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Sample records for transmembrane pore induced

  1. Detecting pore-lining regions in transmembrane protein sequences

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    Nugent Timothy

    2012-07-01

    Full Text Available Abstract Background Alpha-helical transmembrane channel and transporter proteins play vital roles in a diverse range of essential biological processes and are crucial in facilitating the passage of ions and molecules across the lipid bilayer. However, the experimental difficulties associated with obtaining high quality crystals has led to their significant under-representation in structural databases. Computational methods that can identify structural features from sequence alone are therefore of high importance. Results We present a method capable of automatically identifying pore-lining regions in transmembrane proteins from sequence information alone, which can then be used to determine the pore stoichiometry. By labelling pore-lining residues in crystal structures using geometric criteria, we have trained a support vector machine classifier to predict the likelihood of a transmembrane helix being involved in pore formation. Results from testing this approach under stringent cross-validation indicate that prediction accuracy of 72% is possible, while a support vector regression model is able to predict the number of subunits participating in the pore with 62% accuracy. Conclusion To our knowledge, this is the first tool capable of identifying pore-lining regions in proteins and we present the results of applying it to a data set of sequences with available crystal structures. Our method provides a way to characterise pores in transmembrane proteins and may even provide a starting point for discovering novel routes of therapeutic intervention in a number of important diseases. This software is freely available as source code from: http://bioinf.cs.ucl.ac.uk/downloads/memsat-svm/.

  2. Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore

    Science.gov (United States)

    Song, Langzhou; Hobaugh, Michael R.; Shustak, Christopher; Cheley, Stephen; Bayley, Hagan; Gouaux, J. Eric

    1996-12-01

    The structure of the Staphylococcus aureus α-hemolysin pore has been determined to 1.9 overset{circ}{mathrm A} resolution. Contained within the mushroom-shaped homo-oligomeric heptamer is a solvent-filled channel, 100 overset{circ}{mathrm A} in length, that runs along the sevenfold axis and ranges from 14 overset{circ}{mathrm A} to 46 overset{circ}{mathrm A} in diameter. The lytic, transmembrane domain comprises the lower half of a 14-strand antiparallel β barrel, to which each protomer contributes two β strands, each 65 overset{circ}{mathrm A} long. The interior of the β barrel is primarily hydrophilic, and the exterior has a hydrophobic belt 28 overset{circ}{mathrm A} wide. The structure proves the heptameric subunit stoichiometry of the α-hemolysin oligomer, shows that a glycine-rich and solvent-exposed region of a water-soluble protein can self-assemble to form a transmembrane pore of defined structure, and provides insight into the principles of membrane interaction and transport activity of β barrel pore-forming toxins.

  3. 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.

  4. 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

  5. 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)

  6. 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...

  7. 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.

  8. Structural Changes Fundamental to Gating of the Cystic Fibrosis Transmembrane Conductance Regulator Anion Channel Pore.

    Science.gov (United States)

    Linsdell, Paul

    2017-01-01

    Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an epithelial cell anion channel. Potentiator drugs used in the treatment of cystic fibrosis act on the channel to increase overall channel function, by increasing the stability of its open state and/or decreasing the stability of its closed state. The structure of the channel in either the open state or the closed state is not currently known. However, changes in the conformation of the protein as it transitions between these two states have been studied using functional investigation and molecular modeling techniques. This review summarizes our current understanding of the architecture of the transmembrane channel pore that controls the movement of chloride and other small anions, both in the open state and in the closed state. Evidence for different kinds of changes in the conformation of the pore as it transitions between open and closed states is described, as well as the mechanisms by which these conformational changes might be controlled to regulate normal channel gating. The ways that key conformational changes might be targeted by small compounds to influence overall CFTR activity are also discussed. Understanding the changes in pore structure that might be manipulated by such small compounds is key to the development of novel therapeutic strategies for the treatment of cystic fibrosis.

  9. Poisson-Nernst-Planck models of nonequilibrium ion electrodiffusion through a protegrin transmembrane pore.

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    Dan S Bolintineanu

    2009-01-01

    Full Text Available Protegrin peptides are potent antimicrobial agents believed to act against a variety of pathogens by forming nonselective transmembrane pores in the bacterial cell membrane. We have employed 3D Poisson-Nernst-Planck (PNP calculations to determine the steady-state ion conduction characteristics of such pores at applied voltages in the range of -100 to +100 mV in 0.1 M KCl bath solutions. We have tested a variety of pore structures extracted from molecular dynamics (MD simulations based on an experimentally proposed octomeric pore structure. The computed single-channel conductance values were in the range of 290-680 pS. Better agreement with the experimental range of 40-360 pS was obtained using structures from the last 40 ns of the MD simulation, where conductance values range from 280 to 430 pS. We observed no significant variation of the conductance with applied voltage in any of the structures that we tested, suggesting that the voltage dependence observed experimentally is a result of voltage-dependent channel formation rather than an inherent feature of the open pore structure. We have found the pore to be highly selective for anions, with anionic to cationic current ratios (I(Cl-/I(K+ on the order of 10(3. This is consistent with the highly cationic nature of the pore but surprisingly in disagreement with the experimental finding of only slight anionic selectivity. We have additionally tested the sensitivity of our PNP model to several parameters and found the ion diffusion coefficients to have a significant influence on conductance characteristics. The best agreement with experimental data was obtained using a diffusion coefficient for each ion set to 10% of the bulk literature value everywhere inside the channel, a scaling used by several other studies employing PNP calculations. Overall, this work presents a useful link between previous work focused on the structure of protegrin pores and experimental efforts aimed at investigating their

  10. 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.

  11. Reversal of charge selectivity in transmembrane protein pores by using noncovalent molecular adapters

    Science.gov (United States)

    Gu, Li-Qun; Dalla Serra, Mauro; Vincent, J. Bryan; Vigh, Gyula; Cheley, Stephen; Braha, Orit; Bayley, Hagan

    2000-01-01

    In this study, the charge selectivity of staphylococcal α-hemolysin (αHL), a bacterial pore-forming toxin, is manipulated by using cyclodextrins as noncovalent molecular adapters. Anion-selective versions of αHL, including the wild-type pore and various mutants, become more anion selective when β-cyclodextrin (βCD) is lodged within the channel lumen. By contrast, the negatively charged adapter, hepta-6-sulfato-β-cyclodextrin (s7βCD), produces cation selectivity. The cyclodextrin adapters have similar effects when placed in cation-selective mutant αHL pores. Most probably, hydrated Cl− ions partition into the central cavity of βCD more readily than K+ ions, whereas s7βCD introduces a charged ring near the midpoint of the channel lumen and confers cation selectivity through electrostatic interactions. The molecular adapters generate permeability ratios (PK+/PCl−) over a 200-fold range and should be useful in the de novo design of membrane channels both for basic studies of ion permeation and for applications in biotechnology. PMID:10760267

  12. Chimeric Glutamate Receptor Subunits Reveal the Transmembrane Domain Is Sufficient for NMDA Receptor Pore Properties but Some Positive Allosteric Modulators Require Additional Domains.

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

    2016-08-24

    NMDA receptors are ligand-gated ion channels that underlie transmission at excitatory synapses and play an important role in regulating synaptic strength and stability. Functional NMDA receptors require two copies of the GluN1 subunit coassembled with GluN2 (and/or GluN3) subunits into a heteromeric tetramer. A diverse array of allosteric modulators can upregulate or downregulate NMDA receptor activity. These modulators include both synthetic compounds and endogenous modulators, such as cis-unsaturated fatty acids, 24(S)-hydroxycholesterol, and various neurosteroids. To evaluate the structural requirements for the formation and allosteric modulation of NMDA receptor pores, we have replaced portions of the rat GluN1, GluN2A, and GluN2B subunits with homologous segments from the rat GluK2 kainate receptor subunit. Our results with these chimeric constructs show that the NMDA receptor transmembrane domain is sufficient to account for most pore properties, but that regulation by some allosteric modulators requires additional cytoplasmic or extracellular domains. Glutamate receptors mediate excitatory synaptic transmission by forming cation channels through the membrane that open upon glutamate binding. Although many compounds have been identified that regulate glutamate receptor activity, in most cases the detailed mechanisms that underlie modulation are poorly understood. To identify what parts of the receptor are essential for pore formation and sensitivity to allosteric modulators, we generated chimeric subunits that combined segments from NMDA and kainate receptors, subtypes with distinct pharmacological profiles. Surprisingly, our results identify separate domain requirements for allosteric potentiation of NMDA receptor pores by pregnenolone sulfate, 24(S)-hydroxycholesterol, and docosahexaenoic acid, three endogenous modulators derived from membrane constituents. Understanding where and how these compounds act on NMDA receptors should aid in designing better

  13. 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.

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

    Science.gov (United States)

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

    2015-04-01

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

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

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 112; Issue 3. A simulation of earthquake induced undrained pore pressure changes with bearing on some soil liquefaction observations following the 2001 Bhuj earthquake. Irene Sarkar Ramesh Chander. Volume 112 Issue 3 September 2003 pp 471-477 ...

  16. 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.

  17. pH regulation in early endosomes and interferon-inducible transmembrane proteins control avian retrovirus fusion.

    Science.gov (United States)

    Desai, Tanay M; Marin, Mariana; Mason, Caleb; Melikyan, Gregory B

    2017-05-12

    Enveloped viruses infect host cells by fusing their membranes with those of the host cell, a process mediated by viral glycoproteins upon binding to cognate host receptors or entering into acidic intracellular compartments. Whereas the effect of receptor density on viral infection has been well studied, the role of cell type-specific factors/processes, such as pH regulation, has not been characterized in sufficient detail. Here, we examined the effects of cell-extrinsic factors (buffer environment) and cell-intrinsic factors (interferon-inducible transmembrane proteins, IFITMs), on the pH regulation in early endosomes and on the efficiency of acid-dependent fusion of the avian sarcoma and leukosis virus (ASLV), with endosomes. First, we found that a modest elevation of external pH can raise the pH in early endosomes in a cell type-dependent manner and thereby delay the acid-induced fusion of endocytosed ASLV. Second, we observed a cell type-dependent delay between the low pH-dependent and temperature-dependent steps of viral fusion, consistent with the delayed enlargement of the fusion pore. Third, ectopic expression of IFITMs, known to potently block influenza virus fusion with late compartments, was found to only partially inhibit ASLV fusion with early endosomes. Interestingly, IFITM expression promoted virus uptake and the acidification of endosomal compartments, resulting in an accelerated fusion rate when driven by the glycosylphosphatidylinositol-anchored, but not by the transmembrane isoform of the ASLV receptor. Collectively, these results highlight the role of cell-extrinsic and cell-intrinsic factors in regulating the efficiency and kinetics of virus entry and fusion with target cells. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. Prognostic significance of INF-induced transmembrane protein 1 in colorectal cancer

    OpenAIRE

    He, Jingdong; Li, Jin; Feng, Wanting; Chen, Longbang; Yang, Kangqun

    2015-01-01

    Interferon-induced transmembrane protein 1 (IFITM1) has recently been implicated in tumorigenesis. However, the prognostic value of IFITM1 in colorectal cancer remains unknown. The present study aimed to examine the expression and prognostic significance of IFITM1 in human colorectal cancer. IFITM1 expression was analyzed in 144 archived, paraffin-embedded colorectal cancer tissues and corresponding normal colorectal mucosa by immunohistochemistry. The correlation of IFITM1 with clinic-pathol...

  19. 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

  20. Oroxylin A inhibits hemolysis via hindering the self-assembly of α-hemolysin heptameric transmembrane pore.

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    Jing Dong

    Full Text Available Alpha-hemolysin (α-HL is a self-assembling, channel-forming toxin produced by most Staphylococcus aureus strains as a 33.2-kDa soluble monomer. Upon binding to a susceptible cell membrane, the monomer self-assembles to form a 232.4-kDa heptamer that ultimately causes host cell lysis and death. Consequently, α-HL plays a significant role in the pathogenesis of S. aureus infections, such as pneumonia, mastitis, keratitis and arthritis. In this paper, experimental studies show that oroxylin A (ORO, a natural compound without anti-S. aureus activity, can inhibit the hemolytic activity of α-HL. Molecular dynamics simulations, free energy calculations, and mutagenesis assays were performed to understand the formation of the α-HL-ORO complex. This combined approach revealed that the catalytic mechanism of inhibition involves the direct binding of ORO to α-HL, which blocks the conformational transition of the critical "Loop" region of the α-HL protein thereby inhibiting its hemolytic activity. This mechanism was confirmed by experimental data obtained from a deoxycholate-induced oligomerization assay. It was also found that, in a co-culture system with S. aureus and human alveolar epithelial (A549 cells, ORO could protect against α-HL-mediated injury. These findings indicate that ORO hinders the lytic activity of α-HL through a novel mechanism, which should facilitate the design of new and more effective antibacterial agents against S. aureus.

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

    DEFF Research Database (Denmark)

    Shillcock, Julian C.

    2008-01-01

    The dynamics of tension-induced fusion of two vesicles is studied using dissipative particle dynamics (DPD) simulations. The vesicle membranes use an improved DPD parameter set that results in their sustaining only a 10–30% relative area stretch before rupturing on the microsecond timescale...... fusion time on membrane tension implies that the fusion process is completed by overcoming two energy barriers with scales of 13kBT and 11kBT. The fusion pore radius as a function of time has also been extracted from the simulations, and provides a quantitative measure of the fusion dynamics which...

  2. 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.

  3. Cystic fibrosis transmembrane conductance regulator is involved in polyphenol-induced swelling of the endothelial glycocalyx.

    Science.gov (United States)

    Peters, Wladimir; Kusche-Vihrog, Kristina; Oberleithner, Hans; Schillers, Hermann

    2015-08-01

    Previous studies show that polyphenol-rich compounds can induce a swelling of the endothelial glycocalyx (eGC). Our goal was to reveal the mechanism behind the eGC-swelling. As polyphenols are potent modulators of fibrosis transmembrane conductance regulator (CFTR) Cl(-) channel, the hypothesis was tested whether polyphenol-induced increase in CFTR activity is responsible for the eGC-swelling. The impact of the polyphenols resveratrol, (-)-epicatechin, and quercetin on nanomechanics of living endothelial GM7373 cells was monitored by AFM-nanoindentation. The tested polyphenols lead to eGC-swelling with a simultaneous decrease in cortical stiffness. EGC-swelling, but not the change in cortical stiffness, was prevented by the inhibition of CFTR. Polyphenol-induced eGC-swelling could be mimicked by cytochalasin D, an actin-depolymerizing agent. Thus, in the vascular endothelium, polyphenols induce eGC-swelling by softening cortical actin and activating CFTR. Our findings imply that CFTR plays an important role in the maintenance of vascular homeostasis and may explain the vasoprotective properties of polyphenols. Many vascular problems clinically can be attributed to a dysregulation of endothelial glycocalyx (eGC). The underlying mechanism however remains unclear. In this article, the authors used nanoindentation and showed that polyphenols could swell the endothelial glycocalyx and alter its function. This investigative method can lead to further mechanistic studies of other molecular pathways. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Sarker, Muzaddid; de Antueno, Roberto; Langelaan, David N.; Parmar, Hiren B.; Shin, Kyungsoo; Rainey, Jan K.; Duncan, Roy

    2015-01-01

    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. PMID:26061049

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

    Directory of Open Access Journals (Sweden)

    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.

  6. A membrane topology model for human interferon inducible transmembrane protein 1.

    Directory of Open Access Journals (Sweden)

    Stuart Weston

    Full Text Available InterFeron Inducible TransMembrane proteins 1-3 (IFITM1, IFITM2 and IFITM3 are a family of proteins capable of inhibiting the cellular entry of numerous human and animal viruses. IFITM1-3 are unique amongst the currently described viral restriction factors in their apparent ability to block viral entry. This restrictive property is dependant on the localisation of the proteins to plasma and endosomal membranes, which constitute the main portals of viral entry into cells. The topology of the IFITM proteins within cell membranes is an unresolved aspect of their biology. Here we present data from immunofluorescence microscopy, protease cleavage, biotin-labelling and immuno-electron microscopy assays, showing that human IFITM1 has a membrane topology in which the N-terminal domain resides in the cytoplasm, and the C-terminal domain is extracellular. Furthermore, we provide evidence that this topology is conserved for all of the human interferon-induced IFITM proteins. This model is consistent with that recently proposed for murine IFITM3, but differs from that proposed for murine IFITM1.

  7. Experimental Study and Numerical Modeling of Wave Induced Pore Pressure Attenuation Inside a Rubble Mound Breakwater

    DEFF Research Database (Denmark)

    Troch, Peter; Rouck, Julien De; Burcharth, Hans Falk

    2003-01-01

    The main objective of this paper is to study the attenuation of the wave induced pore pressures inside the core of a rubble mound breakwater. The knowledge of the distribution and the attenuation of the pore pressures is important for the design of a stable and safe breakwater. The pore pressure...... and have been re-analysed in detail with respect to the attenuation characteristics. The analysis follows the method by Burcharth et al. (1999) and confirms the practical calculation method for the attenuation of the pore pressure in the core given in this reference. The attenuation of pore pressures...

  8. Prognostic significance of INF-induced transmembrane protein 1 in colorectal cancer.

    Science.gov (United States)

    He, Jingdong; Li, Jin; Feng, Wanting; Chen, Longbang; Yang, Kangqun

    2015-01-01

    Interferon-induced transmembrane protein 1 (IFITM1) has recently been implicated in tumorigenesis. However, the prognostic value of IFITM1 in colorectal cancer remains unknown. The present study aimed to examine the expression and prognostic significance of IFITM1 in human colorectal cancer. IFITM1 expression was analyzed in 144 archived, paraffin-embedded colorectal cancer tissues and corresponding normal colorectal mucosa by immunohistochemistry. The correlation of IFITM1 with clinic-pathological features and overall survival of colorectal cancer patients was evaluated. IFITM1 was overexpressed in colonic cancer tissues but not in rectal cancer tissues, compared to control normal tissues. The expression of IFITM1 was significantly higher in patients with poor differentiation (P=0.031). The patients with higher IFITM1 expression had worse overall survival outcomes than those with lower IFITM1 expression in rectal cancer (P=0.037). Univariate Cox regression suggested that older age and poorly differentiation status predict shorter overall survival in colorectal cancer (Pcancer. IFITM1 may serve as an independent prognostic biomarker for colorectal cancer.

  9. 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.

  10. Bilayer Deformation, Pores, and Micellation Induced by Oxidized Lipids.

    Science.gov (United States)

    Boonnoy, Phansiri; Jarerattanachat, Viwan; Karttunen, Mikko; Wong-Ekkabut, Jirasak

    2015-12-17

    The influence of different oxidized lipids on lipid bilayers was investigated with 16 individual 1 μs atomistic molecular dynamics (MD) simulations. Binary mixtures of lipid bilayers of 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphatidylcholine (PLPC) and its peroxide and aldehyde products were performed at different concentrations. In addition, an asymmetrical short chain lipid, 1-palmitoyl-2-decanoyl-sn-glycero-3-phosphatidylcholine (PDPC), was used to compare the effects of polar/apolar groups in the lipid tail on lipid bilayer. Although water defects occurred with both aldehyde and peroxide lipids, full pore formation was observed only for aldehyde lipids. At medium concentrations the pores were stable. At higher concentrations, however, the pores became unstable and micellation occurred. Data analysis shows that aldehyde lipids' propensity for pore formation is due to their shorter and highly mobile tail. The highly polar peroxide lipids are stabilized by strong hydrogen bonds with interfacial water.

