta2-2beta3 loops of the heptameric precursor to generate a 14-strand transmembrane beta barrel.We examined the effects on pore formation, protein translocation, and cytotoxicity, of mutating two phenylalanines, F313 and F314, that lie at the tip the beta barrel, and a third one, F324, that lies part way up the barrel.Our results show that the function of these phenylalanine residues is to mediate membrane insertion and formation of stable transmembrane channels. Unlike F427, a key luminal residue in the cap of the pore, F313, F314, and F324 do not directly affect protein translocation through the pore. Our findings add to our knowledge of structure-function relationships of a key virulence factor of the anthrax bacillus.

  12. Molecular pharmacological phenotyping of EBI2. An orphan seven-transmembrane receptor with constitutive activity

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Benned-Jensen, Tau; Holst, Peter J

    2006-01-01

    Epstein-Barr virus (EBV)-induced receptor 2 (EBI2) is an orphan seven-transmembrane (7TM) receptor originally identified as the most up-regulated gene (>200-fold) in EBV-infected cells. Here we show that EBI2 signals with constitutive activity through Galpha(i) as determined by a receptor...

  13. [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.

  14. Radial symmetry in a chimeric glutamate receptor pore

    Science.gov (United States)

    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.

  15. Pore-Scale Study of Transverse Mixing Induced CaCO 3 Precipitation and Permeability Reduction in a Model Subsurface Sedimentary System

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Changyong; Dehoff, Karl; Hess, Nancy; Oostrom, Mart; Wietsma, Thomas W.; Valocchi, Albert J.; Fouke, Bruce W.; Werth, Charles J.

    2010-10-15

    A microfluidic pore structure etched into a silicon wafer was used as a two-dimensional model subsurface sedimentary system (i.e., a micromodel) to study mineral precipitation and permeability reduction relevant to groundwater remediation and geological carbon sequestration. Solutions containing CaCl2 and Na2CO3 at four different saturation states (Ω = [Ca2+] [CO32-] / KspCaCO3) were introduced through two separate inlets and they mixed by diffusion transverse to the main flow direction along the center of the micromodel resulting in CaCO3 precipitation. Precipitation rates increased and the total amount of precipitates decreased with increasing saturation state, and only vaterite and calcite crystals were formed (no aragonite). The relative amount of vaterite increased from 80% at the lowest saturation (Ωv = 2.8 for vaterite) state to 95% at the highest saturation state (Ωv = 4.5). Fluorescent tracer tests conducted before and after CaCO3 precipitation indicate that pore spaces were completely occluded by CaCO3 precipitates along the transverse mixing zone, thus significantly reducing porosity and permeability, and potentially limiting transformation from vaterite to the more stable calcite. The results suggest that mineral precipitation along plume margins can decrease both reactant mixing during groundwater remediation, and injection and storage efficiency during CO2 sequestration.

  16. 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.

  17. 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

  18. 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...

  19. 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.

  20. A study on chloride induced depassivation of Fe-P-C-Si and Fe-P-C-Si-N steels in simulated concrete pore solution

    Science.gov (United States)

    Mehta, Yashwant; Chaudhari, Gajanan P.; Dabhade, Vikram V.

    2018-03-01

    The corrosion behaviour of high phosphorous steels containing varying amounts of silicon and nitrogen was studied by potentiodynamic polarization, linear polarization resistance (LPR) and electrochemical impedance spectroscopy (EIS) measurements. The morphology of a steel specimen tested in chloride containing concrete pore solution was studied using scanning electron microscope (SEM) and the elemental distribution at the pitting corrosion area was investigated using electron dispersive spectroscopy (EDS). The results showed that the capacitance increased and resistance declined with immersion time in Ca(OH)2 solution containing 0.1% chloride for plain carbon steel. The opposite was observed in the case of the high phosphorous steels. The potentiodynamic polarization and LPR results complement the EIS findings. Corrosion behaviour could be described with an equivalent circuit having two time constants. The creation, expansion and degradation of the passive layer were discussed with the help of the equivalent circuit elements. The SEM-EDS studies revealed that MnS inclusions at the surface could have a role in the initiation and growth of pits and that phosphorous was present at the pit free surface of the steel.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. A monocyte chemotaxis inhibiting factor in serum of HIV infected men shares epitopes with the HIV transmembrane protein gp41

    NARCIS (Netherlands)

    Tas, M.; Drexhage, H. A.; Goudsmit, J.

    1988-01-01

    This report describes that gp41, the transmembranous envelope protein of HIV, is able to inhibit monocyte chemotaxis (measured as FMLP-induced polarization). To study the presence of such immunosuppressive HIV env proteins in the circulation of HIV-infected men, fractions were prepared from serum

  7. Selective elimination of high constitutive activity or chemokine binding in the human herpesvirus 8 encoded seven transmembrane oncogene ORF74

    DEFF Research Database (Denmark)

    Rosenkilde, M M; Kledal, T N; Holst, Peter Johannes

    2000-01-01

    Open reading frame 74 (ORF74) encoded by human herpesvirus 8 is a highly constitutively active seven transmembrane (7TM) receptor stimulated by angiogenic chemokines, e.g. growth-related oncogene-alpha, and inhibited by angiostatic chemokines e.g. interferon-gamma-inducible protein. Transgenic mice...

  8. Three-dimensional structures of the mammalian multidrug resistance P-glycoprotein demonstrate major conformational changes in the transmembrane domains upon nucleotide binding.

    Science.gov (United States)

    Rosenberg, Mark F; Kamis, Alhaji Bukar; Callaghan, Richard; Higgins, Christopher F; Ford, Robert C

    2003-03-07

    P-glycoprotein is an ATP-binding cassette transporter that is associated with multidrug resistance and the failure of chemotherapy in human patients. We have previously shown, based on two-dimensional projection maps, that P-glycoprotein undergoes conformational changes upon binding of nucleotide to the intracellular nucleotide binding domains. Here we present the three-dimensional structures of P-glycoprotein in the presence and absence of nucleotide, at a resolution limit of approximately 2 nm, determined by electron crystallography of negatively stained crystals. The data reveal a major reorganization of the transmembrane domains throughout the entire depth of the membrane upon binding of nucleotide. In the absence of nucleotide, the two transmembrane domains form a single barrel 5-6 nm in diameter and about 5 nm deep with a central pore that is open to the extracellular surface and spans much of the membrane depth. Upon binding nucleotide, the transmembrane domains reorganize into three compact domains that are each 2-3 nm in diameter and 5-6 nm deep. This reorganization opens the central pore along its length in a manner that could allow access of hydrophobic drugs (transport substrates) directly from the lipid bilayer to the central pore of the transporter.

  9. Cationic PAMAM dendrimers as pore-blocking binary toxin inhibitors.

    Science.gov (United States)

    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.

  10. Intrinsic potential of cell membranes: opposite effects of lipid transmembrane asymmetry and asymmetric salt ion distribution

    DEFF Research Database (Denmark)

    Gurtovenko, Andrey A; Vattulainen, Ilpo

    2009-01-01

    Using atomic-scale molecular dynamics simulations, we consider the intrinsic cell membrane potential that is found to originate from a subtle interplay between lipid transmembrane asymmetry and the asymmetric distribution of monovalent salt ions on the two sides of the cell membrane. It turns out......Cl saline solution and the PE leaflet is exposed to KCl, the outcome is that the effects of asymmetric lipid and salt ion distributions essentially cancel one another almost completely. Overall, our study highlights the complex nature of the intrinsic potential of cell membranes under physiological...... that both the asymmetric distribution of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) lipids across a membrane and the asymmetric distribution of NaCl and KCl induce nonzero drops in the transmembrane potential. However, these potential drops are opposite in sign. As the PC leaflet faces a Na...

  11. 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.

  12. Tracking the Chemical Transformations at the Brønsted Acid Site upon Water-Induced Deprotonation in a Zeolite Pore

    Energy Technology Data Exchange (ETDEWEB)

    Vjunov, Aleksei; Wang, Meng; Govind, Niranjan; Huthwelker, Thomas; Shi, Hui; Mei, Donghai; Fulton, John L.; Lercher, Johannes A.

    2017-10-23

    We report the structural changes induced by Brønsted acidic site deprotonation in a zeolite with MFI structure as a function of temperature up to 430°C using in situ Al K-edge X-ray absorption fine structure spectroscopy (XAFS). At ambient conditions, the protons are present as hydrated hydronium ions (H3O+(H2O)n) that are ion-paired to the anionic, Al tetrahedral (T) site. At elevated temperatures, loss of water molecules hydrating the hydronium ions leads to an unstable free hydronium ion that disso-ciates to form the hydroxylated T-site. The formation of this (-O3)-Al-(OH-) species leads to the elongation of one of the four Al-O bonds and causes significant distortion of the tetrahedral symmetry about the Al atom. This distortion leads to the appearance of new pre-edge features in the Al K-edge X-ray absorption near edge structure (XANES) spectra. The pre-edge peak assignment is confirmed by time-dependent density functional theory calculation of the XANES spectrum. The XANES spectra are also sensitive to solutes or solvent that are in proximity to the T-site. A second structural transition occurs at about the same temperature, namely the conversion of a minor fraction of extra-framework octahedral Al present in the sample at ambient conditions to a tetrahedral species through the de-coordination of H2O-ligands. Both IR spectroscopy and thermogravimetric analysis (TGA) are further used to confirm the overall chemical transformation of the T-site.

  13. Co-Assembled Supported Catalysts: Synthesis of Nano-Structured Supported Catalysts with Hierarchic Pores through Combined Flow and Radiation Induced Co-Assembled Nano-Reactors

    Directory of Open Access Journals (Sweden)

    Galip Akay

    2016-05-01

    Full Text Available A novel generic method of silica supported catalyst system generation from a fluid state is presented. The technique is based on the combined flow and radiation (such as microwave, thermal or UV induced co-assembly of the support and catalyst precursors forming nano-reactors, followed by catalyst precursor decomposition. The transformation from the precursor to supported catalyst oxide state can be controlled from a few seconds to several minutes. The resulting nano-structured micro-porous silica supported catalyst system has a surface area approaching 300 m2/g and X-ray Diffraction (XRD-based catalyst size controlled in the range of 1–10 nm in which the catalyst structure appears as lamellar sheets sandwiched between the catalyst support. These catalyst characteristics are dependent primarily on the processing history as well as the catalyst (Fe, Co and Ni studied when the catalyst/support molar ratio is typically 0.1–2. In addition, Ca, Mn and Cu were used as co-catalysts with Fe and Co in the evaluation of the mechanism of catalyst generation. Based on extensive XRD, Scanning Electron Microscopy (SEM and Transmission Electron Microscopy (TEM studies, the micro- and nano-structure of the catalyst system were evaluated. It was found that the catalyst and silica support form extensive 0.6–2 nm thick lamellar sheets of 10–100 nm planar dimensions. In these lamellae, the alternate silica support and catalyst layer appear in the form of a bar-code structure. When these lamellae structures pack, they form the walls of a micro-porous catalyst system which typically has a density of 0.2 g/cm3. A tentative mechanism of catalyst nano-structure formation is provided based on the rheology and fluid mechanics of the catalyst/support precursor fluid as well as co-assembly nano-reactor formation during processing. In order to achieve these structures and characteristics, catalyst support must be in the form of silane coated silica nano

  14. Particles in Pores

    DEFF Research Database (Denmark)

    Yuan, Hao

    migration and recapture; (6) Induced colloid migration for enhanced oil recovery; (7) Estimating filtration coefficients for straining. These studies have been spearately published as journal papers, conference papers and book chapters. Nevertheless, they are not independent of one another but logically...... cakes in the injection wells gives rise to the steady stage of the injectivity and filling rat holes in the well (Chapter 4). The migration of surfaceassociated colloids gives rise to non-monotonic deposition profiles (Chapter 5). Migration and straining of reservoir fines may enhance oil receovery...

  15. Transmembrane helices can induce domain formation in crowded model membranes

    NARCIS (Netherlands)

    Domanski, Jan; Marrink, Siewert J.; Schäfer, Lars V.

    We studied compositionally heterogeneous multi-component model membranes comprised of saturated lipids, unsaturated lipids, cholesterol, and a-helical TM protein models using coarse-grained molecular dynamics simulations. Reducing the mismatch between the length of the saturated and unsaturated

  16. 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.

  17. 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.

  18. Diffusion and electromigration in clay bricks influenced by differences in the pore system resulting from firing

    DEFF Research Database (Denmark)

    Rörig-Dalgaard, Inge; Ottosen, Lisbeth M.; Hansen, Kurt Kielsgaard

    2012-01-01

    Ion transport in porous materials has been subject of study for several decades. However, the interaction between the pores and the overall pore system make it complicated to obtain a clear picture and predict diffusion and electromigration (transport induced by an applied electric field). Specific...... to the distance to the surface.The influence of the pore system on ion transport through the water saturated pore system of the bricks was supported by measurements for calculation of the electrical resistance and an increasing resistance was found for increasing brick firing temperatures. The effective diffusion...... the pore system to contribute to an overall understanding of ion transport in porous materials.The pore system in bricks are influenced by the firing degree, clay mixture composition and ion content. The present paper focuses on the pore system and effects from clay mixture composition and ion content were...

  19. 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.

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

    Science.gov (United States)

    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

  1. An investigation of fractal characteristics of mesoporous carbon electrodes with various pore structures

    International Nuclear Information System (INIS)

    Pyun, Su-Il; Rhee, Chang-Kyu

    2004-01-01

    Fractal characteristics of mesoporous carbon electrodes were investigated with various pore structures using the N 2 gas adsorption method and the transmission electron microscopy (TEM) image analysis method. The mesoporous carbons with various pore structures were prepared by imprinting mesophase pitch used as a carbonaceous precursor with different colloidal silica particles. All imprinted mesoporous carbons were composed of two groups of pores produced from the carbonisation of mesophase pitch and from the silica imprinting. The overall surface fractal dimensions of the carbon specimens were determined from the analyses of the N 2 gas adsorption isotherms. In order to distinguish the surface fractal dimension of the carbonisation-induced pore surface from that fractal dimension of the silica-imprinted pore surface, the individual surface fractal dimensions were determined from the image analyses of the TEM images. From the comparison of the overall surface fractal dimension with the individual surface fractal dimensions, it was recognised that the overall surface fractal dimension is crucially influenced by the individual surface fractal dimension of the silica-imprinted pore surface. Moreover, from the fact that the silica-imprinted pore surface with broad relative pore size distribution (PSD) gave lower value of the individual surface fractal dimension than that pore surface with narrow relative PSD, it is concluded that as the silica-imprinted pores comprising the carbon specimen agglomerate, the individual surface fractal dimension of that pore surface decreases

  2. 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

  3. Killing machines: three pore-forming proteins of the immune system

    Science.gov (United States)

    McCormack, Ryan; de Armas, Lesley; Shiratsuchi, Motoaki

    2014-01-01

    The evolution of early multicellular eukaryotes 400–500 million years ago required a defensive strategy against microbial invasion. Pore-forming proteins containing the membrane-attack-complex-perforin (MACPF) domain were selected as the most efficient means to destroy bacteria or virally infected cells. The mechanism of pore formation by the MACPF domain is distinctive in that pore formation is purely physical and unspecific. The MACPF domain polymerizes, refolds, and inserts itself into bilayer membranes or bacterial outer cell walls. The displacement of surface lipid/carbohydrate molecules by the polymerizing MACPF domain creates clusters of large, water-filled holes that destabilize the barrier function and provide access for additional anti-bacterial or anti-viral effectors to sensitive sites that complete the destruction of the invader via enzymatic or chemical attack. The highly efficient mechanism of anti-microbial defense by a combined physical and chemical strategy using pore-forming MACPF-proteins has been retargeted during evolution of vertebrates and mammals for three purposes: (1) to kill extracellular bacteria C9/polyC9 evolved in conjunction with complement, (2) to kill virus infected and cancer cells perforin-1/polyperforin-1 CTL evolved targeted by NK and CTL, and (3) to kill intracellular bacteria transmembrane perforin-2/putative polyperforin-2 evolved targeted by phagocytic and nonphagocytic cells. Our laboratory has been involved in the discovery and description of each of the three pore-formers that will be reviewed here. PMID:24293008

  4. 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.

  5. Coating of silicon pore optics

    DEFF Research Database (Denmark)

    Cooper-Jensen, Carsten P.; Ackermann, M.; Christensen, Finn Erland

    2009-01-01

    For the International X-ray observatory (IXO), a mirror module with an effective area of 3 m2 at 1.25 keV and at least 0.65 m2 at 6 keV has to be realized. To achieve this goal, coated silicon pore optics has been developed over the last years. One of the challenges is to coat the Si plates...

  6. 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.

  7. 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...

  8. 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.

  9. 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...

  10. Solid-State Nuclear Magnetic Resonance Investigation of the Structural Topology and Lipid Interactions of a Viral Fusion Protein Chimera Containing the Fusion Peptide and Transmembrane Domain.

    Science.gov (United States)

    Yao, Hongwei; Lee, Myungwoon; Liao, Shu-Yu; Hong, Mei

    2016-12-13

    The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of parainfluenza virus 5 (PIV5) fusion protein F using solid-state nuclear magnetic resonance. These studies provide structural information about the two domains when they are spatially well separated in the fusion process. To investigate how these two domains are structured relative to each other in the postfusion state, when the ectodomain forms a six-helix bundle that is thought to force the FP and TMD together in the membrane, we have now expressed and purified a chimera of the FP and TMD, connected by a Gly-Lys linker, and measured the chemical shifts and interdomain contacts of the protein in several lipid membranes. The FP-TMD chimera exhibits α-helical chemical shifts in all the membranes examined and does not cause strong curvature of lamellar membranes or membranes with negative spontaneous curvature. These properties differ qualitatively from those of the separate peptides, indicating that the FP and TMD interact with each other in the lipid membrane. However, no 13 C- 13 C cross peaks are observed in two-dimensional correlation spectra, suggesting that the two helices are not tightly associated. These results suggest that the ectodomain six-helix bundle does not propagate into the membrane to the two hydrophobic termini. However, the loosely associated FP and TMD helices are found to generate significant negative Gaussian curvature to membranes that possess spontaneous positive curvature, consistent with the notion that the FP-TMD assembly may

  11. 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

  12. 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 ...

  13. 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.

  14. 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

  15. Effect of Pore Geometry on Gas Adsorption: Grand Canonical Monte Carlo Simulation Studies

    International Nuclear Information System (INIS)

    Lee, Eon Ji; Chang, Rak Woo; Han, Ji Hyung; Chung, Taek Dong

    2012-01-01

    In this study, we investigated the pure geometrical effect of porous materials in gas adsorption using the grand canonical Monte Carlo simulations of primitive gas-pore models with various pore geometries such as planar, cylindrical, and random pore geometries. Although the model does not possess atomistic level details of porous materials, our simulation results provided many insightful information in the effect of pore geometry on the adsorption behavior of gas molecules. First, the surface curvature of porous materials plays a significant role in the amount of adsorbed gas molecules: the concave surface such as in cylindrical pores induces more attraction between gas molecules and pore, which results in the enhanced gas adsorption. On the contrary, the convex surface of random pores gives the opposite effect. Second, this geometrical effect shows a nonmonotonic dependence on the gas-pore interaction strength and length. Third, as the external gas pressure is increased, the change in the gas adsorption due to pore geometry is reduced. Finally, the pore geometry also affects the collision dynamics of gas molecules. Since our model is based on primitive description of fluid molecules, our conclusion can be applied to any fluidic systems including reactant-electrode systems

  16. 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....

  17. 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

    major findings were: (i) the FL strain encodes 16 virion transmembrane proteins; (ii) eight of these proteins are essential for viral growth in vitro ; (iii) seven of the nonessential proteins affect viral growth in vitro , and two affect virulence in vivo ; and (iv) a mutant lacking ORF25 is highly attenuated but induces moderate immune protection. This study represents a major breakthrough in understanding the biology of CyHV-3 and will contribute to the development of prophylactic methods. It also provides a firm basis for the further research on alloherpesvirus virion transmembrane proteins. Copyright © 2017 Vancsok et al.

  18. Staphylococcus aureus α-Toxin Induces Actin Filament Remodeling in Human Airway Epithelial Model Cells.

    Science.gov (United States)

    Ziesemer, Sabine; Eiffler, Ina; Schönberg, Alfrun; Müller, Christian; Hochgräfe, Falko; Beule, Achim G; Hildebrandt, Jan-Peter

    2018-04-01

    Exposure of cultured human airway epithelial model cells (16HBE14o-, S9) to Staphylococcus aureus α-toxin (hemolysin A, Hla) induces changes in cell morphology and cell layer integrity that are due to the inability of the cells to maintain stable cell-cell or focal contacts and to properly organize their actin cytoskeletons. The aim of this study was to identify Hla-activated signaling pathways involved in regulating the phosphorylation level of the actin-depolymerizing factor cofilin. We used recombinant wild-type hemolysin A (rHla) and a variant of Hla (rHla-H35L) that is unable to form functional transmembrane pores to treat immortalized human airway epithelial cells (16HBE14o-, S9) as well as freshly isolated human nasal tissue. Our results indicate that rHla-mediated changes in cofilin phosphorylation require the formation of functional Hla pores in the host cell membrane. Formation of functional transmembrane pores induced hypophosphorylation of cofilin at Ser3, which was mediated by rHla-induced attenuation of p21-activated protein kinase and LIM kinase activities. Because dephosphorylation of pSer3-cofilin results in activation of this actin-depolymerizing factor, treatment of cells with rHla resulted in loss of actin stress fibers from the cells and destabilization of cell shape followed by the appearance of paracellular gaps in the cell layers. Activation of protein kinase A or activation of small GTPases (Rho, Rac, Cdc42) do not seem to be involved in this response.

  19. 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.

  20. 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.

  1. Low rate doses effects of gamma radiation on glycoproteins of transmembrane junctions in fibroblasts

    International Nuclear Information System (INIS)

    Bringas, J.E.; Caceres, J.L.

    1996-01-01

    Glycoproteins of trans-membrane junctions are molecules that help to bind cells with the extracellular matrix. Integrins are the most important trans-membrane molecules among others. The damage of gamma radiation on those proteins could be an important early event that causes membrane abnormalities which may lead to cell malfunction and cancer induced by radiation due to cell dissociation. Randomized blocks with 3 repetitions of mouse embryo fibroblast cultures, were irradiated with Cobalt-60 gamma rays, during 20 days. Biological damage to glycoproteins and integrins was evaluated by cellular growth and fibroblast proliferative capacity. Integrins damage was studied by isolation by column immunoaffinity chromatography migrated on SDS-Page under reducing and non reducing conditions, and inhibition of integrins extracellular matrix adhesion by monoclonal antibodies effect. The dose/rate (0.05 Gy/day-0.2 Gy/day) of gamma given to cells did not show damage evidence on glycoproteins and integrins. If damage happened, it was repaired by cells very soon, was delayed by continuous cellular division or by glycoproteins characteristic of being multiple extracellular ligatures. Bio effects became more evident with an irradiation time greater than 20 days or a high dose/rate. (authors). 6 refs

  2. Evolution of magnetic and transport properties in pore-modified CoAlO antidot arrays

    International Nuclear Information System (INIS)

    Ma, Y G; Lim, S L; Ong, C K

    2007-01-01

    CoAlO composite antidot arrays were fabricated on self-organized porous anodic aluminium oxide (AAO) membranes. The effects of pore size and film thickness on the magnetism and magnetotransport properties of the CoAlO films were investigated. On increasing the pore dimensions in the arrays, an anisotropic to isotropic magnetism transition was observed. The result is discussed based on the competitive contributions from the external field induced uniaxial anisotropy and the topology-induced shape anisotropy superimposed by the stray fields from the pore channels. Magnetoresistance showed corresponding variations with increasing pore sizes, as evidenced by a magnetoresistance variation from typically anisotropic to nearly isotropic behaviour. When deposited on large-pored AAO membranes, the antidot arrays showed no obvious anisotropy at different film thicknesses. It led to negligible magnetoresistive loops in the thick films of high structural continuity. The possible reasons for spin-independent electron scatterings are discussed

  3. 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.

  4. Variation of Pore Water Pressure in Tailing Sand under Dynamic Loading

    Directory of Open Access Journals (Sweden)

    Jia-xu Jin

    2018-01-01

    Full Text Available Intense vibration affects the pore water pressure in a tailing dam, with the tendency to induce dam liquefaction. In this study, experiments were performed wherein model tailing dams were completely liquefied by sustained horizontal dynamic loading to determine the effects of the vibration frequency, vibration amplitude, and tailing density on the pore water pressure. The results revealed four stages in the increase of the tailing pore water pressure under dynamic loading, namely, a slow increase, a rapid increase, inducement of structural failure, and inducement of complete liquefaction. A lower frequency and smaller amplitude of the vibration were found to increase the time required to achieve a given pore water pressure in dense tailings. Under the effect of these three factors—vibration frequency and amplitude and tailing density—the tailing liquefaction time varied nonlinearly with the height from the base of the tailing dam, with an initial decrease followed by an increase. The pore pressure that induced structural failure also gradually decreased with increasing height. The increase in the tailing pore pressure could be described by an S-shaped model. A complementary multivariate nonlinear equation was also derived for predicting the tailing pore water pressure under dynamic loading.

  5. Mechanical constraint and release generates long, ordered horizontal pores in anodic alumina templates

    International Nuclear Information System (INIS)

    Bolger, Ciara T; Petkov, Nikolay; Holmes, Justin D; Fois, Giovanni; Cross, Graham L W; Sassiat, Nicolas; Burke, Micheál; Quinn, Aidan J

    2012-01-01

    We describe the formation of long, highly ordered arrays of planar oriented anodic aluminum oxide (AAO) pores during plane parallel anodization of thin aluminum ‘finger’ microstructures fabricated on thermally oxidized silicon substrates and capped with a silicon oxide layer. The pore morphology was found to be strongly influenced by mechanical constraint imposed by the oxide layers surrounding the Al fingers. Tractions induced by the SiO 2 substrate and capping layer led to frustrated volume expansion and restricted oxide flow along the interface, with extrusion of oxide into the primary pore volume, leading to the formation of dendritic pore structures and meandering pore growth. However, partial relief of the constraint by a delaminating interfacial fracture, with its tip closely following the anodization front, led to pore growth that was highly ordered with regular, hexagonally packed arrays of straight horizontal pores up to 3 µm long. Detailed characterization of both straight and dendritic planar pores over a range of formation conditions using advanced microscopy techniques is reported, including volume reconstruction, enabling high quality 3D visualization of pore formation. (paper)

  6. 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.

  7. 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.

  8. 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.

  9. Transmembrane START domain proteins: in silico identification, characterization and expression analysis under stress conditions in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Satheesh, Viswanathan; Chidambaranathan, Parameswaran; Jagannadham, Prasanth Tejkumar; Kumar, Vajinder; Jain, Pradeep K; Chinnusamy, Viswanathan; Bhat, Shripad R; Srinivasan, R

    2016-01-01

    Steroidogenic acute regulatory related transfer (StART) proteins that are involved in transport of lipid molecules, play a myriad of functions in insects, mammals and plants. These proteins consist of a modular START domain of approximately 200 amino acids which binds and transfers the lipids. In the present study we have performed a genome-wide search for all START domain proteins in chickpea. The search identified 36 chickpea genes belonging to the START domain family. Through a phylogenetic tree reconstructed with Arabidopsis, rice, chickpea, and soybean START proteins, we were able to identify four transmembrane START (TM-START) proteins in chickpea. These four proteins are homologous to the highly conserved mammalian phosphatidylcholine transfer proteins. Multiple sequence alignment of all the transmembrane containing START proteins from Arabidopsis, rice, chickpea, and soybean revealed that the amino acid residues to which phosphatidylcholine binds in mammals, is also conserved in all these plant species, implying an important functional role and a very similar mode of action of all these proteins across dicots and monocots. This study characterizes a few of the not so well studied transmembrane START superfamily genes that may be involved in stress signaling. Expression analysis in various tissues showed that these genes are predominantly expressed in flowers and roots of chickpea. Three of the chickpea TM-START genes showed induced expression in response to drought, salt, wound and heat stress, suggesting their role in stress response.

  10. Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

    Directory of Open Access Journals (Sweden)

    Peter Spijker

    2010-06-01

    Full Text Available Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

  11. 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.

  12. 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.

  13. 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....

  14. 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.

  15. Role of α and β Transmembrane Domains in Integrin Clustering

    Directory of Open Access Journals (Sweden)

    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.

  16. Structure and function of the cystic fibrosis transmembrane conductance regulator

    Directory of Open Access Journals (Sweden)

    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.