  11. Formation of protein induced micro-pores in Chitosan membranes

    Science.gov (United States)

    Begum, S. N. Suraiya; Aswal, V. K.; Ramasamy, Radha Perumal

    2017-05-01

    Polymer based nanocomposites are important class of materials and have wide applications. Blending two biopolymers can lead to the development of new materials with tailored properties. Chitosan is a naturally occurring polysaccharide with useful properties such as biodegradability and excellent film forming capacity. Bovine serum albumin (BSA) is a abundantly available globular protein. In our research the interaction of chitosan with BSA and the effect of formation of Au nanoparticles on chitosan-BSA system were investigated. Scanning electron microscope (SEM) of the films showed formation of micron sized pores and these pores were hindered with formation of Au nanoparticles. Small angle neutron scattering (SANS) analysis showed that BSA interacts with chitosan chain and affects the Rg value of chitosan. The formation of micro pores decreases the conductivity values (σ'), while the formation of Au nanoparticles increases σ'.

  12. Andrographolide induces autophagic cell death in human liver cancer cells through cyclophilin D-mediated mitochondrial permeability transition pore.

    Science.gov (United States)

    Chen, Wei; Feng, Lina; Nie, Hao; Zheng, Xiaodong

    2012-11-01

    Liver cancer is the third leading cause of cancer death worldwide and about half of the patients with liver cancer require adjuvant therapy after surgical resection. Therefore, development of novel agents to eradicate cancer cells may constitute a viable approach to treat patients with liver cancer. Andrographolide, a diterpenoid lactone isolated from Andrographis paniculata, is known to possess potent antioxidant, anti-inflammatory, antineoplastic and antiviral properties. In this study, we investigated the cytotoxic effect of andrographolide on human liver cancer cells and explored the cell death mechanism. Andrographolide induced a cell death distinct from apoptosis in multiple human liver cancer cells. The death was characterized by autophagy as evidenced by the accumulation of LC3 II and autophagosomes, and the formation of puncta GFP-LC3. This autophagy as well as cytotoxicity caused by andrographolide could be effectively prevented by 3-methyladenine (a chemical inhibitor of autophagy). Mechanistic study indicated that andrographolide induced autophagic cell death by disruption of mitochondrial transmembrane potential and elevation of reactive oxygen species, which were correlated with mitochondrial permeability transition pore Inhibition of cyclophilin D (a component of MPTP) by cyclosporin A or abrogation of its expression by small interfering RNA significantly suppressed the cytotoxicity of andrographolide, suggesting that cyclophilin D may play an important role in mediating andrographolide-induced cytotoxicity. Taken together, our findings unveil a novel mechanism of drug action by andrographolide in liver cancer cells and suggest that andrographolide may represent a promising novel agent in the treatment of liver cancer.

  13. Evolutionary dynamics of the interferon-induced transmembrane gene family in vertebrates.

    Directory of Open Access Journals (Sweden)

    Zhao Zhang

    Full Text Available Vertebrate interferon-induced transmembrane (IFITM genes have been demonstrated to have extensive and diverse functions, playing important roles in the evolution of vertebrates. Despite observance of their functionality, the evolutionary dynamics of this gene family are complex and currently unknown. Here, we performed detailed evolutionary analyses to unravel the evolutionary history of the vertebrate IFITM family. A total of 174 IFITM orthologous genes and 112 pseudogenes were identified from 27 vertebrate genome sequences. The vertebrate IFITM family can be divided into immunity-related IFITM (IR-IFITM, IFITM5 and IFITM10 sub-families in phylogeny, implying origins from three different progenitors. In general, vertebrate IFITM genes are located in two loci, one containing the IFITM10 gene, and the other locus containing IFITM5 and various numbers of IR-IFITM genes. Conservation of evolutionary synteny was observed in these IFITM genes. Significant functional divergence was detected among the three IFITM sub-families. No gene duplication or positive selection was found in IFITM5 sub-family, implying the functional conservation of IFITM5 in vertebrate evolution, which is involved in bone formation. No IFITM5 locus was identified in the marmoset genome, suggesting a potential association with the tiny size of this monkey. The IFITM10 sub-family was divided into two groups: aquatic and terrestrial types. Functional divergence was detected between the two groups, and five IFITM10-like genes from frog were dispersed into the two groups. Both gene duplication and positive selection were observed in aquatic vertebrate IFITM10-like genes, indicating that IFITM10 might be associated with the adaptation to aquatic environments. A large number of lineage- and species-specific gene duplications were observed in IR-IFITM sub-family and positive selection was detected in IR-IFITM of primates and rodents. Because primates have experienced a long history of

  14. 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

  15. 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

  16. 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

  17. Kit- and Fc epsilonRI-induced differential phosphorylation of the transmembrane adaptor molecule NTAL/LAB/LAT2 allows flexibility in its scaffolding function in mast cells

    DEFF Research Database (Denmark)

    Iwaki, Shoko; Spicka, Jiri; Tkaczyk, Christine

    2008-01-01

    The transmembrane adaptor protein (TRAP), NTAL, is phosphorylated in mast cells following FcvarepsilonRI aggregation whereby it cooperates with LAT to induce degranulation. The Kit ligand, stem cell factor (SCF), enhances antigen-induced degranulation and this also appears to be NTAL-dependent. H...

  18. Structural studies of the natriuretic peptide receptor: a novel hormone-induced rotation mechanism for transmembrane signal transduction.

    Science.gov (United States)

    Misono, Kunio S; Ogawa, Haruo; Qiu, Yue; Ogata, Craig M

    2005-06-01

    The atrial natriuretic peptide (ANP) receptor is a single-span transmembrane receptor that is coupled to its intrinsic intracellular guanylate cyclase (GCase) catalytic activity. To investigate the mechanisms of hormone binding and signal transduction, we have expressed the extracellular hormone-binding domain of the ANP receptor (ANPR) and characterized its structure and function. The disulfide-bond structure, state of glycosylation, binding-site residues, chloride-dependence of ANP binding, dimerization, and binding stoichiometry have been determined. More recently, the crystal structures of both the apoANPR dimer and ANP-bound complex have been determined. The structural comparison between the two has shown that, upon ANP binding, two ANPR molecules in the dimer undergo an inter-molecular twist with little intra-molecular conformational change. This motion produces a Ferris wheel-like translocation of two juxtamembrane domains with essentially no change in the inter-domain distance. This movement alters the relative orientation of the two domains equivalent to counter-clockwise rotation of each by 24 degrees . These results suggest that transmembrane signaling by the ANP receptor is mediated by a novel hormone-induced rotation mechanism.

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

    Indian Academy of Sciences (India)

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

    The Bhuj earthquake of January 26th, 2001, induced wide spread liquefaction within the Kachch peninsula. It has been pointed out that inundation due to soil liquefaction was short lived in some parts than in others in the affected region. Several geological, seismological and hydrological factors would have cumulatively ...

  20. Exosome-related multi-pass transmembrane protein TSAP6 is a target of rhomboid protease RHBDD1-induced proteolysis.

    Directory of Open Access Journals (Sweden)

    Chunhua Wan

    Full Text Available We have previously reported that rhomboid domain containing 1 (RHBDD1, a mammalian rhomboid protease highly expressed in the testis, can cleave the Bcl-2 protein Bik. In this study, we identified a multi-pass transmembrane protein, tumor suppressor activated pathway-6 (TSAP6 as a potential substrate of RHBDD1. RHBDD1 was found to induce the proteolysis of TSAP6 in a dose- and activity-dependent manner. The cleavage of TSAP6 was not restricted to its glycosylated form and occurred in three different regions. In addition, mass spectrometry and mutagenesis analyses both indicated that the major cleavage site laid in the C-terminal of the third transmembrane domain of TSAP6. A somatic cell knock-in approach was used to genetically inactivate the endogenous RHBDD1 in HCT116 and RKO colon cancer cells. Exosome secretion was significantly elevated when RHBDD1 was inactivated in the two cells lines. The increased exosome secretion was verfied through the detection of certain exosomal components, including Tsg101, Tf-R, FasL and Trail. In addition, the elevation of exosome secretion by RHBDD1 inactivation was reduced when TSAP6 was knocked down, indicating that the role of RHBDD1 in regulating exosomal trafficking is very likely to be TSAP6-dependent. We found that the increase in FasL and Trail increased exosome-induced apoptosis in Jurkat cells. Taken together, our findings suggest that RHBDD1 is involved in the regulation of a nonclassical exosomal secretion pathway through the restriction of TSAP6.

  1. The water-induced linear reduction gas diffusivity model extended to three pore regions

    DEFF Research Database (Denmark)

    Chamindu, Deepagoda; De Jonge, Lis Wollesen; Kawamoto, Ken

    2015-01-01

    An existing gas diffusivity model developed originally for sieved, repacked soils was extended to characterize gas diffusion in differently structured soils and functional pore networks. A gas diffusivity-derived pore connectivity index was used as a measure of soil structure development. Charact......An existing gas diffusivity model developed originally for sieved, repacked soils was extended to characterize gas diffusion in differently structured soils and functional pore networks. A gas diffusivity-derived pore connectivity index was used as a measure of soil structure development....... 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...

  2. 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

  3. Mashiningan Improves Opioid-Induced Constipation in Rats by Activating Cystic Fibrosis Transmembrane Conductance Regulator Chloride Channel.

    Science.gov (United States)

    Harada, Yumi; Iizuka, Seiichi; Saegusa, Yayoi; Mogami, Sachiko; Fujitsuka, Naoki; Hattori, Tomohisa

    2017-07-01

    Opioid receptor stimulants are analgesics used in patients with and without cancer; however, they often cause constipation, resulting in poor adherence and deterioration of the quality of life. Hence, suitable treatments for constipation are required. In this study, we investigated the pharmacological mechanisms of action of mashiningan (MNG), a Kampo medicine used to treat constipation, and evaluated the effect of MNG on opioid-induced constipation in rats. MNG (100 or 300 mg/kg) was orally administered to normal or codeine phosphate (CPH)-induced constipation in rats, and its effect was evaluated on the basis of fecal counts, characteristics, and weight. Small intestinal fluid secretion was measured after treatment with MNG alone or coadministration with a cystic fibrosis transmembrane conductance regulator (CFTR)-specific inhibitor (CFTRinh-172). The effects of MNG on the CFTR and type-2 chloride channel were determined using patch-clamp or short-circuit current experiments, respectively. MNG increased the fecal weight and proportion of soft feces in normal rats. CPH-induced constipation in rats decreased fecal counts and weight, whereas MNG prevented these effects and increased the proportion of soft feces. MNG increased the electronic chloride current, and this effect was inhibited by the CFTRinh-172 in the CFTR assay. Furthermore, MNG increased small intestinal fluid secretion, and this effect was abolished by coadministration with the CFTRinh-172. MNG improved opioid-induced constipation in rats, and this improvement may have been mediated by increasing intestinal fluid secretion via CFTR chloride channel activation. Therefore, MNG is expected as a medicine of the treatment of constipation in patients taking opioids. Copyright © 2017 by The Author(s).

  4. 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...

  5. Knock-out transmembrane prostate androgen-induced protein gene suppressed triple-negative breast cancer cell proliferation

    Directory of Open Access Journals (Sweden)

    Bantari W.K. Wardhani

    2017-11-01

    Full Text Available Background: Triple negative breast cancer (TNBC tends to grow more rapidly and has poorer prognosis compared to others. High expression of transmembrane prostate androgen-induced protein (TMEPAI correlates with poor prognosis in TNBC patients. However, the mechanistic role of TMEPAI in tumorigenic remains unknown. This study aimed to knock-out TMEPAI in TNBC cell line to determine its function further in cells proliferation.Methods: CRISPR-Cas9 has been used previously to knock-out TMEPAI in Hs857T TNBC cell line. Hs587T TNBC parental cell line (wild-type/WT and TMEPAI knock out Hs 586T cell lines were cultured in Dulbecco’s modified eagle medium (DMEM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and amphotericin B. Both cell lines were seeded in 24-well plates and counted every two days, then proliferation rates were plotted. Afterwards, total RNA were isolated from the cells and Ki-67, and TGF-β mRNA expression levels as proliferation markers were determined.Results: Cell proliferation rates as displayed in growth curve plots showed that WT-TMEPAI cell line grew more rapidly than KO-TMEPAI. In accordance, mRNA expression levels of  Ki-67 and TGF-β  were significantly decreased KO-TMEPAI as compare to TMEPAI-WT.Conclusion: Knock-out of TMEPAI attenuates cell proliferation in TNBC.

  6. 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.

  7. 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.

  8. 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.

  9. Shear-wave anisotropy reveals pore fluid pressure-induced seismicity in the U.S. midcontinent.

    Science.gov (United States)

    Nolte, Keith A; Tsoflias, George P; Bidgoli, Tandis S; Watney, W Lynn

    2017-12-01

    Seismicity in the U.S. midcontinent has increased by orders of magnitude over the past decade. Spatiotemporal correlations of seismicity to wastewater injection operations have suggested that injection-related pore fluid pressure increases are inducing the earthquakes. We present direct evidence linking earthquake occurrence to pore pressure increase in the U.S. midcontinent through time-lapse shear-wave ( S -wave) anisotropy analysis. Since the onset of the observation period in 2010, the orientation of the fast S -wave polarization has flipped from inline with the maximum horizontal stress to inline with the minimum horizontal stress, a change known to be associated with critical pore pressure buildup. The time delay between fast and slow S -wave arrivals exhibits increased variance through time, which is common in critical pore fluid settings. Near-basement borehole fluid pressure measurements indicate pore pressure increase in the region over the earthquake monitoring period.

  10. Trophic cascade induced by molluscivore predator alters pore-water biogeochemistry via competitive release of prey.

    Science.gov (United States)

    van Gils, Jan A; van der Geest, Matthijs; Jansen, Erik J; Govers, Laura L; de Fouw, Jimmy; Piersma, Theunis

    2012-05-01

    Effects of predation may cascade down the food web. By alleviating interspecific competition among prey, predators may promote biodiversity, but the precise mechanisms of how predators alter competition have remained elusive. Here we report on a predator-exclosure experiment carried out in a tropical intertidal ecosystem, providing evidence for a three-level trophic cascade induced by predation by molluscivore Red Knots (Calidris canutus) that affects pore water biogeochemistry. In the exclosures the knots' favorite prey (Dosinia isocardia) became dominant and reduced the individual growth rate in an alternative prey (Loripes lucinalis). Dosinia, a suspension feeder, consumes suspended particulate organic matter (POM), whereas Loripes is a facultative mixotroph, partly living on metabolites produced by sulfur-oxidizing chemoautotrophic bacteria, but also consuming suspended POM. Reduced sulfide concentrations in the exclosures suggest that, without predation on Dosinia, stronger competition for suspended POM forces Loripes to rely on energy produced by endosymbiotic bacteria, thus leading to an enhanced uptake of sulfide from the surrounding pore water. As sulfide is toxic to most organisms, this competition-induced diet shift by Loripes may detoxify the environment, which in turn may facilitate other species. The inference that predators affect the toxicity of their environment via a multi-level trophic cascade is novel, but we believe it may be a general phenomenon in detritus-based ecosystems.

  11. 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

  12. 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.

  13. 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.

  14. Theoretical estimates of magnitudes of earthquakes induced by pore-pressure perturbations with large aspect ratios

    Science.gov (United States)

    Galis, Martin; Ampuero, Jean-Paul; Mai, P. Martin; Cappa, Frédéric

    2017-04-01

    Being able to reliably and accurately estimate the possible maximum magnitude of fluid-injection-induced earthquakes is of critical importance to quantify the associated seismic hazard and to define operational constraints for geo-reservoirs. In previous studies, we developed theoretical estimates of the magnitude of fluid-injection-induced earthquakes based fracture mechanics, assuming circular pressure perturbations. However, natural reservoirs are typically much wider than thicker. Therefore, here we discuss the application of our model to horizontally elongated pressurized regions with realistic aspect ratios. Assuming circular pressure perturbations, we derived a physical model estimating how large a rupture will grow on a given fault and for a given pore-pressure perturbation. We used two approaches. The first, semi-analytical approach is based on pore pressure evolution obtained by solving the diffusion equation for a cylindrical reservoir with no-flow boundaries. The second approach is an approximation to the first one, based on a point-load approximation of the pres-sure perturbation on the fault, allowing derivation of a complete analytical formula relating the magnitude of the largest arrested rupture, Mmax-arr, to injection and slip-weakening friction parameters. We found that the Mmax-arr scales with cumulative injected fluid volume as a power law with exponent of 3/2. In contrast, the Mmax relation by McGarr (2014) is a linear scaling (exponent of 1). While for the dataset used by McGarr (2014) the difference between our and McGarr's models is relatively small, inclusion of datasets with broad range of injected fluid volumes (from 10-10m3 to 1010m3) suggests better agreement with our model. However, inclusion of extended pressure perturbations into our two models, while maintaining the (semi-)analytical character, is not viable. Therefore, we perform numerical dynamic-rupture simulations to investigate rupture nucleation and arrest for pressure

  15. 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

  16. 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...

  17. A synthetic peptide corresponding to the carboxy terminus of human immunodeficiency virus type 1 transmembrane glycoprotein induces alterations in the ionic permeability of Xenopus laevis oocytes.

    Science.gov (United States)

    Comardelle, A M; Norris, C H; Plymale, D R; Gatti, P J; Choi, B; Fermin, C D; Haislip, A M; Tencza, S B; Mietzner, T A; Montelaro, R C; Garry, R F

    1997-11-20

    The carboxy-terminal 29 amino acids of the human immunodeficiency virus type 1 transmembrane glycoprotein (HIV-1 TM) are referred to as lentivirus lytic peptide 1 (LLP-1). Synthetic peptides corresponding to LLP-1 have been shown to induce cytolysis and to alter the permeability of cultured cells to various small molecules. To address the mechanisms by which LLP-1 induces cytolysis and membrane permeability changes, various concentrations of LLP-1 were incubated with Xenopus laevis oocytes, and two-electrode, voltage-clamp recording measurements were performed. LLP-1 at concentrations of 75 nM and above induced dramatic alterations in the resting membrane potential and ionic permeability of Xenopus oocytes. These concentrations of LLP-1 appeared to induce a major disruption of plasma membrane electrophysiological integrity. In contrast, concentrations of LLP-1 of 20-50 nM induced changes in membrane ionic permeability that mimic changes induced by compounds, such as the bee venom peptide melittin, that are known to form channel-like structures in biological membranes at sublytic concentrations. An analog of LLP-1 with greatly reduced cytolytic activity failed to alter the electrophysiological properties of Xenopus oocytes. Thus, by altering plasma membrane ionic permeability, the carboxy terminus of TM may contribute to cytolysis of HIV-1-infected CD4+ cells.

  18. 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.

  19. 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.

  20. 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...

  1. 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

  2. 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.

  3. 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

    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...... 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...... of the wheel rut. Simulations of the stress field in the soil beneath the tyre indicated that the trends in ka were determined by both the mean normal stress and the shear stress, while the trend in εa was determined by the mean normal stress only. At 10 cm depth, the index of pore continuity (N) supported...

  4. 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.

  5. A monodisperse transmembrane α-helical peptide barrel

    Science.gov (United States)

    Mahendran, Kozhinjampara R.; Niitsu, Ai; Kong, Lingbing; Thomson, Andrew R.; Sessions, Richard B.; Woolfson, Derek N.; Bayley, Hagan

    2017-05-01

    The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing.

  6. Melatonin modulates permeability transition pore and 5-hydroxydecanoate induced KATPchannel inhibition in isolated brain mitochondria.

    Science.gov (United States)

    Waseem, Mohammad; Tabassum, Heena; Parvez, Suhel

    2016-11-01

    There is increasing recognition of the magnitude of mitochondria in neurodegenerative disorders. Mitochondria play a key role in apoptotic and necrotic cell death. Melatonin (Mel), an indoleamine produced in several organs including the pineal gland has been known for its neuroprotective actions. In our study, we have investigated whether the mitochondrial ATP sensitive potassium (mtK ATP ) channel blocker 5-hydroxydecanoate (5-HD) and calcium (Ca 2+ ) affects permeability transition pore (PTP) alterations in isolated brain mitochondria treated with melatonin (Mel) and cyclosporin A (CsA). Mitochondrial swelling, mitochondrial membrane potential (Δψ m ), ROS measurement and mitochondrial respiration were evaluated in isolated brain mitochondria. In our results, mitochondrial swelling stimulated by exposing Ca 2+ ions and 5-HD associated by mPTP opening as depicted by modulation of CsA and Mel. In addition, Ca 2+ and 5-HD decreased Δψ m , depleted intracellular ROS, and inhibition of mitochondrial respiration (state 3 and state 4) in isolated brain mitochondria. Addition of Mel and CsA has shown significant restoration in mitochondrial swelling, Δψ m , intracellular ROS measurement and mitochondrial respiration in isolated brain mitochondria. Therefore, we speculate the modulatory effect of Mel and CsA in mitochondria treated with 5-HD and Ca 2+ hinders the mPTP-mediated mitochondrial dysfunction and cellular oxidative stress. We conclude that inhibition of mPT is one likely mechanism of CsA's and its neuroprotective actions. Development of neuroprotective agents including Mel targeting the mPTP therefore bears hope for future treatment of severe neurodegenerative diseases. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  7. Heart failure induces significant changes in nuclear pore complex of human cardiomyocytes.

    Directory of Open Access Journals (Sweden)

    Estefanía Tarazón

    Full Text Available AIMS: The objectives of this study were to analyse the effect of heart failure (HF on several proteins of nuclear pore complex (NPC and their relationship with the human ventricular function. METHODS AND RESULTS: A total of 88 human heart samples from ischemic (ICM, n = 52 and dilated (DCM, n = 36 patients undergoing heart transplant and control donors (CNT, n = 9 were analyzed by Western blot. Subcellular distribution of nucleoporins was analysed by fluorescence and immunocytochemistry. When we compared protein levels according to etiology, ICM showed significant higher levels of NDC1 (65%, p<0.0001, Nup160 (88%, p<0.0001 and Nup153 (137%, p = 0.004 than those of the CNT levels. Furthermore, DCM group showed significant differences for NDC1 (41%, p<0.0001, Nup160 (65%, p<0.0001, Nup153 (155%, p = 0.006 and Nup93 (88%, p<0.0001 compared with CNT. However, Nup155 and translocated promoter region (TPR did not show significant differences in their levels in any etiology. Regarding the distribution of these proteins in cell nucleus, only NDC1 showed differences in HF. In addition, in the pathological group we obtained good relationship between the ventricular function parameters (LVEDD and LVESD and Nup160 (r = -0382, p = 0.004; r = -0.290, p = 0.033; respectively. CONCLUSIONS: This study shows alterations in specific proteins (NDC1, Nup160, Nup153 and Nup93 that compose NPC in ischaemic and dilated human heart. These changes, related to ventricular function, could be accompanied by alterations in the nucleocytoplasmic transport. Therefore, our findings may be the basis for a new approach to HF management.

  8. Transmembrane Signaling Proteoglycans

    DEFF Research Database (Denmark)

    Couchman, John R

    2010-01-01

    and their glycosaminoglycan chains is matched by diverse functions. However, all assume roles as coreceptors, often working alongside high-affinity growth factor receptors or adhesion receptors such as integrins. Other common themes are an ability to signal through their cytoplasmic domains, often to the actin cytoskeleton......, and linkage to PDZ protein networks. Many transmembrane proteoglycans associate on the cell surface with metzincin proteases and can be shed by them. Work with model systems in vivo and in vitro reveal roles in growth, adhesion, migration, and metabolism. Furthermore, a wide range of phenotypes for the core...

  9. The Effect of Membrane Material and Surface Pore Size on the Fouling Properties of Submerged Membranes

    Directory of Open Access Journals (Sweden)

    Sungil Jeon

    2016-12-01

    Full Text Available We aimed to investigate the relationship between membrane material and the development of membrane fouling in a membrane bioreactor (MBR using membranes with different pore sizes and hydrophilicities. Batch filtration tests were performed using submerged single hollow fiber membrane ultrafiltration (UF modules with different polymeric membrane materials including cellulose acetate (CA, polyethersulfone (PES, and polyvinylidene fluoride (PVDF with activated sludge taken from a municipal wastewater treatment plant. The three UF hollow fiber membranes were prepared by a non-solvent-induced phase separation method and had similar water permeabilities and pore sizes. The results revealed that transmembrane pressure (TMP increased more sharply for the hydrophobic PVDF membrane than for the hydrophilic CA membrane in batch filtration tests, even when membranes with similar permeabilities and pore sizes were used. PVDF hollow fiber membranes with smaller pores had greater fouling propensity than those with larger pores. In contrast, CA hollow fiber membranes showed good mitigation of membrane fouling regardless of pore size. The results obtained in this study suggest that the surface hydrophilicity and pore size of UF membranes clearly affect the fouling properties in MBR operation when using activated sludge.

  10. 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.

  11. Tl(+) induces both cationic and transition pore permeability in the inner membrane of rat heart mitochondria.

    Science.gov (United States)

    Korotkov, Sergey M; Nesterov, Vladimir P; Brailovskaya, Irina V; Furaev, Viktor V; Novozhilov, Artemy V

    2013-12-01

    Effects of Tl(+) were studied in experiments with isolated rat heart mitochondria (RHM) injected into 400 mOsm medium containing TlNO3 and a nitrate salt (KNO3 or NH4NO3) or TlNO3 and sucrose. Tl(+) increased permeability of the inner membrane of the RHM to K(+) and H(+). This manifested as an increase of the non-energized RHM swelling, in the order of sucrose rat heart mitochondria increased both the swelling and the inner membrane potential dissipation, as well as decreased basal state and 2,4-dinitrophenol-stimulated respiration. These effects of Tl(+) were suppressed by the MPTP inhibitors (cyclosporine A, ADP, bongkrekic acid, and n-ethylmaleimide), activated in the presence of the MPTP inducer (carboxyatractyloside) or mitoKATP inhibitor (5-hydroxydecanoate), but were not altered in the presence of mitoKATP agonists (diazoxide or pinacidil). We suggest that the greater sensitivity of heart and striated muscles, versus liver, to thallium salts in vivo can result in more vigorous Tl(+) effects on muscle cell mitochondria.

  12. 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

  13. 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

  14. Pore-scale study of dissolution-induced changes in hydrologic properties of rocks with binary minerals

    Science.gov (United States)

    Chen, Li; Kang, Qinjun; Viswanathan, Hari S.; Tao, Wen-Quan

    2014-12-01

    A pore-scale numerical model for reactive transport processes based on the Lattice Boltzmann method is used to study the dissolution-induced changes in hydrologic properties of a fractured medium and a porous medium. The solid phase of both media consists of two minerals, and a structure reconstruction method called quartet structure generation set is employed to generate the distributions of both minerals. Emphasis is put on the effects of undissolved minerals on the changes of permeability and porosity under different Peclet and Damkohler numbers. The simulation results show porous layers formed by the undissolved mineral remain behind the dissolution reaction front. Due to the large flow resistance in these porous layers, the permeability increases very slowly or even remains at a small value although the porosity increases by a large amount. Besides, due to the heterogeneous characteristic of the dissolution, the chemical, mechanical and hydraulic apertures are very different from each other. Further, simulations in complex porous structures demonstrate that the existence of the porous layers of the nonreactive mineral suppresses the wormholing phenomena observed in the dissolution of mono-mineralic rocks.

  15. 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.

  16. Pore formation by human stefin B in its native and oligomeric states and the consequent amyloid induced toxicity.

    Directory of Open Access Journals (Sweden)

    Gregor eAnderluh

    2012-08-01

    Full Text Available It is well documented that amyloid forming peptides and proteins interact with membranes and that this correlates with cytotoxicity. To introduce the theme we give a brief description of some amyloidogenic proteins and note their similarities with pore forming toxins and cell penetrating peptides. Human stefin B, a member of the family of cystatins, is an amyloidogenic protein in vitro. This review describes our studies of the interaction of stefin B oligomers and prefibrillar aggregates with model membranes leading to pore formation. We have studied the interaction between human stefin B and artificial membranes of various compositions. We also have prepared distinct sizes and morphologies of stefin B prefibrillar states and assessed their toxicity. Furthermore, we have measured electrical currents through pores formed by stefin B prefibrillar oligomers in a planar lipid bilayer setup. We finally discuss the possible functional and pathological significance of such pores formed by human stefin B.

  17. Rasagiline and selegiline suppress calcium efflux from mitochondria by PK11195-induced opening of mitochondrial permeability transition pore: a novel anti-apoptotic function for neuroprotection.

    Science.gov (United States)

    Wu, Yuqiu; Kazumura, Kimiko; Maruyama, Wakako; Osawa, Toshihiko; Naoi, Makoto

    2015-10-01

    Rasagiline and selegiline, inhibitors of type B monoamine oxidase (MAO-B), protect neurons from cell death in cellular and animal models. Suppression of mitochondrial membrane permeabilization and subsequent activation of apoptosis cascade, and induction of anti-apoptotic, pro-survival genes are proposed to contribute the anti-apoptotic function. Rasagiline suppresses neurotoxin- and oxidative stress-induced membrane permeabilization in isolated mitochondria, but the mechanism has been not fully clarified. In this paper, regulation of the mitochondrial permeability transition pore by rasagiline and selegiline was examined in apoptosis induced by PK11195, a ligand of the outer membrane translocator protein 18 kDa (TSPO) in SH-SY5Y cells. The pore opening was quantitatively measured using a simultaneous monitoring system for calcium (Ca(2+)) and superoxide (O2(-)) (Ishibashi et al. in Biochem Biophys Res Commun 344:571-580, 2006). The association of the pore opening with Ca(2+) efflux and ROS increase was proved by the inhibition of Bcl-2 overexpression and cyclosporine A treatment. Potency to release Ca(2+) was correlated with the cytotoxicity of TSPO antagonists, PK11195, FGIN-1-27 and protoporphyrin IX, whereas a TSPO agonist, 4-chloro-diazepamine, did not significantly increase Ca(2+) or cause cell death. Rasagiline and selegiline inhibited mitochondrial Ca(2+) efflux through the mitochondrial permeability transition pore dose dependently. Ca(2+) efflux was confirmed as the initial signal in mitochondrial apoptotic cascade, and the suppression of Ca(2+) efflux may account for the neuroprotective function of rasagiline and selegiline. The quantitative measurement of Ca(2+) efflux can be applied to determine anti-apoptotic activity of neuroprotective compounds. The role of mitochondrial Ca(2+) release in neuronal death and also in neuroprotection by MAO-B inhibitors is discussed.

  18. Assessing the Structure and Stability of Transmembrane Oligomeric Intermediates of an α-Helical Toxin.

    Science.gov (United States)

    Desikan, Rajat; Maiti, Prabal K; Ayappa, K Ganapathy

    2017-10-24

    Protein membrane interactions play an important role in our understanding of diverse phenomena ranging from membrane-assisted protein aggregation to oligomerization and folding. Pore-forming toxins (PFTs) are the primary vehicle for infection by several strains of bacteria. These proteins which are expressed in a water-soluble form (monomers) bind to the target membrane and conformationally transform (protomers) and self-assemble to form a multimer transmembrane pore complex through a process of oligomerization. On the basis of the structure of the transmembrane domains, PFTs are broadly classified into β or α toxins. In contrast to β-PFTs, the paucity of available crystal structures coupled with the amphipathic nature of the transmembrane domains has hindered our understanding of α-PFT pore formation. In this article, we use molecular dynamics (MD) simulations to examine the process of pore formation of the bacterial α-PFT, cytolysin A from Escherichia coli (ClyA) in lipid bilayer membranes. Using atomistic MD simulations ranging from 50 to 500 ns, we show that transmembrane oligomeric intermediates or "arcs" form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges. By creating initial conditions where the lipids are contained within the arcs, we study the dynamics of spontaneous lipid evacuation and toroidal edge formation. This process occurs on the time scale of tens of nanoseconds, suggesting that once protomers oligomerize, transmembrane arcs are rapidly stabilized to form functional water channels capable of leakage. Using umbrella sampling with a coarse-grained molecular model, we obtain the free energy of insertion of a single protomer into the membrane. A single inserted protomer has a stabilization free energy of -52.9 ± 1.2 kJ/mol and forms a stable transmembrane water channel capable of leakage. Our simulations reveal that arcs are stable and viable intermediates that can occur during the pore

  19. 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

  20. Curcumin Pretreatment Prevents Potassium Dichromate-Induced Hepatotoxicity, Oxidative Stress, Decreased Respiratory Complex I Activity, and Membrane Permeability Transition Pore Opening

    Directory of Open Access Journals (Sweden)

    Wylly Ramsés García-Niño

    2013-01-01

    Full Text Available Curcumin is a polyphenol derived from turmeric with recognized antioxidant properties. Hexavalent chromium is an environmental toxic and carcinogen compound that induces oxidative stress. The objective of this study was to evaluate the potential protective effect of curcumin on the hepatic damage generated by potassium dichromate (K2Cr2O7 in rats. Animals were pretreated daily by 9-10 days with curcumin (400 mg/kg b.w. before the injection of a single intraperitoneal of K2Cr2O7 (15 mg/kg b.w.. Groups of animals were sacrificed 24 and 48 h later. K2Cr2O7-induced damage to the liver was evident by histological alterations and increase in the liver weight and in the activity of alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, and alkaline phosphatase in plasma. In addition, K2Cr2O7 induced oxidative damage in liver and isolated mitochondria, which was evident by the increase in the content of malondialdehyde and protein carbonyl and decrease in the glutathione content and in the activity of several antioxidant enzymes. Moreover, K2Cr2O7 induced decrease in mitochondrial oxygen consumption, in the activity of respiratory complex I, and permeability transition pore opening. All the above-mentioned alterations were prevented by curcumin pretreatment. The beneficial effects of curcumin against K2Cr2O7-induced liver oxidative damage were associated with prevention of mitochondrial dysfunction.

  1. Curcumin Pretreatment Prevents Potassium Dichromate-Induced Hepatotoxicity, Oxidative Stress, Decreased Respiratory Complex I Activity, and Membrane Permeability Transition Pore Opening

    Science.gov (United States)

    García-Niño, Wylly Ramsés; Tapia, Edilia; Zazueta, Cecilia; Zatarain-Barrón, Zyanya Lucía; Hernández-Pando, Rogelio; Vega-García, Claudia Cecilia; Pedraza-Chaverrí, José

    2013-01-01

    Curcumin is a polyphenol derived from turmeric with recognized antioxidant properties. Hexavalent chromium is an environmental toxic and carcinogen compound that induces oxidative stress. The objective of this study was to evaluate the potential protective effect of curcumin on the hepatic damage generated by potassium dichromate (K2Cr2O7) in rats. Animals were pretreated daily by 9-10 days with curcumin (400 mg/kg b.w.) before the injection of a single intraperitoneal of K2Cr2O7 (15 mg/kg b.w.). Groups of animals were sacrificed 24 and 48 h later. K2Cr2O7-induced damage to the liver was evident by histological alterations and increase in the liver weight and in the activity of alanine aminotransferase, aspartate aminotransferase, lactate dehydrogenase, and alkaline phosphatase in plasma. In addition, K2Cr2O7 induced oxidative damage in liver and isolated mitochondria, which was evident by the increase in the content of malondialdehyde and protein carbonyl and decrease in the glutathione content and in the activity of several antioxidant enzymes. Moreover, K2Cr2O7 induced decrease in mitochondrial oxygen consumption, in the activity of respiratory complex I, and permeability transition pore opening. All the above-mentioned alterations were prevented by curcumin pretreatment. The beneficial effects of curcumin against K2Cr2O7-induced liver oxidative damage were associated with prevention of mitochondrial dysfunction. PMID:23956771

  2. 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.

  3. Trichoderma viride cellulase induces resistance to the antibiotic pore-forming peptide alamethicin associated with changes in the plasma membrane lipid composition of tobacco BY-2 cells

    Directory of Open Access Journals (Sweden)

    Andreasson Erik

    2010-12-01

    Full Text Available Abstract Background Alamethicin is a membrane-active peptide isolated from the beneficial root-colonising fungus Trichoderma viride. This peptide can insert into membranes to form voltage-dependent pores. We have previously shown that alamethicin efficiently permeabilises the plasma membrane, mitochondria and plastids of cultured plant cells. In the present investigation, tobacco cells (Nicotiana tabacum L. cv Bright Yellow-2 were pre-treated with elicitors of defence responses to study whether this would affect permeabilisation. Results Oxygen consumption experiments showed that added cellulase, already upon a limited cell wall digestion, induced a cellular resistance to alamethicin permeabilisation. This effect could not be elicited by xylanase or bacterial elicitors such as flg22 or elf18. The induction of alamethicin resistance was independent of novel protein synthesis. Also, the permeabilisation was unaffected by the membrane-depolarising agent FCCP. As judged by lipid analyses, isolated plasma membranes from cellulase-pretreated tobacco cells contained less negatively charged phospholipids (PS and PI, yet higher ratios of membrane lipid fatty acid to sterol and to protein, as compared to control membranes. Conclusion We suggest that altered membrane lipid composition as induced by cellulase activity may render the cells resistant to alamethicin. This induced resistance could reflect a natural process where the plant cells alter their sensitivity to membrane pore-forming agents secreted by Trichoderma spp. to attack other microorganisms, and thus adding to the beneficial effect that Trichoderma has for plant root growth. Furthermore, our data extends previous reports on artificial membranes on the importance of lipid packing and charge for alamethicin permeabilisation to in vivo conditions.

  4. 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

  5. Betulinic acid induces cytochrome c release and apoptosis in a Bax/Bak-independent, permeability transition pore dependent fashion

    NARCIS (Netherlands)

    Mullauer, Franziska B.; Kessler, Jan H.; Medema, Jan Paul

    2009-01-01

    Betulinic acid (BetA) is a plant-derived pentacyclic triterpenoid that exerts potent anti-cancer effects in vitro and in vivo, but is non toxic to untransformed cells. In our previous study we observed that BetA consistently induced cell death in a broad panel of tumor cell lines. Apoptosis induced

  6. ER reorganization is remarkably induced in COS-7 cells accumulating transmembrane protein receptors not competent for export from the endoplasmic reticulum.

    Science.gov (United States)

    D'Agostino, Massimo; Crespi, Arianna; Polishchuk, Elena; Generoso, Serena; Martire, Gianluca; Colombo, Sara Francesca; Bonatti, Stefano

    2014-11-01

    The newly synthesized mutant L501fsX533 Frizzled-4 form and the alpha3beta4 nicotinic acetylcholine receptor expressed in the absence of nicotine accumulate in the endoplasmic reticulum of COS-7 cells and induce the formation of large areas of smooth and highly convoluted cisternae. This results in a generalized block of the transport to the Golgi complex of newly synthesized proteins. Intriguingly, both effects happen peculiarly in COS-7 cells; HeLa, Huh-7, and HEK293 cells expressing the two receptors at similar level than COS-7 cells show normal ER and normal transport toward the plasma membrane. These results question the conclusion that a dominant-negative mechanism would explain the dominance of the mutant L501fsX533 Fz4 allele in the transmission of a form of Familial exudative vitreoretinopathy. Moreover, they indicate that the coordination of endoplasmic reticulum homeostasis in COS-7 cells is particularly error prone. This finding suggests that COS-7 cells may be extremely useful to study the molecular mechanisms regulating endoplasmic reticulum size and architecture.

  7. Esculetin induces apoptosis in human gastric cancer cells through a cyclophilin D-mediated mitochondrial permeability transition pore associated with ROS.