  17. Fabrication of three-dimensional poly(ε-caprolactone) scaffolds with hierarchical pore structures for tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingchun [Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237 (China); Luo, Houyong [State Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, Shanghai 200237 (China); Zhang, Yan [Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237 (China); Zhou, Yan [State Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, Shanghai 200237 (China); Ye, Zhaoyang, E-mail: zhaoyangye@ecust.edu.cn [State Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, Shanghai 200237 (China); Tan, Wensong [State Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, Shanghai 200237 (China); Lang, Meidong, E-mail: mdlang@ecust.edu.cn [Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237 (China)

    2013-05-01

    The physical properties of tissue engineering scaffolds such as microstructures play important roles in controlling cellular behaviors and neotissue formation. Among them, the pore size stands out as a key determinant factor. In the present study, we aimed to fabricate porous scaffolds with pre-defined hierarchical pore sizes, followed by examining cell growth in these scaffolds. This hierarchical porous microstructure was implemented via integrating different pore-generating methodologies, including salt leaching and thermal induced phase separation (TIPS). Specifically, large (L, 200–300 μm), medium (M, 40–50 μm) and small (S, < 10 μm) pores were able to be generated. As such, three kinds of porous scaffolds with a similar porosity of ∼ 90% creating pores of either two (LS or MS) or three (LMS) different sizes were successfully prepared. The number fractions of different pores in these scaffolds were determined to confirm the hierarchical organization of pores. It was found that the interconnectivity varied due to the different pore structures. Besides, these scaffolds demonstrated similar compressive moduli under dry and hydrated states. The adhesion, proliferation, and spatial distribution of human fibroblasts within the scaffolds during a 14-day culture were evaluated with MTT assay and fluorescence microscopy. While all three scaffolds well supported the cell attachment and proliferation, the best cell spatial distribution inside scaffolds was achieved with LMS, implicating that such a controlled hierarchical microstructure would be advantageous in tissue engineering applications. Highlights: ► The scaffolds with dual-pore and triple-pore structures were fabricated. ► Triple-pore structure had better interconnectivity than dual-pore structures. ► Better cell migration and distribution were found on the triple-pore structures. ► The medium pore size (45–50 μm) was appropriate for cell migration. ► Scaffolds with triple-pore structure

  18. 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.

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

    Science.gov (United States)

    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.

  20. 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

  1. Effect of Spin-Crossover-Induced Pore Contraction on CO2–Host Interactions in the Porous Coordination Polymers [Fe(pyrazine)M(CN)4] (M = Ni, Pt)

    Energy Technology Data Exchange (ETDEWEB)

    Culp, Jeffrey T; Chen, De-Li; Liu, Jinchen; Chirdon, Danielle; Kauffman, Kristi; Goodman, Angela; Johnson, J Karl

    2013-02-01

    Variable-temperature in situ ATR-FTIR spectra are presented for the porous spin-crossover compounds [Fe(pyrazine)Ni(CN)4] and [Fe(pyrazine)Pt(CN)4] under CO2 pressures of up to 8 bar. Significant shifts in the ν3 and ν2 IR absorption bands of adsorbed CO2 are observed as the host materials undergo transition between low- and high-spin states. Computational models used to determine the packing arrangement of CO2 within the pore structures show a preferred orientation of one of the adsorbed CO2 molecules with close O=C=O···H contacts with the pyrazine pillar ligands. The interaction is a consequence of the commensurate distance of the inter-pyrazine separations and the length of the CO2 molecule, which allows the adsorbed CO2 to effectively bridge the pyrazine pillars in the structure. The models were used to assign the distinct shifts in the IR absorption bands of the adsorbed CO2 that arise from changes in the O=C=O···H contacts that strengthen and weaken in correlation with changes in the Fe–N bond lengths as the spin state of Fe changes. The results indicate that spin-crossover compounds can function as a unique type of flexible sorbent in which the pore contractions associated with spin transition can affect the strength of CO2–host interactions.

  2. FINGERPRINT MATCHING BASED ON PORE CENTROIDS

    Directory of Open Access Journals (Sweden)

    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.

  3. 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.

  4. Predicting Reactive Transport Dynamics in Carbonates using Initial Pore Structure

    Science.gov (United States)

    Menke, H. P.; Nunes, J. P. P.; Blunt, M. J.

    2017-12-01

    Understanding rock-fluid interaction at the pore-scale is imperative for accurate predictive modelling of carbon storage permanence. However, coupled reactive transport models are computationally expensive, requiring either a sacrifice of resolution or high performance computing to solve relatively simple geometries. Many recent studies indicate that initial pore structure many be the dominant mechanism in determining the dissolution regime. Here we investigate how well the initial pore structure is predictive of distribution and amount of dissolution during reactive flow using particle tracking on the initial image. Two samples of carbonate rock with varying initial pore space heterogeneity were reacted with reservoir condition CO2-saturated brine and scanned dynamically during reactive flow at a 4-μm resolution between 4 and 40 times using 4D X-ray micro-tomography over the course of 1.5 hours using μ-CT. Flow was modelled on the initial binarized image using a Navier-Stokes solver. Particle tracking was then run on the velocity fields, the streamlines were traced, and the streamline density was calculated both on a voxel-by-voxel and a channel-by-channel basis. The density of streamlines was then compared to the amount of dissolution in subsequent time steps during reaction. It was found that for the flow and transport regimes studied, the streamline density distribution in the initial image accurately predicted the dominant pathways of dissolution and gave good indicators of the type of dissolution regime that would later develop. This work suggests that the eventual reaction-induced changes in pore structure are deterministic rather than stochastic and can be predicted with high resolution imaging of unreacted rock.

  5. Induction of IL-1 during hemodialysis: Transmembrane passage of intact endotoxins (LPS)

    Energy Technology Data Exchange (ETDEWEB)

    Laude-Sharp, M.; Caroff, M.; Simard, L.; Pusineri, C.; Kazatchkine, M.D.; Haeffner-Cavaillon, N. (INSERM U 28, Hopital Broussais, Paris (France))

    1990-12-01

    Circulating monocytes of patients undergoing chronic hemodialysis are triggered to produce interleukin-1 (IL-1) in vivo. Intradialytic induction of IL-1 is associated with complement activation in patients dialyzed with first-use cellulose membranes. Chronic stimulation of IL-1 production occurs because of an yet unidentified mechanism in patients dialyzed with high permeability membranes. The present study demonstrates that intact bacterial lipopolysaccharide (LPS) molecules may cross cuprophan, AN69 and polysulfone membranes under in vitro conditions simulating in vivo hemodialysis. The experiments used purified LPS from Neisseria meningitidis and LPS from Pseudomonas testosteroni, a bacterial strain grown out from a clinically used dialysate. LPS were purified to homogeneity and radiolabeled. Transmembrane passage of 3H-labeled LPS was observed within the first five minutes of dialysis. A total of 0.1 to 1% of 3H-labeled LPS were recovered in the dialysate compartment after one hour of dialysis. High amounts of LPS, representing 40 to 70% of the amount originally present in the dialysate, were absorbed onto high permeability membranes. Low amounts of LPS were absorbed onto cuprophan membranes. The amount of LPS absorbed decreased with the concentration of LPS in the dialysate. LPS recovered from the blood compartment exhibited the same molecular weight as that used to contaminate the dialysate. Biochemically detectable transmembrane passage of LPS was not associated with that of material detectable using the limulus amebocyte lysate (LAL) assay. An IL-1-inducing activity was, however, detected in the blood compartment upon dialysis with high permeability membranes, as previously found by others with cuprophan membranes.

  6. Induction of IL-1 during hemodialysis: Transmembrane passage of intact endotoxins (LPS)

    International Nuclear Information System (INIS)

    Laude-Sharp, M.; Caroff, M.; Simard, L.; Pusineri, C.; Kazatchkine, M.D.; Haeffner-Cavaillon, N.

    1990-01-01

    Circulating monocytes of patients undergoing chronic hemodialysis are triggered to produce interleukin-1 (IL-1) in vivo. Intradialytic induction of IL-1 is associated with complement activation in patients dialyzed with first-use cellulose membranes. Chronic stimulation of IL-1 production occurs because of an yet unidentified mechanism in patients dialyzed with high permeability membranes. The present study demonstrates that intact bacterial lipopolysaccharide (LPS) molecules may cross cuprophan, AN69 and polysulfone membranes under in vitro conditions simulating in vivo hemodialysis. The experiments used purified LPS from Neisseria meningitidis and LPS from Pseudomonas testosteroni, a bacterial strain grown out from a clinically used dialysate. LPS were purified to homogeneity and radiolabeled. Transmembrane passage of 3H-labeled LPS was observed within the first five minutes of dialysis. A total of 0.1 to 1% of 3H-labeled LPS were recovered in the dialysate compartment after one hour of dialysis. High amounts of LPS, representing 40 to 70% of the amount originally present in the dialysate, were absorbed onto high permeability membranes. Low amounts of LPS were absorbed onto cuprophan membranes. The amount of LPS absorbed decreased with the concentration of LPS in the dialysate. LPS recovered from the blood compartment exhibited the same molecular weight as that used to contaminate the dialysate. Biochemically detectable transmembrane passage of LPS was not associated with that of material detectable using the limulus amebocyte lysate (LAL) assay. An IL-1-inducing activity was, however, detected in the blood compartment upon dialysis with high permeability membranes, as previously found by others with cuprophan membranes

  7. 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

  8. Self-assembled isoporous block copolymer membranes with tuned pore sizes

    KAUST Repository

    Yu, Haizhou

    2014-07-23

    The combination of nonsolvent-induced phase separation and the self-assembly of block copolymers can lead to asymmetric membranes with a thin highly ordered isoporous skin layer. The effective pore size of such membranes is usually larger than 15 nm. We reduced the pore size of these membranes by electroless gold deposition. We demonstrate that the pore sizes can be controlled precisely between 3 and 20 nm leading to a tunable sharp size discrimination in filtration processes. Besides fractionation of nanoparticles and biomaterials, controlled drug delivery is an attractive potential application. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Self-assembled isoporous block copolymer membranes with tuned pore sizes

    KAUST Repository

    Yu, Haizhou; Qiu, Xiaoyan; Nunes, Suzanapereira; Peinemann, Klaus-Viktor

    2014-01-01

    The combination of nonsolvent-induced phase separation and the self-assembly of block copolymers can lead to asymmetric membranes with a thin highly ordered isoporous skin layer. The effective pore size of such membranes is usually larger than 15 nm. We reduced the pore size of these membranes by electroless gold deposition. We demonstrate that the pore sizes can be controlled precisely between 3 and 20 nm leading to a tunable sharp size discrimination in filtration processes. Besides fractionation of nanoparticles and biomaterials, controlled drug delivery is an attractive potential application. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Self-assembled isoporous block copolymer membranes with tuned pore sizes.

    Science.gov (United States)

    Yu, Haizhou; Qiu, Xiaoyan; Nunes, Suzana P; Peinemann, Klaus-Viktor

    2014-09-15

    The combination of nonsolvent-induced phase separation and the self-assembly of block copolymers can lead to asymmetric membranes with a thin highly ordered isoporous skin layer. The effective pore size of such membranes is usually larger than 15 nm. We reduced the pore size of these membranes by electroless gold deposition. We demonstrate that the pore sizes can be controlled precisely between 3 and 20 nm leading to a tunable sharp size discrimination in filtration processes. Besides fractionation of nanoparticles and biomaterials, controlled drug delivery is an attractive potential application. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Transmission of integrin β7 transmembrane domain topology enables gut lymphoid tissue development.

    Science.gov (United States)

    Sun, Hao; Lagarrigue, Frederic; Gingras, Alexandre R; Fan, Zhichao; Ley, Klaus; Ginsberg, Mark H

    2018-04-02

    Integrin activation regulates adhesion, extracellular matrix assembly, and cell migration, thereby playing an indispensable role in development and in many pathological processes. A proline mutation in the central integrin β3 transmembrane domain (TMD) creates a flexible kink that uncouples the topology of the inner half of the TMD from the outer half. In this study, using leukocyte integrin α4β7, which enables development of gut-associated lymphoid tissue (GALT), we examined the biological effect of such a proline mutation and report that it impairs agonist-induced talin-mediated activation of integrin α4β7, thereby inhibiting rolling lymphocyte arrest, a key step in transmigration. Furthermore, the α4β7(L721P) mutation blocks lymphocyte homing to and development of the GALT. These studies show that impairing the ability of an integrin β TMD to transmit talin-induced TMD topology inhibits agonist-induced physiological integrin activation and biological function in development. © 2018 Sun et al.

  12. 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

  13. Effect of ionizing radiation on transmembrane potential of Streptococcus

    International Nuclear Information System (INIS)

    Fomenko, B.S.; Akoev, I.G.

    1979-01-01

    Treatment of Streptococcus faecalis with ionizing radiation at doses of 5 to 100 krad is shown to reduce the energy-dependent accumulation of dibenzyldimethylammonium (DDA + ) by the cell. Since transmembrane potential is the moving force of DDA + transport across the membrane, the decrease in DDA + accumulation is suggested to be due to potential reduction. This radiation effect was not due to inactivation of the potential-generating mechanism; thus, the ATPase activity and glycolytic activity of the irradiated cells were higher than in the control. At the same time, the membranes exhibited an increased permeability for K + and protons, which is probably due to structural rearrangements in the membranes after irradiation. It is suggested that the potential reduction results from the increase in proton permeability of membranes

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Transmembrane signalling at the epidermal growth factor receptor. Positive regulation by the C-terminal phosphotyrosine residues

    DEFF Research Database (Denmark)

    Magni, M; Pandiella, A; Helin, K

    1991-01-01

    a positive role in the regulation of transmembrane signalling at the EGF receptor. The stepwise decrease in signal generation observed in single, double and triple point mutants suggest that the role of phosphotyrosine residues is not in the participation in specific amino acid sequences, but rather...... in the double and the triple mutants. In the latter mutant, expression of the EGF-receptor-activated lipolytic enzyme phospholipase C gamma was unchanged, whereas its tyrosine phosphorylation induced by the growth factor was lowered to approx. 25% of that in the controls. In all of the cell clones employed......, the accumulation of inositol phosphates induced by treatment with fetal calf serum varied only slightly, whereas the same effect induced by EGF was consistently lowered in those lines expressing mutated receptors. This decrease was moderate for those receptors missing only the distal tyrosine (point and deletion...

  19. Valve seat pores sealed with thermosetting monomer

    Science.gov (United States)

    Olmore, A. B.

    1966-01-01

    Hard anodic coating provides a smooth wear resistant value seating surface on a cast aluminum alloy valve body. Vacuum impregnation with a thermosetting monomer, diallyl phthalate, seals the pores on the coating to prevent galvanic corrosion.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Different size biomolecules anchoring on porous silicon surface: fluorescence and reflectivity pores infiltration comparative studies

    Energy Technology Data Exchange (ETDEWEB)

    Giovannozzi, Andrea M.; Rossi, Andrea M. [National Institute for Metrological Research, Thermodynamic Division, Strada delle Cacce 91, 10135 Torino (Italy); Renacco, Chiara; Farano, Alessandro [Ribes Ricecrhe Srl, Via Lavoratori Vittime del Col du Mont 24, 11100 Aosta (Italy); Derosas, Manuela [Biodiversity Srl, Via Corfu 71, 25124 Brescia (Italy); Enrico, Emanuele [National Institute for Metrological Research, Electromagnetism Division, Strada delle Cacce 91, 10135 Torino (Italy)

    2011-06-15

    The performance of porous silicon optical based biosensors strongly depends on material nanomorphology, on biomolecules distribution inside the pores and on the ability to link sensing species to the pore walls. In this paper we studied the immobilization of biomolecules with different size, such as antibody anti aflatoxin (anti Aflatox Ab, {proportional_to}150 KDa), malate dehydrogenase (MDH, {proportional_to}36KDa) and metallothionein (MT, {proportional_to}6KDa) at different concentrations on mesoporous silicon samples ({proportional_to}15 nm pores diameter). Fluorescence measurements using FITC- labeled biomolecules and refractive index analysis based on reflectivity spectra have been employed together to detect the amount of proteins bound to the surface and to evaluate their diffusion inside the pores. Here we suggest that these two techniques should be used together to have a better understanding of what happens at the porous silicon surface. In fact, when pores dimensions are not perfectly tuned to the protein size a higher fluorescence signal doesn't often correspond to a higher biomolecules distribution inside the pores. When a too much higher concentration of biomolecule is anchored on the surface, steric crowd effects and repulsive interactions probably take over and hinder pores infiltration, inducing a small or absent shift in the fringe pattern even if a higher fluorescence signal is registered. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  5. 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.

  6. 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.

  7. 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

    Multiple lines of evidence indicate that, during a hydraulic fracture stimulation, the permeability of the unfractured matrix far from the main, induced tensile fracture increases by one to two orders of magnitude. This permeability enhancement is associated with pervasive shear failure in a large region surrounding the main induced fracture. We have performed low-pressure gas sorption, mercury intrusion, and nuclear magnetic resonance measurements along with high-resolution scanning electron microscope imaging on several preserved and unpreserved shale samples from North American basins before and after inducing failure in confined compressive strength tests. We have observed that the pore structure in intact samples exhibits multiscale behavior, with sub-micron-scale pores in organic matter connected in isolated, micron-scale clusters which themselves are connected to each other through a network of microcracks. The organic-hosted pore networks are poorly connected due to a significant number of dead-end pores within the organic matter. Following shear failure, we often observe an increase in pore volume in the sub-micron range, which appears to be related to the formation of microcracks that propagate along grain boundaries and other planes of mechanical strength contrast. This is consistent with other experimental and field evidence. In some cases these microcracks cross or terminate in organic matter, intersecting the organic-hosted pores. The induced microcrack networks typically have low connectivity and do not appreciably increase the connectivity of the overall pore network. However, in other cases the shear deformation results in an overall pore volume decrease; samples which exhibit this behavior tend to have more clay minerals. Our interpretation of these phenomena is as follows. As organic matter is converted to hydrocarbons, organic-hosted pores develop, and the hydrocarbons contained in these pores are overpressured. The disconnected nature of these

  8. 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.

  9. 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.

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

    Directory of Open Access Journals (Sweden)

    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 (Ri 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.

  11. Transmembrane Peptides as Sensors of the Membrane Physical State

    Directory of Open Access Journals (Sweden)

    Stefano Piotto

    2018-05-01

    Full Text Available Cell membranes are commonly considered fundamental structures having multiple roles such as confinement, storage of lipids, sustain and control of membrane proteins. In spite of their importance, many aspects remain unclear. The number of lipid types is orders of magnitude larger than the number of amino acids, and this compositional complexity is not clearly embedded in any membrane model. A diffused hypothesis is that the large lipid palette permits to recruit and organize specific proteins controlling the formation of specialized lipid domains and the lateral pressure profile of the bilayer. Unfortunately, a satisfactory knowledge of lipid abundance remains utopian because of the technical difficulties in isolating definite membrane regions. More importantly, a theoretical framework where to fit the lipidomic data is still missing. In this work, we wish to utilize the amino acid sequence and frequency of the membrane proteins as bioinformatics sensors of cell bilayers. The use of an alignment-free method to find a correlation between the sequences of transmembrane portion of membrane proteins with the membrane physical state (MPS suggested a new approach for the discovery of antimicrobial peptides.

  12. Incorporation of transmembrane hydroxide transport into the chemiosmotic theory.

    Science.gov (United States)

    de Grey, A D

    1999-10-01

    A cornerstone of textbook bioenergetics is that oxidative ATP synthesis in mitochondria requires, in normal conditions of internal and external pH, a potential difference (delta psi) of well over 100 mV between the aqueous compartments that the energy-transducing membrane separates. Measurements of delta psi inferred from diffusion of membrane-permeant ions confirm this, but those using microelectrodes consistently find no such delta psi--a result ostensibly irreconcilable with the chemiosmotic theory. Transmembrane hydroxide transport necessarily accompanies mitochondrial ATP synthesis, due to the action of several carrier proteins; this nullifies some of the proton transport by the respiratory chain. Here, it is proposed that these carriers' structure causes the path of this "lost" proton flow to include a component perpendicular to the membrane but within the aqueous phases, so maintaining a steady-state proton-motive force between the water at each membrane surface and in the adjacent bulk medium. The conflicting measurements of delta psi are shown to be consistent with the response of this system to its chemical environment.

  13. Transmembrane topology of the acetylcholine receptor examined in reconstituted vesicles

    International Nuclear Information System (INIS)

    McCrea, P.D.

    1987-01-01

    Each of the five acetylcholine receptor (AChR) subunits, α 2 β-γδ, is believed to have the same number of transmembrane crossing and to share the same general folding pattern. AChR isolated from the electric organ of electric fish is predominantly dimeric. We have used this bridge as a marker for the C-terminus of the δ subunit, and presumably that of the other subunits in addition. The disulfide's accessibility to hydrophilic reductants, principally glutathione (GSH), was tested in a reconstituted vesicle system. The reduction of the δ-δ desulfide, as evidenced by the transition of AChrR dimers to monomers, was quantitatively monitored on velocity sedimentation sucrose gradients. Alternatively, the reduction of δ 2 to δ was followed by employing non-reducing SDS-PAGE. Reductants such as GSH were able to access the bridge in intact right-side-out vesicles. No acceleration of this process was evident when the vesicles were disrupted by freeze-thaw or by detergents. Control experiments which determined the rate of reduction of entrapped diphtheria toxin, or that of 3 H-GSH efflux, demonstrated that intact reconstituted vesicles provide an adequate permeability barrier to GSH access of their intravesicular space

  14. NMR studies of transmembrane electron transport in human erythrocytes

    International Nuclear Information System (INIS)

    Kennett, E.C.; Bubb, W.A.; Kuchel, P.W.

    2002-01-01

    Full text: Electron transport systems exist in the plasma membranes of all cells. These systems appear to play a role in cell growth and proliferation, intracellular signalling, hormone responses, apoptotic events, cell defence and perhaps most importantly they enable the cell to respond to changes in the redox state of both the intra- and extracellular environments. Previously, 13 C NMR has been used to study transmembrane electron transport in human erythrocytes, specifically the reduction of extracellular 13 C-ferricyanide. NMR is a particularly useful tool for studying such systems as changes in the metabolic state of the cell can be observed concomitantly with extracellular reductase activity. We investigated the oxidation of extracellular NADH by human erythrocytes using 1 H and 31 P NMR spectroscopy. Recent results for glucose-starved human erythrocytes indicate that, under these conditions, extracellular NADH can be oxidised at the plasma membrane with the electron transfer across the membrane resulting in reduction of intracellular NAD + . The activity is inhibited by known trans-plasma membrane electron transport inhibitors (capsaicin and atebrin) and is unaffected by inhibition of the erythrocyte Band 3 anion transporter. These results suggest that electron import from extracellular NADH allows the cell to re-establish a reducing environment after the normal redox balance is disturbed

  15. Transmembrane peptides as sensors of the membrane physical state

    Science.gov (United States)

    Piotto, Stefano; Di Biasi, Luigi; Sessa, Lucia; Concilio, Simona

    2018-05-01

    Cell membranes are commonly considered fundamental structures having multiple roles such as confinement, storage of lipids, sustain and control of membrane proteins. In spite of their importance, many aspects remain unclear. The number of lipid types is orders of magnitude larger than the number of amino acids, and this compositional complexity is not clearly embedded in any membrane model. A diffused hypothesis is that the large lipid palette permits to recruit and organize specific proteins controlling the formation of specialized lipid domains and the lateral pressure profile of the bilayer. Unfortunately, a satisfactory knowledge of lipid abundance remains utopian because of the technical difficulties in isolating definite membrane regions. More importantly, a theoretical framework where to fit the lipidomic data is still missing. In this work, we wish to utilize the amino acid sequence and frequency of the membrane proteins as bioinformatics sensors of cell bilayers. The use of an alignment-free method to find a correlation between the sequences of transmembrane portion of membrane proteins with the membrane physical state suggested a new approach for the discovery of antimicrobial peptides.

  16. 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.)

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

    Directory of Open Access Journals (Sweden)

    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.

  18. 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.

  19. 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...

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

    Directory of Open Access Journals (Sweden)

    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

  1. Epithelial Cell–Derived Secreted and Transmembrane 1a Signals to Activated Neutrophils during Pneumococcal Pneumonia

    Science.gov (United States)

    Kamata, Hirofumi; Yamamoto, Kazuko; Wasserman, Gregory A.; Zabinski, Mary C.; Yuen, Constance K.; Lung, Wing Yi; Gower, Adam C.; Belkina, Anna C.; Ramirez, Maria I.; Deng, Jane C.; Quinton, Lee J.; Jones, Matthew R.

    2016-01-01

    Airway epithelial cell responses are critical to the outcome of lung infection. In this study, we aimed to identify unique contributions of epithelial cells during lung infection. To differentiate genes induced selectively in epithelial cells during pneumonia, we compared genome-wide expression profiles from three sorted cell populations: epithelial cells from uninfected mouse lungs, epithelial cells from mouse lungs with pneumococcal pneumonia, and nonepithelial cells from those same infected lungs. Of 1,166 transcripts that were more abundant in epithelial cells from infected lungs compared with nonepithelial cells from the same lungs or from epithelial cells of uninfected lungs, 32 genes were identified as highly expressed secreted products. Especially strong signals included two related secreted and transmembrane (Sectm) 1 genes, Sectm1a and Sectm1b. Refinement of sorting strategies suggested that both Sectm1 products were induced predominantly in conducting airway epithelial cells. Sectm1 was induced during the early stages of pneumococcal pneumonia, and mutation of NF-κB RelA in epithelial cells did not diminish its expression. Instead, type I IFN signaling was necessary and sufficient for Sectm1 induction in lung epithelial cells, mediated by signal transducer and activator of transcription 1. For target cells, Sectm1a bound to myeloid cells preferentially, in particular Ly6GbrightCD11bbright neutrophils in the infected lung. In contrast, Sectm1a did not bind to neutrophils from uninfected lungs. Sectm1a increased expression of the neutrophil-attracting chemokine CXCL2 by neutrophils from the infected lung. We propose that Sectm1a is an epithelial product that sustains a positive feedback loop amplifying neutrophilic inflammation during pneumococcal pneumonia. PMID:27064756

  2. Epithelial Cell-Derived Secreted and Transmembrane 1a Signals to Activated Neutrophils during Pneumococcal Pneumonia.

    Science.gov (United States)

    Kamata, Hirofumi; Yamamoto, Kazuko; Wasserman, Gregory A; Zabinski, Mary C; Yuen, Constance K; Lung, Wing Yi; Gower, Adam C; Belkina, Anna C; Ramirez, Maria I; Deng, Jane C; Quinton, Lee J; Jones, Matthew R; Mizgerd, Joseph P

    2016-09-01

    Airway epithelial cell responses are critical to the outcome of lung infection. In this study, we aimed to identify unique contributions of epithelial cells during lung infection. To differentiate genes induced selectively in epithelial cells during pneumonia, we compared genome-wide expression profiles from three sorted cell populations: epithelial cells from uninfected mouse lungs, epithelial cells from mouse lungs with pneumococcal pneumonia, and nonepithelial cells from those same infected lungs. Of 1,166 transcripts that were more abundant in epithelial cells from infected lungs compared with nonepithelial cells from the same lungs or from epithelial cells of uninfected lungs, 32 genes were identified as highly expressed secreted products. Especially strong signals included two related secreted and transmembrane (Sectm) 1 genes, Sectm1a and Sectm1b. Refinement of sorting strategies suggested that both Sectm1 products were induced predominantly in conducting airway epithelial cells. Sectm1 was induced during the early stages of pneumococcal pneumonia, and mutation of NF-κB RelA in epithelial cells did not diminish its expression. Instead, type I IFN signaling was necessary and sufficient for Sectm1 induction in lung epithelial cells, mediated by signal transducer and activator of transcription 1. For target cells, Sectm1a bound to myeloid cells preferentially, in particular Ly6G(bright)CD11b(bright) neutrophils in the infected lung. In contrast, Sectm1a did not bind to neutrophils from uninfected lungs. Sectm1a increased expression of the neutrophil-attracting chemokine CXCL2 by neutrophils from the infected lung. We propose that Sectm1a is an epithelial product that sustains a positive feedback loop amplifying neutrophilic inflammation during pneumococcal pneumonia.

  3. Porous media fluid transport and pore structure

    CERN Document Server

    Dullien, F A L

    1992-01-01

    This book examines the relationship between transport properties and pore structure of porous material. Models of pore structure are presented with a discussion of how such models can be used to predict the transport properties of porous media. Portions of the book are devoted to interpretations of experimental results in this area and directions for future research. Practical applications are given where applicable, and are expected to be useful for a large number of different fields, including reservoir engineering, geology, hydrogeology, soil science, chemical process engineering, biomedica

  4. Nuclear pore complex tethers to the cytoskeleton.

    Science.gov (United States)

    Goldberg, Martin W

    2017-08-01

    The nuclear envelope is tethered to the cytoskeleton. The best known attachments of all elements of the cytoskeleton are via the so-called LINC complex. However, the nuclear pore complexes, which mediate the transport of soluble and membrane bound molecules, are also linked to the microtubule network, primarily via motor proteins (dynein and kinesins) which are linked, most importantly, to the cytoplasmic filament protein of the nuclear pore complex, Nup358, by the adaptor BicD2. The evidence for such linkages and possible roles in nuclear migration, cell cycle control, nuclear transport and cell architecture are discussed. Copyright © 2017. Published by Elsevier Ltd.

  5. 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.

  6. Entamoeba histolytica phagocytosis of human erythrocytes involves PATMK, a member of the transmembrane kinase family.

    Directory of Open Access Journals (Sweden)

    Douglas R Boettner

    2008-01-01

    Full Text Available Entamoeba histolytica is the cause of amebic colitis and liver abscess. This parasite induces apoptosis in host cells and utilizes exposed ligands such as phosphatidylserine to ingest the apoptotic corpses and invade deeper into host tissue. The purpose of this work was to identify amebic proteins involved in the recognition and ingestion of dead cells. A member of the transmembrane kinase family, phagosome-associated TMK96 (PATMK, was identified in a proteomic screen for early phagosomal proteins. Anti-peptide affinity-purified antibody produced against PATMK demonstrated that it was a type I integral membrane protein that was expressed on the trophozoite surface, and that co-localized with human erythrocytes at the site of contact. The role of PATMK in erythrophagocytosis in vitro was demonstrated by: (i incubation of ameba with anti-PATMK antibodies; (ii PATMK mRNA knock-down using a novel shRNA expression system; and (iii expression of a carboxy-truncation of PATMK (PATMK(delta932. Expression of the carboxy-truncation of PATMK(delta932 also caused a specific reduction in the ability of E. histolytica to establish infection in the intestinal model of amebiasis, however these amebae retained the ability to cause hepatic abscesses when directly injected in the liver. In conclusion, PATMK was identified as a member of the TMK family that participates in erythrophagocytosis and is uniquely required for intestinal infection.

  7. Entamoeba histolytica phagocytosis of human erythrocytes involves PATMK, a member of the transmembrane kinase family.

    Science.gov (United States)

    Boettner, Douglas R; Huston, Christopher D; Linford, Alicia S; Buss, Sarah N; Houpt, Eric; Sherman, Nicholas E; Petri, William A

    2008-01-01

    Entamoeba histolytica is the cause of amebic colitis and liver abscess. This parasite induces apoptosis in host cells and utilizes exposed ligands such as phosphatidylserine to ingest the apoptotic corpses and invade deeper into host tissue. The purpose of this work was to identify amebic proteins involved in the recognition and ingestion of dead cells. A member of the transmembrane kinase family, phagosome-associated TMK96 (PATMK), was identified in a proteomic screen for early phagosomal proteins. Anti-peptide affinity-purified antibody produced against PATMK demonstrated that it was a type I integral membrane protein that was expressed on the trophozoite surface, and that co-localized with human erythrocytes at the site of contact. The role of PATMK in erythrophagocytosis in vitro was demonstrated by: (i) incubation of ameba with anti-PATMK antibodies; (ii) PATMK mRNA knock-down using a novel shRNA expression system; and (iii) expression of a carboxy-truncation of PATMK (PATMK(delta932)). Expression of the carboxy-truncation of PATMK(delta932) also caused a specific reduction in the ability of E. histolytica to establish infection in the intestinal model of amebiasis, however these amebae retained the ability to cause hepatic abscesses when directly injected in the liver. In conclusion, PATMK was identified as a member of the TMK family that participates in erythrophagocytosis and is uniquely required for intestinal infection.

  8. 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.

  9. Mice deficient in transmembrane prostatic acid phosphatase display increased GABAergic transmission and neurological alterations.

    Directory of Open Access Journals (Sweden)

    Heidi O Nousiainen

    Full Text Available Prostatic acid phosphatase (PAP, the first diagnostic marker and present therapeutic target for prostate cancer, modulates nociception at the dorsal root ganglia (DRG, but its function in the central nervous system has remained unknown. We studied expression and function of TMPAP (the transmembrane isoform of PAP in the brain by utilizing mice deficient in TMPAP (PAP-/- mice. Here we report that TMPAP is expressed in a subpopulation of cerebral GABAergic neurons, and mice deficient in TMPAP show multiple behavioral and neurochemical features linked to hyperdopaminergic dysregulation and altered GABAergic transmission. In addition to increased anxiety, disturbed prepulse inhibition, increased synthesis of striatal dopamine, and augmented response to amphetamine, PAP-deficient mice have enlarged lateral ventricles, reduced diazepam-induced loss of righting reflex, and increased GABAergic tone in the hippocampus. TMPAP in the mouse brain is localized presynaptically, and colocalized with SNARE-associated protein snapin, a protein involved in synaptic vesicle docking and fusion, and PAP-deficient mice display altered subcellular distribution of snapin. We have previously shown TMPAP to reside in prostatic exosomes and we propose that TMPAP is involved in the control of GABAergic tone in the brain also through exocytosis, and that PAP deficiency produces a distinct neurological phenotype.

  10. The cystic fibrosis transmembrane recruiter the alter ego of CFTR as a multi-kinase anchor.

    Science.gov (United States)

    Mehta, Anil

    2007-11-01

    This review focuses on a newly discovered interaction between protein kinases involved in cellular energetics, a process that may be disturbed in cystic fibrosis for unknown reasons. I propose a new model where kinase-mediated cellular transmission of energy provides mechanistic insight to a latent role of the cystic fibrosis transmembrane conductance regulator (CFTR). I suggest that CFTR acts as a multi-kinase recruiter to the apical epithelial membrane. My group finds that, in the cytosol, two protein kinases involved in cell energy homeostasis, nucleoside diphosphate kinase (NDPK) and AMP-activated kinase (AMPK), bind one another. Preliminary data suggest that both can also bind CFTR (function unclear). The disrupted role of this CFTR-kinase complex as 'membrane transmitter to the cell' is proposed as an alternative paradigm to the conventional ion transport mediated and CFTR/chloride-centric view of cystic fibrosis pathogenesis. Chloride remains important, but instead, chloride-induced control of the phosphohistidine content of one kinase component (NDPK, via a multi-kinase complex that also includes a third kinase, CK2; formerly casein kinase 2). I suggest that this complex provides the necessary near-equilibrium conditions needed for efficient transmission of phosphate energy to proteins controlling cellular energetics. Crucially, a new role for CFTR as a kinase controller is proposed with ionic concentration acting as a signal. The model posits a regulatory control relay for energy sensing involving a cascade of protein kinases bound to CFTR.

  11. Dissection of seroreactivity against the tryptophan-rich motif of the feline immunodeficiency virus transmembrane glycoprotein

    International Nuclear Information System (INIS)

    Freer, Giulia; Giannecchini, Simone; Tissot, Alain; Bachmann, Martin F.; Rovero, Paolo; Serres, Pierre Francoise; Bendinelli, Mauro

    2004-01-01

    Immunogenicity of the tryptophan-rich motif (TrpM) in the membrane-proximal ectodomain of the transmembrane (TM) glycoprotein of feline immunodeficiency virus (FIV) was investigated. Peptide 59, a peptide containing the TrpM of the TM of FIV, was covalently coupled to Qβ phage virus-like particles (Qβ-59) in the attempt to induce potent anti-TrpM B cell responses in cats. All Qβ-59 immunized cats, but not cats that received a mixture of uncoupled Qβ and peptide 59, developed antibodies that reacted with a same epitope in extensive binding and binding competition assays. The epitope recognized was composed of three amino acids, two of which are adjacent. However, Qβ-59-immune sera failed to recognize whole FIV in all binding and neutralization assays performed. Furthermore, no reactivity against the TrpM was detected by screening sera from FIV-infected cats that had reacted with TM peptides, confirming that this epitope does not seem to be serologically functional in the FIV virion. The data suggest that TrpM may not be a suitable target for antiviral vaccine design

  12. Poxvirus-encoded TNF decoy receptors inhibit the biological activity of transmembrane TNF.

    Science.gov (United States)

    Pontejo, Sergio M; Alejo, Ali; Alcami, Antonio

    2015-10-01

    Poxviruses encode up to four different soluble TNF receptors, named cytokine response modifier B (CrmB), CrmC, CrmD and CrmE. These proteins mimic the extracellular domain of the cellular TNF receptors to bind and inhibit the activity of TNF and, in some cases, other TNF superfamily ligands. Most of these ligands are released after the enzymic cleavage of a membrane precursor. However, transmembrane TNF (tmTNF) is not only a precursor of soluble TNF but also exerts specific pro-inflammatory and immunological activities. Here, we report that viral TNF receptors bound and inhibited tmTNF and describe some interesting differences in their activity against the soluble cytokine. Thus, CrmE, which does not inhibit mouse soluble TNF, could block murine tmTNF-induced cytotoxicity. We propose that this anti-tmTNF effect should be taken into consideration when assessing the role of viral TNF decoy receptors in the pathogenesis of poxvirus.

  13. 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.

  14. Molecular pharmacology of promiscuous seven transmembrane receptors sensing organic nutrients.

    Science.gov (United States)

    Wellendorph, Petrine; Johansen, Lars Dan; Bräuner-Osborne, Hans

    2009-09-01

    A number of highly promiscuous seven transmembrane (7TM) receptors have been cloned and characterized within the last few years. It is noteworthy that many of these receptors are activated broadly by amino acids, proteolytic degradation products, carbohydrates, or free fatty acids and are expressed in taste tissue, the gastrointestinal tract, endocrine glands, adipose tissue, and/or kidney. These receptors thus hold the potential to act as sensors of food intake, regulating, for example, release of incretin hormones from the gut, insulin/glucagon from the pancreas, and leptin from adipose tissue. The promiscuous tendency in ligand recognition of these receptors is in contrast to the typical specific interaction with one physiological agonist seen for most receptors, which challenges the classic "lock-and-key" concept. We here review the molecular mechanisms of nutrient sensing of the calcium-sensing receptor, the G protein-coupled receptor family C, group 6, subtype A (GPRC6A), and the taste1 receptor T1R1/T1R3, which are sensing L-alpha-amino acids, the carbohydrate-sensing T1R2/T1R3 receptor, the proteolytic degradation product sensor GPR93 (also termed GPR92), and the free fatty acid (FFA) sensing receptors FFA1, FFA2, FFA3, GPR84, and GPR120. The involvement of the individual receptors in sensing of food intake has been validated to different degrees because of limited availability of specific pharmacological tools and/or receptor knockout mice. However, as a group, the receptors represent potential drug targets, to treat, for example, type II diabetes by mimicking food intake by potent agonists or positive allosteric modulators. The ligand-receptor interactions of the promiscuous receptors of organic nutrients thus remain an interesting subject of emerging functional importance.

  15. Functional characterization of transmembrane adenylyl cyclases from the honeybee brain.

    Science.gov (United States)

    Balfanz, Sabine; Ehling, Petra; Wachten, Sebastian; Jordan, Nadine; Erber, Joachim; Mujagic, Samir; Baumann, Arnd

    2012-06-01

    The second messenger cAMP has a pivotal role in animals' physiology and behavior. Intracellular concentrations of cAMP are balanced by cAMP-synthesizing adenylyl cyclases (ACs) and cAMP-cleaving phosphodiesterases. Knowledge about ACs in the honeybee (Apis mellifera) is rather limited and only an ortholog of the vertebrate AC3 isoform has been functionally characterized, so far. Employing bioinformatics and functional expression we characterized two additional honeybee genes encoding membrane-bound (tm)ACs. The proteins were designated AmAC2t and AmAC8. Unlike the common structure of tmACs, AmAC2t lacks the first transmembrane domain. Despite this unusual topography, AmAC2t-activity could be stimulated by norepinephrine and NKH477 with EC(50s) of 0.07 μM and 3 μM. Both ligands stimulated AmAC8 with EC(50s) of 0.24 μM and 3.1 μM. In brain cryosections, intensive staining of mushroom bodies was observed with specific antibodies against AmAC8, an expression pattern highly reminiscent of the Drosophila rutabaga AC. In a current release of the honeybee genome database we identified three additional tmAC- and one soluble AC-encoding gene. These results suggest that (1) the AC-gene family in honeybees is comparably large as in other species, and (2) based on the restricted expression of AmAC8 in mushroom bodies, this enzyme might serve important functions in honeybee behavior. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. Interactions between bedforms, turbulence and pore flow

    Science.gov (United States)

    Blois, G.; Best, J.; Sambrook Smith, G.; Hardy, R. J.; Lead, J.

    2010-12-01

    A widespread occurrence of flow-form interaction in rivers is represented by subaqueous bedforms such as dunes. Many models have been proposed to explain how bedform generation and evolution are driven by turbulent flow structures that control the incipient motion of cohesionless sediments and later bedform development. However, most of these models have assumed such bedforms to be migrating over an impermeable bed, and that any surface-subsurface flow interaction is negligible. However, for some gravel-bed rivers the porosity can be high, up to 43%, which may result in significant flow both through the permeable bed (hyporheic flow) and across the surface-subsurface interface. The mass and momentum exchange occurring at the interface may have a strong impact on the structure of turbulent flow in the near-bed region. In the case of a dune, its topography induces a local pressure gradient that enhances flow across the interface. This results in a flow structure that may be radically different from that commonly proposed by past work. This paper presents results from a simplified laboratory model akin to a fine-grained bedform generated on top of a coarser sediment bed. Particle imaging velocimetry (PIV) measurements were conducted in order to characterise flow both over and underneath an idealised 2-dimensional dune (0.41 m long, 0.056 m high and having a leeside angle of 27°) overlaying a packed bed of uniform size spheres (D = 0.04 m diameter). Experiments were conducted in free surface flow conditions (Froude number = 0.1; Reynolds number = 25,000) for one bedform height: flow depth ratio (0.31). The flow above the dune was measured using a standard PIV technique while a novel endoscopic PIV (EPIV) system allowed collection of flow data within the pore spaces beneath the dune. The results show that topographically-induced subsurface flow significantly modifies the structure of flow in the leeside of the dune, resulting in a flow field that is radically different

  17. 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

  18. Capillary Condensation in Pores with Rough Walls:

    Czech Academy of Sciences Publication Activity Database

    Bryk, P.; Rżysko, W.; Malijevský, Alexandr; Sokołowski, S.

    2007-01-01

    Roč. 313, č. 1 (2007), s. 41-52 ISSN 0021-9797 Grant - others:TOK(XE) 509249 Institutional research plan: CEZ:AV0Z40720504 Source of funding: R - rámcový projekt EK Keywords : adsorption * pore * capillary condensation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.309, year: 2007

  19. Mimicking the nuclear pore complex using nanopores

    NARCIS (Netherlands)

    Ananth, A.N.

    2018-01-01

    Nuclear pore complexes acts as a gatekeeper for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The central NPC channel is filled with intrinsically disordered FG domains (phenylalanine (F), glycine (G)) that are responsible for the fascinating selectivity of NPCs, for

  20. Preliminary Investigation on the Behavior of Pore Air Pressure During Rainfall Infiltration

    Science.gov (United States)

    Ashraf Mohamad Ismail, Mohd; Min, Ng Soon; Hasliza Hamzah, Nur; Hazreek Zainal Abidin, Mohd; Madun, Aziman; Tajudin, Saiful Azhar Ahmad

    2018-04-01

    This paper focused on the preliminary investigation of pore air pressure behaviour during rainfall infiltration in order to substantiate the mechanism of rainfall induced slope failure. The actual behaviour or pore air pressure during infiltration is yet to be clearly understood as it is regularly assumed as atmospheric. Numerical modelling of one dimensional (1D) soil column was utilized in this study to provide a preliminary insight of this highlighted uncertainty. Parametric study was performed by using rainfall intensities of 1.85 x 10-3m/s and 1.16 x 10-4m/s applied on glass beads to simulate intense and modest rainfall conditions. Analysis results show that the high rainfall intensity causes more development of pore air pressure compared to low rainfall intensity. This is because at high rainfall intensity, the rainwater cannot replace the pore air smoothly thus confining the pore air. Therefore, the effect of pore air pressure has to be taken into consideration particularly during heavy rainfall.

  1. Investigating the pore-water chemistry effects on the volume change behaviour of Boom clay

    Science.gov (United States)

    Deng, Y. F.; Cui, Y. J.; Tang, A. M.; Nguyen, X. P.; Li, X. L.; Van Geet, M.

    The Essen site has been chosen as an alternative site for nuclear waste disposal in Belgium. The soil formation involved at this site is the same as at Mol site: Boom clay. However, owing to its geographical situation closer to the sea, Boom clay at Essen presents a pore water salinity 4-5 times higher than Boom clay at Mol. This study aims at studying the effects of pore water salinity on the hydro-mechanical behaviour of Boom clay. Specific oedometer cells were used allowing “flushing” the pore water in soil specimen by synthetic pore water or distilled water. The synthetic pore water used was prepared with the chemistry as that for the site water: 5.037 g/L for core Ess83 and 5.578 g/L for core Ess96. Mechanical loading was then carried out on the soil specimen after flushing. The results show that water salinity effect on the liquid limit is negligible. The saturation or pore water replacement under the in situ effective stress of 2.4 MPa does not induce significant volume change. For Ess83, hydro-mechanical behaviour was found to be slightly influenced by the water salinity; on the contrary, no obvious effect was identified on the hydro-mechanical behaviour of Ess96. This can be attributed to the higher smectite content in Ess83 than in Ess96.

  2. Shifts in pore connectivity from precipitation versus groundwater rewetting increases soil carbon loss after drought

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Ashly P.; Bond-Lamberty, Benjamin; Benscoter, Brian W.; Tfaily, Malak M.; Hinkle, Ross; Liu, Chongxuan; Bailey, Vanessa L.

    2017-11-06

    Droughts and other extreme precipitation events are predicted to increase in intensity, duration and extent, with uncertain implications for terrestrial carbon (C) sequestration. Soil wetting from above (precipitation) results in a characteristically different pattern of pore-filling than wetting from below (groundwater), with larger, well-connected pores filling before finer pore spaces, unlike groundwater rise in which capillary forces saturate the finest pores first. Here we demonstrate that pore-scale wetting patterns interact with antecedent soil moisture conditions to alter pore-, core- and field-scale C dynamics. Drought legacy and wetting direction are perhaps more important determinants of short-term C mineralization than current soil moisture content in these soils. Our results highlight that microbial access to C is not solely limited by physical protection, but also by drought or wetting-induced shifts in hydrologic connectivity. We argue that models should treat soil moisture within a three-dimensional framework emphasizing hydrologic conduits for C and resource diffusion.

  3. Conductometric determination of single pores in polyethyleneterephthalate irradiated by heavy ions

    International Nuclear Information System (INIS)

    Oganesyan, V.R.; Trofimov, V.V.; Doerschel, B.; Hermsdorf, D.; Vetter, J.; Danziger, M.

    2002-01-01

    Most of the previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7·10 3 ions/cm 2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20μm was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation, we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed model. Thus, the developed 'track-by-track' method can be used effectively for description of the sequential appearance of individual pores in an electrolytic etching process

  4. 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.

  5. 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 ...

  6. Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene.

    Science.gov (United States)

    Shahbabaei, Majid; Kim, Daejoong

    2017-08-09

    In this study, molecular dynamics (MD) simulations are used to examine the water transport properties through asymmetric hourglass-shaped pores in multilayer nanoporous graphene with a constant interlayer separation of 6 Å. The properties of the tested asymmetric hourglass-shaped pores [with the models having long cone (l 1 , -P) and short cone (l 2 , +P) entrances] are compared to a symmetric pore model. The study findings indicate that the water occupancy increases across the asymmetric pore (l 1 , -P) compared to (l 2 , +P), because of the length effect. The asymmetric pore, (l 1 , -P), yields higher flux compared to (l 2 , +P) and even the symmetric model, which can be attributed to the increase in the hydrogen bonds. In addition, the single-file water molecules across the narrowest pore diameter inside the (l 2 , +P) pore exhibit higher viscosity compared to those in the (l 1 , -P) pore because of the increase in the water layering effect. Moreover, it is found that the permeability inside the multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules before approaching the layer with the smallest pore diameter. The probability of dipole orientation exhibits wider distribution inside the (l 1 , -P) system compared to (l 2 , +P), implying an enhanced formation of hydrogen bonding of water molecules. This results in the fast flow of water molecules. The MD trajectory shows that the dipole orientation across the single-layer graphene has frequently flipped compared to the dipole orientation across the pores in multilayer graphene, which is maintained during the whole simulation time (although the dipole orientation has flipped for a few picoseconds at the beginning of the simulation). This can be attributed to the energy barrier induced by the individual layer. The diffusion coefficient of water molecules inside the (l 2 , +P) system increases with pressure difference, however, it decreases inside the (l 1 , -P) system because

  7. 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...

  8. A Natural Chimeric Pseudomonas Bacteriocin with Novel Pore-Forming Activity Parasitizes the Ferrichrome Transporter.

    Science.gov (United States)

    Ghequire, Maarten G K; Kemland, Lieselore; Anoz-Carbonell, Ernesto; Buchanan, Susan K; De Mot, René

    2017-02-21

    Modular bacteriocins represent a major group of secreted protein toxins with a narrow spectrum of activity, involved in interference competition between Gram-negative bacteria. These antibacterial proteins include a domain for binding to the target cell and a toxin module at the carboxy terminus. Self-inhibition of producers is provided by coexpression of linked immunity genes that transiently inhibit the toxin's activity through formation of bacteriocin-immunity complexes or by insertion in the inner membrane, depending on the type of toxin module. We demonstrate strain-specific inhibitory activity for PmnH, a Pseudomonas bacteriocin with an unprecedented dual-toxin architecture, hosting both a colicin M domain, potentially interfering with peptidoglycan synthesis, and a novel colicin N-type domain, a pore-forming module distinct from the colicin Ia-type domain in Pseudomonas aeruginosa pyocin S5. A downstream-linked gene product confers PmnH immunity upon susceptible strains. This protein, ImnH, has a transmembrane topology similar to that of Pseudomonas colicin M-like and pore-forming immunity proteins, although homology with either of these is essentially absent. The enhanced killing activity of PmnH under iron-limited growth conditions reflects parasitism of the ferrichrome-type transporter for entry into target cells, a strategy shown here to be used as well by monodomain colicin M-like bacteriocins from pseudomonads. The integration of a second type of toxin module in a bacteriocin gene could offer a competitive advantage against bacteria displaying immunity against only one of both toxic activities. IMPORTANCE In their continuous struggle for ecological space, bacteria face a huge load of contenders, including phylogenetically related strains that compete for the same niche. One important group of secreted antibacterial proteins assisting in eliminating these rivals are modular bacteriocins of Gram-negative bacteria, comprising a domain for docking onto the

  9. The Role of Water Distribution Controlled by Transmembrane Potentials in the Cytochrome c-Cardiolipin Interaction: Revealing from Surface-Enhanced Infrared Absorption Spectroscopy.

    Science.gov (United States)

    Zeng, Li; Wu, Lie; Liu, Li; Jiang, Xiue

    2017-11-02

    The interaction of cytochrome c (cyt c) with cardiolipin (CL) plays a crucial role in apoptotic functions, however, the changes of the transmembrane potential in governing the protein behavior at the membrane-water interface have not been studied due to the difficulties in simultaneously monitoring the interaction and regulating the electric field. Herein, surface-enhanced infrared absorption (SEIRA) spectroelectrochemistry is employed to study the mechanism of how the transmembrane potentials control the interaction of cyt c with CL membranes by regulating the electrode potentials of an Au film. When the transmembrane potential decreases, the water content at the interface of the membranes can be increased to slow down protein adsorption through decreasing the hydrogen-bond and hydrophobic interactions, but regulates the redox behavior of CL-bound cyt c through a possible water-facilitated proton-coupled electron transfer process. Our results suggest that the potential drop-induced restructure of the CL conformation and the hydration state could modify the structure and function of CL-bound cyt c on the lipid membrane. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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

  11. 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

  12. The transmembrane domain of the p75 neurotrophin receptor stimulates phosphorylation of the TrkB tyrosine kinase receptor.

    Science.gov (United States)

    Saadipour, Khalil; MacLean, Michael; Pirkle, Sean; Ali, Solav; Lopez-Redondo, Maria-Luisa; Stokes, David L; Chao, Moses V

    2017-10-06

    The function of protein products generated from intramembraneous cleavage by the γ-secretase complex is not well defined. The γ-secretase complex is responsible for the cleavage of several transmembrane proteins, most notably the amyloid precursor protein that results in Aβ, a transmembrane (TM) peptide. Another protein that undergoes very similar γ-secretase cleavage is the p75 neurotrophin receptor. However, the fate of the cleaved p75 TM domain is unknown. p75 neurotrophin receptor is highly expressed during early neuronal development and regulates survival and process formation of neurons. Here, we report that the p75 TM can stimulate the phosphorylation of TrkB (tyrosine kinase receptor B). In vitro phosphorylation experiments indicated that a peptide representing p75 TM increases TrkB phosphorylation in a dose- and time-dependent manner. Moreover, mutagenesis analyses revealed that a valine residue at position 264 in the rat p75 neurotrophin receptor is necessary for the ability of p75 TM to induce TrkB phosphorylation. Because this residue is just before the γ-secretase cleavage site, we then investigated whether the p75(αγ) peptide, which is a product of both α- and γ-cleavage events, could also induce TrkB phosphorylation. Experiments using TM domains from other receptors, EGFR and FGFR1, failed to stimulate TrkB phosphorylation. Co-immunoprecipitation and biochemical fractionation data suggested that p75 TM stimulates TrkB phosphorylation at the cell membrane. Altogether, our results suggest that TrkB activation by p75(αγ) peptide may be enhanced in situations where the levels of the p75 receptor are increased, such as during brain injury, Alzheimer's disease, and epilepsy. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. 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.

  14. Pores and Void in Asclepiades’ Physical Theory

    Science.gov (United States)

    Leith, David

    2012-01-01

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

  15. Active Pore Volume in Danish Peat Soils

    DEFF Research Database (Denmark)

    Forsmann, Ditte M.; Kjærgaard, Charlotte

    2012-01-01

    Phosphorus release within the soil matrix caused by the changed redox conditions due to re-establishment of a riparian wetland can be critical for the aquatic environment. However, phosphorous released in the soil will not always result in an immediate contribution to this loss to the aquatic...... environment. Lowland soils are primarily peat soils, and only a minor part of the total soil volume of peat soils is occupied by macropores (>30 µm). Since water primarily flows in these macropores, the majority of the soil matrix is bypassed (the immobile domain). Phosphorus released in the immobile domain...... is not actively transported out of the system, but is only transported via diffusion, which is a very slow process. Thus it is interesting to investigate the size of the active pore volume in peat soils. The hypothesis of this study is that the active pores volume of a peat soil can be expressed using bulk...

  16. 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.

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

    Science.gov (United States)

    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.

  18. [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.

  19. Facial skin pores: a multiethnic study

    Directory of Open Access Journals (Sweden)

    Flament F

    2015-02-01

    Full Text Available Frederic Flament,1 Ghislain Francois,1 Huixia Qiu,2 Chengda Ye,2 Tomoo Hanaya,3 Dominique Batisse,3 Suzy Cointereau-Chardon,1 Mirela Donato Gianeti Seixas,4 Susi Elaine Dal Belo,4 Roland Bazin5 1Department of Applied Research and Development, L’Oreal Research and Innovation, Paris, France; 2Department of Applied Research and Development, L’Oreal Research and Innovation, Shanghai, People’s Republic of China; 3Department of Applied Research and Development, L’Oreal Research and Innovation, Tokyo, Japan; 4Department of Applied Research and Development, L’Oreal Research and Innovation, Rio de Janeiro, Brazil; 5RB Consult, Bievres, France Abstract: Skin pores (SP, as they are called by laymen, are common and benign features mostly located on the face (nose, cheeks, etc that generate many aesthetic concerns or complaints. Despite the prevalence of skin pores, related literature is scarce. With the aim of describing the prevalence of skin pores and anatomic features among ethnic groups, a dermatoscopic instrument, using polarized lighting, coupled to a digital camera recorded the major features of skin pores (size, density, coverage on the cheeks of 2,585 women in different countries and continents. A detection threshold of 250 µm, correlated to clinical scorings by experts, was input into a specific software to further allow for automatic counting of the SP density (N/cm2 and determination of their respective sizes in mm2. Integrating both criteria also led to establishing the relative part of the skin surface (as a percentage that is actually covered by SP on cheeks. The results showed that the values of respective sizes, densities, and skin coverage: 1 were recorded in all studied subjects; 2 varied greatly with ethnicity; 3 plateaued with age in most cases; and 4 globally reflected self-assessment by subjects, in particular those who self-declare having “enlarged pores” like Brazilian women. Inversely, Chinese women were clearly

  20. Evaluation of pore structures and cracking in cement paste exposed to elevated temperatures by X-ray computed tomography

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kwang Yeom, E-mail: kimky@kict.re.kr [Korea Institute of Construction Technology, 283 Goyangdae-ro, Ilsanseo-gu, Goyang 411-712 (Korea, Republic of); Yun, Tae Sup, E-mail: taesup@yonsei.ac.kr [School of Civil and Environmental Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 120-749 (Korea, Republic of); Park, Kwang Pil, E-mail: bamtol97@kict.re.kr [Korea Institute of Construction Technology, 283 Goyangdae-ro, Ilsanseo-gu, Goyang 411-712 (Korea, Republic of)

    2013-08-15

    When cement-based materials are exposed to the high temperatures induced by fire, which can rapidly cause temperatures of over 1000 °C, the changes in pore structure and density prevail. In the present study, mortar specimens were subjected to a series of increasing temperatures to explore the temperature-dependent evolution of internal pore structure. High-performance X-ray computed tomography (CT) was used to observe the evolution of temperature-induced discontinuities at the sub-millimeter level. X-ray diffraction (XRD) and scanning electron microscopy (SEM) were employed to investigate the cause of physical changes in the heated mortar specimens. Results exhibit the changes in pore structure caused by elevated temperatures, and thermally induced fractures. We discuss the progressive formation of thermally induced fracture networks, which is a prerequisite for spalling failure of cement-based materials by fire, based on visual observations of the 3D internal structures revealed by X-ray CT.

  1. Evaluation of pore structures and cracking in cement paste exposed to elevated temperatures by X-ray computed tomography

    International Nuclear Information System (INIS)

    Kim, Kwang Yeom; Yun, Tae Sup; Park, Kwang Pil

    2013-01-01

    When cement-based materials are exposed to the high temperatures induced by fire, which can rapidly cause temperatures of over 1000 °C, the changes in pore structure and density prevail. In the present study, mortar specimens were subjected to a series of increasing temperatures to explore the temperature-dependent evolution of internal pore structure. High-performance X-ray computed tomography (CT) was used to observe the evolution of temperature-induced discontinuities at the sub-millimeter level. X-ray diffraction (XRD) and scanning electron microscopy (SEM) were employed to investigate the cause of physical changes in the heated mortar specimens. Results exhibit the changes in pore structure caused by elevated temperatures, and thermally induced fractures. We discuss the progressive formation of thermally induced fracture networks, which is a prerequisite for spalling failure of cement-based materials by fire, based on visual observations of the 3D internal structures revealed by X-ray CT

  2. Function and expression of cystic fibrosis transmembrane conductance regulator after small intestinal transplantation in mice.