    Science.gov (United States)

    Pan, Hui; Wang, Bao-Hui; Lv, Wang; Jiang, Yan; He, Lei

    2015-12-05

    Esculetin is a coumarin derivative from natural plants that has been commonly used as a folk medicine and has been reported to have beneficial pharmacological and biochemical activities; however, the mechanism by which esculetin prevents human gastric cancer cell growth is still largely unknown. In this study, we investigated the effect of esculetin on human gastric cancer cells and explored the cell death mechanism. Our data indicated that esculetin inhibited the growth of human gastric cancer cells in a dose- and time-dependent manner and apoptosis was the main cause of decreased cell viability in esculetin-treated cells. Additionally, esculetin treatment increased the activity of caspase-9 and caspase-3, and resulted in the appearance of the PARP cleavage product; and esculetin-induced cell death and apoptosis was decreased by pretreatment with CsA and NAC, but not BA; these results demonstrate that esculetin induced apoptosis via the caspase-dependent mitochondrial pathway in human gastric cancer cells in which cyclophilin D mediated the cytotoxic action by triggering the opening of the mitochondrial permeability transition pore; and the generation of ROS not only was a consequence of mitochondrial dysfunction, but also triggered esculetin-induced apoptosis. These results reveal a novel mechanism of esculetin on gastric cancer cells and suggest that esculetin could be a novel agent in the treatment of gastric cancer. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Tl+ induces the permeability transition pore in Ca2+-loaded rat liver mitochondria energized by glutamate and malate.

    Science.gov (United States)

    Korotkov, Sergey M; Emelyanova, Larisa V; Konovalova, Svetlana A; Brailovskaya, Irina V

    2015-08-01

    It is known that Ca2+ and heavy metals more actively induce MPTP opening in mitochondria, energized by the I complex substrates. Thus, a rise in a Tl+-induced MPTP was proposed in experiments on isolated rat liver mitochondria energized by the complex I substrate (glutamate and malate). Expose of the mitochondria to Ca2+ into a medium containing TlNO3, glutamate, and malate as well as sucrose or KNO3 resulted in a decrease in state 3, state 4, or DNP-stimulated respiration as well as an increase of both mitochondrial swelling and ΔΨmito dissipation. The MPTP inhibitors, CsA and ADP, almost completely eliminated the effect of Ca2+, which was more pronounced in the presence of the complex I substrates than the complex II substrate (succinate) and rotenone (Korotkov and Saris, 2011). The present study concludes that Tl+-induced MPTP opening is more appreciable in mitochondria energized by glutamate and malate but not succinate in the presence of rotenone. We assume that the Tl+-induced MPTP opening along with followed swelling and possible structural deformations of the complex I in Ca2+-loaded mitochondria may be a part of the thallium toxicity mechanism on mitochondria in living organisms. At the same time, oxidation of Tl+ to Tl3+ by mitochondrial oxygen reactive species is proposed for the mechanism. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Pore-scale network modeling of microbially induced calcium carbonate precipitation : Insight into scale dependence of biogeochemical reaction rates

    NARCIS (Netherlands)

    Qin, Chao-Zhong; Hassanizadeh, S. Majid; Ebigbo, Anozie

    2016-01-01

    The engineering of microbially induced calcium carbonate precipitation (MICP) has attracted much attention in a number of applications, such as sealing of CO2 leakage pathways, soil stabilization, and subsurface remediation of radionuclides and toxic metals. The goal of this work is to gain insight

  10. Salicylate-inducible antibiotic resistance in Pseudomonas cepacia associated with absence of a pore-forming outer membrane protein.

    OpenAIRE

    Burns, J L; Clark, D K

    1992-01-01

    The most common mechanism of antibiotic resistance in multiply resistant Pseudomonas cepacia is decreased porin-mediated outer membrane permeability. In some gram-negative organisms this form of antibiotic resistance can be induced by growth in the presence of weak acids, such as salicylates, which suppress porin synthesis. To determine the effects of salicylates on outer membrane permeability of P. cepacia, a susceptible laboratory strain, 249-2, was grown in 10 mM sodium salicylate. Antibio...

  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. CO2 Reaction Induced Wettability Alteration and its Impacts on CO2 Storage: Pore to Core Scale Reservoir Condition Experimental Studies

    Science.gov (United States)

    Wan, J.; Tokunaga, T. K.; Kim, Y.; Jung, J.; Kim, T.; Dong, W.

    2013-12-01

    Wettability of the mineral surfaces plays an important role in subsurface multiphase flow and transport. Wettability affects the capillary pressure-saturation (Pc- S) relations, relative permeability (kr) of each fluid phase, and relative phase occupancy in reservoir pores. Although wettability issues have been studied extensively in other fields, significant knowledge gaps remain when applying the existing understanding to geological carbon sequestration; due largely to the unique physical-chemical properties of supercritical (sc) CO2 relative to other common non-wetting fluids such as air and oil. Here, we report our recent progress on wettability alteration upon reaction with CO2 and the resulting differences in capillary trapping of CO2 versus air. (1) Pore Scale Studies. There are conflict predictions in the literature concerning the effect of wettability on capillary trapping; some find that larger contact angles lead to lower capillary trapping while others have found opposite behavior. We hypothesized that spontaneous imbibition becomes energetically unfavorable with decreased wettability, so that increased residual trapping of scCO2 should occur during the post-injection inbibition stage. We developed a laboratory high-pressure and elevated temperature microscopic-micromodel system that is capable of controlling fine scale capillary pressure of scCO2-brine, and enabled us to conduct imbibition under controlled capillary pressures at the pore scale. We found that the de-wetting enhanced scCO2 capillary trapping is significant. These results suggest that scCO2 reaction induced dewetting can result in higher degrees of CO2 residual trapping in the post-injection stage than previously predicted. (2) Core Scale Studies. Capillary scaling is used routinely to predict Pc(S) relations for scCO2-brine systems at field scale, based on relations measured with air-water or mercury porosimetry. However, scaling-based predictions for CO2-brine systems have not been

  13. Acyclic αγα-Tripeptides with Fluorinated- and Nonfluorinated-Furanoid Sugar Framework: Importance of Fluoro Substituent in Reverse-Turn Induced Self-Assembly and Transmembrane Ion-Transport Activity.

    Science.gov (United States)

    Burade, Sachin S; Shinde, Sopan Valiba; Bhuma, Naresh; Kumbhar, Navanath; Kotmale, Amol; Rajamohanan, Pattuparambil R; Gonnade, Rajesh G; Talukdar, Pinaki; Dhavale, Dilip D

    2017-06-02

    Acyclic αγα-tripeptides derived from fluorinated-furanoid sugar amino acid frameworks act as reverse-turn inducers with a U-shaped conformation, whereas the corresponding nonfluorinated αγα-tripeptides show random peptide conformations. The NMR studies showed the presence of bifurcated weak intramolecular hydrogen bonding (F···HN) and N + ···F δ- charge-dipole attraction compel the amide carbonyl groups to orient antiperiplanar to the C-F bond, thus, demonstrating the role of the fluorine substituent in stabilizing the U-shaped conformation. The NOESY data indicate that the U-shaped tripeptides self-assembly formation is stabilized by the intermolecular hydrogen bonding between C═O···HN with antiparallel orientation. This fact is supported by ESI-MS data, which showed mass peaks up to the pentameric self-assembly, even in the gas phase. The morphological analysis by FE-SEM, on solid samples, showed arrangement of fibers into nanorods. The antiparallel self-assembled pore of the fluorinated tripeptides illustrates the selective ion-transport activity. The experimental findings were supported by DFT studies.

  14. 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.

  15. Giant osmotic energy conversion measured in a single transmembrane boron nitride nanotube.

    Science.gov (United States)

    Siria, Alessandro; Poncharal, Philippe; Biance, Anne-Laure; Fulcrand, Rémy; Blase, Xavier; Purcell, Stephen T; Bocquet, Lydéric

    2013-02-28

    New models of fluid transport are expected to emerge from the confinement of liquids at the nanoscale, with potential applications in ultrafiltration, desalination and energy conversion. Nevertheless, advancing our fundamental understanding of fluid transport on the smallest scales requires mass and ion dynamics to be ultimately characterized across an individual channel to avoid averaging over many pores. A major challenge for nanofluidics thus lies in building distinct and well-controlled nanochannels, amenable to the systematic exploration of their properties. Here we describe the fabrication and use of a hierarchical nanofluidic device made of a boron nitride nanotube that pierces an ultrathin membrane and connects two fluid reservoirs. Such a transmembrane geometry allows the detailed study of fluidic transport through a single nanotube under diverse forces, including electric fields, pressure drops and chemical gradients. Using this device, we discover very large, osmotically induced electric currents generated by salinity gradients, exceeding by two orders of magnitude their pressure-driven counterpart. We show that this result originates in the anomalously high surface charge carried by the nanotube's internal surface in water at large pH, which we independently quantify in conductance measurements. The nano-assembly route using nanostructures as building blocks opens the way to studying fluid, ionic and molecule transport on the nanoscale, and may lead to biomimetic functionalities. Our results furthermore suggest that boron nitride nanotubes could be used as membranes for osmotic power harvesting under salinity gradients.

  16. 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.

  17. Pressure-Induced Amorphization of Small Pore Zeolites-the Role of Cation-H2O Topology and Anti-glass Formation.

    Science.gov (United States)

    Chan Hwang, Gil; Joo Shin, Tae; Blom, Douglas A; Vogt, Thomas; Lee, Yongjae

    2015-10-12

    Systematic studies of pressure-induced amorphization of natrolites (PIA) containing monovalent extra-framework cations (EFC) Li(+), Na(+), K(+), Rb(+), Cs(+) allow us to assess the role of two different EFC-H2O configurations within the pores of a zeolite: one arrangement has H2O molecules (NATI) and the other the EFC (NATII) in closer proximity to the aluminosilicate framework. We show that NATI materials have a lower onset pressure of PIA than the NATII materials containing Rb and Cs as EFC. The onset pressure of amorphization (PA) of NATII materials increases linearly with the size of the EFC, whereas their initial bulk moduli (P1 phase) decrease linearly. Only Cs- and Rb-NAT reveal a phase separation into a dense form (P2 phase) under pressure. High-Angle Annular Dark Field Scanning Transmission Electron Microscopy (HAADF-STEM) imaging shows that after recovery from pressures near 25 and 20 GPa long-range ordered Rb-Rb and Cs-Cs correlations continue to be present over length scales up to 100 nm while short-range ordering of the aluminosilicate framework is significantly reduced-this opens a new way to form anti-glass structures.

  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. 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...

  20. Effect of pore size on the calculated pressure at biological cells pore wall.

    Science.gov (United States)

    El-Hag, Ayman H; Zheng, Zhong; Boggs, Steven A; Jayaram, Shesha H

    2006-09-01

    A transient nonlinear finite-element program has been used to calculate the electric field distribution as a function of time for a spherical cell with a pore in a conducting medium during application of a subnanosecond rise time "step" wave, including the effects of dipolar saturation in the water-based cytoplasm and cell medium. The time-dependent pressure on the pore wall has been computed as a function of time as the system polarizes from the change of the energy in the electric field to the left (inside the pore) and to the right (inside the membrane) of the pore wall. The computations suggest that dipolar saturation, while significant, has little effect on the time-dependent electric field distribution but a substantial effect on the field-induced pore wall pressure. Also, the effect of pore size on both the computed electric field and field-induced pressure was studied. As the pore size increases, a collapse in both the electric field and field-induced pressure has been noticed. This suggests that as the pore size increases, the driving force for further opening the pore is not electrical.

  1. Chemotherapy Drugs Thiocolchicoside and Taxol Permeabilize Lipid Bilayer Membranes by Forming Ion Pores

    International Nuclear Information System (INIS)

    Ashrafuzzaman, Md; Tuszynski, J A; Duszyk, M

    2011-01-01

    We report ion channel formation by chemotherapy drugs: thiocolchicoside (TCC) and taxol (TXL) which primarily target tubulin but not only. For example, TCC has been shown to interact with GABA A , nuclear envelope and strychnine-sensitive glycine receptors. TXL interferes with the normal breakdown of microtubules inducing mitotic block and apoptosis. It also interacts with mitochondria and found significant chemotherapeutic applications for breast, ovarian and lung cancer. In order to better understand the mechanisms of TCC and TXL actions, we examined their effects on phospholipid bilayer membranes. Our electrophysiological recordings across membranes constructed in NaCl aqueous phases consisting of TCC or TXL under the influence of an applied transmembrane potential (V) indicate that both molecules induce stable ion flowing pores/channels in membranes. Their discrete current versus time plots exhibit triangular shapes which is consistent with a spontaneous time-dependent change of the pore conductance in contrast to rectangular conductance events usually induced by ion channels. These events exhibit conductance (∼0.01-0.1 pA/mV) and lifetimes (∼5-30 ms) within the ranges observed in e.g., gramicidin A and alamethicin channels. The channel formation probability increases linearly with TCC/TXL concentration and V and is not affected by pH (5.7 - 8.4). A theoretical explanation on the causes of chemotherapy drug induced ion pore formation and the pore stability has also been found using our recently discovered binding energy between lipid bilayer and the bilayer embedded ion channels using gramicidin A channels as tools. This picture of energetics suggests that as the channel forming agents approach to the lipids on bilayer the localized charge properties in the constituents of both channel forming agents (e.g., chemotherapy drugs in this study) and the lipids determine the electrostatic drug-lipid coupling energy through screened Coulomb interactions between

  2. The effect of wind turbine-induced microclimates and plant functional types on peatland greenhouse gas emissions and pore water dissolved organic carbon concentrations

    Science.gov (United States)

    Armstrong, A.; Waldron, S.; Ostle, N.; Whitaker, J.

    2012-04-01

    Wind turbines can affect the local climate by removing energy from the wind and increasing air turbulence with a recent study showing a cooling effect of 1.5C during the day (Baidya & Roy, 2010). Wind farms are commonly located on peatlands where both greenhouse gas carbon dioxide (CO2) and methane (CH4) fluxes and dissolved organic carbon concentrations ([DOC]) are significantly influenced by temperature and water table depth. In this paper we present data from Black Law Wind Farm, Scotland, where we examined the effect of wind turbines on (1) Microclimate - peatland surface and subsurface temperatures, soil moisture and water table depth and (2) Carbon cycling - greenhouse gas fluxes and pore water dissolved organic carbon concentrations. Within our experimental framework we examined the impact of the three main peatland plant functional types (shrubs, mosses and sedges) and their interactions with wind microclimate changes on ecosystem CO2 and CH4 fluxes and [DOC]. The sampling plots are divided into four sites along a hypothesized wind turbine-induced microclimatic gradient. At each site twelve sampling plots were established, four in areas dominated by mosses, four in areas dominated by sedges and four in areas dominated by shrubs. The results show that there are significant relationships between plot location on the hypothesized microclimatic gradient, plant functional type and their interactions and CO2 and CH4 fluxes and [DOC]. Consequently, the long-term effects of wind farms on peatland microclimates may need to be taken into account when considering their life cycle carbon budget.

  3. Biophysics, Pathophysiology and Pharmacology of Ion Channel Gating Pores

    Directory of Open Access Journals (Sweden)

    Adrien eMoreau

    2014-04-01

    Full Text Available Voltage sensor domain (VSDs are a feature of voltage gated ion channel (VGICs and voltage sensitive proteins. They are composed of four transmembrane (TM segments (S1 to S4. Currents leaking through VSDs are called omega or gating pore currents.Gating pores are caused by mutations of the highly conserved positively charged amino acids in the S4 segment that disrupt interactions between the S4 segment and the gating charge transfer center (GCTC. The GCTC separates the intracellular and extracellular water crevices. The disruption of S4–GCTC interactions allows these crevices to communicate and create a fast activating and non-inactivating alternative cation-selective permeation pathway of low conductance, or a gating pore.Gating pore currents have recently been shown to cause periodic paralysis phenotypes. There is also increasing evidence that gating pores are linked to several other familial diseases. For example, gating pores in Nav1.5 and Kv7.2 channels may underlie mixed arrhythmias associated with dilated cardiomyopathy (DCM phenotypes and peripheral nerve hyperexcitability (PNH respectively. There is little evidence for the existence of gating pore blockers. Moreover, it is known that a number of toxins bind to the VSD of a specific domain of Na+ channels. These toxins may thus modulate gating pore currents. This focus on the VSD motif opens up a new area of research centered on developing molecules to treat a number of cell excitability disorders such as epilepsy, cardiac arrhythmias, and pain.The purpose of the present review is to summarize existing knowledge of the pathophysiology, biophysics, and pharmacology of gating pore currents and to serve as a guide for future studies aimed at improving our understanding of gating pores and their pathophysiological roles.

  4. Reconstituted Fusion Pore

    OpenAIRE

    Jeremic, Aleksandar; Kelly, Marie; Cho, Sang-Joon; Stromer, Marvin H.; Jena, Bhanu P.

    2003-01-01

    Fusion pores or porosomes are basket-like structures at the cell plasma membrane, at the base of which, membrane-bound secretory vesicles dock and fuse to release vesicular contents. Earlier studies using atomic force microscopy (AFM) demonstrated the presence of fusion pores at the cell plasma membrane in a number of live secretory cells, revealing their morphology and dynamics at nm resolution and in real time. ImmunoAFM studies demonstrated the release of vesicular contents through the por...

  5. Accurate computational design of multipass transmembrane proteins.

    Science.gov (United States)

    Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo; Fallas, Jorge A; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U; Baker, David

    2018-03-02

    The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  6. Characterization of reactive flow-induced evolution of carbonate rocks using digital core analysis- part 1: Assessment of pore-scale mineral dissolution and deposition.

    Science.gov (United States)

    Qajar, Jafar; Arns, Christoph H

    2016-09-01

    The application of X-ray micro-computed tomography (μ-CT) for quantitatively characterizing reactive-flow induced pore structure evolution including local particle detachment, displacement and deposition in carbonate rocks is investigated. In the studies conducted in this field of research, the experimental procedure has involved alternating steps of imaging and ex-situ core sample alteration. Practically, it is impossible to return the sample, with micron precision, to the same position and orientation. Furthermore, successive images of a sample in pre- and post-alteration states are usually taken at different conditions such as different scales, resolutions and signal-to-noise ratios. These conditions accompanying with subresolution features in the images make voxel-by-voxel comparisons of successive images problematic. In this paper, we first address the respective challenges in voxel-wise interpretation of successive images of carbonate rocks subject to reactive flow. Reactive coreflood in two carbonate cores with different rock types are considered. For the first rock, we used the experimental and imaging results published by Qajar et al. (2013) which showed a quasi-uniform dissolution regime. A similar reactive core flood was conducted in the second rock which resulted in wormhole-like dissolution regime. We particularly examine the major image processing operations such as transformation of images to the same grey-scale, noise filtering and segmentation thresholding and propose quantitative methods to evaluate the effectiveness of these operations in voxel-wise analysis of successive images of a sample. In the second part, we generalize the methodology based on the three-phase segmentation of normalized images, microporosity assignment and 2D histogram of image intensities to estimate grey-scale changes of individual image voxels for a general case where the greyscale images are segmented into arbitrary number of phases. The results show that local (voxel

  7. MD simulations of the central pore of ryanodine receptors and sequence comparison with 2B protein from coxsackie virus.

    Science.gov (United States)

    Schilling, Roman; Fink, Rainer H A; Fischer, Wolfgang B

    2014-04-01

    The regulation of intracellular Ca(2+) triggers a multitude of vital processes in biological cells. Ca(2+) permeable ryanodine receptors (RyRs) are the biggest known ion channels and play a key role in the regulation of intracellular calcium concentrations, particularly in muscle cells. In this study, we construct a computational model of the pore region of the skeletal RyR and perform molecular dynamics (MD) simulations. The dynamics and distribution of Ca(2+) around the luminal pore entry of the RyR suggest that Ca(2+) ions are channeled to the pore entry due to the arrangement of (acidic) amino acids at the extramembrane surface of the protein. This efficient mechanism of Ca(2+) supply is thought to be part of the mechanism of Ca(2+) conductance of RyRs. Viral myocarditis is predominantly caused by coxsackie viruses that induce the expression of the protein 2B which is known to affect intracellular Ca(2+) homeostasis in infected cells. From our sequence comparison, it is hypothesized, that modulation of RyR could be due to replacement of its transmembrane domains (TMDs) by those domains of the viral channel forming protein 2B of coxsackie virus. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. 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.