    Directory of Open Access Journals (Sweden)

    Penghong Song

    Full Text Available The secretion function of intestinal graft is one of the most important factors for successful intestinal transplantation. Cystic fibrosis transmembrane conductance regulator (CFTR mediates HCO3(- and Cl(- secretions in intestinal epithelial cells. In this study, we made investigation on the expression and function of CFTR in an experimental model of murine small intestinal transplantation. Heterotopic intestinal transplantations were performed in syngeneic mice. The mRNA and protein expressions of CFTR were analyzed by real time PCR and western blot. Murine intestinal mucosal HCO3(- and Cl(- secretions were examined in vitro in Ussing chambers by the pH stat and short circuit current (I(sc techniques. The results showed that forskolin, an activator of CFTR, stimulated jejunal mucosal epithelial HCO3(- and Cl(- secretions in mice, but forskolin-stimulated HCO3(- and Cl(- secretions in donor and recipient jejunal mucosae of mice after heterotopic jejunal transplantation were markedly decreased, compared with controls (P<0.001. The mRNA and protein expression levels of CFTR in donor and recipient jejunal mucosae of mice were also markedly lower than those in controls (P<0.001, and the mRNA and protein expression levels of tumor necrosis factor α (TNFα were markedly increased in donor jejunal mucosae of mice (P<0.001, compared with controls. Further experiments showed that TNFα down-regulated the expression of CFTR mRNA in murine jejunal mucosa. In conclusion, after intestinal transplantation, the function of CFTR was impaired, and its mRNA and protein expressions were down-regulated, which may be induced by TNFα.

  3. Distinct neurobehavioural effects of cannabidiol in transmembrane domain neuregulin 1 mutant mice.

    Directory of Open Access Journals (Sweden)

    Leonora E Long

    Full Text Available The cannabis constituent cannabidiol (CBD possesses anxiolytic and antipsychotic properties. We have previously shown that transmembrane domain neuregulin 1 mutant (Nrg1 TM HET mice display altered neurobehavioural responses to the main psychoactive constituent of cannabis, Δ(9-tetrahydrocannabinol. Here we investigated whether Nrg1 TM HET mice respond differently to CBD and whether CBD reverses schizophrenia-related phenotypes expressed by these mice. Adult male Nrg1 TM HET and wild type-like littermates (WT received vehicle or CBD (1, 50 or 100 mg/kg i.p. for 21 days. During treatment and 48 h after withdrawal we measured behaviour, whole blood CBD concentrations and autoradiographic receptor binding. Nrg1 HET mice displayed locomotor hyperactivity, PPI deficits and reduced 5-HT(2A receptor binding density in the substantia nigra, but these phenotypes were not reversed by CBD. However, long-term CBD (50 and 100 mg/kg selectively enhanced social interaction in Nrg1 TM HET mice. Furthermore, acute CBD (100 mg/kg selectively increased PPI in Nrg1 TM HET mice, although tolerance to this effect was manifest upon repeated CBD administration. Long-term CBD (50 mg/kg also selectively increased GABA(A receptor binding in the granular retrosplenial cortex in Nrg1 TM HET mice and reduced 5-HT(2A binding in the substantia nigra in WT mice. Nrg1 appears necessary for CBD-induced anxiolysis since only WT mice developed decreased anxiety-related behaviour with repeated CBD treatment. Altered pharmacokinetics in mutant mice could not explain our findings since no genotype differences existed in CBD blood concentrations. Here we demonstrate that Nrg1 modulates acute and long-term neurobehavioural effects of CBD, which does not reverse the schizophrenia-relevant phenotypes.

  4. 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

  5. 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.

  6. The voltage-sensing domain of a phosphatase gates the pore of a potassium channel.

    Science.gov (United States)

    Arrigoni, Cristina; Schroeder, Indra; Romani, Giulia; Van Etten, James L; Thiel, Gerhard; Moroni, Anna

    2013-03-01

    The modular architecture of voltage-gated K(+) (Kv) channels suggests that they resulted from the fusion of a voltage-sensing domain (VSD) to a pore module. Here, we show that the VSD of Ciona intestinalis phosphatase (Ci-VSP) fused to the viral channel Kcv creates Kv(Synth1), a functional voltage-gated, outwardly rectifying K(+) channel. Kv(Synth1) displays the summed features of its individual components: pore properties of Kcv (selectivity and filter gating) and voltage dependence of Ci-VSP (V(1/2) = +56 mV; z of ~1), including the depolarization-induced mode shift. The degree of outward rectification of the channel is critically dependent on the length of the linker more than on its amino acid composition. This highlights a mechanistic role of the linker in transmitting the movement of the sensor to the pore and shows that electromechanical coupling can occur without coevolution of the two domains.

  7. Physiological and pharmacological characterization of transmembrane acid extruders in cultured human umbilical artery smooth muscle cells

    Directory of Open Access Journals (Sweden)

    Gunng-Shinng Chen

    2015-01-01

    Full Text Available Background: Intracellular pH (pH i is a pivotal factor for cellular functions and homeostasis. Apart from passive intracellular buffering capacity, active transmembrane transporters responsible for kinetic changes of pH i impacts. Acid extrusion transporters such as Na + /H + exchanger (NHE and Na + /HCO3− cotransporter (NBC have been found to be activated when cells are in an acidic condition in different cell types. However, such far, the pH i regulators have not been characterized in human umbilical artery smooth muscle cells (HUASMCs. Materials and Methods: We, therefore, investigated the mechanism of pH i recovery from intracellular acidosis, induced by NH 4 Cl-prepulse, using pH-sensitive fluorescence dye: 2′,7′-bis(2-carboxethyl-5(6-carboxy-fluorescein in HUASMCs. Cultured HUASMCs were derived from the segments of the human umbilical artery that were obtained from women undergoing children delivery. Results: The resting pH i is 7.23 ± 0.03 when cells in HEPES (nominally HCO 3− -free buffered solution. The resting pH i is higher as 7.27 ± 0.03 when cells in CO 2 /HCO3− -buffered solution. In HEPES-buffered solution, a pH i recovery following induced intracellular acidosis could be inhibited completely by 30 μM HOE 694 (a specific NHE inhibitor or by removing [Na +]o . In 5% CO2/HCO3− -buffered solution, 30 μM HOE 694 slowed the pH i recovery from the induced intracellular acidosis only. On the contrary, HOE 694 adding together with 0.2 mM 4,4′-diisothiocyanatostilbene-2,2′-disulphonic acid (a specific NBC inhibitor or removal of [Na +]o entirely blocked the acid extrusion. By using Western blot technique, we demonstrated that four different isoforms of NBC, that is, SLC4A8 (NBCBE, SLC4A7 (NBCn1, SLC4A5 (NBCe2 and SLC4A4 (NBCe1, co-exist in the HUASMCs. Conclusions: We demonstrate, for the 1 st time, that apart from the housekeeping NHE1, another Na + couple HCO3− -transporter, that is, NBC, functionally coexists to

  8. Conductometric Determination of Single Pores in Polyethyleneterephthalate Irradiated by Heavy Ions

    CERN Document Server

    Oganesyan, V R; Dörschel, B; Vetter, J E; Danziger, M; Hermsdorf, D

    2002-01-01

    Most of previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7\\cdot 10^{3} ions/cm^2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20 m was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed model. Thus, the de...

  9. Conductometric determination of single pores in polyethyleneterephthalate irradiated by heavy ions

    CERN Document Server

    Oganesyan, V R; Dörschel, B; Hermsdorf, D; Trofimov, V V; Vetter, J

    2002-01-01

    Most of the previous works devoted to the problem of track formation processes did not pay enough attention to direct measurement of the appearance of every individual pore in an array of many pores induced by the irradiation of polymer films with ions. Such measurements are not easy to carry out due to the extremely high electric resistance in the moment of pore opening. In this work the analysis of films irradiated with low particle fluences up to 3.7 centre dot 10 sup 3 ions/cm sup 2 is described. Polyethyleneterephthalate (PET) Hostaphan with a thickness of 20 mu m was used. The samples were irradiated with Bi ions of 11.4 MeV/amu energy. Using optimized etching conditions and computer aided data evaluation, we obtained results, which are in good agreement with theoretical predictions and model calculations. The measured increase of conductivity beginning from the breakthrough of a single track up to the next pore opening in dependence on the etching time and the number of opened pores confirm the assumed...

  10. Type IIA photosensitivity and formation of pores in optical fibers under intense ultraviolet irradiation

    International Nuclear Information System (INIS)

    Kukushkin, S. A.; Shlyagin, M. G.; Swart, P. L.; Chtcherbakov, A. A.; Osipov, A. V.

    2007-01-01

    Formation of the type IIA Bragg gratings in germanosilicate optical fibers is studied. We report the observation of such a type of gratings in the standard single-mode fiber (Corning SMF-28) under different experimental conditions. A mechanism for the type IIA photosensitivity in optical fibers is proposed which is based on nucleation and evolution of pores from vacancy-type defects in fiber areas where a high level of mechanical stress is induced under intense ultraviolet (UV) light. Evolution of fiber core temperature under influence of a single 20 ns light pulse from a KrF excimer laser was measured and compared with theoretical calculations. It was shown that transient thermoinduced stress in the fiber core can achieve a level sufficient for effective nucleation of pores. A theory describing formation of pores in optical fibers has been developed and was used to estimate the pore nucleation rate, concentration, and other parameters of pore evolution for different levels of UV fluence and fiber core stress

  11. 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.

  12. Pore ordering in mesoporous matrices induced by different directing agents

    Czech Academy of Sciences Publication Activity Database

    Putz, A.-M.; Cecilia, S.; Ianasi, C.; Dudás, Z.; Székely, N. K.; Plocek, Jiří; Sfarloaga, P.; Sacarescu, L.; Almásy, L.

    2015-01-01

    Roč. 22, č. 2 (2015), s. 321-331 ISSN 1380-2224 Institutional support: RVO:61388980 Keywords : Mesoporous silica * MCM-41 * Dodecyl-trimethyl ammonium bromide * Hexadecyl-trimethylammonium bromide Subject RIV: CA - Inorganic Chemistry Impact factor: 1.385, year: 2015

  13. Bcl-2 overexpression: effects on transmembrane calcium movement

    International Nuclear Information System (INIS)

    Rangaswami, Arun A.; Premack, Brett; Walleczek, Jan; Killoran, Pamela; Gardner, Phyllis; Knox, Susan J.

    1996-01-01

    Purpose/Objective: High levels of expression of the proto-oncogene bcl-2 and its 26 kD protein product Bcl-2 have been correlated with the inhibition of apoptosis and the increased resistance of tumor cells to cytotoxic drugs and ionizing radiation. Unfortunately, the specific mechanism of action of Bcl-2 remains poorly understood. In the studies described here, the role of intracellular calcium fluxes and plasma membrane calcium cycling in the induction of apoptosis, and the effect of Bcl-2 expression on the modulation of transmembrane calcium fluxes following treatment of cells with cytotoxic agents were studied. The relationship between intracellular calcium release, capacitive calcium entry, and the plasma membrane potential were also investigated. Materials and Methods: Human B-cell lymphoma (PW) and human promyelocytic leukemia (HL60) cell lines were transfected with Bcl-2 and a control vector. The Bcl-2 transfectants over expressed the Bcl-2 onco-protein and were more resistant to irradiation than the control cells. Cells were loaded with fluorescent indicators indo-1 and fura-2 AM to quantify the cytosolic calcium concentration and subsequent calcium responses to a variety of cytotoxic stimuli, including the microsomal ATPase inhibitor, thapsigargin, using fluorometric measurements. Comparisons of resting and stimulated cytosolic calcium concentrations were made between the parental, neomycin control, and bcl-2 transfected cells. In order to determine the actual calcium influx rate, cells were loaded with either indo-1 or fura-2 and then exposed to 0.1 mM extracellular manganese, which enters the cells through calcium influx channels and quenches the fluorescent signal in proportion to the calcium influx rate. In order to determine the role of the membrane potential in driving calcium influx, cells were treated with either 0.1 μM Valinomycin or isotonic potassium chloride to either hyper polarize or depolarize the resting membrane potential, and the

  14. 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.

  15. 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.

  16. 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...

  17. Silicon pore optics developments and status

    DEFF Research Database (Denmark)

    Bavdaz, Marcos; Wille, Eric; Wallace, Kotska

    2012-01-01

    Silicon Pore Optics (SPO) is a lightweight high performance X-ray optics technology being developed in Europe, driven by applications in observatory class high energy astrophysics missions. An example of such application is the former ESA science mission candidate ATHENA (Advanced Telescope...... for High Energy Astrophysics), which uses the SPO technology for its two telescopes, in order to provide an effective area exceeding 1 m2 at 1 keV, and 0.5 m2 at 6 keV, featuring an angular resolution of 10" or better [1 to 24]. This paper reports on the development activities led by ESA, and the status...

  18. 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.

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

    Science.gov (United States)

    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

  20. Identification of a probable pore-forming domain in the multimeric vacuolar anion channel AtALMT9.

    Science.gov (United States)

    Zhang, Jingbo; Baetz, Ulrike; Krügel, Undine; Martinoia, Enrico; De Angeli, Alexis

    2013-10-01

    Aluminum-activated malate transporters (ALMTs) form an important family of anion channels involved in fundamental physiological processes in plants. Because of their importance, the role of ALMTs in plant physiology is studied extensively. In contrast, the structural basis of their functional properties is largely unknown. This lack of information limits the understanding of the functional and physiological differences between ALMTs and their impact on anion transport in plants. This study aimed at investigating the structural organization of the transmembrane domain of the Arabidopsis (Arabidopsis thaliana) vacuolar channel AtALMT9. For that purpose, we performed a large-scale mutagenesis analysis and found two residues that form a salt bridge between the first and second putative transmembrane α-helices (TMα1 and TMα2). Furthermore, using a combination of pharmacological and mutagenesis approaches, we identified citrate as an "open channel blocker" of AtALMT9 and used this tool to examine the inhibition sensitivity of different point mutants of highly conserved amino acid residues. By this means, we found a stretch within the cytosolic moiety of the TMα5 that is a probable pore-forming domain. Moreover, using a citrate-insensitive AtALMT9 mutant and biochemical approaches, we could demonstrate that AtALMT9 forms a multimeric complex that is supposedly composed of four subunits. In summary, our data provide, to our knowledge, the first evidence about the structural organization of an ion channel of the ALMT family. We suggest that AtALMT9 is a tetramer and that the TMα5 domains of the subunits contribute to form the pore of this anion channel.

  1. Expression of transmembrane carbonic anhydrases, CAIX and CAXII, in human development

    Directory of Open Access Journals (Sweden)

    Lerman Michael I

    2009-03-01

    Full Text Available Abstract Background Transmembrane CAIX and CAXII are members of the alpha carbonic anhydrase (CA family. They play a crucial role in differentiation, proliferation, and pH regulation. Expression of CAIX and CAXII proteins in tumor tissues is primarily induced by hypoxia and this is particularly true for CAIX, which is regulated by the transcription factor, hypoxia inducible factor-1 (HIF-1. Their distributions in normal adult human tissues are restricted to highly specialized cells that are not always hypoxic. The human fetus exists in a relatively hypoxic environment. We examined expression of CAIX, CAXII and HIF-1α in the developing human fetus and postnatal tissues to determine whether expression of CAIX and CAXII is exclusively regulated by HIF-1. Results The co-localization of CAIX and HIF-1α was limited to certain cell types in embryonic and early fetal tissues. Those cells comprised the primitive mesenchyma or involved chondrogenesis and skin development. Transient CAIX expression was limited to immature tissues of mesodermal origin and the skin and ependymal cells. The only tissues that persistently expressed CAIX protein were coelomic epithelium (mesothelium and its remnants, the epithelium of the stomach and biliary tree, glands and crypt cells of duodenum and small intestine, and the cells located at those sites previously identified as harboring adult stem cells in, for example, the skin and large intestine. In many instances co-localization of CAIX and HIF-1α was not evident. CAXII expression is restricted to cells involved in secretion and water absorption such as parietal cells of the stomach, acinar cells of the salivary glands and pancreas, epithelium of the large intestine, and renal tubules. Co-localization of CAXII with CAIX or HIF-1α was not observed. Conclusion The study has showed that: 1 HIF-1α and CAIX expression co- localized in many, but not all, of the embryonic and early fetal tissues; 2 There is no evidence of

  2. Performance characterization of silicon pore optics

    Science.gov (United States)

    Collon, M. J.; Kraft, S.; Günther, R.; Maddox, E.; Beijersbergen, M.; Bavdaz, M.; Lumb, D.; Wallace, K.; Krumrey, M.; Cibik, L.; Freyberg, M.

    2006-06-01

    The characteristics of the latest generation of assembled silicon pore X-ray optics are discussed in this paper. These very light, stiff and modular high performance pore optics (HPO) have been developed [1] for the next generation of astronomical X-ray telescopes, which require large collecting areas whilst achieving angular resolutions better than 5 arcseconds. The suitability of 12 inch silicon wafers as high quality optical mirrors and the automated assembly process are discussed elsewhere in this conference. HPOs with several tens of ribbed silicon plates are assembled by bending the plates into an accurate cylindrical shape and directly bonding them on top of each other. The achievable figure accuracy is measured during assembly and in test campaigns at X-ray testing facilities like BESSY-II and PANTER. Pencil beam measurements allow gaining information on the quality achieved by the production process with high spatial resolution. In combination with full beam illumination a complete picture of the excellent performance of these optics can be derived. Experimental results are presented and discussed in detail. The results of such campaigns are used to further improve the production process in order to match the challenging XEUS requirements [2] for imaging resolution and mass.

  3. A novel bio-safe phase separation process for preparing open-pore biodegradable polycaprolactone microparticles.

    Science.gov (United States)

    Salerno, Aurelio; Domingo, Concepción

    2014-09-01

    Open-pore biodegradable microparticles are object of considerable interest for biomedical applications, particularly as cell and drug delivery carriers in tissue engineering and health care treatments. Furthermore, the engineering of microparticles with well definite size distribution and pore architecture by bio-safe fabrication routes is crucial to avoid the use of toxic compounds potentially harmful to cells and biological tissues. To achieve this important issue, in the present study a straightforward and bio-safe approach for fabricating porous biodegradable microparticles with controlled morphological and structural features down to the nanometer scale is developed. In particular, ethyl lactate is used as a non-toxic solvent for polycaprolactone particles fabrication via a thermal induced phase separation technique. The used approach allows achieving open-pore particles with mean particle size in the 150-250 μm range and a 3.5-7.9 m(2)/g specific surface area. Finally, the combination of thermal induced phase separation and porogen leaching techniques is employed for the first time to obtain multi-scaled porous microparticles with large external and internal pore sizes and potential improved characteristics for cell culture and tissue engineering. Samples were characterized to assess their thermal properties, morphology and crystalline structure features and textural properties. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2017-04-01

    Soil pore structure has a strong influence on water retention, and is itself influenced by plant and microbial dynamics such as root proliferation and microbial exudation. Although increased nitrogen (N) availability and elevated atmospheric CO 2 concentrations (eCO 2 ) often have interacting effects on root and microbial dynamics, it is unclear whether these biotic effects can translate into altered soil pore structure and water retention. This study was based on a long-term experiment (7 yr at the time of sampling) in which a C 4 pasture grass (Paspalum notatum) was grown on a sandy loam soil while provided factorial additions of N and CO 2 . Through an analysis of soil aggregate fractal properties supported by 3D microtomographic imagery, we found that N fertilization induced an increase in intra-aggregate porosity and a simultaneous shift toward greater accumulation of pore space in larger aggregates. These effects were enhanced by eCO 2 and yielded an increase in water retention at pressure potentials near the wilting point of plants. However, eCO 2 alone induced changes in the opposite direction, with larger aggregates containing less pore space than under control conditions, and water retention decreasing accordingly. Results on biotic factors further suggested that organic matter gains or losses induced the observed structural changes. Based on our results, we postulate that the pore structure of many mineral soils could undergo N-dependent changes as atmospheric CO 2 concentrations rise, having global-scale implications for water balance, carbon storage, and related rhizosphere functions. © 2016 John Wiley & Sons Ltd.

  5. [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.

  6. 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...

  7. Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO

    NARCIS (Netherlands)

    Duarte, A.M.; Mierlo, van C.P.M.; Hemminga, M.A.

    2008-01-01

    10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are

  8. The transmembrane region is responsible for targeting of adaptor protein LAX into "heavy rafts''

    Czech Academy of Sciences Publication Activity Database

    Hrdinka, Matouš; Otáhal, Pavel; Hořejší, Václav

    2012-01-01

    Roč. 7, č. 5 (2012), e36330 E-ISSN 1932-6203 R&D Projects: GA ČR GEMEM/09/E011; GA MŠk 1M0506 Institutional research plan: CEZ:AV0Z50520514 Keywords : LAX * transmembrane domain * DRM Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.730, year: 2012

  9. 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.

  10. Intact transmembrane isoforms of the neural cell adhesion molecule are released from the plasma membrane

    DEFF Research Database (Denmark)

    Olsen, M; Krog, L; Edvardsen, K

    1993-01-01

    . By density-gradient centrifugation it was shown that shed transmembrane NCAM-B was present in fractions of high, as well as low, density, indicating that a fraction of the shed NCAM is associated with minor plasma membrane fragments. Finally, it was shown that isolated soluble NCAM inhibited cell binding...

  11. 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

  12. Transmembrane Domain Single-Nucleotide Polymorphisms Impair Expression and Transport Activity of ABC Transporter ABCG2

    NARCIS (Netherlands)

    Sjostedt, N.; Heuvel, J.J.M.W. van den; Koenderink, J.B.; Kidron, H.

    2017-01-01

    PURPOSE: To study the function and expression of nine naturally occurring single-nucleotide polymorphisms (G406R, F431L, S441N, P480L, F489L, M515R, L525R, A528T and T542A) that are predicted to reside in the transmembrane regions of the ABC transporter ABCG2. METHODS: The transport activity of the

  13. 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

  14. 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....

  15. SCIMP, a transmembrane adaptor protein involved in major histocompatibility complex class II signaling

    Czech Academy of Sciences Publication Activity Database

    Dráber, Peter; Vonková, Ivana; Štěpánek, Ondřej; Hrdinka, Matouš; Kucová, Markéta; Skopcová, Tereza; Otáhal, Pavel; Angelisová, Pavla; Hořejší, Václav; Yeung, M.; Weiss, A.; Brdička, Tomáš

    2011-01-01

    Roč. 31, č. 22 (2011), s. 4550-4562 ISSN 0270-7306 R&D Projects: GA MŠk 1M0506; GA ČR GEMEM/09/E011 Institutional research plan: CEZ:AV0Z50520514 Keywords : SCIMP * transmembrane adaptor protein * MHC II Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.527, year: 2011

  16. 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.

  17. Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments

    Czech Academy of Sciences Publication Activity Database

    Vít, O.; Man, Petr; Kádek, Alan; Hausner, Jiří; Sklenář, A.; Harant, K.; Novák, Petr; Scigelová, M.; Wofferndin, G.; Petrák, J.

    2016-01-01

    Roč. 146, SI (2016), s. 15-22 ISSN 1874-3919 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : Integral membrane proteins * CNBr * Transmembrane Subject RIV: CE - Biochemistry Impact factor: 3.914, year: 2016

  18. Effect of Pore Pressure on Slip Failure of an Impermeable Fault: A Coupled Micro Hydro-Geomechanical Model

    Science.gov (United States)

    Yang, Z.; Juanes, R.

    2015-12-01

    The geomechanical processes associated with subsurface fluid injection/extraction is of central importance for many industrial operations related to energy and water resources. However, the mechanisms controlling the stability and slip motion of a preexisting geologic fault remain poorly understood and are critical for the assessment of seismic risk. In this work, we develop a coupled hydro-geomechanical model to investigate the effect of fluid injection induced pressure perturbation on the slip behavior of a sealing fault. The model couples single-phase flow in the pores and mechanics of the solid phase. Granular packs (see example in Fig. 1a) are numerically generated where the grains can be either bonded or not, depending on the degree of cementation. A pore network is extracted for each granular pack with pore body volumes and pore throat conductivities calculated rigorously based on geometry of the local pore space. The pore fluid pressure is solved via an explicit scheme, taking into account the effect of deformation of the solid matrix. The mechanics part of the model is solved using the discrete element method (DEM). We first test the validity of the model with regard to the classical one-dimensional consolidation problem where an analytical solution exists. We then demonstrate the ability of the coupled model to reproduce rock deformation behavior measured in triaxial laboratory tests under the influence of pore pressure. We proceed to study the fault stability in presence of a pressure discontinuity across the impermeable fault which is implemented as a plane with its intersected pore throats being deactivated and thus obstructing fluid flow (Fig. 1b, c). We focus on the onset of shear failure along preexisting faults. We discuss the fault stability criterion in light of the numerical results obtained from the DEM simulations coupled with pore fluid flow. The implication on how should faults be treated in a large-scale continuum model is also presented.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Pore size matters for potassium channel conductance

    Science.gov (United States)

    Moldenhauer, Hans; Pincuntureo, Matías

    2016-01-01

    Ion channels are membrane proteins that mediate efficient ion transport across the hydrophobic core of cell membranes, an unlikely process in their absence. K+ channels discriminate K+ over cations with similar radii with extraordinary selectivity and display a wide diversity of ion transport rates, covering differences of two orders of magnitude in unitary conductance. The pore domains of large- and small-conductance K+ channels share a general architectural design comprising a conserved narrow selectivity filter, which forms intimate interactions with permeant ions, flanked by two wider vestibules toward the internal and external openings. In large-conductance K+ channels, the inner vestibule is wide, whereas in small-conductance channels it is narrow. Here we raise the idea that the physical dimensions of the hydrophobic internal vestibule limit ion transport in K+ channels, accounting for their diversity in unitary conductance. PMID:27619418

  4. Pore structure in blended cement pastes

    DEFF Research Database (Denmark)

    Canut, Mariana Moreira Cavalcanti

    Supplementary cementitious materials (SCMs), such as slag and fly ash, are increasingly used as a substitute for Portland cement in the interests of improvement of engineering properties and sustainability of concrete. According to studies improvement of engineering properties can be explained by...... on assumptions of degree of reaction and product densities gave for plain cement pastes results comparable to MIP data.......Supplementary cementitious materials (SCMs), such as slag and fly ash, are increasingly used as a substitute for Portland cement in the interests of improvement of engineering properties and sustainability of concrete. According to studies improvement of engineering properties can be explained...... supplement each other. Cement pastes (w/b=0.4) with and without slag and fly ash cured at two moisture (sealed and saturated) and temperature (20 and 55ºC) conditions were used to investigate the combined impact of SCMs addition and curing on the pore structure of pastes cured up to two years. Also...

  5. Conservation agriculture effects on soil pore characteristics

    DEFF Research Database (Denmark)

    Munkholm, Lars Juhl; Abdollahi, Lotfollah

    ploughing to a depth of 20 cm (MP), harrowing to a depth of 8-10 cm (H) and direct drilling (D). Minimally disturbed core samples were taken at 4-8, 12-16 and 18-27 cm depths 11 years after experimental start. Water retention characteristics were measured for a range of matric potential ranging from -10......Conservation tillage in combination with crop rotation, residue management and cover crops are key components of conservation agriculture. A positive long-term effect of applying all components of conservation agriculture on soil structural quality is expected. However, there is a lack...... of quantitative knowledge to support this statement. This study examines the long-term effects of crop rotations, residue management and tillage on soil pore characteristics of two sandy loam soils in Denmark. Results are reported from a split plot field experiment rotation as main plot factor and tillage...

  6. Preferential flow from pore to landscape scales

    Science.gov (United States)

    Koestel, J. K.; Jarvis, N.; Larsbo, M.

    2017-12-01

    In this presentation, we give a brief personal overview of some recent progress in quantifying preferential flow in the vadose zone, based on our own work and those of other researchers. One key challenge is to bridge the gap between the scales at which preferential flow occurs (i.e. pore to Darcy scales) and the scales of interest for management (i.e. fields, catchments, regions). We present results of recent studies that exemplify the potential of 3-D non-invasive imaging techniques to visualize and quantify flow processes at the pore scale. These studies should lead to a better understanding of how the topology of macropore networks control key state variables like matric potential and thus the strength of preferential flow under variable initial and boundary conditions. Extrapolation of this process knowledge to larger scales will remain difficult, since measurement technologies to quantify macropore networks at these larger scales are lacking. Recent work suggests that the application of key concepts from percolation theory could be useful in this context. Investigation of the larger Darcy-scale heterogeneities that generate preferential flow patterns at the soil profile, hillslope and field scales has been facilitated by hydro-geophysical measurement techniques that produce highly spatially and temporally resolved data. At larger regional and global scales, improved methods of data-mining and analyses of large datasets (machine learning) may help to parameterize models as well as lead to new insights into the relationships between soil susceptibility to preferential flow and site attributes (climate, land uses, soil types).

  7. Phase transitions of fluids in heterogeneous pores

    Directory of Open Access Journals (Sweden)

    A. Malijevský

    2016-03-01

    Full Text Available We study phase behaviour of a model fluid confined between two unlike parallel walls in the presence of long range (dispersion forces. Predictions obtained from macroscopic (geometric and mesoscopic arguments are compared with numerical solutions of a non-local density functional theory. Two capillary models are considered. For a capillary comprising two (differently adsorbing walls we show that simple geometric arguments lead to the generalized Kelvin equation locating very accurately capillary condensation, provided both walls are only partially wet. If at least one of the walls is in complete wetting regime, the Kelvin equation should be modified by capturing the effect of thick wetting films by including Derjaguin's correction. Within the second model, we consider a capillary formed of two competing walls, so that one tends to be wet and the other dry. In this case, an interface localized-delocalized transition occurs at bulk two-phase coexistence and a temperature T*(L depending on the pore width L. A mean-field analysis shows that for walls exhibiting first-order wetting transition at a temperature T_{w}, T_{s} > T*(L > T_{w}, where the spinodal temperature Ts can be associated with the prewetting critical temperature, which also determines a critical pore width below which the interface localized-delocalized transition does not occur. If the walls exhibit critical wetting, the transition is shifted below Tw and for a model with the binding potential W(l=A(Tl-2+B(Tl-3+..., where l is the location of the liquid-gas interface, the transition can be characterized by a dimensionless parameter κ=B/(AL, so that the fluid configuration with delocalized interface is stable in the interval between κ=-2/3 and κ ~ -0.23.

  8. The HIV-1 envelope transmembrane domain binds TLR2 through a distinct dimerization motif and inhibits TLR2-mediated responses.

    Directory of Open Access Journals (Sweden)

    Eliran Moshe Reuven

    2014-08-01

    Full Text Available HIV-1 uses a number of means to manipulate the immune system, to avoid recognition and to highjack signaling pathways. HIV-1 infected cells show limited Toll-Like Receptor (TLR responsiveness via as yet unknown mechanisms. Using biochemical and biophysical approaches, we demonstrate that the trans-membrane domain (TMD of the HIV-1 envelope (ENV directly interacts with TLR2 TMD within the membrane milieu. This interaction attenuates TNFα, IL-6 and MCP-1 secretion in macrophages, induced by natural ligands of TLR2 both in in vitro and in vivo models. This was associated with decreased levels of ERK phosphorylation. Furthermore, mutagenesis demonstrated the importance of a conserved GxxxG motif in driving this interaction within the membrane milieu. The administration of the ENV TMD in vivo to lipotechoic acid (LTA/Galactosamine-mediated septic mice resulted in a significant decrease in mortality and in tissue damage, due to the weakening of systemic macrophage activation. Our findings suggest that the TMD of ENV is involved in modulation of the innate immune response during HIV infection. Furthermore, due to the high functional homology of viral ENV proteins this function may be a general character of viral-induced immune modulation.

  9. 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.

  10. 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...

  11. 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.

  12. 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)

  13. Beer Clarification by Novel Ceramic Hollow-Fiber Membranes: Effect of Pore Size on Product Quality.

    Science.gov (United States)

    Cimini, Alessio; Moresi, Mauro

    2016-10-01

    In this work, the crossflow microfiltration performance of rough beer samples was assessed using ceramic hollow-fiber (HF) membrane modules with a nominal pore size ranging from 0.2 to 1.4 μm. Under constant operating conditions (that is, transmembrane pressure difference, TMP = 2.35 bar; feed superficial velocity, v S = 2.5 m/s; temperature, T = 10 °C), quite small steady-state permeation fluxes (J * ) of 32 or 37 L/m 2 /h were achieved using the 0.2- or 0.5-μm symmetric membrane modules. Both permeates exhibited turbidity beer quality parameters. Moreover, it exhibited J * values of the same order of magnitude of those claimed for the polyethersulfone HF membrane modules currently commercialized. The 1.4-μm asymmetric membrane module yielded quite a high steady-state permeation flux (196 ± 38 L/m 2 /h), and a minimum decline in permeate quality parameters, except for the high levels of turbidity at room temperature and chill haze. In the circumstances, such a membrane module might be regarded as a real valid alternative to conventional powder filters on condition that the resulting permeate were submitted to a final finishing step using 0.45- or 0.65-μm microbially rated membrane cartridges prior to aseptic bottling. A novel combined beer clarification process was thus outlined. © 2016 Institute of Food Technologists®.

  14. 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.

  15. 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.

  16. Coarse and fine root plants affect pore size distributions differently

    OpenAIRE

    Bodner, G.; Leitner, D.; Kaul, H.-P.

    2014-01-01

    Aims Small scale root-pore interactions require validation of their impact on effective hydraulic processes at the field scale. Our objective was to develop an interpretative framework linking root effects on macroscopic pore parameters with knowledge at the rhizosphere scale. Methods A field experiment with twelve species from different families was conducted. Parameters of Kosugi?s pore size distribution (PSD) model were determined inversely from tension infiltrometer data. Measured root tr...

  17. 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.

  18. 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.

  19. Fusion Pore Diameter Regulation by Cations Modulating Local Membrane Anisotropy

    Directory of Open Access Journals (Sweden)

    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.

  20. 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.

  1. 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.

  2. 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.

  3. Pore-size Distributions from Nitrogen Adsorption Revisited: Models Comparison with Controlled-pore Glasses

    Czech Academy of Sciences Publication Activity Database

    Šolcová, Olga; Matějová, Lenka; Schneider, Petr

    2006-01-01

    Roč. 313, č. 2 (2006), s. 167-176 ISSN 0926-860X R&D Projects: GA ČR(CZ) GA104/04/2116; GA ČR GD203/03/H140; GA AV ČR IAA4072404 Institutional research plan: CEZ:AV0Z40720504 Keywords : pore size distribution * physical adsorption * standard nitrogen isotherm Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.630, year: 2006

  4. 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.

  5. 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

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

    Science.gov (United States)

    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.

  7. 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.

  8. ZnO Coatings with Controlled Pore Size, Crystallinity and Electrical Conductivity

    Directory of Open Access Journals (Sweden)

    Roman SCHMACK

    2016-05-01

    Full Text Available Zinc oxide is a wide bandgap semiconductor with unique optical, electrical and catalytic properties. Many of its practical applications rely on the materials pore structure, crystallinity and electrical conductivity. We report a synthesis method for ZnO films with ordered mesopore structure and tuneable crystallinity and electrical conductivity. The synthesis relies on dip-coating of solutions containing micelles of an amphiphilic block copolymer and complexes of Zn2+ ions with aliphatic ligands. A subsequent calcination at 400°C removes the template and induces crystallization of the pore walls. The pore structure is controlled by the template polymer, whereas the aliphatic ligands control the crystallinity of the pore walls. Complexes with a higher thermal stability result in ZnO films with a higher content of residual carbon, smaller ZnO crystals and therefore lower electrical conductivity. The paper discusses the ability of different types of ligands to assist in the synthesis of mesoporous ZnO and relates the structure and thermal stability of the precursor complexes to the crystallinity and electrical conductivity of the zinc oxide.DOI: http://dx.doi.org/10.5755/j01.ms.22.1.8634

  9. 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.

  10. Role of ATP binding and hydrolysis in the gating of the cystic fibrosis transmembrane conductance regulator

    Directory of Open Access Journals (Sweden)

    Taras Gout

    2012-01-01

    Full Text Available The CFTR gene is unique within the ATP-binding cassette (ABC protein family, predominantly of transporters, by coding a chloride channel. The gating mechanism of ABC proteins has been characterized by the ATP Switch model in terms cycles of dimer formation and dissociation linked to ATP binding and hydrolysis, respectively. It would be of interest to assess the extent that Cystic Fibrosis Transmembrane Conductance Regulator (CFTR, a functional channel, fits the ATP Switch model for ABC transporters. Additional transporter mechanisms, namely those of Pgp and HlyB, are discussed for perspective. Literature search of databases selected key references in comparing and contrasting the gating mechanism. CFTR is a functional chloride channel facilitating transmembrane anion flow down electrochemical gradients. A dysfunctional CFTR protein results in cystic fibrosis, a fatal pleiotropic disease currently managed symptomatically. Understanding the gating mechanism will help target drug development aimed at alleviating and curing the disease.

  11. 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.

  12. 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.

  13. 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.

  14. [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.

  15. 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.

  16. 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....

  17. Performance of multilayer coated silicon pore optics

    Science.gov (United States)

    Ackermann, M. D.; Collon, M. J.; Jensen, C. P.; Christensen, F. E.; Krumrey, M.; Cibik, L.; Marggraf, S.; Bavdaz, M.; Lumb, D.; Shortt, B.

    2010-07-01

    The requirements for the IXO (International X-ray Observatory) telescope are very challenging in respect of angular resolution and effective area. Within a clear aperture with 1.7 m > R > 0.25 m that is dictated by the spacecraft envelope, the optics technology must be developed to satisfy simultaneously requirements for effective area of 2.5 m2 at 1.25 keV, 0.65 m2 at 6 keV and 150 cm2 at 30 keV. The reflectivity of the bare mirror substrate materials does not allow these requirements to be met. As such the IXO baseline design contains a coating layout that varies as a function of mirror radius and in accordance with the variation in grazing incidence angle. The higher energy photon response is enhanced through the use of depth-graded multilayer coatings on the inner radii mirror modules. In this paper we report on the first reflectivity measurements of wedged ribbed silicon pore optics mirror plates coated with a depth graded W/Si multilayer. The measurements demonstrate that the deposition and performance of the multilayer coatings is compatible with the SPO production process.

  18. Current concepts in nuclear pore electrophysiology.

    Science.gov (United States)

    Bustamante, José Omar

    2006-01-01

    Over 4 decades ago, microelectrode studies of in situ nuclei showed that, under certain conditions, the nuclear envelope (NE) behaves as a barrier opposing the nucleocytoplasmic flow of physiological ions. As the nuclear pore complexes (NPCs) of the NE are the only pathways for direct nucleocytoplasmic flow, those experiments implied that the NPCs are capable of restricting ion flow. These early studies validated electrophysiology as a useful approach to quantify some of the mechanisms by which NPCs mediate gene activity and expression. Since electron microscopy (EM) and other non-electrophysiological investigations, showed that the NPC lumen is a nanochannel, the opinion prevailed that the NPC could not oppose the flow of ions and, therefore, that electrophysiological observations resulted from technical artifacts. Consequently, the initial enthusiasm with nuclear electrophysiology faded out in less than a decade. In 1990, nuclear electrophysiology was revisited with patch-clamp, the most powerful electrophysiological technique to date. Patch-clamp has consistently demonstrated that the NE has intrinsic ion channel activity. Direct demonstrations of the NPC on-off ion channel gating behavior were published for artificial conditions in 1995 and for intact living nuclei in 2002. This on-off switching/gating behavior can be interpreted in terms of a metastable energy barrier. In the hope of advancing nuclear electrophysiology, and to complement the other papers contained in this special issue of the journal, here I review some of the main technical, experimental, and theoretical issues of the field, with special focus on NPCs.

  19. The hydraulic conductivity of sediments: A pore size perspective

    KAUST Repository

    Ren, X.W.; Santamarina, Carlos

    2017-01-01

    in the void ratio is higher than the theoretical value due to two concurrent phenomena: 1) percolating large pores are responsible for most of the flow, and 2) the larger pores close first during compaction. The prediction of hydraulic conductivity based

  20. Pore fluids from the argillaceous rocks of the Harwell region

    International Nuclear Information System (INIS)

    Brightman, M.A.; Bath, A.H.; Cave, M.R.; Darling, W.G.

    1985-06-01

    The aim of this work was to obtain samples of pore water from argillaceous formations in the Harwell area for chemical analysis to provide a background for radionuclide migration studies and regional groundwater flow pattern. This report describes the samples, development of a pore-water squeezing cell and its operation. Chemical and analytical studies are summarized. (UK)

  1. Fouling layer characterization and pore-blocking mechanisms in an ...

    African Journals Online (AJOL)

    Fouling layer characterization and pore-blocking mechanisms in an UF membrane externally coupled to a UASB reactor. ... Regarding pore-blocking mechanisms, standard blocking was the predominant mechanism at the beginning of filtration, coexisting at the end of it with cake filtration. In the first filtration cycle (1 h), after ...

  2. 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

  3. The study of the relationship between pore structure and ...

    Indian Academy of Sciences (India)

    Administrator

    The pore structure was determined by the N2 adsorption/desorption method below. 73 K and calculated using the BJH model. TEM characterizations show that the pores are ... Mesoporous TiO2 was obtained by calcination of the gel at 500°C for 6 h in air to remove the surfactant species. The samples were designated as ...

  4. Pore size distribution in tablets measured with a morphological sieve

    NARCIS (Netherlands)

    Wu, Yu San; van Vliet, Lucas J.; Frijlink, Henderik W.; van der Voort Maarschalk, Kees

    2007-01-01

    Porosity and pore structure are important characteristics of tablets, since they influence mechanical strength and many other proper-ties. This paper proposes an alternative method for the characterization of pore structure based on image analysis of SEM micrographs. SEM images were made of sodium

  5. The Pore Structure of Direct Methanol Fuel Cell Electrodes

    DEFF Research Database (Denmark)

    Lund, Peter Brilner

    2005-01-01

    The pore structure and morphology of direct methanol fuel cell electrodes are characterized using mercury intrusion porosimetry and scanning electron microscopy. It is found that the pore size distributions of printed primer and catalyst layers are largely dictated by the powders used to make...

  6. 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.)

  7. A FILTRATION METHOD AND APPARATUS INCLUDING A ROLLER WITH PORES

    DEFF Research Database (Denmark)

    2008-01-01

    The present invention offers a method for separating dry matter from a medium. A separation chamber is at least partly defined by a plurality of rollers (2,7) and is capable of being pressure regulated. At least one of the rollers is a pore roller (7) having a surface with pores allowing permeabi...

  8. Expression and regulation of transmembrane transporters in healthy intestine and gastrointestinal diseases

    OpenAIRE

    Hruz, Petr

    2006-01-01

    Transmembrane transporters mediate energy dependent or independent translocation of drugs, potentially toxic compounds, and of various endogenous substrates such as bile acids and bilirubin across membranes. In this thesis the focus is on two classes of transporters, the ATPbinding cassette (ABC) transporters, which mediate ATP dependent transport and the solute carriers (SLC) which use electrochemical gradients for their transport. The transporters are expressed on membranes o...

  9. 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

  10. Functional relevance of aromatic residues in the first transmembrane domain of P2X receptors

    Czech Academy of Sciences Publication Activity Database

    Jindřichová, Marie; Vávra, Vojtěch; Obšil, Tomáš; Stojilkovic, S. S.; Zemková, Hana

    2009-01-01

    Roč. 109, č. 3 (2009), s. 923-934 ISSN 0022-3042 R&D Projects: GA MŠk(CZ) LC554; GA AV ČR(CZ) IAA5011408; GA AV ČR(CZ) IAA500110702; GA AV ČR(CZ) IAA500110910 Institutional research plan: CEZ:AV0Z50110509 Keywords : purinergic receptors * gating * transmembrane domain Subject RIV: FH - Neuro logy Impact factor: 3.999, year: 2009

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

    Science.gov (United States)

    Sikder, Md. Kabir Uddin; Stone, Kyle A.; Kumar, P. B. Sunil; Laradji, Mohamed

    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 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. PMID:25106608

  12. 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

  13. 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

  14. Damage Effects and Fractal Characteristics of Coal Pore Structure during Liquid CO2 Injection into a Coal Bed for E-CBM

    Directory of Open Access Journals (Sweden)

    Li Ma

    2018-05-01

    Full Text Available Pore structure has a significant influence on coal-bed methane (CBM enhancement. Injecting liquid CO2 into coal seams is an effective way to increase CBM recovery. However, there has been insufficient research regarding the damage effects and fractal characteristics of pore structure at low temperature induced by injecting liquid CO2 into coal samples. Therefore, the methods of low-pressure nitrogen adsorption-desorption (LP-N2-Ad and mercury intrusion porosimetry (MIP were used to investigate the damage effects and fractal characteristics of pore structure with full aperture as the specimens were frozen by liquid CO2. The adsorption isotherms revealed that the tested coal samples belonged to type B, indicating that they contained many bottle and narrow-slit shaped pores. The average pore diameter (APD; average growth rate of 18.20%, specific surface area (SSA; average growth rate of 7.38%, and total pore volume (TPV; average growth rate of 18.26% increased after the specimens were infiltrated by liquid CO2, which indicated the generation of new pores and the transformation of original pores. Fractal dimensions D1 (average of 2.58 and D2 (average of 2.90 of treated coal samples were both larger the raw coal (D1, average of 2.55 and D2, average of 2.87, which indicated that the treated specimens had more rough pore surfaces and complex internal pore structures than the raw coal samples. The seepage capacity was increased because D4 (average of 2.91 of the treated specimens was also higher than the raw specimens (D4, average of 2.86. The grey relational coefficient between the fractal dimension and pore structure parameters demonstrated that the SSA, APD, and porosity positively influenced the fractal features of the coal samples, whereas the TPV and permeability exerted negative influences.

  15. Integrative structure and functional anatomy of a nuclear pore complex

    Science.gov (United States)

    Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

    2018-03-01

    Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

  16. Integrative structure and functional anatomy of a nuclear pore complex.

    Science.gov (United States)

    Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

    2018-03-22

    Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. The role of membrane microdomains in transmembrane signaling through the epithelial glycoprotein Gp140/CDCP1

    Science.gov (United States)

    Alvares, Stacy M.; Dunn, Clarence A.; Brown, Tod A.; Wayner, Elizabeth E.; Carter, William G.

    2008-01-01

    Cell adhesion to the extracellular matrix (ECM) via integrin adhesion receptors initiates signaling cascades leading to changes in cell behavior. While integrin clustering is necessary to initiate cell attachment to the matrix, additional membrane components are necessary to mediate the transmembrane signals and the cell adhesion response that alter downstream cell behavior. Many of these signaling components reside in glycosphingolipid-rich and cholesterol-rich membrane domains such as Tetraspanin Enriched Microdomains (TEMs)/Glycosynapse 3 and Detergent-Resistant Microdomains (DRMs), also known as lipid rafts. In the following article, we will review examples of how components in these membrane microdomains modulate integrin adhesion after initial attachment to the ECM. Additionally, we will present data on a novel adhesion-responsive transmembrane glycoprotein Gp140/CUB Domain Containing Protein 1, which clusters in epithelial cell-cell contacts. Gp140 can then be phosphorylated by Src Family Kinases at tyrosine 734 in response to outside-in signals- possibly through interactions involving the extracellular CUB domains. Data presented here suggests that outside-in signals through Gp140 in cell-cell contacts assemble membrane clusters that associate with membrane microdomains to recruit and activate SFKs. Active SFKs then mediate phosphorylation of Gp140, SFK and PKCδ with Gp140 acting as a transmembrane scaffold for these kinases. We propose that the clustering of Gp140 and signaling components in membrane microdomains in cell-cell contacts contributes to changes in cell behavior. PMID:18269919

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Effect of Tissue Heterogeneity on the Transmembrane Potential of Type-1 Spiral Ganglion Neurons: A Simulation Study.

    Science.gov (United States)

    Sriperumbudur, Kiran Kumar; Pau, Hans Wilhelm; van Rienen, Ursula

    2018-03-01

    Electric stimulation of the auditory nerve by cochlear implants has been a successful clinical intervention to treat the sensory neural deafness. In this pathological condition of the cochlea, type-1 spiral ganglion neurons in Rosenthal's canal play a vital role in the action potential initiation. Various morphological studies of the human temporal bones suggest that the spiral ganglion neurons are surrounded by heterogeneous structures formed by a variety of cells and tissues. However, the existing simulation models have not considered the tissue heterogeneity in the Rosenthal's canal while studying the electric field interaction with spiral ganglion neurons. Unlike the existing models, we have implemented the tissue heterogeneity in the Rosenthal's canal using a computationally inexpensive image based method in a two-dimensional finite element model. Our simulation results suggest that the spatial heterogeneity of surrounding tissues influences the electric field distribution in the Rosenthal's canal, and thereby alters the transmembrane potential of the spiral ganglion neurons. In addition to the academic interest, these results are especially useful to understand how the latest tissue regeneration methods such as gene therapy and drug-induced resprouting of peripheral axons, which probably modify the density of the tissues in the Rosenthal's canal, affect the cochlear implant functionality.

  8. Joint inversion of NMR and SIP data to estimate pore size distribution of geomaterials

    Science.gov (United States)

    Niu, Qifei; Zhang, Chi

    2018-03-01

    There are growing interests in using geophysical tools to characterize the microstructure of geomaterials because of the non-invasive nature and the applicability in field. In these applications, multiple types of geophysical data sets are usually processed separately, which may be inadequate to constrain the key feature of target variables. Therefore, simultaneous processing of multiple data sets could potentially improve the resolution. In this study, we propose a method to estimate pore size distribution by joint inversion of nuclear magnetic resonance (NMR) T2 relaxation and spectral induced polarization (SIP) spectra. The petrophysical relation between NMR T2 relaxation time and SIP relaxation time is incorporated in a nonlinear least squares problem formulation, which is solved using Gauss-Newton method. The joint inversion scheme is applied to a synthetic sample and a Berea sandstone sample. The jointly estimated pore size distributions are very close to the true model and results from other experimental method. Even when the knowledge of the petrophysical models of the sample is incomplete, the joint inversion can still capture the main features of the pore size distribution of the samples, including the general shape and relative peak positions of the distribution curves. It is also found from the numerical example that the surface relaxivity of the sample could be extracted with the joint inversion of NMR and SIP data if the diffusion coefficient of the ions in the electrical double layer is known. Comparing to individual inversions, the joint inversion could improve the resolution of the estimated pore size distribution because of the addition of extra data sets. The proposed approach might constitute a first step towards a comprehensive joint inversion that can extract the full pore geometry information of a geomaterial from NMR and SIP data.

  9. Fabrication of beta-PVDF membranes by track etching and specific functionalization of nano-pores

    International Nuclear Information System (INIS)

    Cuscito, O.

    2008-01-01

    Poly(vinylidene fluoride)(β-PVDF) nano-porous membranes were made by chemical revealing of tracks induced from swift heavy ions irradiation. Pore opening and radii can be varied in a controllable manner with the etching time. nano-pores size in nano-meter scale (from 12 nm to 50 nm) appears to be linearly dependent to the etching time. It was then necessary to adapt the characterization tools to these membranes. Consequently, we resorted to the use of structural analysis methods (Scanning Electron Microscopy, Small Angle Neutron Scattering) and developed evaluation methods of the membranes transport properties like gas permeation and ionic diffusion. Results obtained confirm the pores opening (break through) and the hydrophobicity of material, which we have modified with hydrophilic molecules. In this precise case, the grafting of acrylic acid was initiated by the radicals still remains after track-etching (called radio-grafting). This key result was obtained by a study of Electron Paramagnetic Resonance. The labelling of introduced chemical functionalities with fluorescent probes was a very effective mean to visualize very few amounts of molecules by confocal microscopy. The radio-grafting was found specifically localized inside etched tracks. The protocol offers the possibility to create a double functionality, the one localized inside the nano-pores and the other on the surface of membranes. The modification of radio-grafting parameters (the acrylic acid concentration, solvent nature, use of transfer agent) and the chemical properties of the nano-pore walls have a direct incidence on the transport properties. (author) [fr

  10. Pore-scale dynamics of salt transport and distribution in drying porous media

    International Nuclear Information System (INIS)

    Shokri, Nima

    2014-01-01

    Understanding the physics of water evaporation from saline porous media is important in many natural and engineering applications such as durability of building materials and preservation of monuments, water quality, and mineral-fluid interactions. We applied synchrotron x-ray micro-tomography to investigate the pore-scale dynamics of dissolved salt distribution in a three dimensional drying saline porous media using a cylindrical plastic column (15 mm in height and 8 mm in diameter) packed with sand particles saturated with CaI 2 solution (5% concentration by mass) with a spatial and temporal resolution of 12 μm and 30 min, respectively. Every time the drying sand column was set to be imaged, two different images were recorded using distinct synchrotron x-rays energies immediately above and below the K-edge value of Iodine. Taking the difference between pixel gray values enabled us to delineate the spatial and temporal distribution of CaI 2 concentration at pore scale. Results indicate that during early stages of evaporation, air preferentially invades large pores at the surface while finer pores remain saturated and connected to the wet zone at bottom via capillary-induced liquid flow acting as evaporating spots. Consequently, the salt concentration increases preferentially in finer pores where evaporation occurs. Higher salt concentration was observed close to the evaporating surface indicating a convection-driven process. The obtained salt profiles were used to evaluate the numerical solution of the convection-diffusion equation (CDE). Results show that the macro-scale CDE could capture the overall trend of the measured salt profiles but fail to produce the exact slope of the profiles. Our results shed new insight on the physics of salt transport and its complex dynamics in drying porous media and establish synchrotron x-ray tomography as an effective tool to investigate the dynamics of salt transport in porous media at high spatial and temporal resolution

  11. 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.

  12. Bioactive glass-poly (ε-caprolactone) composite scaffolds with 3 dimensionally hierarchical pore networks

    International Nuclear Information System (INIS)

    Yun, Hui-suk; Kim, Seung-eon; Park, Eui Kyun

    2011-01-01

    Hierarchically mesoporous-macroporous-giant-porous bioactive glass/poly ε-caprolactone (PCL) composite scaffolds were prepared using a combination of the sol-gel method, evaporation-induced self-assembly process in the presence of nonionic triblock copolymer, EO 100 PO 65 EO 100 (F127), as template, salt leaching method, and rapid prototyping techniques. F127 acts as a template, inducing the formation of mesopores, NaCl with sizes between 25 and 33 μm provides macro-pores after leaching, and rapid prototyping produces giant-pores. The structure and morphology of the scaffolds were characterized by the field emission scanning electron microscopy, transmission electron microscopy, and Hg porosimetry. The mechanical properties of the scaffolds were examined by the dynamic mechanical analysis. Their in vitro bioactivities were confirmed by immersing the scaffolds in simulated body fluid. Their biocompatibilities were also evaluated by culturing human bone marrow stromal cells on the scaffolds. The scaffolds show good molding capabilities, mechanical properties, 3 dimensionally well-interconnected pore structures, bioactivities, and biocompatibilities in vitro. Depending on the amount of NaCl, the scaffolds also show unique sponge-like properties, but still retain better mechanical properties than general salt leaching derived PCL scaffolds. All of the data provide good evidence that the obtained scaffolds possess excellent potential for applications in the fields of tissue engineering and drug storage.

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

    Science.gov (United States)

    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.

  14. Pore Scale Dynamics of Microemulsion Formation.

    Science.gov (United States)

    Unsal, Evren; Broens, Marc; Armstrong, Ryan T

    2016-07-19

    Experiments in various porous media have shown that multiple parameters come into play when an oleic phase is displaced by an aqueous solution of surfactant. In general, the displacement efficiency is improved when the fluids become quasi-miscible. Understanding the phase behavior oil/water/surfactant systems is important because microemulsion has the ability to generate ultralow interfacial tension (microemulsion formation and the resulting properties under equilibrium conditions. However, the majority of applications where microemulsion is present also involve flow, which has received relatively less attention. It is commonly assumed that the characteristics of an oil/water/surfactant system under flowing conditions are identical to the one under equilibrium conditions. Here, we show that this is not necessarily the case. We studied the equilibrium phase behavior of a model system consisting of n-decane and an aqueous solution of olefin sulfonate surfactant, which has practical applications for enhanced oil recovery. The salt content of the aqueous solution was varied to provide a range of different microemulsion compositions and oil-water interfacial tensions. We then performed microfluidic flow experiments to study the dynamic in situ formation of microemulsion by coinjecting bulk fluids of n-decane and surfactant solution into a T-junction capillary geometry. A solvatochromatic fluorescent dye was used to obtain spatially resolved compositional information. In this way, we visualized the microemulsion formation and the flow of it along with the excess phases. A complex interaction between the flow patterns and the microemulsion properties was observed. The formation of microemulsion influenced the flow regimes, and the flow regimes affected the characteristics of the microemulsion formation. In particular, at low flow rates, slug flow was observed, which had profound consequences on the pore scale mixing behavior and resulting microemulsion properties.

  15. Nonpolar interactions between trans-membrane helical EGF peptide and phosphatidylcholines, sphingomyelins and cholesterol. Molecular dynamics simulation studies

    NARCIS (Netherlands)

    Róg, T.; Murzyn, K.; Karttunen, M.E.J.; Pasenkiewicz-Gierula, M.

    2008-01-01

    A molecular dynamics simulation study of four lipid bilayers with inserted trans-membrane helical fragment of epithelial growth factor (EGF) receptor (EGF peptide) was performed. The lipid bilayers differ in their lipid composition and consist of (i) unsaturated phosphatidylcholine

  16. 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.

  17. Can The Pore Scale Geometry Explain Soil Sample Scale Hydrodynamic Properties?

    Directory of Open Access Journals (Sweden)

    Sarah Smet

    2018-04-01

    also showed a link between pores of different sizes. Identifying the key geometrical indicators that induce soil hydrodynamic behavior is of major interest for the generation of phenomenological pore network models. These models are useful to test physical equations of fluid transport that ultimately depend on a multitude of processes, and induce numerous biological processes.

  18. A Three-Dimensional Pore-Scale Model for Non-Wetting Phase Mobilization with Ferrofluid

    Science.gov (United States)

    Wang, N.; Prodanovic, M.