  9. 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

  10. 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

  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. 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.

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

    OpenAIRE

    Kozma, D?niel; Simon, Istv?n; Tusn?dy, G?bor E.

    2012-01-01

    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 la...

  14. 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

  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. Role of the synaptobrevin C terminus in fusion pore formation

    DEFF Research Database (Denmark)

    Ngatchou, Annita N; Kisler, Kassandra; Fang, Qinghua

    2010-01-01

    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......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...

  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. 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.

  19. Chloride induced localized corrosion in simulated concrete pore solution: effect of a phosphate-based inhibitor on the behavior of 304L stainless steel compared to carbon steel

    International Nuclear Information System (INIS)

    Nahali, Haifa; Dhouibi, Leila

    2013-01-01

    In this paper, the acoustic emission technique coupled with electrochemical measurements was used to determine, in simulated concrete pore solution (Ca(OH) 2 ), the critical value [Cl - ] / [OH - ], which prevents the pitting corrosion initiation of AISI 304L austenitic stainless steel, and to compare this critical value with that of the carbon steel in the same medium with and without inhibitor Na 3 PO 4 . The results show that for the austenitic stainless steel, the critical threshold of pitting corrosion initiation is around 5, while for carbon steel without inhibitor in Ca(OH) 2 solution, it has a low value of about 0.6. However, the presence of the inhibitor Na 3 PO 4 in this solution leads to the formation of a protective phosphate layer on the steel surface, increasing the critical ratio [Cl - ] / [OH - ] from 0.6 to 15. Under these conditions, the corrosion behavior of carbon steel is improved and, thanks to the blocking of pitting sites by the Na 3 PO 4 inhibitor, it becomes much more resistant to localized corrosion than AISI 304L austenitic steel. (authors)

  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. Pore roller filtration apparatus

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to the field of filtering, more precisely the present invention concerns an apparatus and a method for the separation of dry matter from a medium and the use of said apparatus. One embodiment discloses an apparatus for the separation of dry matter from a medium, comp...... of a pore roller and one other roller, means for establishing a pressure difference across the filter, means for passing filter and filter cake through the set of rollers, and a closure mechanism configured to control the transverse tension between the rollers......., comprising a pressure regulated separation chamber defined, in cross section, by a plurality of rollers mounted between opposing sidewalls, each of said rollers having a shaft adapted to be engaged with the sidewalls, a filter arranged so that it passes between at least one set of said rollers consisting...

  2. Nanometer-Scale Pores: Potential Applications for Analyte Detection and DNA Characterization

    Directory of Open Access Journals (Sweden)

    John J. Kasianowicz

    2002-01-01

    Full Text Available Several classes of transmembrane protein ion channels function in vivo as sensitive and selective detection elements for analytes. Recent studies on single channels reconstituted into planar lipid bilayer membranes suggest that nanometer-scale pores can be used to detect, quantitate and characterize a wide range of analytes that includes small ions and single stranded DNA. We briefly review here these studies and identify leaps in technology that, if realized, might lead to innovations for the early detection of cancer.

  3. Transmembrane protein sorting driven by membrane curvature

    Science.gov (United States)

    Strahl, H.; Ronneau, S.; González, B. Solana; Klutsch, D.; Schaffner-Barbero, C.; Hamoen, L. W.

    2015-11-01

    The intricate structure of prokaryotic and eukaryotic cells depends on the ability to target proteins to specific cellular locations. In most cases, we have a poor understanding of the underlying mechanisms. A typical example is the assembly of bacterial chemoreceptors at cell poles. Here we show that the classical chemoreceptor TlpA of Bacillus subtilis does not localize according to the consensus stochastic nucleation mechanism but accumulates at strongly curved membrane areas generated during cell division. This preference was confirmed by accumulation at non-septal curved membranes. Localization appears to be an intrinsic property of the protein complex and does not rely on chemoreceptor clustering, as was previously shown for Escherichia coli. By constructing specific amino-acid substitutions, we demonstrate that the preference for strongly curved membranes arises from the curved shape of chemoreceptor trimer of dimers. These findings demonstrate that the intrinsic shape of transmembrane proteins can determine their cellular localization.

  4. Virus-Encoded 7 Transmembrane Receptors

    DEFF Research Database (Denmark)

    Mølleskov-Jensen, Ann-Sofie; Oliveira, MarthaTrindade; Farrell, Helen Elizabeth

    2015-01-01

    have acquired a range of distinctive characteristics. This chapter reviews key features of the v7TMRs which are likely to impact upon their functional roles: trafficking properties, ligand specificity, and signaling capacity. Rapid, constitutive endocytosis, reminiscent of cellular “scavenger......Herpesviruses are an ancient group which have exploited gene capture of multiple cellular modulators of the immune response. Viral homologues of 7 transmembrane receptors (v7TMRs) are a consistent feature of beta- and gammaherpesviruses; the majority of the v7TMRs are homologous to cellular...... chemokine receptors (CKRs). Conserved families of v7TMRs distinguish between beta- versus gammaherpesviruses; furthermore, significant divisions within these subfamilies, such as between genera of the gammaherpesviruses or between the primate and rodent cytomegaloviruses, coincide with specific v7TMR gene...

  5. 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

  6. Molecular mechanisms for generating transmembrane proton gradients

    Science.gov (United States)

    Gunner, M.R.; Amin, Muhamed; Zhu, Xuyu; Lu, Jianxun

    2013-01-01

    Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side. PMID:23507617

  7. 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.

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

    OpenAIRE

    Galip Akay

    2016-01-01

    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 s...

  9. 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

  10. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface*

    OpenAIRE

    Chin, Stephanie; Yang, Donghe; Miles, Andrew J.; Eckford, Paul D. W.; Molinski, Steven; Wallace, B. A.; Bear, Christine E.

    2016-01-01

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein...

  11. 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.

  12. 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.

  13. Guided Transport of a Transmembrane Nanochannel

    Science.gov (United States)

    Dutt, Meenakshi; Kuksenok, Olga; Balazs, Anna

    2011-03-01

    Via the Dissipative Particle Dynamics approach, we design a system that allows transport of a nanochannel to a desired location by applying an external force. Each nanochannel encompasses an ABA architecture, with a hydrophobic shaft (B) with two hydrophilic ends (A). One of the hydrophilic ends of the nanochannel is functionalized with hydrophilic functional groups, or hairs. The hydrophilic hairs serve a dual role: (1) control transport across the membrane barrier when the channel diffuses freely in the membrane, and (2) enable the channel relocation to a specific membrane site. Our system comprises a transmembrane hairy nanochannel with the hairs extending into solution. In our earlier work, we demonstrated the spontaneous insertion of such a hairy nanochannel into a lipid bilayer (Nanoscale DOI: 10.1039/C0NR00578A). First, we hold a suitably functionalized pipette stationary above the membrane while the nanochannel freely diffuses within the membrane. For an optimal range of parameters, we demonstrate that the hairs find the pipette and spontaneously anchor onto it. We then show that by moving the pipette for a range of velocities, we can effectively transport the channel to any location within the membrane. This prototype system can provide guidelines for designing a number of biomimetic applications.

  14. The Origins of Transmembrane Ion Channels

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Even though membrane proteins that mediate transport of ions and small molecules across cell walls are among the largest and least understood biopolymers in contemporary cells, it is still possible to shed light on their origins and early evolution. The central observation is that transmembrane portions of most ion channels are simply bundles of -helices. By combining results of experimental and computer simulation studies on synthetic models and natural channels, mostly of non-genomic origin, we show that the emergence of -helical channels was protobiologically plausible, and did not require highly specific amino acid sequences. Despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. Specifically, we explain how the antiamoebin channels, which are made of identical helices, 16 amino acids in length, achieve efficiency comparable to that of highly evolved channels. We further show that antiamoebin channels are extremely flexible, compared to modern, genetically coded channels. On the basis of our results, we propose that channels evolved further towards high structural complexity because they needed to acquire stable rigid structures and mechanisms for precise regulation rather than improve efficiency. In general, even though architectures of membrane proteins are not nearly as diverse as those of water-soluble proteins, they are sufficiently flexible to adapt readily to the functional demands arising during evolution.

  15. 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

  16. Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions

    DEFF Research Database (Denmark)

    He, Li; Steinocher, Helena; Shelar, Ashish

    2017-01-01

    of leucine and isoleucine (called LIL traptamers) that specifically activate the erythropoietin receptor (EPOR) in mouse cells to confer growth factor independence. We discovered that the placement of a single side chain methyl group at specific positions in a traptamer determined whether it associated......Transmembrane domains (TMDs) engage in protein-protein interactions that regulate many cellular processes, but the rules governing the specificity of these interactions are poorly understood. To discover these principles, we analyzed 26-residue model transmembrane proteins consisting exclusively...... productively with the TMD of the human EPOR, the mouse EPOR, or both receptors. Association of the traptamers with the EPOR induced EPOR oligomerization in an orientation that stimulated receptor activity. These results highlight the high intrinsic specificity of TMD interactions, demonstrate that a single...

  17. 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.

  18. Metal structures with parallel pores

    Science.gov (United States)

    Sherfey, J. M.

    1976-01-01

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

  19. 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

  20. Pathophysiological role of omega pore current in channelopathies

    Directory of Open Access Journals (Sweden)

    Karin eJurkat-Rott

    2012-06-01

    Full Text Available In voltage-gated cation channels, a recurrent pattern for mutations is the neutralization of positively charged residues in the voltage-sensing S4 transmembrane segments. These mutations cause dominant ion channelopathies affecting many tissues such as brain, heart, and skeletal muscle. Recent studies suggest that the pathogenesis of associated phenotypes is not limited to alterations in the gating of the ion-conducting alpha pore. Instead, aberrant so-called omega currents facilitated by the movement of the S4 segments during activation and during recovery are thought to cause symptoms. Surprisingly, these omega currents display uni- or bi-directionality and conduct cations with varying ion selectivity. Additionally, the voltage-sensitivity enables the channels to conduct different omega currents in the various voltage ranges. This review gives an overview of voltage sensor channelopathies in general and focuses on pathogenesis of skeletal muscle S4 disorders for which current knowledge is most advanced.

  1. Nano pores evolution in hydroxyapatite microsphere during spark plasma sintering

    Directory of Open Access Journals (Sweden)

    Lin C.

    2011-01-01

    Full Text Available Micron-spherical granules of hydroxyapatite (HAp nanoparticles were prepared by powder granulation methods. Through subsequent sintering, porous HAp microspheres with tailored pore and grain framework structures were obtained. Detailed microstructure investigation by SEM and TEM revealed the correlation of the pore structure and the necking strength with the sintering profiles that determine the coalescence features of the nanoparticles. The partially sintered porous HAp microspheres containing more than 50% porosity consisting of pores and grains both in nano-scale are active in inducing the precipitation of HAp in simulated body fluid. The nano-porous HAp microspheres with an extensive surface and interconnecting pores thus demonstrate the potential of stimulating the formation of collagen and bone and the integration with the newly formed bones during physiological bone remodeling.

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

    OpenAIRE

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

    2017-01-01

    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 ...

  3. Cystic fibrosis transmembrane conductance regulator chloride channel blockers: Pharmacological, biophysical and physiological relevance.

    Science.gov (United States)

    Linsdell, Paul

    2014-02-26

    Dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel causes cystic fibrosis, while inappropriate activity of this channel occurs in secretory diarrhea and polycystic kidney disease. Drugs that interact directly with CFTR are therefore of interest in the treatment of a number of disease states. This review focuses on one class of small molecules that interacts directly with CFTR, namely inhibitors that act by directly blocking chloride movement through the open channel pore. In theory such compounds could be of use in the treatment of diarrhea and polycystic kidney disease, however in practice all known substances acting by this mechanism to inhibit CFTR function lack either the potency or specificity for in vivo use. Nevertheless, this theoretical pharmacological usefulness set the scene for the development of more potent, specific CFTR inhibitors. Biophysically, open channel blockers have proven most useful as experimental probes of the structure and function of the CFTR chloride channel pore. Most importantly, the use of these blockers has been fundamental in developing a functional model of the pore that includes a wide inner vestibule that uses positively charged amino acid side chains to attract both permeant and blocking anions from the cell cytoplasm. CFTR channels are also subject to this kind of blocking action by endogenous anions present in the cell cytoplasm, and recently this blocking effect has been suggested to play a role in the physiological control of CFTR channel function, in particular as a novel mechanism linking CFTR function dynamically to the composition of epithelial cell secretions. It has also been suggested that future drugs could target this same pathway as a way of pharmacologically increasing CFTR activity in cystic fibrosis. Studying open channel blockers and their mechanisms of action has resulted in significant advances in our understanding of CFTR as a pharmacological target in disease

  4. 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.

  5. NMDA receptor structures reveal subunit arrangement and pore architecture.

    Science.gov (United States)

    Lee, Chia-Hsueh; Lü, Wei; Michel, Jennifer Carlisle; Goehring, April; Du, Juan; Song, Xianqiang; Gouaux, Eric

    2014-07-10

    N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present X-ray crystal structures of the Xenopus laevis GluN1-GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains. The transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ∼twofold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors.

  6. NMDA receptor structures reveal subunit arrangement and pore architecture

    Science.gov (United States)

    Lee, Chia-Hsueh; Lü, Wei; Michel, Jennifer Carlisle; Goehring, April; Du, Juan; Song, Xianqiang; Gouaux, Eric

    2014-01-01

    Summary N-methyl-d-aspartate (NMDA) receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore across the membrane bilayer. Despite the importance of the NMDA receptor in the development and function of the brain, a molecular structure of an intact receptor has remained elusive. Here we present x-ray crystal structures of the GluN1/GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino terminal and ligand binding domains. The transmembrane domains harbor a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a ~2-fold symmetric arrangement of ion channel pore loops. These structures provide new insights into the architecture, allosteric coupling and ion channel function of NMDA receptors. PMID:25008524

  7. 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.

  8. Cystic fibrosis transmembrane conductance regulator: temperature-dependent cysteine reactivity suggests different stable conformers of the conduction pathway.

    Science.gov (United States)

    Liu, Xuehong; Dawson, David C

    2011-11-29

    Cysteine scanning has been widely used to identify pore-lining residues in mammalian ion channels, including the cystic fibrosis transmembrane conductance regulator (CFTR). These studies, however, have been typically conducted at room temperature rather than human body temperature. Reports of substantial effects of temperature on gating and anion conduction in CFTR channels as well as an unexpected pattern of cysteine reactivity in the sixth transmembrane segment (TM6) prompted us to investigate the effect of temperature on the reactivity of cysteines engineered into TM6 of CFTR. We compared reaction rates at temperatures ranging from 22 to 37 °C for cysteines placed on either side of an apparent size-selective accessibility barrier previously defined by comparing reactivity toward channel-permeant and channel-impermeant, thiol-directed reagents. The results indicate that the reactivity of cysteines at three positions extracellular to the position of the accessibility barrier, 334, 336, and 337, is highly temperature-dependent. At 37 °C, cysteines at these positions were highly reactive toward MTSES(-), whereas at 22 °C, the reaction rates were 2-6-fold slower to undetectable. An activation energy of 157 kJ/mol for the reaction at position 337 is consistent with the hypothesis that, at physiological temperature, the extracellular portion of the CFTR pore can adopt conformations that differ significantly from those that can be accessed at room temperature. However, the position of the accessibility barrier defined empirically by applying channel-permeant and channel-impermeant reagents to the extracellular aspect of the pore is not altered. The results illuminate previous scanning results and indicate that the assay temperature is a critical variable in studies designed to use chemical modification to test structural models for the CFTR anion conduction pathway.

  9. 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

  10. Vitamin B1 thiazole derivative reduces transmembrane current through ionic channels formed by toxins from black widow spider venom and sea anemone in planar phospholipid membranes.

    Science.gov (United States)

    Shatursky, Oleg Ya; Volkova, Tatyana M; Romanenko, Olexander V; Himmelreich, Nina H; Grishin, Eugene V

    2007-02-01

    The vitamin B1 (thiamine) structural analogue 3-decyloxycarbonylmethyl-4-methyl-5-(beta-hydroxyethyl) thiazole chloride (DMHT) (0.1 mM) reversibly reduced transmembrane currents in CaCl2 and KCl solutions via ionic channels produced by latrotoxins (alpha-latrotoxin (alpha-LT) and alpha-latroinsectotoxin (alpha-LIT)) from black widow spider venom and sea anemone toxin (RTX) in the bilayer lipid membranes (BLMs). Introduction of DMHT from the cis-side of BLM bathed in 10 mM CaCl2 inhibited transmembrane current by 31.6+/-3% and by 61.8+/-3% from the trans-side of BLM for alpha-LT channels. Application of DMHT in the solution of 10 mM CaCl2 to the cis-side of BLM decreased the current through the alpha-LIT and RTX channels by 52+/-4% and 50+/-5%, respectively. Addition of Cd2+ (1 mM) to the cis- or trans-side of the membrane after the DMHT-induced depression of Ca2+-current across the alpha-LT channels caused its further decrease by 85+/-5% that coincides favorably with the intensity of Cd2+ blocking in control experiments without DMHT. These data suggest that DMHT inhibiting is not specific for latrotoxin channels only and DMHT may exert its action on alpha-LT channels without considerable influence on the ionogenic groups of Ca2+-selective site inside the channel cavity. The binding kinetics of DMHT with the alpha-LT channel shows no cooperativity and allows to expect that the DMHT binding site of the toxin is formed by one ionogenic group as the slopes of inhibition rate determined in log-log coordinates are 1.25 on the trans-side and 0.68 on the cis-side. Similar pK of binding (5.4 on the trans-side and 5.7 on the cis-side) also suggest that DMHT may interact with the same high affinity site of alpha-LT channel on either side of the BLM. The comparative analysis of effective radii measured for alpha-LT, alpha-LIT and RTX channels on the cis-side (0.9 nm, 0.53 nm and 0.55 nm, correspondingly) and for alpha-LT channel on the trans-side (0.28+/-0.18 nm) with the

  11. 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

  12. Effect of support material pore size on the filtration behavior of dynamic membrane bioreactor.

    Science.gov (United States)

    Cai, Donglong; Huang, Ju; Liu, Guoqiang; Li, Mingyu; Yu, Yang; Meng, Fangang

    2018-05-01

    The effect of support material pore size on the filtration behaviors during start-up and stabilized stages in the dynamic membrane bioreactors (DMBR) was studied. Before the dynamic membrane (DM) was formed, the turbidity at 50-μm could be more than 250 NTU, while it was less than 40 and 10 NTU at 25- and 10-μm, respectively. After the DM was formed, the stabilized stage lasted for 61 days with low transmembrane pressure pressure filtration, a mesh size of ∼25 μm is more suitable for DMBR. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. 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.

  14. Probing single nanometer-scale pores with polymeric molecular rulers

    Science.gov (United States)

    Henrickson, Sarah E.; DiMarzio, Edmund A.; Wang, Qian; Stanford, Vincent M.; Kasianowicz, John J.

    2010-04-01

    We previously demonstrated that individual molecules of single-stranded DNA can be driven electrophoretically through a single Staphylococcus aureus α-hemolysin ion channel. Polynucleotides thread through the channel as extended chains and the polymer-induced ionic current blockades exhibit stable modes during the interactions. We show here that polynucleotides can be used to probe structural features of the α-hemolysin channel itself. Specifically, both the pore length and channel aperture profile can be estimated. The results are consistent with the channel crystal structure and suggest that polymer-based "molecular rulers" may prove useful in deducing the structures of nanometer-scale pores in general.

  15. Pore Pressure Measurements Inside Rubble Mound Breakwaters

    DEFF Research Database (Denmark)

    Helgason, Einar; Burcharth, H. F.; Grüne, Joachim

    2004-01-01

    The present paper presents pore pressure measurements from large scale model tests performed at the Large Wave Channel, Hannover, Germany and small scale model test performed at the Hydraulic & Coastal Engineering Laboratory, Aalborg University, Denmark. Information on pore pressure attenuation...

  16. Contributions of H G Khorana to Understanding Transmembrane ...

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL | ARTICLE. Contributions of H G Khorana to Understanding. Transmembrane Signal Transduction. David L Farrens and Thomas P Sakmar. Heptahelical G protein-coupled receptors (GPCRs) are lo- cated in the cell's plasma membrane and are responsible for transmitting chemical signals across the lipid bilayer.

  17. 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

  18. ER-associated complexes (ERACs) containing aggregated cystic fibrosis transmembrane conductance regulator (CFTR) are degraded by autophagy

    OpenAIRE

    Fua, Lianwu; Sztula, Elizabeth

    2009-01-01

    The ubiquitin-proteasome pathway and autophagy are the two major mechanisms responsible for the clearance of cellular proteins. We have used the yeast Saccharomyces cerevisiae as a model system and the cystic fibrosis transmembrane conductance regulator (CFTR) as a model substrate to study the interactive function of these two pathways in the degradation of misfolded proteins. EGFP-tagged human CFTR was introduced into yeast and expressed under a copper-inducible promoter. The localization an...

  19. 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

  20. 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

  1. Multifractal Characterization of Soil Pore Shapes

    Science.gov (United States)

    Gimenez, Daniel; Posadas, Adolfo; Cooper, Miguel

    2010-05-01

    Two dimensional (2-D) images representing pores and solids are used for direct quantification of soil structure using tools that are sensitive to the spatial arrangement of pores or by grouping pores by morphological properties such as shape and size. Pore shapes and sizes are related and have been used to interpret soil processes. Fractal and multifractal methods of pore characterization have been applied separately to spatial arrangement of soil pores and to pore size distributions derived from 2-D images. The objective of this work was to estimate fractal dimensions of spatial arrangement of soil pores of predetermined shapes. Images covering a range of soil structures were analyzed. Pore shape was classified using a shape factor S that quantifies the circularity of pores (S=1 for circular pores). Images containing only pores with S values smaller than 0.1, between 0.1 and 0.2, 0.2 and 0.5, 0.5 and 0.7 and greater than 0.7 were derived from the initial images and analyzed with a multifractal algorithm. The findings of this work will be discussed in relation to models of soil hydraulic properties.

  2. 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.

  3. Microfiltration of red berry juice with thread filters: Effects of temperature, flow and filter pore size

    DEFF Research Database (Denmark)

    Bagger-Jørgensen, Rico; Casani, Sandra Dobon; Meyer, Anne Boye Strunge

    2002-01-01

    A series of experiments was conducted to demonstrate the applicability of a new Filtomat(R) thread filtration principle for microfiltration of semiprocessed blackcurrant juice and cherry juice. The effect of juice temperature (3-20C), flow (20-80 L/h), and filter pore size (3-10 mum) on the trans......A series of experiments was conducted to demonstrate the applicability of a new Filtomat(R) thread filtration principle for microfiltration of semiprocessed blackcurrant juice and cherry juice. The effect of juice temperature (3-20C), flow (20-80 L/h), and filter pore size (3-10 mum......) on the transmembrane pressure, juice turbidity, protein, sugar, and total phenols levels was evaluated in a lab scale microfiltration unit employing statistically designed factorial experiments. Thread microfiltration reduced significantly the turbidity of both juices. For blackcurrant juice, in all experiments...

  4. 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

  5. Aromatic Residues in the Fourth Transmembrane-Spanning Helix M4 Are Important for GABAρ Receptor Function.

    Science.gov (United States)

    Cory-Wright, James; Alqazzaz, Mona; Wroe, Francesca; Jeffreys, Jenny; Zhou, Lu; Lummis, Sarah C R

    2018-02-21

    GABAρ receptors are a subfamily of the GABA A receptor family of pentameric ligand-gated ion channels (pLGICs). Each of the five subunits has four transmembrane α-helices (M1-M4), with M4 most distant from the central pore. Aromatic residues in this M4 helix are important for receptor assembly in pLGICs and also may interact with adjacent lipids and/or residues in neighboring α-helices and the extracellular domain to modify or enable channel gating. This study examines the role of M4 receptor aromatic residues in the GABAρ receptor transmembrane domain using site-directed mutagenesis and subsequent expression in HEK293 cells, probing functional parameters using a fluorescent membrane-potential-sensitive dye. The data indicate that many of the aromatic residues in M4 play a role in receptor function, as substitution with other residues can ablate and/or modify functional parameters. Modeling showed that these residues likely interact with residues in the adjacent M1 and M3 α-helices and/or residues in the Cys-loop in the extracellular domain. We suggest that many of these aromatic interactions contribute to an "aromatic zipper", which allows interactions between M4 and the rest of the receptor that are essential for function. Thus, the data support other studies showing that M4 does not play a passive role in "protecting" the other transmembrane helices from the lipid bilayer but is actively involved in the function of the protein.

  6. Inhibition of Ebola virus glycoprotein-mediated cytotoxicity by targeting its transmembrane domain and cholesterol.

    Science.gov (United States)

    Hacke, Moritz; Björkholm, Patrik; Hellwig, Andrea; Himmels, Patricia; Ruiz de Almodóvar, Carmen; Brügger, Britta; Wieland, Felix; Ernst, Andreas M

    2015-07-09

    The high pathogenicity of the Ebola virus reflects multiple concurrent processes on infection. Among other important determinants, Ebola fusogenic glycoprotein (GP) has been associated with the detachment of infected cells and eventually leads to vascular leakage and haemorrhagic fever. Here we report that the membrane-anchored GP is sufficient to induce the detachment of adherent cells. The results show that the detachment induced through either full-length GP1,2 or the subunit GP2 depends on cholesterol and the structure of the transmembrane domain. These data reveal a novel molecular mechanism in which GP regulates Ebola virus assembly and suggest that cholesterol-reducing agents could be useful as therapeutics to counteract GP-mediated cell detachment.

  7. A missense mutation in the second transmembrane segment of the luteinizing hormone receptor causes familial male-limited precocious puberty

    Energy Technology Data Exchange (ETDEWEB)

    Kraaij, R.; Post, M.; Grootegoed, J.A. [Erasmus Univ. Rotterdam (Netherlands)] [and others

    1995-10-01

    Patients with familial male-limited precocious puberty present with early onset of puberty. Several missense mutations in the LH receptor gene that cause amino acid substitutions in the sixth transmembrane segment of the receptor protein have been shown to be a cause of the disorder. We have identified a novel LH receptor gene mutation in a patient with familial male-limited precocious puberty that results in a threonine for methionine substitution at position 398 in the second transmembrane segment of the receptor protein. In vitro expression in human embryonic kidney 293 cells of this LH receptor mutant and two previously described LH receptor mutants showed that cAMP production in the absence of hormone was elevated up to 25-fold compared to the basal level of the wild-type receptor. The ED{sub 50} values of hormone-induced cAMP production was relatively low for mutant receptors. We also produced receptors containing amino acid substitutions in both the second and sixth transmembrane segments. For these double mutants, basal receptor activities were similar to the basal activities observed in single mutants, whereas hormone-induced receptor activation was almost completely abolished. 31 refs., 2 figs.

  8. The ER membrane protein complex is a transmembrane domain insertase

    Science.gov (United States)

    Guna, Alina; Volkmar, Norbert; Christianson, John C.; Hegde, Ramanujan S.

    2018-01-01

    Insertion of proteins into membranes is an essential cellular process. The extensive biophysical and topological diversity of membrane proteins necessitates multiple insertion pathways that remain incompletely defined. Here, we found that known membrane insertion pathways fail to effectively engage tail-anchored membrane proteins with moderately hydrophobic transmembrane domains. These proteins are instead shielded in the cytosol by calmodulin. Dynamic release from calmodulin allowed sampling of the endoplasmic reticulum (ER), where the conserved ER membrane protein complex (EMC) was shown to be essential for efficient insertion in vitro and in cells. Purified EMC in synthetic liposomes catalyzed insertion of its substrates in a reconstituted system. Thus, EMC is a transmembrane domain insertase, a function that may explain its widely pleiotropic membrane-associated phenotypes across organisms. PMID:29242231

  9. Crystal structure of hormone-bound atrial natriuretic peptide receptor extracellular domain: rotation mechanism for transmembrane signal transduction.

    Science.gov (United States)

    Ogawa, Haruo; Qiu, Yue; Ogata, Craig M; Misono, Kunio S

    2004-07-02

    A cardiac hormone, atrial natriuretic peptide (ANP), plays a major role in blood pressure and volume regulation. ANP activities are mediated by a single span transmembrane receptor carrying intrinsic guanylate cyclase activity. ANP binding to its extracellular domain stimulates guanylate cyclase activity by an as yet unknown mechanism. Here we report the crystal structure of dimerized extracellular hormone-binding domain in complex with ANP. The structural comparison with the unliganded receptor reveals that hormone binding causes the two receptor monomers to undergo an intermolecular twist with little intramolecular conformational change. This motion produces a Ferris wheel-like translocation of two juxtamembrane domains in the dimer with essentially no change in the interdomain distance. This movement alters the relative orientation of the two domains by a shift equivalent to counterclockwise rotation of each by 24 degrees. These results suggest that transmembrane signaling by the ANP receptor is initiated via a hormone-induced rotation mechanism.

  10. Transmembrane electron transport and the neutral theory of evolution.

    Science.gov (United States)

    Scherer, S

    1984-01-01

    Based on the concept of "pairs of basic functional states" the evolution of the first chemiosmotic mechanism of energy conversion is discussed in terms of point mutations, gene duplications and of the neutral theory of evolution. A model for estimating the overall probability of the evolutionary step in question is presented, both for the "selectionist" and "neutralist" position. It is concluded that, concerning the present stage of knowledge, the evolution of transmembrane electron transport is an unsolved problem in evolutionary biology.

  11. Structural basis for pore-forming mechanism of staphylococcal α-hemolysin.

    Science.gov (United States)

    Sugawara, Takaki; Yamashita, Daichi; Kato, Koji; Peng, Zhao; Ueda, Junki; Kaneko, Jun; Kamio, Yoshiyuki; Tanaka, Yoshikazu; Yao, Min

    2015-12-15

    Staphylococcal α-hemolysin (α-HL) is a β-barrel pore-forming toxin (PFT) expressed by Staphylococcus aureus. α-HL is secreted as a water-soluble monomeric protein, which binds to target membranes and forms membrane-inserted heptameric pores. To explore the pore-forming mechanism of α-HL in detail, we determined the crystal structure of the α-HL monomer and prepore using H35A mutant and W179A/R200A mutant, respectively. Although the overall structure of the monomer was similar to that of other staphylococcal PFTs, a marked difference was observed in the N-terminal amino latch, which bent toward the prestem. Moreover, the prestem was fastened by the cap domain with a key hydrogen bond between Asp45 and Tyr118. Prepore structure showed that the transmembrane region is roughly formed with flexibility, although the upper half of the β-barrel is formed appropriately. Structure comparison among monomer, prepore and pore revealed a series of motions, in which the N-terminal amino latch released upon oligomerization destroys its own key hydrogen bond between Asp45-Tyr118. This action initiated the protrusion of the prestem. Y118F mutant and the N-terminal truncated mutant markedly decreased in the hemolytic activity, indicating the importance of the key hydrogen bond and the N-terminal amino latch on the pore formation. Based on these observations, we proposed a dynamic molecular mechanism of pore formation for α-HL. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. 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.

  13. Antamanide, a derivative of Amanita phalloides, is a novel inhibitor of the mitochondrial permeability transition pore.

    Directory of Open Access Journals (Sweden)

    Luca Azzolin

    2011-01-01

    Full Text Available Antamanide is a cyclic decapeptide derived from the fungus Amanita phalloides. Here we show that antamanide inhibits the mitochondrial permeability transition pore, a central effector of cell death induction, by targeting the pore regulator cyclophilin D. Indeed, (i permeability transition pore inhibition by antamanide is not additive with the cyclophilin D-binding drug cyclosporin A, (ii the inhibitory action of antamanide on the pore requires phosphate, as previously shown for cyclosporin A; (iii antamanide is ineffective in mitochondria or cells derived from cyclophilin D null animals, and (iv abolishes CyP-D peptidyl-prolyl cis-trans isomerase activity. Permeability transition pore inhibition by antamanide needs two critical residues in the peptide ring, Phe6 and Phe9, and is additive with ubiquinone 0, which acts on the pore in a cyclophilin D-independent fashion. Antamanide also abrogates mitochondrial depolarization and the ensuing cell death caused by two well-characterized pore inducers, clotrimazole and a hexokinase II N-terminal peptide. Our findings have implications for the comprehension of cyclophilin D activity on the permeability transition pore and for the development of novel pore-targeting drugs exploitable as cell death inhibitors.

  14. RNase A does not translocate the alpha-hemolysin pore.

    Directory of Open Access Journals (Sweden)

    Besnik Krasniqi

    Full Text Available The application of nanopore sensing utilizing the α-hemolysin pore to probe proteins at single-molecule resolution has expanded rapidly. In some studies protein translocation through the α-hemolysin has been reported. However, there is no direct evidence, as yet, that proteins can translocate the α-hemolysin pore. The biggest challenge to obtaining direct evidence is the lack of a highly sensitive assay to detect very low numbers of protein molecules. Furthermore, if an activity based assay is applied then the proteins translocating by unfolding should refold back to an active confirmation for the assay technique to work. To overcome these challenges we selected a model enzyme, ribonuclease A, that readily refolds to an active conformation even after unfolding it with denaturants. In addition we have developed a highly sensitive reverse transcription polymerase chain reaction based activity assay for ribonuclease A. Initially, ribonuclease A, a protein with a positive net charge and dimensions larger than the smallest diameter of the pore, was subjected to nanopore analysis under different experimental conditions. Surprisingly, although the protein was added to the cis chamber (grounded and a positive potential was applied, the interaction of ribonuclease A with α-hemolysin pore induced small and large blockade events in the presence and the absence of a reducing and/or denaturing agent. Upon measuring the zeta potential, it was found that the protein undergoes a charge reversal under the experimental conditions used for nanopore sensing. From the investigation of the effect of voltage on the interaction of ribonuclease A with the α-hemolysin pore, it was impossible to conclude if the events observed were translocations. However, upon testing for ribonuclease A activity on the trans chamber it was found that ribonuclease A does not translocate the α-hemolysin pore.

  15. 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...... and still to realize Si-Si bonding. It has been demonstrated that ribbed silicon plates can be produced and assembled into stacks. All previously work has been done using uncoated Si plates. In this paper we describe how to coat the ribbed Si plates with an Ir coating and a top C coating through a mask so...

  16. Wet winter pore pressures in railway embankments

    OpenAIRE

    Briggs, Kevin M; Smethurst, Joel A; Powrie, William; O'Brien, Anthony S

    2013-01-01

    This paper demonstrates the influence of extreme wet winter weather on pore water pressures within clay fill railway embankments, using field monitoring data and numerical modelling. Piezometer readings taken across the London Underground Ltd network following the wet winter of 2000/2001 were examined, and showed occurrences of hydrostatic pore water pressure within embankments but also many readings below this. A correlation was found between the maximum pore water pressures and the permeabi...

  17. 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.

  18. Structural models of the transmembrane region of voltage-gated and other K+ channels in open, closed, and inactivated conformations.

    Science.gov (United States)

    Durell, S R; Hao, Y; Guy, H R

    1998-01-01

    A large collaborative, multidisciplinary effort involving many research laboratories continues which uses indirect methods of molecular biology and membrane biophysics to analyze the three-dimensional structures and functional mechanisms of K+ channels. This work also extends to the distant relatives of these channels, including the voltage-gated Na+ and Ca2+ channels. The role that our group plays in this process is to combine the information gained from experimental studies with molecular modeling techniques to generate atomic-scale structural models of these proteins. The modeling process involves three stages which are summarized as: (I) prediction of the channel sequence transmembrane topology, including the functionality and secondary structure of the segments; (II) prediction of the relative positions of the transmembrane segments, and (III) filling in all atoms of the amino acid residues, with conformations for energetically stabilized interactions. Both physiochemical and evolutionary principles (including sequence homology analysis) are used to guide the development. In addition to testing the steric and energetic feasibilities of different structural hypotheses, the models provide guidance for the design of new experiments. Structural modeling also serves to "fill in the gaps" of experimental data, such as predicting additional residue interactions and conformational changes responsible for functional processes. The modeling process is currently at the stage that experimental studies have definitely confirmed most of our earlier predictions about the transmembrane topology and functionality of different segments. Additionally, this report describes the detailed, three-dimensional models we have developed for the entire transmembrane region and important functional sites of the voltage-gated Shaker K+ channel in the open, closed, and inactivated conformations (including the ion-selective pore and voltage-sensor regions). As part of this effort, we also

  19. Interaction of amphipathic α-helical peptides with a lipid membrane: Adsorption and pore formation

    Science.gov (United States)

    Zhdanov, Vladimir P.

    2014-05-01

    Amphipathic α-helical peptides often exhibit antimicrobial or antiviral properties. Adsorption of such peptides at a lipid membrane may result in pore formation. Current phenomenological models of the latter process imply that the peptide-peptide lateral interaction is repulsive and that the conditions for pore formation depend on the difference of the peptide energies at the membrane surface and in a pore. There is, however, experimental evidence that the kinetics of peptide adsorption at small vesicles (about 100 nm diameter) may be cooperative and accordingly the peptide-peptide lateral interaction may be attractive. In addition, the experiments indicate that the peptide-induced pore formation is often observed at the conditions close to those corresponding to pore formation under externally induced tensile stress where the difference of the peptide energies at the membrane surface and in a pore is irrelevant. Here, a model describing both types of peptide-peptide lateral interactions at a membrane is proposed. In addition, a new scenario of peptide-induced pore formation naturally explaining the similarity of this process under different conditions is suggested.

  20. The pore-load modulus of ordered nanoporous materials with surface effects

    Science.gov (United States)

    Liu, Mingchao; Wu, Jian; Gan, Yixiang; Chen, C. Q.

    2016-03-01

    Gas and liquid adsorption-induced deformation of ordered porous materials is an important physical phenomenon with a wide range of applications. In general, the deformation can be characterized by the pore-load modulus and, when the pore size reduces to nanoscale, it is affected by surface effects and shows prominent size-dependent features. In this Letter, the influence of surface effects on the elastic properties of ordered nanoporous materials with internal pressure is accounted for in a single pore model. A porosity and surface elastic constants dependent closed form solution for the size dependent pore-load modulus is obtained and verified by finite element simulations and available experimental results. In addition, it is found to depend on the geometrical arrangement of pores. This study provides an efficient tool to analyze the surface effects on the elastic response of ordered nanoporous materials.

  1. 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.

  2. 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.

  3. Reverse endocytosis of transmembrane ephrin-B ligands via a clathrin-mediated pathway

    International Nuclear Information System (INIS)

    Parker, Monica; Roberts, Richard; Enriquez, Miriam; Zhao Xia; Takahashi, Takamune; Pat Cerretti, Douglas; Daniel, Tom; Chen Jin

    2004-01-01

    Eph/ephrin receptors and ligands mediate cell-cell interaction through reciprocal signaling upon juxtacrine contact, and play a critical role in embryonic patterning, neuronal targeting, and vascular assembly. To study transmembrane ephrin-B ligand trafficking, we determined the cellular localization of ephrin-B1-GFP upon engagement by EphB1. Under normal culture conditions ephrin-B1-GFP is localized to the plasma membrane, mostly at the lateral cell borders. Addition of soluble EphB1-Fc receptor induces ephrin-B1-GFP clustering on the cell surface and subsequent internalization, as judged by biochemical studies, electron microscopy, and co-localization with endosomal markers. A dominant-negative mutant of dynamin or potassium depletion blocks ephrin-B1 endocytosis. These results suggest that ephrin-B1 internalization is an active receptor-mediated process that utilizes the clathrin-mediated endocytic pathway

  4. 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.