    2017-12-01

    Ferrofluid, a stable dispersion of paramagnetic nanoparticles in water, can generate a distributed pressure difference across the phase interface in an immiscible two-phase flow under an external magnetic field. In water-wet porous media, this non-uniform pressure difference may be used to mobilize the non-wetting phase, e.g. oil, trapped in the pores. Previous numerical work by Soares et al. of two-dimensional single-pore model showed enhanced non-wetting phase recovery with water-based ferrofluid under certain magnetic field directions and decreased recovery under other directions. However, the magnetic field selectively concentrates in the high magnetic permeability ferrofluid which fills the small corners between the non-wetting phase and the solid wall. The magnetic field induced pressure is proportional to the square of local magnetic field strength and its normal component, and makes a significant impact on the non-wetting phase deformation. The two-dimensional model omitted the effect of most of these corners and is not sufficient to compute the magnetic-field-induced pressure difference or to predict the non-wetting blob deformation. Further, it is not clear that 3D effects on magnetic field in an irregular geometry can be approximated in 2D. We present a three-dimensional immiscible two-phase flow model to simulate the deformation of a non-wetting liquid blob in a single pore filled with a ferrofluid under a uniform external magnetic field. The ferrofluid is modeled as a uniform single phase because the nanoparticles are 104 times smaller than the pore. The open source CFD solver library OpenFOAM is used for the simulations based on the volume of fluid method. Simulations are performed in a converging-diverging channel model on different magnetic field direction, different initial oil saturations, and different pore shapes. Results indicate that the external magnetic field always stretches the non-wetting blob away from the solid channel wall. A magnetic

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Pore Structures in the Biomineralized Byssus of Anomia simplex

    DEFF Research Database (Denmark)

    Frølich, Simon; Leemreize, Hanna; Thomsen, Jesper Skovhus

    2016-01-01

    that uses a biomineralized byssus to permanently anchor itself to substrates. The byssus has a highly complex hierarchical structure and contains over 90 wt% CaCO3. The byssus features a complex set of porosities, presumed to be highly important for the function of the attachment system. The pore space...... is the main focus of the present work. We characterize the three dimensional distribution of pore spaces in the byssus using micro-computed tomography (µCT) through a combination of in house CT and high-resolution synchrotron CT. The pore structures are observed to fall into distinct categories in various...

  6. Crystalline mesoporous zirconia catalysts having stable tetragonal pore wall structure

    Science.gov (United States)

    Sachtler, W.M.H.; Huang, Y.Y.

    1998-07-28

    Methods are disclosed for the preparation of new sulfated mesoporous zirconia materials/catalysts with crystalline pore walls of predominantly tetragonal crystal structure, characterized by nitrogen physical sorption measurement, X-ray diffraction, transmission electron microscopy and catalytic tests using n-butane isomerization to iso-butane and alkylation of 1-naphthol with 4-tert-butylstyrene as probe reactions. Sulfate deposition is preferred for the transformation of a mesoporous precursor with amorphous pore walls into a material with crystalline pore walls maintaining the mesoporous characteristics. 17 figs.

  7. Time evolution of pore system in lime - Pozzolana composites

    Science.gov (United States)

    Doleželová, Magdaléna; Čáchová, Monika; Scheinherrová, Lenka; Keppert, Martin

    2017-11-01

    The lime - pozzolana mortars and plasters are used in restoration works on building cultural heritage but these materials are also following the trend of energy - efficient solutions in civil engineering. Porosity and pore size distribution is one of crucial parameters influencing engineering properties of porous materials. The pore size distribution of lime based system is changing in time due to chemical processes occurring in the material. The present paper describes time evolution of pore system in lime - pozzolana composites; the obtained results are useful in prediction of performance of lime - pozzolana systems in building structures.

  8. The Destabilization of Protected Soil Organic Carbon Following Experimental Drought at the Pore and Core scale

    Science.gov (United States)

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

    2015-12-01

    The movement of water and solutes through the pore matrix controls the distribution and transformation of carbon (C) in soils. Thus, a change in the hydrologic connectivity, such as increased saturation, disturbance or drought, may alter C mineralization and greenhouse gas (GHG) fluxes to the atmosphere. While these processes occur at the pore scale, they are often investigated at coarser scale. This project investigates pore- and core-scale soil C dynamics with varying hydrologic factors (simulated precipitation, groundwater-led saturation, and drought) to assess how climate-change induced shifts in hydrologic connectivity influences the destabilization of protected C in soils. Surface soil cores (0-15 cm depth) were collected from the Disney Wilderness Preserve, Florida, USA where water dynamics, particularly water table rise and fall, appear to exert a strong control on the emissions of GHGs and the persistence of soil organic matter in these soils. We measured CO2 and CH4 from soils allowed to freely imbibe water from below to a steady state starting from either field moist conditions or following experimental drought. Parallel treatments included the addition of similar quantities of water from above to simulate precipitation. Overall respiration increased in soil cores subjected to drought compared to field moist cores independent of wetting type. Cumulative CH4 production was higher in drought-induced soils, especially in the soils subjected to experimental groundwater-led saturation. Overall, the more C (from CO2 and CH4) was lost in drought-induced soils compared to field moist cores. Our results indicate that future drought events could have profound effects on the destabilization of protected C, especially in groundwater-fed soils. Our next steps focus on how to accurately capture drought-induced C destabilization mechanisms in earth system models.

  9. 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.

  10. 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.

  11. Microfiltration of distillery stillage: Influence of membrane pore size

    Directory of Open Access Journals (Sweden)

    Vasić Vesna M.

    2012-01-01

    Full Text Available Stillage is one of the most polluted waste products of the food industry. Beside large volume, the stillage contains high amount of suspended solids, high values of chemical oxygen demand and biological oxygen demand, so it should not be discharged in the nature before previous purification. In this work, three ceramic membranes for microfiltration with different pore sizes were tested for stillage purification in order to find the most suitable membrane for the filtration process. Ceramic membranes with a nominal pore size of 200 nm, 450 nm and 800 nm were used for filtration. The influence of pore size on permeate flux and removal efficiency was investigated. A membrane with the pore size of 200 nm showed the best filtration performance so it was chosen for the microfiltration process.

  12. Mesoporous Akaganeite of Adjustable Pore Size Synthesized using Mixed Templates

    Science.gov (United States)

    Zhang, Y.; Ge, D. L.; Ren, H. P.; Fan, Y. J.; Wu, L. M.; Sun, Z. X.

    2017-12-01

    Mesoporous akaganeite with large and adjustable pore size was synthesized through a co-template method, which was achieved by the combined interaction between PEG2000 and alkyl amines with different lengths of the straight carbon chain. The characterized results indicate that the synthesized samples show comparatively narrow BJH pore size distributions and centered at 14.3 nm when PEG and HEPA was used, and it could be enlarged to 16.8 and 19.4 nm respectively through changing the alkyl amines to DDA and HDA. Meanwhile, all the synthesized akaganeite possess relativity high specific surface area ranging from 183 to 281 m2/g and high total pore volume of 0.98 to 1.5 cm3/g. A possible mechanism leading to the pore size changing was also proposed.

  13. 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

    Glycosylphosphatidylinositol (GPI) anchoring of the prion protein (PrP C ) influences PrP C misfolding into the disease-associated isoform, PrP res , as well as prion propagation and infectivity. GPI proteins are found in cholesterol- and sphingolipid-rich membrane regions called rafts. Exchanging the GPI anchor for a nonraft transmembrane sequence redirects PrP C away from rafts. Previous studies showed that nonraft transmembrane PrP C variants resist conversion to PrP res when transfected into scrapie-infected N2a neuroblastoma cells, likely due to segregation of transmembrane PrP C and GPI-anchored PrP res in distinct membrane environments. Thus, it remained unclear whether transmembrane PrP C might convert to PrP res if seeded by an exogenous source of PrP res not associated with host cell rafts and without the potential influence of endogenous expression of GPI-anchored PrP C To further explore these questions, constructs containing either a C-terminal wild-type GPI anchor signal sequence or a nonraft transmembrane sequence containing a flexible linker were expressed in a cell line derived from PrP knockout hippocampal neurons, NpL2. NpL2 cells have physiological similarities to primary neurons, representing a novel and advantageous model for studying transmissible spongiform encephalopathy (TSE) infection. Cells were infected with inocula from multiple prion strains and in different biochemical states (i.e., membrane bound as in brain microsomes from wild-type mice or purified GPI-anchorless amyloid fibrils). Only GPI-anchored PrP C supported persistent PrP res propagation. Our data provide strong evidence that in cell culture GPI anchor-directed membrane association of PrP C is required for persistent PrP res propagation, implicating raft microdomains as a location for conversion. Mechanisms of prion propagation, and what makes them transmissible, are poorly understood. Glycosylphosphatidylinositol (GPI) membrane anchoring of the prion protein (PrP C

  14. 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

  15. 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

  16. Pore Pressure and Field stress variation from Salt Water Injection; A case Study from Beaver Lodge Field in Williston Basin

    Science.gov (United States)

    Mohammed, R. A.; Khatibi, S.

    2017-12-01

    One of the major concerns in producing from oil and gas reservoirs in North American Basins is the disposal of high salinity salt water. It is a misconception that Hydro frack triggers Earthquakes, but due to the high salinity and density of water being pumped to the formation that has pore space of the rock already filled, which is not the case in Hydro-frack or Enhanced Oil Recovery in which fracturing fluid is pumped into empty pore space of rocks in depleted reservoirs. A review on the Bakken history showed that the concerns related to induce seismicity has increased over time due to variations in Pore pressure and In-situ stress that have shown steep changes in the region over the time. In this study, we focused on Pore pressure and field Stress variations in lower Cretaceous Inyan Kara and Mississippian Devonian Bakken, Inyan Kara is the major source for class-II salt-water disposal in the basin. Salt-water disposal is the major cause for induced seismicity. A full field study was done on Beaver Lodge Field, which has many salt-water disposal wells Adjacent to Oil and Gas Wells. We analyzed formation properties, stresses, pore-pressure, and fracture gradient profile in the field and. The constructed Mechanical Earth Model (MEM) revealed changes in pore pressure and stresses over time due to saltwater injection. Well drilled in the past were compared to recently drilled wells, which showed much stress variations. Safe mud weight Window of wells near proximity of injection wells was examined which showed many cases of wellbore instabilities. Results of this study will have tremendous impact in studying environmental issues and the future drilling and Fracking operations.

  17. Transmembrane neural cell-adhesion molecule (NCAM), but not glycosyl-phosphatidylinositol-anchored NCAM, down-regulates secretion of matrix metalloproteinases

    DEFF Research Database (Denmark)

    Edvardsen, K; Chen, W; Rucklidge, G

    1993-01-01

    proteinases, and proteinase inhibitors all participate in the construction, maintenance, and remodeling of extracellular matrix by cells. The neural cell-adhesion molecule (NCAM)-negative rat glioma cell line BT4Cn secretes substantial amounts of metalloproteinases, as compared with its NCAM-positive mother......During embryogenesis interactions between cells and extracellular matrix play a central role in the modulation of cell motility, growth, and differentiation. Modulation of matrix structure is therefore crucial during development; extracellular matrix ligands, their receptors, extracellular...... cell line BT4C. We have transfected the BT4Cn cell line with cDNAs encoding the human NCAM-B and -C isoforms. We report here that the expression of transmembrane NCAM-B, but not of glycosyl-phosphatidylinositol-linked NCAM-C, induces a down-regulation of 92-kDa gelatinase (matrix metalloproteinase 9...

  18. Resolving the biophysics of axon transmembrane polarization in a single closed-form description

    Energy Technology Data Exchange (ETDEWEB)

    Melendy, Robert F., E-mail: rfmelendy@liberty.edu [School of Engineering and Computational Sciences, Liberty University, Lynchburg, Virginia 24515 (United States)

    2015-12-28

    When a depolarizing event occurs across a cell membrane there is a remarkable change in its electrical properties. A complete depolarization event produces a considerably rapid increase in voltage that propagates longitudinally along the axon and is accompanied by changes in axial conductance. A dynamically changing magnetic field is associated with the passage of the action potential down the axon. Over 75 years of research has gone into the quantification of this phenomenon. To date, no unified model exist that resolves transmembrane polarization in a closed-form description. Here, a simple but formative description of propagated signaling phenomena in the membrane of an axon is presented in closed-form. The focus is on using both biophysics and mathematical methods for elucidating the fundamental mechanisms governing transmembrane polarization. The results presented demonstrate how to resolve electromagnetic and thermodynamic factors that govern transmembrane potential. Computational results are supported by well-established quantitative descriptions of propagated signaling phenomena in the membrane of an axon. The findings demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation function together in generating an action potential in a unified closed-form description. The work presented in this paper provides compelling evidence that three basic factors contribute to the propagated signaling in the membrane of an axon. It is anticipated this work will compel those in biophysics, physical biology, and in the computational neurosciences to probe deeper into the classical and quantum features of membrane magnetization and signaling. It is hoped that subsequent investigations of this sort will be advanced by the computational features of this model without having to resort to numerical methods of analysis.

  19. 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.

  20. Obif, a Transmembrane Protein, Is Required for Bone Mineralization and Spermatogenesis in Mice.

    Directory of Open Access Journals (Sweden)

    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.

  1. 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.

  2. Pore Structure and Fractal Characteristics of Niutitang Shale from China

    Directory of Open Access Journals (Sweden)

    Zhaodong Xi

    2018-04-01

    Full Text Available A suite of shale samples from the Lower Cambrian Niutitang Formation in northwestern Hunan Province, China, were investigated to better understand the pore structure and fractal characteristics of marine shale. Organic geochemistry, mineralogy by X-ray diffraction, porosity, permeability, mercury intrusion and nitrogen adsorption and methane adsorption experiments were conducted for each sample. Fractal dimension D was obtained from the nitrogen adsorption data using the fractal Frenkel-Halsey-Hill (FHH model. The relationships between total organic carbon (TOC content, mineral compositions, pore structure parameters and fractal dimension are discussed, along with the contributions of fractal dimension to shale gas reservoir evaluation. Analysis of the results showed that Niutitang shale samples featured high TOC content (2.51% on average, high thermal maturity (3.0% on average, low permeability and complex pore structures, which are highly fractal. TOC content and mineral compositions are two major factors affecting pore structure but they have different impacts on the fractal dimension. Shale samples with higher TOC content had a larger specific surface area (SSA, pore volume (PV and fractal dimension, which enhanced the heterogeneity of the pore structure. Quartz content had a relatively weak influence on shale pore structure, whereas SSA, PV and fractal dimension decreased with increasing clay mineral content. Shale with a higher clay content weakened pore structure heterogeneity. The permeability and Langmuir volume of methane adsorption were affected by fractal dimension. Shale samples with higher fractal dimension had higher adsorption capacity but lower permeability, which is favorable for shale gas adsorption but adverse to shale gas seepage and diffusion.

  3. Direct Numerical Simulation of Low Capillary Number Pore Scale Flows

    Science.gov (United States)

    Esmaeilzadeh, S.; Soulaine, C.; Tchelepi, H.

    2017-12-01

    The arrangement of void spaces and the granular structure of a porous medium determines multiple macroscopic properties of the rock such as porosity, capillary pressure, and relative permeability. Therefore, it is important to study the microscopic structure of the reservoir pores and understand the dynamics of fluid displacements through them. One approach for doing this, is direct numerical simulation of pore-scale flow that requires a robust numerical tool for prediction of fluid dynamics and a detailed understanding of the physical processes occurring at the pore-scale. In pore scale flows with a low capillary number, Eulerian multiphase methods are well-known to produce additional vorticity close to the interface. This is mainly due to discretization errors which lead to an imbalance of capillary pressure and surface tension forces that causes unphysical spurious currents. At the pore scale, these spurious currents can become significantly stronger than the average velocity in the phases, and lead to unphysical displacement of the interface. In this work, we first investigate the capability of the algebraic Volume of Fluid (VOF) method in OpenFOAM for low capillary number pore scale flow simulations. Afterward, we compare VOF results with a Coupled Level-Set Volume of Fluid (CLSVOF) method and Iso-Advector method. It has been shown that the former one reduces the VOF's unphysical spurious currents in some cases, and both are known to capture interfaces sharper than VOF. As the conclusion, we will investigate that whether the use of CLSVOF or Iso-Advector will lead to less spurious velocities and more accurate results for capillary driven pore-scale multiphase flows or not. Keywords: Pore-scale multiphase flow, Capillary driven flows, Spurious currents, OpenFOAM

  4. Rock Physics of Reservoir Rocks with Varying Pore Water Saturation and Pore Water Salinity

    DEFF Research Database (Denmark)

    Katika, Konstantina

    experiments, the rock is subjected to high external stresses that resemble the reservoir stresses; 2) the fluid distribution within the pore space changes during the flow through experiments and wettability alterations may occur; 3) different ions, present in the salt water injected in the core, interact......Advanced waterflooding (injection of water with selective ions in reservoirs) is a method of enhanced oil recovery (EOR) that has attracted the interest of oil and gas companies that exploit the Danish oil and gas reservoirs. This method has been applied successfully in oil reservoirs...... and in the Smart Water project performed in a laboratory scale in order to evaluate the EOR processes in selected core plugs. A major step towards this evaluation is to identify the composition of the injected water that leads to increased oil recovery in reservoirs and to define changes in the petrophysical...

  5. 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

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

    International Nuclear Information System (INIS)

    Ewing, R.P.

    2008-01-01

    A central concept for the geological barrier at the proposed Yucca Mountain radioactive waste repository is diffusive retardation: solute moving through a fracture diffuses into and out of the rock matrix. This diffusive exchange retards overall solute movement, and retardation both dilutes waste being released, and allows additional decay. The original concept of diffusive retardation required knowledge only of the fracture conductivity and the matrix diffusion. But that simple concept is unavoidably complicated by other issues and processes: contaminants may sorb to the rock matrix, fracture flow may be episodic, a given fracture may or may not flow depending on the volume of flow and the fracture's connection to the overall fracture network, the matrix imbibes water during flow episodes and dries between episodes, and so on. Some of these issues have been examined by other projects. This particular project is motivated by a simple fact: Yucca Mountain tuff has low pore connectivity. This fact is not widely recognized, nor are its implications widely appreciated. Because low pore connectivity affects many processes, it may invalidate many assumptions that are basic (though perhaps not stated) to other investigations. The overall project's objective statement (from the proposal) was: This proposal aims to improve our understanding of diffusive retardation of radionuclides due to fracture/matrix interactions. Results from this combined experimental/modeling work will (1) determine whether the current understanding and model representation of matrix diffusion is valid, (2) provide insights into the upscaling of laboratory-scale diffusion experiments, and (3) evaluate the impact on diffusive retardation of episodic fracture flow and pore connectivity in Yucca Mountain tuffs. An obvious data gap addressed by the project was that there were only a few limited measurements of the diffusion coefficient of the rock at the repository level. That is, at the time we wrote

  7. Artificial Diels–Alderase based on the transmembrane protein FhuA

    Directory of Open Access Journals (Sweden)

    Hassan Osseili

    2016-06-01

    Full Text Available Copper(I and copper(II complexes were covalently linked to an engineered variant of the transmembrane protein Ferric hydroxamate uptake protein component A (FhuA ΔCVFtev. Copper(I was incorporated using an N-heterocyclic carbene (NHC ligand equipped with a maleimide group on the side arm at the imidazole nitrogen. Copper(II was attached by coordination to a terpyridyl ligand. The spacer length was varied in the back of the ligand framework. These biohybrid catalysts were shown to be active in the Diels–Alder reaction of a chalcone derivative with cyclopentadiene to preferentially give the endo product.

  8. 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.

  9. Trafficking and function of the cystic fibrosis transmembrane conductance regulator: a complex network of posttranslational modifications

    Science.gov (United States)

    McClure, Michelle L.; Barnes, Stephen; Brodsky, Jeffrey L.

    2016-01-01

    Posttranslational modifications add diversity to protein function. Throughout its life cycle, the cystic fibrosis transmembrane conductance regulator (CFTR) undergoes numerous covalent posttranslational modifications (PTMs), including glycosylation, ubiquitination, sumoylation, phosphorylation, and palmitoylation. These modifications regulate key steps during protein biogenesis, such as protein folding, trafficking, stability, function, and association with protein partners and therefore may serve as targets for therapeutic manipulation. More generally, an improved understanding of molecular mechanisms that underlie CFTR PTMs may suggest novel treatment strategies for CF and perhaps other protein conformational diseases. This review provides a comprehensive summary of co- and posttranslational CFTR modifications and their significance with regard to protein biogenesis. PMID:27474090

  10. 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

  11. Structure, function and physiological consequences of virally encoded chemokine seven transmembrane receptors

    DEFF Research Database (Denmark)

    Rosenkilde, M M; Smit, M J; Waldhoer, M

    2008-01-01

    A number of human and animal herpes viruses encode G-protein coupled receptors with seven transmembrane (7TM) segments-most of which are clearly related to human chemokine receptors. It appears, that these receptors are used by the virus for immune evasion, cellular transformation, tissue targeting...... pathogenesis is still poorly understood. Here we focus on the current knowledge of structure, function and trafficking patterns of virally encoded chemokine receptors and further address the putative roles of these receptors in virus survival and host -cell and/or -immune system modulation. Finally, we...

  12. Exploiting hydrophobicity for efficient production of transmembrane helices for structure determination by NMR spectroscopy

    DEFF Research Database (Denmark)

    Bugge, Katrine Østergaard; Steinocher, Helena; Brooks, Andrew J.

    2015-01-01

    -labeled protein. In this work, we have exploited the hydrophobic nature of membrane proteins to develop a simple and efficient production scheme for isotope-labeled single-pass transmembrane domains (TMDs) with or without intrinsically disordered regions. We have evaluated the applicability and limitations...... of the strategy using seven membrane protein variants that differ in their overall hydrophobicity and length and show a recovery for suitable variants of >70%. The developed production scheme is cost-efficient and easy to implement and has the potential to facilitate an increase in the number of structures...

  13. Transmembrane adaptor proteins in the high-affinity IgE receptor signaling

    Czech Academy of Sciences Publication Activity Database

    Dráber, Petr; Hálová, Ivana; Levi-Schaffer, F.; Dráberová, Lubica

    2012-01-01

    Roč. 2, 11.1. (2012), s. 95 ISSN 1664-3224 R&D Projects: GA MŠk 1M0506; GA ČR GA301/09/1826; GA ČR GAP302/10/1759; GA AV ČR KAN200520701 Grant - others:AV ČR(CZ) M200520901 Institutional research plan: CEZ:AV0Z50520514 Institutional support: RVO:68378050 Keywords : IgE receptor * LAT/LAT1 * LAX * NTAL/Lab/LAT2 * PAG/Cbp * mast cells * plasma membrane * transmembrane adaptor proteins Subject RIV: EB - Genetics ; Molecular Biology

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. The effect of the pore-fluid factor on strength and failure mechanism of Wilkeson sandstone

    Science.gov (United States)

    Kätker, A. K.; Rempe, M.; Renner, J.

    2016-12-01

    The effective stress law, σn,eff = σn - αpf, is a central tool in analysing phenomena related to hydromechanical coupling, such as fluid-induced seismicity or aftershock activity. The effective-stress coefficient α assumes different values for specific physical properties and may deviate from 1. The limited number of studies suggest that brittle compressive strength obeys an effective-stress law when effective drainage is achieved. Yet, open questions remain regarding, e.g., the role of the loading path. We performed suites of triaxial compression tests on samples of Wilkeson sandstone at a range of pore-fluid pressures but identical effective confining pressure (60, 100, and 120 MPa) maintaining the pore-fluid factor λ = pf / pc constant (0.05, 0.2, 0.4, 0.55) during the isostatic loading stage to ensure uniform loading paths. Samples were shortened with a strain rate of 4×10-7 s-1 yielding drained conditions. All tests were terminated at a total axial strain of 4.5% for comparability of microstructures. The tests also included continuous permeability determination and ultrasonic p-wave-velocity measurements to monitor microstructural evolution. Results from experiments conducted at peff = 100 MPa show that dry samples exhibit a higher peak strength and brittle failure while water-saturated samples tend to deform at lower stress by cataclastic flow indicating physico-chemical weakening. Regardless of pore-fluid factor, the saturated experiments exhibit similar peak and residual strength. Differences in failure mechanism (degree of macroscopic localization) and volumetric strain evolution are however noticed, albeit without systematic relation to pore-fluid factor. Microstructure analyses by optical and scanning electron microscopy revealed an evolution from localized shear zones in dry experiments and experiments with a low pore-fluid factor to rather distributed cataclastic flow for experiments with high pore fluid factors. Yet, mechanical and structural

  20. PBO Borehole Strainmeters and Pore Pressure Sensors: Recording Hydrological Strain Signals

    Science.gov (United States)

    Gottlieb, M. H.; Hodgkinson, K. M.; Mencin, D.; Henderson, D. B.; Johnson, W.; Van Boskirk, E.; Pyatt, C.; Mattioli, G. S.

    2017-12-01

    UNAVCO operates a network of 75 borehole strainmeters along the west coast of the United States and Vancouver Island, Canada as part of the Plate Boundary Observatory (PBO), the geodetic component of the NSF-funded Earthscope program. Borehole strainmeters are designed to detect variations in the strain field at the nanostrain level and can easily detect transient strains caused by aseismic creep events, Episodic Tremor and Slip (ETS) events and seismically induced co- and post-seimic signals. In 2016, one strainmeter was installed in an Oklahoma oil field to characterize in-situ deformation during CO2 injection. Twenty-three strainmeter sites also have pore pressure sensors to measure fluctuations in groundwater pressure. Both the strainmeter network and the pore pressure sensors provide unique data against which those using water-level measurements, GPS time-series or InSAR data can compare possible subsidence signals caused by groundwater withdrawal or fluid re-injection. Operating for 12 years, the PBO strainmeter and pore pressure network provides a long-term, continuous, 1-sps record of deformation. PBO deploys GTSM21 tensor strainmeters from GTSM Technologies, which consist of four horizontal strain gauges stacked vertically, at different orientations, within a single 2 m-long instrument. The strainmeters are typically installed at depths of 200 to 250 m and grouted into the bottom of 15 cm diameter boreholes. The pore pressure sensors are Digiquartz Depth Sensors from Paros Scientific. These sensors are installed in 2" PVC, sampling groundwater through a screened section 15 m above the co-located strainmeter. These sensors are also recording at 1-sps with a resolution in the hundredths of hPa. High-rate local barometric pressure data and low-rate rainfall data also available at all locations. PBO Strainmeter and pore pressure data are available in SEED, SAC-ASCII and time-stamped ASCII format from the IRIS Data Managements Center. Strainmeter data are

  1. 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.

  2. The effect of the atmosphere and the role of pore filling on the sintering of aluminium

    International Nuclear Information System (INIS)

    Schaffer, G.B.; Hall, B.J.; Bonner, S.J.; Huo, S.H.; Sercombe, T.B.

    2006-01-01

    Alloys of Al-3.8Cu-1Mg-0.7Si, Al-4Cu-0.6Si-0.1Mg, Al-4Cu-1.2Mg and Al-1.9Mg-1.9Si were made using air atomised powder and conventional press-and-sinter powder metallurgy techniques. These were sintered under nitrogen with a controlled water content which varied from 3 to 630 ppm (a dew point of -69 to -25 deg. C), nitrogen-5%hydrogen, argon and argon-5%hydrogen, all at atmospheric pressure, or a vacuum of -2 torr. Dry nitrogen is the most efficacious atmosphere. Vacuum is more effective than argon while hydrogen, and thus water, is extremely prejudicial to sintered density. The minimum dew point for optimum sintering is -60 deg. C (10.5 ppm H 2 O). The key feature in the beneficial effect of nitrogen is the formation of aluminium nitride. This reduces the pressure in the pore spaces relative to the external atmosphere, which induces pore filling at grain sizes that are smaller than those required for sintering in inert atmospheres. It is suggested that pore filling is an important densification mechanism during the sintering of aluminium

  3. 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

  4. 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)

  5. Investigating textural controls on Archie's porosity exponent using process-based, pore-scale modelling

    Science.gov (United States)

    Niu, Q.; Zhang, C.

    2017-12-01

    Archie's law is an important empirical relationship linking the electrical resistivity of geological materials to their porosity. It has been found experimentally that the porosity exponent m in Archie's law in sedimentary rocks might be related to the degree of cementation, and therefore m is termed as "cementation factor" in most literatures. Despite it has been known for many years, there is lack of well-accepted physical interpretations of the porosity exponent. Some theoretical and experimental evidences have also shown that m may be controlled by the particle and/or pore shape. In this study, we conduct a pore-scale modeling of the porosity exponent that incorporates different geological processes. The evolution of m of eight synthetic samples with different particle sizes and shapes are calculated during two geological processes, i.e., compaction and cementation. The numerical results show that in dilute conditions, m is controlled by the particle shape. As the samples deviate from dilute conditions, m increases gradually due to the strong interaction between particles. When the samples are at static equilibrium, m is noticeably larger than its values at dilution condition. The numerical simulation results also show that both geological compaction and cementation induce a significant increase in m. In addition, the geometric characteristics of these samples (e.g., pore space/throat size, and their distributions) during compaction and cementation are also calculated. Preliminary analysis shows a unique correlation between the pore size broadness and porosity exponent for all eight samples. However, such a correlation is not found between m and other geometric characteristics.

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

    Directory of Open Access Journals (Sweden)

    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.

  7. 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.

  8. 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.

  9. Monolayer freeze-fracture autoradiography: quantitative analysis of the transmembrane distribution of radioiodinated concanavalin A

    International Nuclear Information System (INIS)

    Fisher, K.A.