  5. 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.

  6. 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.

  7. 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 characteristi...

  8. Nuclear pore structure: warming up the core.

    Science.gov (United States)

    Harel, Amnon; Gruenbaum, Yosef

    2011-07-22

    Structural determination of the nuclear pore complex has been limited by the complexity and size of this cellular megalith. By taking advantage of exceptionally stable nucleoporins from the thermophilic fungus Chaetomium thermophilum, Amlacher et al. (2011) provide new insight into a core element of the nuclear pore scaffold. Copyright © 2011 Elsevier Inc. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...... 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...

  10. 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...... and computation have been used to study receptor dynamics. Recent studies on three distinct classes of receptors (G-protein coupled receptors, ligand-gated ion-channels and single-pass receptors) are highlighted to show that conformational changes across a range of time-scales and length-scales are central...

  11. Structure of the transmembrane domain of HIV-1 envelope glycoprotein.

    Science.gov (United States)

    Chen, Bing; Chou, James J

    2017-04-01

    HIV-1 envelope spike (Env) is a heavily glycosylated, type I membrane protein that mediates fusion of viral and cell membranes to initiate infection. It is also a primary target of neutralizing antibodies and thus an important candidate for vaccine development. We have recently reported a nuclear magnetic resonance structure of the transmembrane (TM) domain of HIV-1 Env reconstituted in a membrane-like environment. Taking HIV-1 as an example, we discuss here how a TM domain can anchor, stabilize, and modulate a viral envelope spike and how its high-resolution structure can contribute to understanding viral membrane fusion and to immunogen design. © 2016 Federation of European Biochemical Societies.

  12. 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. T....... 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....

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. Stability analysis of the inverse transmembrane potential problem in electrocardiography

    Science.gov (United States)

    Burger, Martin; Mardal, Kent-André; Nielsen, Bjørn Fredrik

    2010-10-01

    In this paper we study some mathematical properties of an inverse problem arising in connection with electrocardiograms (ECGs). More specifically, we analyze the possibility for recovering the transmembrane potential in the heart from ECG recordings, a challenge currently investigated by a growing number of groups. Our approach is based on the bidomain model for the electrical activity in the myocardium, and leads to a parameter identification problem for elliptic partial differential equations (PDEs). It turns out that this challenge can be split into two subproblems: the task of recovering the potential at the heart surface from body surface recordings; the problem of computing the transmembrane potential inside the heart from the potential determined at the heart surface. Problem (1), which can be formulated as the Cauchy problem for an elliptic PDE, has been extensively studied and is well known to be severely ill-posed. The main purpose of this paper is to prove that problem (2) is stable and well posed if a suitable prior is available. Moreover, our theoretical findings are illuminated by a series of numerical experiments. Finally, we discuss some aspects of uniqueness related to the anisotropy in the heart.

  19. 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.

  20. A mechanistic view of mitochondrial death decision pores

    Directory of Open Access Journals (Sweden)

    J.E. Belizário

    2007-08-01

    Full Text Available Mitochondria increase their outer and inner membrane permeability to solutes, protons and metabolites in response to a variety of extrinsic and intrinsic signaling events. The maintenance of cellular and intraorganelle ionic homeostasis, particularly for Ca2+, can determine cell survival or death. Mitochondrial death decision is centered on two processes: inner membrane permeabilization, such as that promoted by the mitochondrial permeability transition pore, formed across inner membranes when Ca2+ reaches a critical threshold, and mitochondrial outer membrane permeabilization, in which the pro-apoptotic proteins BID, BAX, and BAK play active roles. Membrane permeabilization leads to the release of apoptogenic proteins: cytochrome c, apoptosis-inducing factor, Smac/Diablo, HtrA2/Omi, and endonuclease G. Cytochrome c initiates the proteolytic activation of caspases, which in turn cleave hundreds of proteins to produce the morphological and biochemical changes of apoptosis. Voltage-dependent anion channel, cyclophilin D, adenine nucleotide translocase, and the pro-apoptotic proteins BID, BAX, and BAK may be part of the molecular composition of membrane pores leading to mitochondrial permeabilization, but this remains a central question to be resolved. Other transporting pores and channels, including the ceramide channel, the mitochondrial apoptosis-induced channel, as well as a non-specific outer membrane rupture may also be potential release pathways for these apoptogenic factors. In this review, we discuss the mechanistic models by which reactive oxygen species and caspases, via structural and conformational changes of membrane lipids and proteins, promote conditions for inner/outer membrane permeabilization, which may be followed by either opening of pores or a rupture of the outer mitochondrial membrane.

  1. Location of the β4 transmembrane helices in the BK potassium channel

    Science.gov (United States)

    Wu, Roland S.; Chudasama, Neelesh; Zakharov, Sergey I.; Doshi, Darshan; Motoike, Howard; Liu, Guoxia; Yao, Yongneng; Niu, Xiaowei; Deng, Shi-Xian; Landry, Donald W.; Karlin, Arthur; Marx, Steven O.

    2009-01-01

    Large-conductance, voltage- and Ca2+-gated potassium (BK) channels control excitability in a number of cell types. BK channels are composed of α subunits, which contain the voltage-sensor domains and the Ca2+- sensor domains, and form the pore, and often one of four types of β subunits, which modulate the channel in a cell-specific manner. β4 is expressed in neurons throughout the brain. Deletion of β4 in mice causes temporal lobe epilepsy. Compared to channels composed of α alone, channels composed of α and β4 activate and deactivate more slowly. We inferred the locations of the two β4 transmembrane (TM) helices, TM1 and TM2, relative to the seven αTM helices, S0-S6, from the extent of disulfide bond formation between cysteines substituted in the extracellular flanks of these TM helices. We found that β4 TM2 is close to α S0 and that β4 TM1 is close to both α S1 and S2. At least at their extracellular ends, TM1 and TM2 are not close to S3 through S6. In six of eight of the most highly crosslinked cysteine pairs, four crosslinks from TM2 to S0 and one each from TM1 to S1 and S2 had small effects on the V50 and on the rates of activation and deactivation. That disulfide crosslinking caused only small functional perturbations is consistent with the proximity of the extracellular ends of TM2 to S0 and of TM1 to S1 and to S2, in both the open and closed states. PMID:19571123

  2. 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.

  3. Particle diffusion in complex nanoscale pore networks

    DEFF Research Database (Denmark)

    Müter, Dirk; Sørensen, Henning Osholm; Bock, H.

    2015-01-01

    We studied the diffusion of particles in the highly irregular pore networks of chalk, a very fine-grained rock, by combining three-dimensional X-ray imaging and dissipative particle dynamics (DPD) simulations. X-ray imaging data were collected at 25 nm voxel dimension for two chalk samples...... with very different porosities (4% and 26%). The three-dimensional pore systems derived from the tomograms were imported into DPD simulations and filled with spherical particles of variable diameter and with an optional attractive interaction to the pore surfaces. We found that diffusion significantly...

  4. 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.

  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. Prostaglandin E1 protects coronary microvascular function via the glycogen synthase kinase 3β-mitochondrial permeability transition pore pathway in rat hearts subjected to sodium laurate-induced coronary microembolization.

    Science.gov (United States)

    Zhu, Houyong; Ding, Yu; Xu, Xiaoqun; Li, Meiya; Fang, Yangliang; Gao, Beibei; Mao, Hengyi; Tong, Guoxin; Zhou, Liang; Huang, Jinyu

    2017-01-01

    Prostaglandin E1 (PGE1) is used as a pretreatment for ischemia reperfusion injury in many biological systems. However, its value as a pretreatment for coronary microembolization (CME) is unknown. The goal of this study was to determine whether PGE1 would protect against CME. In a CME rat model, we observed microthrombi and early myocardial ischemia, with endothelium appearing exfoliated and mitochondria having irregular morphology and decreased internal complexity. The level of fibrinogen-like protein 2 prothrombinase was increased and superoxide dismutase and catalase levels were decreased. Moreover, mitochondria copy number and mitochondrial permeability transition pore (mPTP) opening were increased. Pretreatment with PGE1 (1 or 2 μg/kg) significantly improved these cardiological deficits, acting via the glycogen synthase kinase 3β (GSK-3β)-mPTP pathway. Unexpectedly, the phosphorylation of Akt at Ser473 decreased in the PGE1 at high dose. Overall, our findings suggested an important role for PGE1 in pretreatment of coronary microvascular dysfunction.

  7. 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.

  8. 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.

  9. Block copolymer structures in nano-pores

    Science.gov (United States)

    Pinna, Marco; Guo, Xiaohu; Zvelindovsky, Andrei

    2010-03-01

    We present results of coarse-grained computer modelling of block copolymer systems in cylindrical and spherical nanopores on Cell Dynamics Simulation. We study both cylindrical and spherical pores and systematically investigate structures formed by lamellar, cylinders and spherical block copolymer systems for various pore radii and affinity of block copolymer blocks to the pore walls. The obtained structures include: standing lamellae and cylinders, ``onions,'' cylinder ``knitting balls,'' ``golf-ball,'' layered spherical, ``virus''-like and mixed morphologies with T-junctions and U-type defects [1]. Kinetics of the structure formation and the differences with planar films are discussed. Our simulations suggest that novel porous nano-containers can be formed by confining block copolymers in pores of different geometries [1,2]. [4pt] [1] M. Pinna, X. Guo, A.V. Zvelindovsky, Polymer 49, 2797 (2008).[0pt] [2] M. Pinna, X. Guo, A.V. Zvelindovsky, J. Chem. Phys. 131, 214902 (2009).

  10. 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...... 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...... volume and threshold pore size were found when comparing with plain cement paste at the same curing conditions. The porosity methods MIP, LTC and SEM have been shown to be suitable to characterise pore parameters of the pastes. MIP is a simple and fast method which covers a large range of pore sizes...

  11. 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.

  12. Glycosylation and the cystic fibrosis transmembrane conductance regulator

    Science.gov (United States)

    Scanlin, Thomas F; Glick, Mary Catherine

    2001-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) has been known for the past 11 years to be a membrane glycoprotein with chloride channel activity. Only recently has the glycosylation of CFTR been examined in detail, by O'Riordan et al in Glycobiology. Using cells that overexpress wild-type (wt)CFTR, the presence of polylactosamine was noted on the fully glycosylated form of CFTR. In the present commentary the results of that work are discussed in relation to the glycosylation phenotype of cystic fibrosis (CF), and the cellular localization and processing of ΔF508 CFTR. The significance of the glycosylation will be known when endogenous CFTR from primary human tissue is examined. PMID:11686896

  13. Glycosylation and the cystic fibrosis transmembrane conductance regulator

    Directory of Open Access Journals (Sweden)

    Glick Mary Catherine

    2001-08-01

    Full Text Available Abstract The cystic fibrosis transmembrane conductance regulator (CFTR has been known for the past 11 years to be a membrane glycoprotein with chloride channel activity. Only recently has the glycosylation of CFTR been examined in detail, by O'Riordan et al in Glycobiology. Using cells that overexpress wild-type (wtCFTR, the presence of polylactosamine was noted on the fully glycosylated form of CFTR. In the present commentary the results of that work are discussed in relation to the glycosylation phenotype of cystic fibrosis (CF, and the cellular localization and processing of ΔF508 CFTR. The significance of the glycosylation will be known when endogenous CFTR from primary human tissue is examined.

  14. 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

  15. 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

  16. The transmembrane channel-like protein family and human papillomaviruses

    Science.gov (United States)

    Horton, Jaime S; Stokes, Alexander J

    2014-01-01

    Epidermodysplasia verruciformis (EV) is a rare genodermatosis characterized by increased sensitivity to infection by the β-subtype of human papillomaviruses (β-HPVs), causing persistent, tinea versicolor-like dermal lesions. In a majority of affected individuals, these macular lesions progress to invasive cutaneous squamous cell carcinoma (CSCC) in sun-exposed areas. While mutations in transmembrane channel-like 6 (TMC6 / EVER1) and 8 (TMC8 / EVER2) have been causally linked to EV, their molecular functions are unclear. It is likely that their protective effects involve regulation of the β-HPV life cycle, host keratinocyte apoptosis vs. survival balance and/or T-cell interaction with infected host cells. PMID:24800179

  17. Molecular Dynamics Simulation of Membranes and a Transmembrane Helix

    Science.gov (United States)

    Duong, Tap Ha; Mehler, Ernest L.; Weinstein, Harel

    1999-05-01

    Three molecular dynamics (MD) simulations of 1.5-ns length were carried out on fully hydrated patches of dimyristoyl phosphatidylcholine (DMPC) bilayers in the liquid-crystalline phase. The simulations were performed using different ensembles and electrostatic conditions: a microcanonical ensemble or constant pressure-temperature ensemble, with or without truncated electrostatic interactions. Calculated properties of the membrane patches from the three different protocols were compared to available data from experiments. These data include the resulting overall geometrical dimensions, the order characteristics of the lipid hydrocarbon chains, as well as various measures of the conformations of the polar head groups. The comparisons indicate that the simulation carried out within the microcanonical ensemble with truncated electrostatic interactions yielded results closest to the experimental data, provided that the initial equilibration phase preceding the production run was sufficiently long. The effects of embedding a non-ideal helical protein domain in the membrane patch were studied with the same MD protocols. This simulation was carried out for 2.5 ns. The protein domain corresponds to the seventh transmembrane segment (TMS7) of the human serotonin 5HT 2Areceptor. The peptide is composed of two α-helical segments linked by a hinge domain around a perturbing Asn-Pro motif that produces at the end of the simulation a kink angle of nearly 80° between the two helices. Several aspects of the TMS7 structure, such as the bending angle, backbone Φ and Ψ torsion angles, the intramolecular hydrogen bonds, and the overall conformation, were found to be very similar to those determined by NMR for the corresponding transmembrane segment of the tachykinin NK-1 receptor. In general, the simulations were found to yield structural and dynamic characteristics that are in good agreement with experiment. These findings support the application of simulation methods to the study

  18. Transmembrane protein topology prediction using support vector machines

    Directory of Open Access Journals (Sweden)

    Nugent Timothy

    2009-05-01

    Full Text Available Abstract Background Alpha-helical transmembrane (TM proteins are involved in a wide range of important biological processes such as cell signaling, transport of membrane-impermeable molecules, cell-cell communication, cell recognition and cell adhesion. Many are also prime drug targets, and it has been estimated that more than half of all drugs currently on the market target membrane proteins. However, due to the experimental difficulties involved in obtaining high quality crystals, this class of protein is severely under-represented in structural databases. In the absence of structural data, sequence-based prediction methods allow TM protein topology to be investigated. Results We present a support vector machine-based (SVM TM protein topology predictor that integrates both signal peptide and re-entrant helix prediction, benchmarked with full cross-validation on a novel data set of 131 sequences with known crystal structures. The method achieves topology prediction accuracy of 89%, while signal peptides and re-entrant helices are predicted with 93% and 44% accuracy respectively. An additional SVM trained to discriminate between globular and TM proteins detected zero false positives, with a low false negative rate of 0.4%. We present the results of applying these tools to a number of complete genomes. Source code, data sets and a web server are freely available from http://bioinf.cs.ucl.ac.uk/psipred/. Conclusion The high accuracy of TM topology prediction which includes detection of both signal peptides and re-entrant helices, combined with the ability to effectively discriminate between TM and globular proteins, make this method ideally suited to whole genome annotation of alpha-helical transmembrane proteins.

  19. 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.

  20. 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.)

  1. Evaluation of the capacity of mosaic-like porous ceramics with designed pores to support osteoconduction.

    Science.gov (United States)

    Teraoka, Kay; Kato, Tomotaka; Hattori, Koji; Ohgushi, Hajime

    2013-12-01

    Under osteoconductive conditions, porous calcium phosphate ceramics are known to induce new bone formation within their pores. A critical aspect of the design of porous ceramics is the geometrical features of their pores, with regard to promoting bone formation and mass transfer management in pore networks. However, the pore geometries of common porous ceramics lack clear details. Further, the connections between pores are hard to characterize and thus have not been thoroughly researched. To address these issues, we have developed an original method for fabricating porous ceramics, which we have termed "mosaic-like ceramics fabrication (MLCF)." Using MLCF, pore geometries can be designed and fabricated by each unit, and a network covering all the pores can be fabricated. Furthermore, MLCF can be used to build porous ceramics with custom-made shapes. In this study, we assessed the osteogenic influences of MLCF products (MLPC) composed of hydroxyapatite units on the differentiation of rat bone-marrow-derived mesenchymal stem cells (MSCs) in vitro and in vivo. Two types of commercial porous artificial bone were used as positive controls. MLPC was superior in osteogenic potential, and proved to be a reliable scaffold for bone tissue engineering. Furthermore, this study succeeded in defining the important geometries for osteoconduction. Copyright © 2013 Wiley Periodicals, Inc.

  2. Quantitative Studies of Antimicrobial Peptide Pore Formation in Large Unilamellar Vesicles by Fluorescence Correlation Spectroscopy (FCS)

    DEFF Research Database (Denmark)

    Kristensen, Kasper; Henriksen, Jonas Rosager; Andresen, Thomas Lars

    2013-01-01

    leakage of fluorescent probes of different sizes through transmembrane pores formed by each of the three representative antimicrobial peptides: melittin, magainin 2, and mastoparan X. The experimental results demonstrate that leakage assays based on fluorescence correlation spectroscopy offer new...... highly warranted. Fluorescence correlation spectroscopy is a biophysical technique that can be used to quantify leakage of fluorescent probes of different sizes from large unilamellar vesicle, thereby potentially becoming such a new tool. However, the usage of fluorescence correlation spectroscopy...... to quantify leakage from large unilamellar vesicles is associated with a number of experimental pitfalls. Based on theoretical and experimental considerations, we discuss how to properly design experiments to avoid these pitfalls. Subsequently, we apply fluorescence correlation spectroscopy to quantify...

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

    Science.gov (United States)

    Lee, Y.

    2011-12-01

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

  4. Single Particle Tracking to Characterize the Mechanism of Pore Formation by Pore Forming Proteins

    OpenAIRE

    Subburaj, Yamunadevi

    2014-01-01

    Pore formation is a common natural mechanism occurring in large number of organisms where proteins are involved as toxins, effectors in immune response or apoptosis. Despite intense research, the structural and dynamic aspects of oligomerization and membrane permeabilization by pore forming proteins remains poorly understood. In this work we have aimed to provide a better understanding on dynamics, oligomerization and pore forming process of two proteins; a) Equinatoxin II, b) Bax (Bcl2 famil...

  5. 21 CFR 866.5900 - Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation detection system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Cystic fibrosis transmembrane conductance... DEVICES Immunological Test Systems § 866.5900 Cystic fibrosis transmembrane conductance regulator (CFTR... intended as an aid in confirmatory diagnostic testing of individuals with suspected cystic fibrosis (CF...

  6. Modeling the structure of SARS 3a transmembrane protein using a ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 12. Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach. S Ramakrishna ... Keywords. Membrane protein modeling; ion channel; transmembrane helices; viroporin; molecular dynamics; SARS 3a.

  7. 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.