    1982-01-01

    The technique of monolayer freeze-fracture autoradiography (MONOFARG) has been developed and the principles, quantitation, and application of the method are described. Cell monolayers attached to polylysine-treated glass were freeze-fractured, shadowed, and coated with dry, Parlodion-supported Ilford L4 photographic emulsion at room temperature. Quantitative aspects of MONOFARG were examined using radioiodinated test systems. Background was routinely -4 grains/μm 2 /day, the highest overall efficiency was between 25% and 45%, and grain density and efficiency were dependent on radiation dose for iodine-125 and D-19 development. Corrected grain densities were linearly proportional to iodine-125 concentration. The method was applied to an examination of the transmembrane distribution of radioiodinated and fluoresceinated concanavalin A ( 125 I-FITC-Con-A). Human erythrocytes were labeled, column-purified, freeze-dried or freeze-fractured, autoradiographed, and examined by electron microscopy. The number of silver grains per square micrometer of unsplit single membrane was essentially identical to that of split extracellular membrane halves. These data demonstrate that 125 I-FITC-Con-A partitions exclusively with the extracellular half of the membrane upon freeze-fracturing and can be used as a quantitative marker for the fraction of extracellular split membrane halves. This method should be able to provide new information about certain transmembrane properties of biological membrane molecules and probes, as well as about the process of freeze-fracture per se

  10. Impact of axial velocity and transmembrane pressure (TMP) on ARP filter performance

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Burket, P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-02-29

    The Savannah River Site (SRS) is currently treating radioactive liquid waste with the Actinide Removal Process (ARP) and the Modular Caustic Side Solvent Extraction Unit (MCU). Recently, the low filter flux through the ARP of approximately 5 gallons per minute has limited the rate at which radioactive liquid waste can be treated. Salt Batch 6 had a lower processing rate and required frequent filter cleaning. Savannah River Remediation (SRR) has a desire to understand the causes of the low filter flux and to increase ARP/MCU throughput. One potential method for increasing filter flux is to adjust the axial velocity and transmembrane pressure (TMP). SRR requested SRNL to conduct bench-scale filter tests to evaluate the effects of axial velocity and transmembrane pressure on crossflow filter flux. The objective of the testing was to determine whether increasing the axial velocity at the ARP could produce a significant increase in filter flux. The authors conducted the tests by preparing slurries containing 6.6 M sodium Salt Batch 6 supernate and 2.5 g MST/L, processing the slurry through a bench-scale crossflow filter unit at varying axial velocity and TMP, and measuring filter flux as a function of time.

  11. 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.

  12. Requirement of transmembrane domain for CD154 association to lipid rafts and subsequent biological events.

    Directory of Open Access Journals (Sweden)

    Nadir Benslimane

    Full Text Available Interaction of CD40 with CD154 leads to recruitment of both molecules into lipid rafts, resulting in bi-directional cell activation. The precise mechanism by which CD154 is translocated into lipid rafts and its impact on CD154 signaling remain largely unknown. Our aim is to identify the domain of CD154 facilitating its association to lipid rafts and the impact of such association on signaling events and cytokine production. Thus, we generated Jurkat cell lines expressing truncated CD154 lacking the cytoplasmic domain or chimeric CD154 in which the transmembrane domain was replaced by that of transferrin receptor I, known to be excluded from lipid rafts. Our results show that cell stimulation with soluble CD40 leads to the association of CD154 wild-type and CD154-truncated, but not CD154-chimera, with lipid rafts. This is correlated with failure of CD154-chimera to activate Akt and p38 MAP kinases, known effectors of CD154 signaling. We also found that CD154-chimera lost the ability to promote IL-2 production upon T cell stimulation with anti-CD3/CD28 and soluble CD40. These results demonstrate the implication of the transmembrane domain of CD154 in lipid raft association, and that this association is necessary for CD154-mediated Akt and p38 activation with consequent enhancement of IL-2 production.

  13. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors

    Directory of Open Access Journals (Sweden)

    Kelly J Culhane

    2015-11-01

    Full Text Available Although family B G protein-coupled receptors (GPCRs contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Synthesis of Novel Mesoporous Silica Materials with Hierarchical Pore Structures

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Suk Bon; Choi, Wang Kyu; Choi, Byung Seon; Moon, Jei Kwon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    Porous materials with various pore sizes in the range of micropore (< 2 nm), mesopore (2-50 nm), and macropore (> 50 nm) are attractive due to their many emerging applications such as catalysts, separation systems, and low dielectric constant materials. The discovery of new M41S mesoporous silica families with pore sizes larger than 2 nm in diameter in 1992 extended the applications into much wider pore ranges, bringing in a new prosperous era in porous material research. The synthesis of these silica materials has been mainly accomplished through a self-assembly between surfactant molecules and inorganic species under various pH conditions. Recently, core-shell nanoparticles with a silica core and mesoporous shell under basic conditions were synthesized using the silica nanoparticles as a core, and a silica precursor (TEOS) and cationic surfactant (CTABr) as a material for the formation of the mesoporous shell. The resultant materials were very monodispersive in size and showed a narrow pore size distribution in the range of ca 2-3 nm in diameter, depending on the alkyl-chain length of the surfactants used. In this work, the mesoporous shell coated-fumed silicas (denoted as MS M-5s) were synthesized by using fumed silica instead of the silica nanoparticle as a core based on previous reports. Also, the structural properties of the MS M-5s such as the specific surface area and pore volume were easily controlled by varying the amount of the silica precursor and surfactant. The resultant materials exhibited a BET surface area of ca 279-446 m{sup 2}/g and total pore volume of ca 0.64-0.74 cm{sup 3}/g and showed a narrow pore size distribution (PSD) due to the removal of the organic surfactant molecules

  17. Effect resonance radiation transfer of excitation porous silicon to I sub 2 molecules sorbed in pores

    CERN Document Server

    Zakharchenko, K V; Kuznetsov, M B; Chistyakov, A A; Karavanskij, V A

    2001-01-01

    One studies the effect of resonance radiation-free transfer of electronic excitation between silicon nanocrystals and iodine molecules sorbed in pores. The experiment procedure includes laser-induced luminescence and laser desorption mass spectrometry. One analyzes photoluminescence spectra prior to and upon iodine sorption. Excitation of iodine through the mechanism of resonance transfer is determined to result in desorption of the iodine sorbed molecules with relatively high kinetic energies (3-1 eV). One evaluated the peculiar distance of resonance transfer the approximate value of which was equal to 2 nm

  18. Sex difference in the sensitivity of cardiac mitochondrial permeability transition pore to calcium load

    Czech Academy of Sciences Publication Activity Database

    Milerová, Marie; Drahota, Zdeněk; Chytilová, Anna; Tauchmannová, Kateřina; Houštěk, Josef; Ošťádal, Bohuslav

    2016-01-01

    Roč. 412, 1-2 (2016), s. 147-154 ISSN 0300-8177 R&D Projects: GA ČR(CZ) GB14-36804G; GA MZd(CZ) NT14050; GA ČR(CZ) GA13-10267S; GA ČR(CZ) GAP303/12/1162 Institutional support: RVO:67985823 Keywords : heart * mitochondrial permeability transition pore * sex difference * calcium-induced swelling Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 2.669, year: 2016

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

    International Nuclear Information System (INIS)

    Ewing, R.P.

    2009-01-01

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

  20. Acoustic characteristics of sand sediment with circular cylindrical pores

    International Nuclear Information System (INIS)

    Roh, Heui-Seol; Lee, Kang-Il; Yoon, Suk-Wang

    2004-01-01

    The acoustic pressure transmission coefficient and the phase velocity are experimentally measured as functions of the frequency and the porosity in sand sediment slabs with circular cylindrical pores filled with water and air. They are also theoretically estimated with the modified Biot-Attenborough (MBA) model, which uses a separate treatment of the viscous and the thermal effects in a non-rigid porous medium with water- and air-filled cylindrical pores. In this study, the fast (first kind) wave and the slow (second kind) wave are not separated in the transmitted signals through a sediment slab without the circular cylindrical pores, but they are separated in the transmitted signals through a sediment slab with pores. Both the phase velocities and the transmission coefficients of the fast wave and the slow wave in the sediment slabs with water- and air-filled cylindrical pores are sensitive to the air and the water porosities. It is proposed that the fast and the slow waves have opposite behaviors for several acoustic characteristics. The generalized tortuosity factor and the dynamic shape factor are introduced from the acoustic characteristics of the fast wave. The experimental results show reasonable agreement with the theoretical results estimated with the MBA model. These results suggest the possibility of predicting the acoustic characteristics of a sediment as functions of arbitrary water and air porosities. This study may also be applicable to understanding acoustic wave propagations in a bubbly liquid sediment for underwater applications and in cancellous bone for the diagnosis of osteoporosis.

  1. Blocking of Single α-Hemolysin Pore by Rhodamine Derivatives.

    Science.gov (United States)

    Rokitskaya, Tatyana I; Nazarov, Pavel A; Golovin, Andrey V; Antonenko, Yuri N

    2017-06-06

    Measurements of ion conductance through α-hemolysin pore in a bilayer lipid membrane revealed blocking of the ion channel by a series of rhodamine 19 and rhodamine B esters. The longest dwell closed time of the blocking was observed with rhodamine 19 butyl ester (C4R1), whereas the octyl ester (C8R1) was of poor effect. Voltage asymmetry in the binding kinetics indicated that rhodamine derivatives bound to the stem part of the aqueous pore lumen. The binding frequency was proportional to a quadratic function of rhodamine concentrations, thereby showing that the dominant binding species were rhodamine dimers. Two levels of the pore conductance and two dwell closed times of the pore were found. The dwell closed times lengthened as the voltage increased, suggesting impermeability of the channel for the ligands. Molecular docking analysis revealed two distinct binding sites within the lumen of the stem of the α-hemolysin pore for the C4R1 dimer, but only one binding site for the C8R1 dimer. The blocking of the α-hemolysin nanopore by rhodamines could be utilized in DNA sequencing as additional optical sensing owing to bright fluorescence of rhodamines if used for DNA labeling. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. MODERN ROUTES TO EXPLORE CONCRETE’S COMPLEX PORE SPACE

    Directory of Open Access Journals (Sweden)

    Piet Stroeven

    2011-05-01

    Full Text Available This paper concentrates on discrete element computer-simulation of concrete. It is argued on the basis of stochastic heterogeneity theory that modern concurrent-algorithm-based systems should be employed for the assessment of pore characteristics underlying durability performance of cementitious materials. The SPACE system was developed at Delft University of Technology for producing realistic schematizations of realcrete for a wide range of other particle packing problems, involving aggregate and fresh cement, and for the purpose of exploring characteristics in the hardened state of concrete, including of the pore network structure because of obvious durability problems. Since structure-sensitive properties are involved, schematization of reality should explicitly deal with the configuration of the cement particles in the fresh state. The paper concentrates on the stereological and mathematical morphology operations executed to acquire information on particle size, global porosity, and on distribution of porosity and of the connected pore fraction as a result of the near neighbourhood of aggregate grains. Goal is to provide information obtained along different exploration routes of concrete's pore space for setting up a pore network modelling approach. This type of methodological papers is scarce in concrete technology, if not missing at all. Technical publications that report on obtained results in our investigations are systematically referred to.

  3. Cu(II) promotes amyloid pore formation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hangyu, E-mail: hangyuz@uw.edu [Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 (United States); Rochet, Jean-Christophe [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907 (United States); Stanciu, Lia A. [Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907 (United States); School of Materials Engineering, Purdue University, West Lafayette, IN 47907 (United States)

    2015-08-14

    The aggregation of α-synuclein is associated with dopamine neuron death in Parkinson's disease. There is controversy in the field over the question of which species of the aggregates, fibrils or protofibrils, are toxic. Moreover, compelling evidence suggested the exposure to heavy metals to be a risk of PD. Nevertheless, the mechanism of metal ions in promoting PD remains unclear. In this research, we investigated the structural basis of Cu(II) induced aggregation of α-synuclein. Using transmission electron microscopy experiments, Cu(II) was found to promote in vitro aggregation of α-synuclein by facilitating annular protofibril formation rather than fibril formation. Furthermore, neuroprotective baicalein disaggregated annular protofibrils accompanied by considerable decrease of β-sheet content. These results strongly support the hypothesis that annular protofibrils are the toxic species, rather than fibrils, thereby inspiring us to search novel therapeutic strategies for the suppression of the toxic annular protofibril formation. - Highlights: • Cu(II) promoted the annular protofibril formation of α-synuclein in vitro. • Cu(II) postponed the in vitro fibrillization of α-synuclein. • Neuroprotective baicalein disaggregated annular protofibrils.

  4. Cu(II) promotes amyloid pore formation

    International Nuclear Information System (INIS)

    Zhang, Hangyu; Rochet, Jean-Christophe; Stanciu, Lia A.

    2015-01-01

    The aggregation of α-synuclein is associated with dopamine neuron death in Parkinson's disease. There is controversy in the field over the question of which species of the aggregates, fibrils or protofibrils, are toxic. Moreover, compelling evidence suggested the exposure to heavy metals to be a risk of PD. Nevertheless, the mechanism of metal ions in promoting PD remains unclear. In this research, we investigated the structural basis of Cu(II) induced aggregation of α-synuclein. Using transmission electron microscopy experiments, Cu(II) was found to promote in vitro aggregation of α-synuclein by facilitating annular protofibril formation rather than fibril formation. Furthermore, neuroprotective baicalein disaggregated annular protofibrils accompanied by considerable decrease of β-sheet content. These results strongly support the hypothesis that annular protofibrils are the toxic species, rather than fibrils, thereby inspiring us to search novel therapeutic strategies for the suppression of the toxic annular protofibril formation. - Highlights: • Cu(II) promoted the annular protofibril formation of α-synuclein in vitro. • Cu(II) postponed the in vitro fibrillization of α-synuclein. • Neuroprotective baicalein disaggregated annular protofibrils

  5. 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.

  6. Why liquid displacement methods are sometimes wrong in estimating the pore-size distribution

    NARCIS (Netherlands)

    Gijsbertsen-Abrahamse, A.J.; Boom, R.M.; Padt, van der A.

    2004-01-01

    The liquid displacement method is a commonly used method to determine the pore size distribution of micro- and ultrafiltration membranes. One of the assumptions for the calculation of the pore sizes is that the pores are parallel and thus are not interconnected. To show that the estimated pore size

  7. Highly Aminated Mesoporous Silica Nanoparticles with Cubic Pore Structure

    KAUST Repository

    Suteewong, Teeraporn

    2011-01-19

    Mesoporous silica with cubic symmetry has attracted interest from researchers for some time. Here, we present the room temperature synthesis of mesoporous silica nanoparticles possessing cubic Pm3n symmetry with very high molar ratios (>50%) of 3-aminopropyl triethoxysilane. The synthesis is robust allowing, for example, co-condensation of organic dyes without loss of structure. By means of pore expander molecules, the pore size can be enlarged from 2.7 to 5 nm, while particle size decreases. Adding pore expander and co-condensing fluorescent dyes in the same synthesis reduces average particle size further down to 100 nm. After PEGylation, such fluorescent aminated mesoporous silica nanoparticles are spontaneously taken up by cells as demonstrated by fluorescence microscopy.

  8. Highly Aminated Mesoporous Silica Nanoparticles with Cubic Pore Structure

    KAUST Repository

    Suteewong, Teeraporn; Sai, Hiroaki; Cohen, Roy; Wang, Suntao; Bradbury, Michelle; Baird, Barbara; Gruner, Sol M.; Wiesner, Ulrich

    2011-01-01

    Mesoporous silica with cubic symmetry has attracted interest from researchers for some time. Here, we present the room temperature synthesis of mesoporous silica nanoparticles possessing cubic Pm3n symmetry with very high molar ratios (>50%) of 3-aminopropyl triethoxysilane. The synthesis is robust allowing, for example, co-condensation of organic dyes without loss of structure. By means of pore expander molecules, the pore size can be enlarged from 2.7 to 5 nm, while particle size decreases. Adding pore expander and co-condensing fluorescent dyes in the same synthesis reduces average particle size further down to 100 nm. After PEGylation, such fluorescent aminated mesoporous silica nanoparticles are spontaneously taken up by cells as demonstrated by fluorescence microscopy.

  9. Fines Classification Based on Sensitivity to Pore-Fluid Chemistry

    KAUST Repository

    Jang, Junbong

    2015-12-28

    The 75-μm particle size is used to discriminate between fine and coarse grains. Further analysis of fine grains is typically based on the plasticity chart. Whereas pore-fluid-chemistry-dependent soil response is a salient and distinguishing characteristic of fine grains, pore-fluid chemistry is not addressed in current classification systems. Liquid limits obtained with electrically contrasting pore fluids (deionized water, 2-M NaCl brine, and kerosene) are combined to define the soil "electrical sensitivity." Liquid limit and electrical sensitivity can be effectively used to classify fine grains according to their fluid-soil response into no-, low-, intermediate-, or high-plasticity fine grains of low, intermediate, or high electrical sensitivity. The proposed methodology benefits from the accumulated experience with liquid limit in the field and addresses the needs of a broader range of geotechnical engineering problems. © ASCE.

  10. Fines classification based on sensitivity to pore-fluid chemistry

    Science.gov (United States)

    Jang, Junbong; Santamarina, J. Carlos

    2016-01-01

    The 75-μm particle size is used to discriminate between fine and coarse grains. Further analysis of fine grains is typically based on the plasticity chart. Whereas pore-fluid-chemistry-dependent soil response is a salient and distinguishing characteristic of fine grains, pore-fluid chemistry is not addressed in current classification systems. Liquid limits obtained with electrically contrasting pore fluids (deionized water, 2-M NaCl brine, and kerosene) are combined to define the soil “electrical sensitivity.” Liquid limit and electrical sensitivity can be effectively used to classify fine grains according to their fluid-soil response into no-, low-, intermediate-, or high-plasticity fine grains of low, intermediate, or high electrical sensitivity. The proposed methodology benefits from the accumulated experience with liquid limit in the field and addresses the needs of a broader range of geotechnical engineering problems.

  11. Influence of crosslinking agents on the pore structure of skin.

    Science.gov (United States)

    Fathima, N Nishad; Dhathathreyan, Aruna; Ramasami, T

    2007-05-15

    Analysis of pore structure of skin is important to understand process of diffusion and adsorption involved during any application of the skin matrix. In this study, the effect of thermal shrinkage on the pore structure of chromium and vegetable treated skin has been analyzed as these tanning agents are known to bring about thermal stability to the matrix. The changes brought about in the pore structure have been studied using mercury intrusion porosimetry and scanning electron microscopy. Response of the chromium treated and vegetable tanning treated skin structure to heat has been found to be quite different from each other. About 41% decrease in porosity is observed for chromium treated skin as against 97% decrease for the skin treated with vegetable tannins. This is primarily attributed to the basic nature of these materials and the nature of interaction of them towards skin.

  12. Coordinated movement of cytoplasmic and transmembrane domains of RyR1 upon gating.

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó

    2009-04-01

    Full Text Available Ryanodine receptor type 1 (RyR1 produces spatially and temporally defined Ca2+ signals in several cell types. How signals received in the cytoplasmic domain are transmitted to the ion gate and how the channel gates are unknown. We used EGTA or neuroactive PCB 95 to stabilize the full closed or open states of RyR1. Single-channel measurements in the presence of FKBP12 indicate that PCB 95 inverts the thermodynamic stability of RyR1 and locks it in a long-lived open state whose unitary current is indistinguishable from the native open state. We analyzed two datasets of 15,625 and 18,527 frozen-hydrated RyR1-FKBP12 particles in the closed and open conformations, respectively, by cryo-electron microscopy. Their corresponding three-dimensional structures at 10.2 A resolution refine the structure surrounding the ion pathway previously identified in the closed conformation: two right-handed bundles emerging from the putative ion gate (the cytoplasmic "inner branches" and the transmembrane "inner helices". Furthermore, six of the identifiable transmembrane segments of RyR1 have similar organization to those of the mammalian Kv1.2 potassium channel. Upon gating, the distal cytoplasmic domains move towards the transmembrane domain while the central cytoplasmic domains move away from it, and also away from the 4-fold axis. Along the ion pathway, precise relocation of the inner helices and inner branches results in an approximately 4 A diameter increase of the ion gate. Whereas the inner helices of the K+ channels and of the RyR1 channel cross-correlate best with their corresponding open/closed states, the cytoplasmic inner branches, which are not observed in the K+ channels, appear to have at least as important a role as the inner helices for RyR1 gating. We propose a theoretical model whereby the inner helices, the inner branches, and the h1 densities together create an efficient novel gating mechanism for channel opening by relaxing two right

  13. Lysosomal-associated Transmembrane Protein 4B (LAPTM4B) Decreases Transforming Growth Factor β1 (TGF-β1) Production in Human Regulatory T Cells.

    Science.gov (United States)

    Huygens, Caroline; Liénart, Stéphanie; Dedobbeleer, Olivier; Stockis, Julie; Gauthy, Emilie; Coulie, Pierre G; Lucas, Sophie

    2015-08-14

    Production of active TGF-β1 is one mechanism by which human regulatory T cells (Tregs) suppress immune responses. This production is regulated by glycoprotein A repetitions predominant (GARP), a transmembrane protein present on stimulated Tregs but not on other T lymphocytes (Th and CTLs). GARP forms disulfide bonds with proTGF-β1, favors its cleavage into latent inactive TGF-β1, induces the secretion and surface presentation of GARP·latent TGF-β1 complexes, and is required for activation of the cytokine in Tregs. We explored whether additional Treg-specific protein(s) associated with GARP·TGF-β1 complexes regulate TGF-β1 production in Tregs. We searched for such proteins by yeast two-hybrid assay, using GARP as a bait to screen a human Treg cDNA library. We identified lysosomal-associated transmembrane protein 4B (LAPTM4B), which interacts with GARP in mammalian cells and is expressed at higher levels in Tregs than in Th cells. LAPTM4B decreases cleavage of proTGF-β1, secretion of soluble latent TGF-β1, and surface presentation of GARP·TGF-β1 complexes by Tregs but does not contribute to TGF-β1 activation. Therefore, LAPTM4B binds to GARP and is a negative regulator of TGF-β1 production in human Tregs. It may play a role in the control of immune responses by decreasing Treg immunosuppression. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. Dispersion upscaling from a pore scale characterization of Lagrangian velocities

    Science.gov (United States)

    Turuban, Régis; de Anna, Pietro; Jiménez-Martínez, Joaquín; Tabuteau, Hervé; Méheust, Yves; Le Borgne, Tanguy

    2013-04-01

    Mixing and reactive transport are primarily controlled by the interplay between diffusion, advection and reaction at pore scale. Yet, how the distribution and spatial correlation of the velocity field at pore scale impact these processes is still an open question. Here we present an experimental investigation of the distribution and correlation of pore scale velocities and its relation with upscaled dispersion. We use a quasi two-dimensional (2D) horizontal set up, consisting of two glass plates filled with cylinders representing the grains of the porous medium : the cell is built by soft lithography technique, wich allows for full control of the system geometry. The local velocity field is quantified from particle tracking velocimetry using microspheres that are advected with the pore scale flow. Their displacement is purely advective, as the particle size is chosen large enough to avoid diffusion. We thus obtain particle trajectories as well as lagrangian velocities in the entire system. The measured velocity field shows the existence of a network of preferential flow paths in channels with high velocities, as well as very low velocity in stagnation zones, with a non Gaussian distribution. Lagrangian velocities are long range correlated in time, which implies a non-fickian scaling of the longitudinal variance of particle positions. To upscale this process we develop an effective transport model, based on correlated continous time random walk, which is entirely parametrized by the pore scale velocity distribution and correlation. The model predictions are compared with conservative tracer test data for different Peclet numbers. Furthermore, we investigate the impact of different pore geometries on the distribution and correlation of Lagrangian velocities and we discuss the link between these properties and the effective dispersion behavior.

  17. Pore-water chemistry explains zinc phytotoxicity in soil.

    Science.gov (United States)

    Kader, Mohammed; Lamb, Dane T; Correll, Ray; Megharaj, Mallavarapu; Naidu, Ravi

    2015-12-01

    Zinc (Zn) is a widespread soil contaminant arising from a numerous anthropogenic sources. However, adequately predicting toxicity of Zn to ecological receptors remains difficult due to the complexity of soil characteristics. In this study, we examined solid-solution partitioning using pore-water data and toxicity of Zn to cucumber (Cucumis sativus L.) in spiked soils. Pore-water effective concentration (ECx, x=10%, 20% and 50% reduction) values were negatively related to pH, indicating lower Zn pore water concentration were needed to cause phytotoxicity at high pH soils. Total dissolved zinc (Znpw) and free zinc (Zn(2+)) in soil-pore water successfully described 78% and 80.3% of the variation in relative growth (%) in the full dataset. When the complete data set was used (10 soils), the estimated EC50pw was 450 and 79.2 µM for Znpw and Zn(2+), respectively. Total added Zn, soil pore water pH (pHpw) and dissolve organic carbon (DOC) were the best predictors of Znpw and Zn(2+) in pore-water. The EC10 (total loading) values ranged from 179 to 5214 mg/kg, depending on soil type. Only pH measurements in soil were related to ECx total Zn data. The strongest relationship to ECx overall was pHca, although pHw and pHpw were in general related to Zn ECx. Similarly, when a solution-only model was used to predict Zn in shoot, DOC was negatively related to Zn in shoot, indicating a reduction in uptake/ translocation of Zn from solution with increasing DOC. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Chen, M.; Kocar, B. D.

    2016-12-01

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

  19. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    International Nuclear Information System (INIS)

    Frazier, Shane D.; Srubar, Wil V.

    2016-01-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm"3) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  20. Evaporation-based method for preparing gelatin foams with aligned tubular pore structures

    Energy Technology Data Exchange (ETDEWEB)

    Frazier, Shane D.; Srubar, Wil V., E-mail: wsrubar@colorado.edu

    2016-05-01

    Gelatin-based foams with aligned tubular pore structures were prepared via liquid-to-gas vaporization of tightly bound water in dehydrated gelatin hydrogels. This study elucidates the mechanism of the foaming process by investigating the secondary (i.e., helical) structure, molecular interactions, and water content of gelatin films before and after foaming using X-ray diffraction, Fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry and thermogravimetric analysis (TGA), respectively. Experimental data from gelatin samples prepared at various gelatin-to-water concentrations (5–30 wt.%) substantiate that resulting foam structures are similar in pore diameter (approximately 350 μm), shape, and density (0.05–0.22 g/cm{sup 3}) to those fabricated using conventional methods (e.g., freeze-drying). Helical structures were identified in the films but were not evident in the foamed samples after vaporization (~ 150 °C), suggesting that the primary foaming mechanism is governed by the vaporization of water that is tightly bound in secondary structures (i.e., helices, β-turns, β-sheets) that are present in dehydrated gelatin films. FTIR and TGA data show that the foaming process leads to more disorder and reduced hydrogen bonding to hydroxyl groups in gelatin and that no thermal degradation of gelatin occurs before or after foaming. - Highlights: • A new method is presented for fabricating gelatin foams with aligned, tubular pores. • Gelatin hydrogels were dehydrated then heated to 150 °C to induce foaming. • Vaporization of tightly (vs. loosely) bound water is the primary foaming mechanism • Foaming induced no thermal degradation but caused disorder in secondary structures • Foam microstructures are similar to those prepared using conventional methods.

  1. Bauhinia championii Flavone Attenuates Hypoxia-Reoxygenation Induced Apoptosis in H9c2 Cardiomyocytes by Improving Mitochondrial Dysfunction.

    Science.gov (United States)

    Liao, Ping; Sun, Guibo; Zhang, Chan; Wang, Min; Sun, Yao; Zhou, Yuehan; Sun, Xiaobo; Jian, Jie

    2016-11-04

    This study aimed to determine the effects of Bauhinia championii flavone (BCF) on hypoxia-reoxygenation (H/R) induced apoptosis in H9c2 cardiomyocytes and to explore potential mechanisms. The H/R model in H9c2 cardiomyocytes was established by 6 h of hypoxia and 12 h of reoxygenation. Cell viability was detected by CCK-8 assay. Apoptotic rate was measured by Annexin V/PI staining. Levels of mitochondria-associated ROS, mitochondrial transmembrane potential (∆Ψm) and mitochondrial permeability transition pores (MPTP) opening were assessed by fluorescent probes. ATP production was measured by ATP assay kit. The release of cytochrome c, translocation of Bax, and related proteins were measured by western blotting. Our results showed that pretreatment with BCF significantly improved cell viability and attenuated the cardiomyocyte apoptosis caused by H/R. Furthermore, BCF increased ATP production and inhibited ROS-generating mitochondria, depolarization of ΔΨm, and MPTP opening. Moreover, BCF pretreatment decreased Bax mitochondrial translocation, cytochrome c release, and activation of caspase-3, as well as increased the expression of p-PI3K, p-Akt, and the ratio of Bcl-2 to Bax. Interestingly, a specific inhibitor of phosphatidylinositol 3-kinase, LY294002, partly reversed the anti-apoptotic effect of BCF. These observations indicated that BCF pretreatment attenuates H/R-induced myocardial apoptosis strength by improving mitochondrial dysfunction via PI3K/Akt signaling pathway.

  2. Silicon pore optics for future x-ray telescopes

    DEFF Research Database (Denmark)

    Wille, Eric; Bavdaz, Marcos; Wallace, Kotska

    2017-01-01

    arcsec or better. These specifications can only be achieved with a novel technology like Silicon Pore Optics, which is being developed by ESA together with a consortium of European industry. Silicon Pore Optics are made of commercial Si wafers using process technology adapted from the semiconductor...... industry. We present the recent upgrades made to the manufacturing processes and equipment, ranging from the manufacture of single mirror plates towards complete focusing mirror modules mounted in flight configuration, and results from first vibration tests. The performance of the mirror modules is tested...

  3. Gas Adsorption in Novel Environments, Including Effects of Pore Relaxation

    International Nuclear Information System (INIS)

    Cole, Milton W; Gatica, Silvina M; Kim, Hye-Young; Lueking, Angela D; Sircar, Sarmishtha

    2012-01-01

    Adsorption experiments have been interpreted frequently with simplified model geometries, such as ideally flat surfaces and slit or cylindrical pores. Recent explorations of unusual environments, such as fullerenes and metal-organic-framework materials, have led to a broadened scope of experimental, theoretical and simulation investigations. This paper reviews a number of such studies undertaken by our group. Among the topics receiving emphasis are these: universality of gas uptake in pores, relaxation of a porous absorbent due to gas uptake and the novel phases of gases on a single nanotube, all of which studies have been motivated by recent experiments.

  4. Role of scaffold mean pore size in meniscus regeneration.

    Science.gov (United States)

    Zhang, Zheng-Zheng; Jiang, Dong; Ding, Jian-Xun; Wang, Shao-Jie; Zhang, Lei; Zhang, Ji-Ying; Qi, Yan-Song; Chen, Xue-Si; Yu, Jia-Kuo

    2016-10-01

    Recently, meniscus tissue engineering offers a promising management for meniscus regeneration. Although rarely reported, the microarchitectures of scaffolds can deeply influence the behaviors of endogenous or exogenous stem/progenitor cells and subsequent tissue formation in meniscus tissue engineering. Herein, a series of three-dimensional (3D) poly(ε-caprolactone) (PCL) scaffolds with three distinct mean pore sizes (i.e., 215, 320, and 515μm) were fabricated via fused deposition modeling. The scaffold with the mean pore size of 215μm significantly improved both the proliferation and extracellular matrix (ECM) production/deposition of mesenchymal stem cells compared to all other groups in vitro. Moreover, scaffolds with mean pore size of 215μm exhibited the greatest tensile and compressive moduli in all the acellular and cellular studies. In addition, the relatively better results of fibrocartilaginous tissue formation and chondroprotection were observed in the 215μm scaffold group after substituting the rabbit medial meniscectomy for 12weeks. Overall, the mean pore size of 3D-printed PCL scaffold could affect cell behavior, ECM production, biomechanics, and repair effect significantly. The PCL scaffold with mean pore size of 215μm presented superior results both in vitro and in vivo, which could be an alternative for meniscus tissue engineering. Meniscus tissue engineering provides a promising strategy for meniscus regeneration. In this regard, the microarchitectures (e.g., mean pore size) of scaffolds remarkably impact the behaviors of cells and subsequent tissue formation, which has been rarely reported. Herein, three three-dimensional poly(ε-caprolactone) scaffolds with different mean pore sizes (i.e., 215, 320, and 515μm) were fabricated via fused deposition modeling. The results suggested that the mean pore size significantly affected the behaviors of endogenous or exogenous stem/progenitor cells and subsequent tissue formation. This study furthers

  5. Dynamics of phase ordering of nematics in a pore

    International Nuclear Information System (INIS)

    Bhattacharya, A.; Chakrabarti, A.

    1994-06-01

    We study the kinetics of phase ordering of a nematic liquid crystal, modeled by a spin-rotor Hamiltonian, confined within a parallel piped pore. The dynamics of the rotor obeys the time-dependent Ginzburg-Landau equation. We study the generation and evolution of a variety of defect structures, and the growth of domains, with different anchoring conditions at the pore surface. Unlike in binary fluids, mere confinement with no anchoring field, does not result in slow dynamics. Homeotropic anchoring, however, leads to slow logarithmic growth. Interestingly, homogeneous anchoring dynamically generates wall defects, resulting in an Ising like structure factor at late times. (author). 27 refs, 4 figs

  6. Quantitative phosphoproteomics dissection of seven-transmembrane receptor signaling using full and biased agonists

    DEFF Research Database (Denmark)

    Christensen, Gitte L; Kelstrup, Christian D; Lyngsø, Christina

    2010-01-01

    (q)-dependent and -independent AT(1)R signaling. This study provides substantial novel insight into angiotensin II signal transduction and is the first study dissecting the differences between a full agonist and a biased agonist from a 7TMR on a systems-wide scale. Importantly, it reveals a previously unappreciated diversity......Seven-transmembrane receptors (7TMRs) signal through the well described heterotrimeric G proteins but can also activate G protein-independent signaling pathways of which the impact and complexity are less understood. The angiotensin II type 1 receptor (AT(1)R) is a prototypical 7TMR...... and quantity of Galpha(q) protein-independent signaling and uncovers novel signaling pathways. We foresee that the amount and diversity of G protein-independent signaling may be more pronounced than previously recognized for other 7TMRs as well. Quantitative mass spectrometry is a promising tool for evaluation...

  7. Fluorophores, environments, and quantification techniques in the analysis of transmembrane helix interaction using FRET.

    Science.gov (United States)

    Khadria, Ambalika S; Senes, Alessandro

    2015-07-01

    Förster resonance energy transfer (FRET) has been widely used as a spectroscopic tool in vitro to study the interactions between transmembrane (TM) helices in detergent and lipid environments. This technique has been instrumental to many studies that have greatly contributed to quantitative understanding of the physical principles that govern helix-helix interactions in the membrane. These studies have also improved our understanding of the biological role of oligomerization in membrane proteins. In this review, we focus on the combinations of fluorophores used, the membrane mimetic environments, and measurement techniques that have been applied to study model systems as well as biological oligomeric complexes in vitro. We highlight the different formalisms used to calculate FRET efficiency and the challenges associated with accurate quantification. The goal is to provide the reader with a comparative summary of the relevant literature for planning and designing FRET experiments aimed at measuring TM helix-helix associations. © 2015 Wiley Periodicals, Inc.

  8. Emerging role of cystic fibrosis transmembrane conductance regulator- an epithelial chloride channel in gastrointestinal cancers

    Institute of Scientific and Technical Information of China (English)

    Yuning Hou; Xiaoqing Guan; Zhe Yang; Chunying Li

    2016-01-01

    Cystic fibrosis transmembrane conductance regulator(CFTR), a glycoprotein with 1480 amino acids, has been well established as a chloride channel mainly expressed in the epithelial cells of various tissues and organs such as lungs, sweat glands, gastrointestinal system, and reproductive organs. Although defective CFTR leads to cystic fibrosis, a common genetic disorder in the Caucasian population, there is accumulating evidence that suggests a novel role of CFTR in various cancers, especially in gastroenterological cancers, such as pancreatic cancer and colon cancer. In this review, we summarize the emerging findings that link CFTR with various cancers, with focus on the association between CFTR defects and gastrointestinal cancers as well as the underlying mechanisms. Further study of CFTR in cancer biology may help pave a new way for the diagnosis and treatment of gastrointestinal cancers.

  9. Purification and crystallization of the cystic fibrosis transmembrane conductance regulator (CFTR).

    Science.gov (United States)

    Rosenberg, Mark F; Kamis, Alhaji Bukar; Aleksandrov, Luba A; Ford, Robert C; Riordan, John R

    2004-09-10

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a membrane protein that is mutated in patients suffering from cystic fibrosis. Here we report the purification and first crystallization of wild-type human CFTR. Functional characterization of the material showed it to be highly active. Electron crystallography of negatively stained two-dimensional crystals of CFTR has revealed the overall architecture of this channel for two different conformational states. These show a strong structural homology to two conformational states of another eukaryotic ATP-binding cassette transporter, P-glycoprotein. In contrast to P-glycoprotein, however, both conformational states can be observed in the presence of a nucleotide, which may be related to the role of CFTR as an ion channel rather than a transporter. The hypothesis that the two conformations could represent the "open" and "closed" states of the channel is considered.

  10. Research Advances in CKLFSF-like MARVEL Transmembrane Domain Containing Member 3.

    Science.gov (United States)

    Hu, Feng-zhan; Sheng, Zheng-zuo; Qin, Cai-peng; Xu, Tao

    2016-06-10

    CKLF-like MARVEL transmembrane domain containing member/chemokine-like factor super family member (CKLFSF/CMTM) is a novel tumor suppressor gene. CMTM3 is broadly expressed in normal human tissues and evolutionary conserved,especially in testis,spleen,and some cells of peripheral blood mononuclear cells. However,its expression is undetectable or down-regulated in most carcinoma cell lines and tissues. Restoration of CMTM3 may inhibit the proliferation,migration,and invasion of carcinoma cells. Although the exact mechanism of its anti-tumor activity remains unclear,CKLFSF3/CMTM3 is closely connected with immune system and associated with sex during tumorigenesis. The study advances of CKLFSF3/CMTM3 are elaborated in this review as CMTM3 may be a new target in the gene therapies for tumors,especially genitourinary tumors,while further studies on CMTM3 and its anti-tumor mechanisms are warranted.

  11. Deorphanizing the human transmembrane genome: A landscape of uncharacterized membrane proteins.

    Science.gov (United States)

    Babcock, Joseph J; Li, Min

    2014-01-01

    The sequencing of the human genome has fueled the last decade of work to functionally characterize genome content. An important subset of genes encodes membrane proteins, which are the targets of many drugs. They reside in lipid bilayers, restricting their endogenous activity to a relatively specialized biochemical environment. Without a reference phenotype, the application of systematic screens to profile candidate membrane proteins is not immediately possible. Bioinformatics has begun to show its effectiveness in focusing the functional characterization of orphan proteins of a particular functional class, such as channels or receptors. Here we discuss integration of experimental and bioinformatics approaches for characterizing the orphan membrane proteome. By analyzing the human genome, a landscape reference for the human transmembrane genome is provided.

  12. Characterization of the single transmembrane domain of human receptor activity-modifying protein 3 in adrenomedullin receptor internalization

    International Nuclear Information System (INIS)

    Kuwasako, Kenji; Kitamura, Kazuo; Nagata, Sayaka; Nozaki, Naomi; Kato, Johji

    2012-01-01

    Highlights: ► RAMP3 mediates CLR internalization much less effectively than does RAMP2. ► The RAMP3 TMD participates in the negative regulation of CLR/RAMP3 internalization. ► A new strategy of promoting internalization and resensitization of the receptor was found. -- Abstract: Two receptor activity-modifying proteins (RAMP2 and RAMP3) enable calcitonin receptor-like receptor (CLR) to function as two heterodimeric receptors (CLR/RAMP2 and CLR/RAMP3) for adrenomedullin (AM), a potent cardiovascular protective peptide. Following AM stimulation, both receptors undergo rapid internalization through a clathrin-dependent pathway, after which CLR/RAMP3, but not CLR/RAMP2, can be recycled to the cell surface for resensitization. However, human (h)RAMP3 mediates CLR internalization much less efficiently than does hRAMP2. Therefore, the molecular basis of the single transmembrane domain (TMD) and the intracellular domain of hRAMP3 during AM receptor internalization was investigated by transiently transfecting various RAMP chimeras and mutants into HEK-293 cells stably expressing hCLR. Flow cytometric analysis revealed that substituting the RAMP3 TMD with that of RAMP2 markedly enhanced AM-induced internalization of CLR. However, this replacement did not enhance the cell surface expression of CLR, [ 125 I]AM binding affinity or AM-induced cAMP response. More detailed analyses showed that substituting the Thr 130 –Val 131 sequence in the RAMP3 TMD with the corresponding sequence (Ile 157 –Pro 158 ) from RAMP2 significantly enhanced AM-mediated CLR internalization. In contrast, substituting the RAMP3 target sequence with Ala 130 –Ala 131 did not significantly affect CLR internalization. Thus, the RAMP3 TMD participates in the negative regulation of CLR/RAMP3 internalization, and the aforementioned introduction of the Ile–Pro sequence into the RAMP3 TMD may be a strategy for promoting receptor internalization/resensitization.

  13. 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.

  14. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

    Science.gov (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-05-01

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  15. 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)

  16. Effect of pore-size distribution on the collapse behaviour of anthropogenic sandy soil deposits

    Directory of Open Access Journals (Sweden)

    Baille Wiebke

    2016-01-01

    Full Text Available In the former open-pit mines of the Lusatian region in Germany, several liquefaction events have occurred during the recent years in the anthropogenic deposits made of very loose sandy soils. These events are related to the rising ground water table after the stop of controlled ground water lowering. The very loose state is due to the formation of sand aggregates (pseudo-grains during the deposition process. The pseudo-grains enclose larger voids of dimension greater than the single sand grain. Wetting induced collapse of the pseudo-grains is presumed to be one of the possible mechanisms triggering liquefaction. In the present study, the effect of larger voids on the wetting induced deformation behaviour of sandy soils is experimentally investigated by laboratory box tests. The deformation field in the sample during wetting was measured using Digital Image Correlation (DIC technique. The results show that the observed deformations are affected by the pore size distribution, thus the amount of voids between the pseudo-grains (macro-void ratio and the voids inside the pseudo-grains (matrix void ratio. The global void ratio of a sandy soil is not sufficient as single state parameter, but the pore size distribution has to be taken into account, experimentally as well as in modelling.

  17. 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.

  18. Comparative analysis of histopathologic effects of synthetic meshes based on material, weight, and pore size in mice.

    Science.gov (United States)

    Orenstein, Sean B; Saberski, Ean R; Kreutzer, Donald L; Novitsky, Yuri W

    2012-08-01

    While synthetic prosthetics have essentially become mandatory for hernia repair, mesh-induced chronic inflammation and scarring can lead to chronic pain and limited mobility. Mesh propensity to induce such adverse effects is likely related to the prosthetic's material, weight, and/or pore size. We aimed to compare histopathologic responses to various synthetic meshes after short- and long-term implantations in mice. Samples of macroporous polyester (Parietex [PX]), heavyweight microporous polypropylene (Trelex[TX]), midweight microporous polypropylene (ProLite[PL]), lightweight macroporous polypropylene (Ultrapro[UP]), and expanded polytetrafluoroethylene (DualMesh[DM]) were implanted subcutaneously in mice. Four and 12 wk post-implantation, meshes were assessed for inflammation, foreign body reaction (FBR), and fibrosis. All meshes induced varying levels of inflammatory responses. PX induced the greatest inflammatory response and marked FBR. DM induced moderate FBR and a strong fibrotic response with mesh encapsulation at 12 wk. UP and PL had the lowest FBR, however, UP induced a significant chronic inflammatory response. Although inflammation decreased slightly for TX, marked FBR was present throughout the study. Of the three polypropylene meshes, fibrosis was greatest for TX and slightly reduced for PL and UP. For UP and PL, there was limited fibrosis within each mesh pore. Polyester mesh induced the greatest FBR and lasting chronic inflammatory response. Likewise, marked fibrosis and encapsulation was seen surrounding ePTFE. Heavier polypropylene meshes displayed greater early and persistent fibrosis; the reduced-weight polypropylene meshes were associated with the least amount of fibrosis. Mesh pore size was inversely proportional to bridging fibrosis. Moreover, reduced-weight polypropylene meshes demonstrated the smallest FBR throughout the study. Overall, we demonstrated that macroporous, reduced-weight polypropylene mesh exhibited the highest degree of

  19. Seismically induced landslides: current research by the US Geological Survey.

    Science.gov (United States)

    Harp, E.L.; Wilson, R.C.; Keefer, D.K.; Wieczorek, G.F.

    1986-01-01

    We have produced a regional seismic slope-stability map and a probabilistic prediction of landslide distribution from a postulated earthquake. For liquefaction-induced landslides, in situ measurements of seismically induced pore-water pressures have been used to establish an elastic model of pore pressure generation. -from Authors

  20. Isolating the effect of pore size distribution on electrochemical double-layer capacitance using activated fluid coke

    Science.gov (United States)

    Zuliani, Jocelyn E.; Tong, Shitang; Kirk, Donald W.; Jia, Charles Q.

    2015-12-01

    Electrochemical double-layer capacitors (EDLCs) use physical ion adsorption in the capacitive electrical double layer of high specific surface area (SSA) materials to store electrical energy. Previous work shows that the SSA-normalized capacitance increases when pore diameters are less than 1 nm. However, there still remains uncertainty about the charge storage mechanism since the enhanced SSA-normalized capacitance is not observed in all microporous materials. In previous studies, the total specific surface area and the chemical composition of the electrode materials were not controlled. The current work is the first reported study that systematically compares the performance of activated carbon prepared from the same raw material, with similar chemical composition and specific surface area, but different pore size distributions. Preparing samples with similar SSAs, but different pores sizes is not straightforward since increasing pore diameters results in decreasing the SSA. This study observes that the microporous activated carbon has a higher SSA-normalized capacitance, 14.1 μF cm-2, compared to the mesoporous material, 12.4 μF cm-2. However, this enhanced SSA-normalized capacitance is only observed above a threshold operating voltage. Therefore, it can be concluded that a minimum applied voltage is required to induce ion adsorption in these sub-nanometer micropores, which increases the capacitance.

  1. 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

  2. Enhanced water transport and salt rejection through hydrophobic zeolite pores

    Science.gov (United States)

    Humplik, Thomas; Lee, Jongho; O'Hern, Sean; Laoui, Tahar; Karnik, Rohit; Wang, Evelyn N.

    2017-12-01

    The potential of improvements to reverse osmosis (RO) desalination by incorporating porous nanostructured materials such as zeolites into the selective layer in the membrane has spurred substantial research efforts over the past decade. However, because of the lack of methods to probe transport across these materials, it is still unclear which pore size or internal surface chemistry is optimal for maximizing permeability and salt rejection. We developed a platform to measure the transport of water and salt across a single layer of zeolite crystals, elucidating the effects of internal wettability on water and salt transport through the ≈5.5 Å pores of MFI zeolites. MFI zeolites with a more hydrophobic (i.e., less attractive) internal surface chemistry facilitated an approximately order of magnitude increase in water permeability compared to more hydrophilic MFI zeolites, while simultaneously fully rejecting both potassium and chlorine ions. However, our results also demonstrated approximately two orders of magnitude lower permeability compared to molecular simulations. This decreased performance suggests that additional transport resistances (such as surface barriers, pore collapse or blockages due to contamination) may be limiting the performance of experimental nanostructured membranes. Nevertheless, the inclusion of hydrophobic sub-nanometer pores into the active layer of RO membranes should improve both the water permeability and salt rejection of future RO membranes (Fasano et al 2016 Nat. Commun. 7 12762).

  3. 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.

  4. The dimension of the pore space in sponges

    International Nuclear Information System (INIS)

    Silva, L H F; Yamashita, M T

    2009-01-01

    A simple experiment to reveal the dimension of the pore space in sponges is proposed. This experiment is suitable for the first year of a physics or engineering course. The calculated dimension of the void space in a sponge of density 16 mg cm -3 was 2.948± 0.008

  5. Microstructural characterization and pore structure analysis of nuclear graphite

    International Nuclear Information System (INIS)

    Kane, J.; Karthik, C.; Butt, D.P.; Windes, W.E.; Ubic, R.

    2011-01-01

    Graphite will be used as a structural and moderator material in next-generation nuclear reactors. While the overall nature of the production of nuclear graphite is well understood, the historic nuclear grades of graphite are no longer available. This paper reports the virgin microstructural characteristics of filler particles and macro-scale porosity in virgin nuclear graphite grades of interest to the Next Generation Nuclear Plant program. Optical microscopy was used to characterize filler particle size and shape as well as the arrangement of shrinkage cracks. Computer aided image analysis was applied to optical images to quantitatively determine the variation of pore structure, area, eccentricity, and orientation within and between grades. The overall porosity ranged between ∼14% and 21%. A few large pores constitute the majority of the overall porosity. The distribution of pore area in all grades was roughly logarithmic in nature. The average pore was best fit by an ellipse with aspect ratio of ∼2. An estimated 0.6-0.9% of observed porosity was attributed to shrinkage cracks in the filler particles. Finally, a preferred orientation of the porosity was observed in all grades.

  6. Energetics of Transport through the Nuclear Pore Complex

    NARCIS (Netherlands)

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

    2016-01-01

    Molecular transport across the nuclear envelope in eukaryotic cells is solely controlled by the nuclear pore complex (NPC). The NPC provides two types of nucleocytoplasmic transport: passive diffusion of small molecules and active chaperon-mediated translocation of large molecules. It has been shown

  7. The hydraulic conductivity of sediments: A pore size perspective

    KAUST Repository

    Ren, X.W.

    2017-12-06

    This article presents an analysis of previously published hydraulic conductivity data for a wide range of sediments. All soils exhibit a prevalent power trend between the hydraulic conductivity and void ratio. Data trends span 12 orders of magnitude in hydraulic conductivity and collapse onto a single narrow trend when the hydraulic conductivity data are plotted versus the mean pore size, estimated using void ratio and specific surface area measurements. The sensitivity of hydraulic conductivity to changes in the void ratio is higher than the theoretical value due to two concurrent phenomena: 1) percolating large pores are responsible for most of the flow, and 2) the larger pores close first during compaction. The prediction of hydraulic conductivity based on macroscale index parameters in this and similar previous studies has reached an asymptote in the range of kmeas/5≤kpredict≤5kmeas. The remaining uncertainty underscores the important role of underlying sediment characteristics such as pore size distribution, shape, and connectivity that are not measured with index properties. Furthermore, the anisotropy in hydraulic conductivity cannot be recovered from scalar parameters such as index properties. Overall, results highlight the robustness of the physics inspired data scrutiny based Hagen–Poiseuille and Kozeny-Carman analyses.

  8. On the Mechanism of Pore Formation by Melittin

    NARCIS (Netherlands)

    van den Bogaart, Geert; Guzman, Jeanette Velasquez; Mika, Jacek T.; Poolman, Bert

    2008-01-01

    The mechanism of pore formation of lytic peptides, such as melittin from bee venom, is thought to involve binding to the membrane surface, followed by insertion at threshold levels of bound peptide. We show that in membranes composed of zwitterionic lipids, i.e. phosphatidylcholine, melittin not

  9. Plastic strain caused by contraction of pores in polycrystalline graphites

    International Nuclear Information System (INIS)

    Ioka, Ikuo; Yoda, Shinichi; Konishi, Takashi.

    1989-01-01

    The effects of porosity on mechanical properties and deformation behavior of four isotropic polycrystalline graphites were studied. The pore size distributions of the graphites were measured using a conventional mercury penetration technique. The average pore radius of ISO-88 graphite was about one-tenth of that of ISEM-1, IG-11 or IG-15 graphites. Young's modulus of the graphites decreased with increasing porosity. The stress-strain curve of each graphite was measured in its lateral and axial directions. Young's modulus of graphite decreased with increasing load. The plastic strain at a given compressive load was calculated from the stress-strain curve and the initial gradient of the unloading curve at the load. The ratio of lateral plastic strain to axial plastic strain for the graphites was less than 0.5, indicating that the volume of the graphites decreased during compressive loading. By assuming that the volume change was caused by contraction of pores, plastic strain associated with contraction of pores was calculated from the axial plastic strain and lateral plastic strain by slips along the basal planes. The plastic strain increased with increasing axial plastic strain and porosity of graphite. (author)

  10. Pore collapse and regrowth in silicon electrodes for rechargeable batteries

    Energy Technology Data Exchange (ETDEWEB)

    DeCaluwe, S. C. [Department of Mechanical Engineering; Colorado School of Mines; USA; Center for Neutron Research; National Institute of Standards and Technology; Dhar, B. M. [Institute for Materials Research and Dept. of Mechanical Engineering; State University of New York; Binghamton; USA; Material Measurement Laboratory; Huang, L. [Institute for Materials Research and Dept. of Mechanical Engineering; State University of New York; Binghamton; USA; He, Y. [Institute for Materials Research and Dept. of Mechanical Engineering; State University of New York; Binghamton; USA; Department of Physics and Astronomy; Yang, K. [Institute for Materials Research and Dept. of Mechanical Engineering; State University of New York; Binghamton; USA; Owejan, J. P. [Department of Mechanical and Electrical Engineering Technology; State University of New York; Alfred; USA; Zhao, Y. [Department of Physics and Astronomy; University of Georgia; Athens; USA; Talin, A. A. [Center for Nanoscale Science and Technology; National Institute of Standards and Technology; Gaithersburg; USA; Sandia National Laboratories; Dura, J. A. [Center for Neutron Research; National Institute of Standards and Technology; Gaithersburg; USA; Wang, H. [Department of Materials Science and Engineering; University of Maryland; College Park; USA; Institute for Materials Research and Dept. of Mechanical Engineering

    2015-01-01

    In-operando Neutron Reflectometry establishes the pore collapse and regrowth (PCRG) mechanism in amorphous Si. Upon lithiation, porosity is first consumed by expansion of solid Si domains, with little thickness increase. After, the whole film expands. Porosity returns upon delithiation.

  11. Alumina ceramics prepared with new pore-forming agents

    Directory of Open Access Journals (Sweden)

    Zuzana Živcová

    2008-06-01

    Full Text Available Porous ceramics have a wide range of applications at all length scales, ranging from fi ltration membranes and catalyst supports to biomaterials (scaffolds for bone ingrowths and thermally or acoustically insulating bulk materials or coating layers. Organic pore-forming agents (PFAs of biological origin can be used to control porosity, pore size and pore shape. This work concerns the characterization and testing of several less common pore-forming agents (lycopodium, coffee, fl our and semolina, poppy seed, which are of potential interest from the viewpoint of size, shape or availability. The performance of these new PFAs is compared to that of starch, which has become a rather popular PFA for ceramics during the last decade. The PFAs investigated in this work are in the size range from 5 μm (rice starch to approximately 1 mm (poppy seed, all with more or less isometric shape. The burnout behavior of PFAs is studied by thermal analysis, i.e. thermogravimetry and differential thermal analysis. For the preparation of porous alumina ceramics from alumina suspensions containing PFAs traditional slip casting (into plaster molds and starch consolidation casting (using metal molds are used in this work. The resulting microstructures are investigated using optical microscopy, combined with image analysis, as well as other methods (Archimedes method of double-weighing in water, mercury intrusion porosimetry.

  12. Enhanced water transport and salt rejection through hydrophobic zeolite pores.

    Science.gov (United States)

    Humplik, Thomas; Lee, Jongho; O'Hern, Sean; Laoui, Tahar; Karnik, Rohit; Wang, Evelyn N

    2017-12-15

    The potential of improvements to reverse osmosis (RO) desalination by incorporating porous nanostructured materials such as zeolites into the selective layer in the membrane has spurred substantial research efforts over the past decade. However, because of the lack of methods to probe transport across these materials, it is still unclear which pore size or internal surface chemistry is optimal for maximizing permeability and salt rejection. We developed a platform to measure the transport of water and salt across a single layer of zeolite crystals, elucidating the effects of internal wettability on water and salt transport through the ≈5.5 Å pores of MFI zeolites. MFI zeolites with a more hydrophobic (i.e., less attractive) internal surface chemistry facilitated an approximately order of magnitude increase in water permeability compared to more hydrophilic MFI zeolites, while simultaneously fully rejecting both potassium and chlorine ions. However, our results also demonstrated approximately two orders of magnitude lower permeability compared to molecular simulations. This decreased performance suggests that additional transport resistances (such as surface barriers, pore collapse or blockages due to contamination) may be limiting the performance of experimental nanostructured membranes. Nevertheless, the inclusion of hydrophobic sub-nanometer pores into the active layer of RO membranes should improve both the water permeability and salt rejection of future RO membranes (Fasano et al 2016 Nat. Commun. 7 12762).

  13. Concentration Polarization to Measure Nano-pore Accessibility

    NARCIS (Netherlands)

    Solsona, Miguel; Eijkel, Jan C.T.; Olthuis, Wouter; Papadimitriou, Vasileios; van den Berg, Albert; Abelmann, Leon; Weckhuysen, Bert M.; Nieuwelink, A. E.

    2017-01-01

    Understanding the deactivation process in porous catalysts is of tremendous economic significance. We demonstrate the feasibility of using the concentration polarization method to obtain the pore accessibility distribution at single particle level for the first time. By using this technique we could

  14. Fines Classification Based on Sensitivity to Pore-Fluid Chemistry

    KAUST Repository

    Jang, Junbong; Santamarina, Carlos

    2015-01-01

    The 75-μm particle size is used to discriminate between fine and coarse grains. Further analysis of fine grains is typically based on the plasticity chart. Whereas pore-fluid-chemistry-dependent soil response is a salient and distinguishing

  15. Impact of biofilm accumulation on transmembrane and feed channel pressure drop: Effects of crossflow velocity, feed spacer and biodegradable nutrient

    KAUST Repository

    Dreszer, C.; Flemming, H. C.; Zwijnenburg, A.; Kruithof, J. C.; Vrouwenvelder, Johannes S.

    2014-01-01

    . As biodegradable nutrient, acetate was dosed to the feed water (1.0 and 0.25mgL-1 carbon) to enhance biofilm accumulation in the monitors. The studies showed that biofilm formation caused an increased transmembrane resistance and feed channel pressure drop

  16. Localization of the transmembrane proteoglycan syndecan-4 and its regulatory kinases in costameres of rat cardiomyocytes: a deconvolution microscopic study

    DEFF Research Database (Denmark)

    VanWinkle, W Barry; Snuggs, Mark B; De Hostos, Eugenio L

    2002-01-01

    Syndecan-4 (syn-4), a transmembrane