  8. A Model of Electrostimulation Based on the Membrane Capacitance as Electromechanical Transducer for Pore Gating.

    Science.gov (United States)

    Irnich, Werner; Kroll, Mark W

    2015-07-01

    Electrostimulation has gained enormous importance in modern medicine, for example, in implantable pacemakers and defibrillators, pain stimulators, and cochlear implants. Most electrostimulation macromodels use the electrical current as the primary parameter to describe the conventional strength-duration relationship of the output of a generator. These models normally assume that the stimulation pulse charges up the passive cell membrane capacitance, and then the increased (less-negative) transmembrane potential activates voltage-gated sodium channels. However, this model has mechanistic and accuracy limitations. Our model assumes that the membrane capacitance is an electromechanical transducer and that the membrane is compressed by the endogenous electric field. The pressure is quadratically correlated with the transmembrane voltage. If the pressure is reduced by an exogenous field, the compression is released and, thus, opening the pores for Na(+) influx initiates excitation. The exogenous electric field must always be equal to or greater than the rheobase field strength (rheobase condition). This concept yields a final result that the voltage-pulse-content produced by the exogenous field between the two ends of a cell is a linear function of the pulse duration at threshold level. Thus, the model yields mathematical formulations that can describe and explain the characteristic features of electrostimulation. Our model of electrostimulation can describe and explain electrostimulation at cellular level. The model's predictions are consistent with published experimental studies. Practical applications in cardiology are discussed in the light of this model of electrostimulation. ©2015 The Authors. Pacing and Clinical Electrophysiology Published by Wiley Periodicals, Inc.

  9. 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

  10. 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.

  11. 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.

  12. New bimodal pore catalysts for Fischer-Tropsch synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Shinoda, Misao; Zhang, Yi; Yoneyama, Yoshiharu; Hasegawa, Kiyoshi; Tsubaki, Noritatsu [Department of Material System and Life Science, School of Engineering, Toyama University, Gofuku 3190, Toyama 930-8555 (Japan)

    2004-11-15

    A simple preparation method of bimodal pore supports was developed by introducing SiO{sub 2} or ZrO{sub 2} sols into large pores of SiO{sub 2} gel pellets directly. The pores of the obtained bimodal pore supports distributed distinctly as two kinds of main pores. On the other hand, the increased BET surface area and decreased pore volume, compared to those of original silica gel, indicated that the obtained bimodal pore supports formed according to the designed route. The obtained bimodal pore supports were applied in liquid-phase Fischer-Tropsch synthesis (FTS) where cobalt was supported. The bimodal pore catalysts presented the best reaction performance in liquid-phase Fischer-Tropsch synthesis (FTS) as higher reaction rate and lower methane selectivities, because the spatial promotional effect of bimodal pore structure and chemical effect of the porous zirconia behaved inside the large pores of original silica gel.

  13. 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

    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......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...... coefficient was empirically determined for chloride and sodium through the application of an electric DC field across the bricks. The lowest effective diffusion coefficient was found for the dark colored brick, increasing for the medium and bright colored respectively. This finding suggests that in clay...

  14. 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.

  15. 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.

  16. Pore fluid pressure and the seismic cycle

    Science.gov (United States)

    French, M. E.; Zhu, W.; Hirth, G.; Belzer, B.

    2017-12-01

    In the brittle crust, the critical shear stress required for fault slip decreases with increasing pore fluid pressures according to the effective stress criterion. As a result, higher pore fluid pressures are thought to promote fault slip and seismogenesis, consistent with observations that increasing fluid pressure as a result of wastewater injection is correlated with increased seismicity. On the other hand, elevated pore fluid pressure is also proposed to promote slow stable failure rather than seismicity along some fault zones, including during slow slip in subduction zones. Here we review recent experimental evidence for the roles that pore fluid pressure and the effective stress play in controlling fault slip behavior. Using two sets of experiments on serpentine fault gouge, we show that increasing fluid pressure does decrease the shear stress for reactivation under brittle conditions. However, under semi-brittle conditions as expected near the base of the seismogenic zone, high pore fluid pressures are much less effective at reducing the shear stress of reactivation even though deformation is localized and frictional. We use an additional study on serpentinite to show that cohesive fault rocks, potentially the product of healing and cementation, experience an increase in fracture energy during faulting as fluid pressures approach lithostatic, which can lead to more stable failure. Structural observations show that the increased fracture energy is associated with a greater intensity of transgranular fracturing and delocalization of deformation. Experiments on several lithologies indicate that the stabilizing effect of fluid pressure occurs independent of rock composition and hydraulic properties. Thus, high pore fluid pressures have the potential to either enhance seismicity or promote stable faulting depending on pressure, temperature, and fluid pressure conditions. Together, the results of these studies indicate that pore fluid pressure promotes

  17. Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment.

    Science.gov (United States)

    Loo, Jason S E; Emtage, Abigail L; Ng, Kar Weng; Yong, Alene S J; Doughty, Stephen W

    2018-03-01

    GPCR crystal structures have become more readily accessible in recent years. However, homology models of GPCRs continue to play an important role as many GPCR structures remain unsolved. The new crystal structures now available provide not only additional templates for homology modelling but also the opportunity to assess the performance of homology models against their respective crystal structures and gain insight into the performance of such models. In this study we have constructed homology models from templates of various transmembrane sequence identities for eight GPCR targets to better understand the relationship between transmembrane sequence identity and model quality. Model quality was assessed relative to the crystal structure in terms of structural accuracy as well as performance in two typical structure-based drug design applications: ligand binding pose prediction and docking enrichment in virtual screening. Crystal structures significantly outperformed homology models in both assessments. Accurate ligand binding pose prediction was possible but difficult to achieve using homology models, even with the use of induced fit docking. In virtual screening using homology models still conferred significant enrichment compared to random selection, with a clear benefit also observed in using models optimized through induced fit docking. Our results indicate that while homology models that are reasonably accurate structurally can be constructed, without significant refinement homology models will be outperformed by crystal structures in ligand binding pose prediction and docking enrichment regardless of the template used, primarily due to the extremely high level of structural accuracy needed for such applications. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Pore Structure Characterization of Indiana Limestone and Pink Dolomite from Pore Network Reconstructions

    Directory of Open Access Journals (Sweden)

    Freire-Gormaly Marina

    2016-05-01

    Full Text Available Carbon sequestration in deep underground saline aquifers holds significant promise for reducing atmospheric carbon dioxide emissions (CO2. However, challenges remain in predicting the long term migration of injected CO2. Addressing these challenges requires an understanding of pore-scale transport of CO2 within existing brine-filled geological reservoirs. Studies on the transport of fluids through geological porous media have predominantly focused on oil-bearing formations such as sandstone. However, few studies have considered pore-scale transport within limestone and other carbonate formations, which are found in potential storage sites. In this work, high-resolution micro-Computed Tomography (microCT was used to obtain pore-scale structural information of two model carbonates: Indiana Limestone and Pink Dolomite. A modified watershed algorithm was applied to extract pore network from the reconstructed microCT volumetric images of rock samples and compile a list of pore-scale characteristics from the extracted networks. These include statistical distributions of pore size and radius, pore-pore separation, throat radius, and network coordination. Finally, invasion percolation algorithms were applied to determine saturation-pressure curves for the rock samples. The statistical distributions were comparable to literature values for the Indiana Limestone. This served as validation for the network extraction approach for Pink Dolomite, which has not been considered previously. Based on the connectivity and the pore-pore separation, formations such as Pink Dolomite may present suitable storage sites for carbon storage. The pore structural distributions and saturation curves obtained in this study can be used to inform core- and reservoir-scale modeling and experimental studies of sequestration feasibility.

  19. Modeling branching pore structures in membrane filters

    Science.gov (United States)

    Sanaei, Pejman; Cummings, Linda J.

    2016-11-01

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

  20. Modeling Tissue Growth Within Nonwoven Scaffolds Pores

    Science.gov (United States)

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

    2011-01-01

    In this study we present a novel approach for predicting tissue growth within the pores of fibrous tissue engineering scaffolds. Thin nonwoven polyethylene terephthalate scaffolds were prepared to characterize tissue growth within scaffold pores, by mouse NR6 fibroblast cells. On the basis of measurements of tissue lengths at fiber crossovers and along fiber segments, mathematical models were determined during the proliferative phase of cell growth. Tissue growth at fiber crossovers decreased with increasing interfiber angle, with exponential relationships determined on day 6 and 10 of culture. Analysis of tissue growth along fiber segments determined two growth profiles, one with enhanced growth as a result of increased tissue lengths near the fiber crossover, achieved in the latter stage of culture. Derived mathematical models were used in the development of a software program to visualize predicted tissue growth within a pore. This study identifies key pore parameters that contribute toward tissue growth, and suggests models for predicting this growth, based on fibroblast cells. Such models may be used in aiding scaffold design, for optimum pore infiltration during the tissue engineering process. PMID:20687775

  1. Transmembrane TNF-α is sufficient for articular inflammation and hypernociception in a mouse model of gout.

    Science.gov (United States)

    Amaral, Flávio A; Bastos, Leandro F S; Oliveira, Thiago H C; Dias, Ana C F; Oliveira, Vívian L S; Tavares, Lívia D; Costa, Vivian V; Galvão, Izabela; Soriani, Frederico M; Szymkowski, David E; Ryffel, Bernhard; Souza, Danielle G; Teixeira, Mauro M

    2016-01-01

    Gout manifests as recurrent episodes of acute joint inflammation and pain due to the deposition of monosodium urate (MSU) crystals within the affected tissue in a process dependent on NLRP3 inflammasome activation. The synthesis, activation, and release of IL-1β are crucial for MSU-induced inflammation. The current study evaluated the mechanism by which TNF-α contributed to MSU-induced inflammation. Male C57BL/6J or transgenic mice were used in this study and inflammation was induced by the injection of MSU crystals into the joint. TNF-α was markedly increased in the joint after the injection of MSU. There was inhibition in the infiltration of neutrophils, production of CXCL1 and IL-1β, and decreased hypernociception in mice deficient for TNF-α or its receptors. Pharmacological blockade of TNF-α with Etanercept or pentoxyfylline produced similar results. Mechanistically, TNF-α blockade resulted in lower amounts of IL-1β protein and pro-IL-1β mRNA transcripts in joints. Gene-modified mice that express only transmembrane TNF-α had an inflammatory response similar to that of WT mice and blockade of soluble TNF-α (XPro™1595) did not decrease MSU-induced inflammation. In conclusion, TNF-α drives expression of pro-IL-1β mRNA and IL-1β protein in experimental gout and that its transmembrane form is sufficient to trigger MSU-induced inflammation in mice. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. An improved and robust DNA immunization method to develop antibodies against extra-cellular loops of multi-transmembrane proteins

    Science.gov (United States)

    Hazen, Meredith; Bhakta, Sunil; Vij, Rajesh; Randle, Steven; Kallop, Dara; Chiang, Vicki; Hötzel, Isidro; Jaiswal, Bijay S; Ervin, Karen E; Li, Bing; Weimer, Robby M; Polakis, Paul; Scheller, Richard H; Junutula, Jagath R; Hongo, Jo-Anne S

    2014-01-01

    Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry. As expected, the use of the immune modulators fetal liver tyrosine kinase 3 ligand (Flt3L) and granulocyte-macrophage colony-stimulating factor positively enhanced the immune response against MRP4. Imaging studies using CMV-based plasmids expressing luciferase showed that the in vivo half-life of the target antigen was less than 48 h using CMV-based plasmids, thus necessitating frequent boosting with DNA to achieve an adequate immune response. We also describe a comparison of plasmids, which contained MRP4 cDNA with either the CMV or CAG promoters, used for immunizations. The observed luciferase activity in this comparison demonstrated that the CAG promoter-containing plasmid pCAGGS induced prolonged constitutive expression of MRP4 and an increased anti-MRP4 specific immune response even when the plasmid was injected less frequently. The method described here is one that can be broadly applicable as a general immunization strategy to develop antibodies against multi-transmembrane proteins, as well as target antigens that are difficult to express or purify in native and functionally active conformation. PMID:24121517

  3. 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

  4. Unplugging the callose plug from sieve pores.

    Science.gov (United States)

    Xie, Bo; Hong, Zonglie

    2011-04-01

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

  5. Pore-forming toxins in Cnidaria.

    Science.gov (United States)

    Podobnik, Marjetka; Anderluh, Gregor

    2017-12-01

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

  6. 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.

  7. A new way to parameterize hydraulic conductances of pore elements: A step towards creating pore-networks without pore shape simplifications

    Science.gov (United States)

    Miao, Xiuxiu; Gerke, Kirill M.; Sizonenko, Timofey O.

    2017-07-01

    Pore-network models were found useful in describing important flow and transport mechanisms and in predicting flow properties of different porous media relevant to numerous fundamental and industrial applications. Pore-networks provide very fast computational framework and permit simulations on large volumes of pores. This is possible due to significant pore space simplifications and linear/exponential relationships between effective properties and geometrical characteristics of the pore elements. To make such relationships work, pore-network elements are usually simplified by circular, triangular, square and other basic shapes. However, such assumptions result in inaccurate prediction of transport properties. In this paper, we propose that pore-networks can be constructed without pore shape simplifications. To test this hypothesize we extracted 3292 2D pore element cross-sections from 3D X-ray microtomography images of sandstone and carbonate rock samples. Based on the circularity, convexity and elongation of each pore element we trained neural networks to predict the dimensionless hydraulic conductance. The optimal neural network provides 90% of predictions lying within the 20% error bounds compared against direct numerical simulation results. Our novel approach opens a new way to parameterize pore-networks and we outlined future improvements to create a new class of pore-network models without pore shape simplifications.

  8. 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

  9. 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.

  10. A Novel Type III Endosome Transmembrane Protein, TEMP

    Directory of Open Access Journals (Sweden)

    Rohan D. Teasdale

    2012-11-01

    Full Text Available As part of a high-throughput subcellular localisation project, the protein encoded by the RIKEN mouse cDNA 2610528J11 was expressed and identified to be associated with both endosomes and the plasma membrane. Based on this, we have assigned the name TEMP for Type III Endosome Membrane Protein. TEMP encodes a short protein of 111 amino acids with a single, alpha-helical transmembrane domain. Experimental analysis of its membrane topology demonstrated it is a Type III membrane protein with the amino-terminus in the lumenal, or extracellular region, and the carboxy-terminus in the cytoplasm. In addition to the plasma membrane TEMP was localized to Rab5 positive early endosomes, Rab5/Rab11 positive recycling endosomes but not Rab7 positive late endosomes. Video microscopy in living cells confirmed TEMP's plasma membrane localization and identified the intracellular endosome compartments to be tubulovesicular. Overexpression of TEMP resulted in the early/recycling endosomes clustering at the cell periphery that was dependent on the presence of intact microtubules. The cellular function of TEMP cannot be inferred based on bioinformatics comparison, but its cellular distribution between early/recycling endosomes and the plasma membrane suggests a role in membrane transport.

  11. MemBrain: improving the accuracy of predicting transmembrane helices.

    Directory of Open Access Journals (Sweden)

    Hongbin Shen

    Full Text Available Prediction of transmembrane helices (TMH in alpha helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/.

  12. 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

  13. Transmembrane channel-like (tmc) gene regulates Drosophila larval locomotion.

    Science.gov (United States)

    Guo, Yanmeng; Wang, Yuping; Zhang, Wei; Meltzer, Shan; Zanini, Damiano; Yu, Yue; Li, Jiefu; Cheng, Tong; Guo, Zhenhao; Wang, Qingxiu; Jacobs, Julie S; Sharma, Yashoda; Eberl, Daniel F; Göpfert, Martin C; Jan, Lily Yeh; Jan, Yuh Nung; Wang, Zuoren

    2016-06-28

    Drosophila larval locomotion, which entails rhythmic body contractions, is controlled by sensory feedback from proprioceptors. The molecular mechanisms mediating this feedback are little understood. By using genetic knock-in and immunostaining, we found that the Drosophila melanogaster transmembrane channel-like (tmc) gene is expressed in the larval class I and class II dendritic arborization (da) neurons and bipolar dendrite (bd) neurons, both of which are known to provide sensory feedback for larval locomotion. Larvae with knockdown or loss of tmc function displayed reduced crawling speeds, increased head cast frequencies, and enhanced backward locomotion. Expressing Drosophila TMC or mammalian TMC1 and/or TMC2 in the tmc-positive neurons rescued these mutant phenotypes. Bending of the larval body activated the tmc-positive neurons, and in tmc mutants this bending response was impaired. This implicates TMC's roles in Drosophila proprioception and the sensory control of larval locomotion. It also provides evidence for a functional conservation between Drosophila and mammalian TMCs.

  14. Pore-scale modeling of pore structure effects on P-wave scattering attenuation in dry rocks.

    Science.gov (United States)

    Wang, Zizhen; Wang, Ruihe; Li, Tianyang; Qiu, Hao; Wang, Feifei

    2015-01-01

    Underground rocks usually have complex pore system with a variety of pore types and a wide range of pore size. The effects of pore structure on elastic wave attenuation cannot be neglected. We investigated the pore structure effects on P-wave scattering attenuation in dry rocks by pore-scale modeling based on the wave theory and the similarity principle. Our modeling results indicate that pore size, pore shape (such as aspect ratio), and pore density are important factors influencing P-wave scattering attenuation in porous rocks, and can explain the variation of scattering attenuation at the same porosity. From the perspective of scattering attenuation, porous rocks can safely suit to the long wavelength assumption when the ratio of wavelength to pore size is larger than 15. Under the long wavelength condition, the scattering attenuation coefficient increases as a power function as the pore density increases, and it increases exponentially with the increase in aspect ratio. For a certain porosity, rocks with smaller aspect ratio and/or larger pore size have stronger scattering attenuation. When the pore aspect ratio is larger than 0.5, the variation of scattering attenuation at the same porosity is dominantly caused by pore size and almost independent of the pore aspect ratio. These results lay a foundation for pore structure inversion from elastic wave responses in porous rocks.

  15. Tryptophan Scanning Reveals Dense Packing of Connexin Transmembrane Domains in Gap Junction Channels Composed of Connexin32*

    Science.gov (United States)

    Brennan, Matthew J.; Karcz, Jennifer; Vaughn, Nicholas R.; Woolwine-Cunningham, Yvonne; DePriest, Adam D.; Escalona, Yerko; Perez-Acle, Tomas; Skerrett, I. Martha

    2015-01-01

    Tryptophan was substituted for residues in all four transmembrane domains of connexin32. Function was assayed using dual cell two-electrode voltage clamp after expression in Xenopus oocytes. Tryptophan substitution was poorly tolerated in all domains, with the greatest impact in TM1 and TM4. For instance, in TM1, 15 substitutions were made, six abolished coupling and five others significantly reduced function. Only TM2 and TM3 included a distinct helical face that lacked sensitivity to tryptophan substitution. Results were visualized on a comparative model of Cx32 hemichannel. In this model, a region midway through the membrane appears highly sensitive to tryptophan substitution and includes residues Arg-32, Ile-33, Met-34, and Val-35. In the modeled channel, pore-facing regions of TM1 and TM2 were highly sensitive to tryptophan substitution, whereas the lipid-facing regions of TM3 and TM4 were variably tolerant. Residues facing a putative intracellular water pocket (the IC pocket) were also highly sensitive to tryptophan substitution. Although future studies will be required to separate trafficking-defective mutants from those that alter channel function, a subset of interactions important for voltage gating was identified. Interactions important for voltage gating occurred mainly in the mid-region of the channel and focused on TM1. To determine whether results could be extrapolated to other connexins, TM1 of Cx43 was scanned revealing similar but not identical sensitivity to TM1 of Cx32. PMID:25969535

  16. Characterization of a nuclear pore protein sheds light on the roles and composition of the Toxoplasma gondii nuclear pore complex.

    Science.gov (United States)

    Courjol, Flavie; Mouveaux, Thomas; Lesage, Kevin; Saliou, Jean-Michel; Werkmeister, Elisabeth; Bonabaud, Maurine; Rohmer, Marine; Slomianny, Christian; Lafont, Franck; Gissot, Mathieu

    2017-06-01

    The nuclear pore is a key structure in eukaryotes regulating nuclear-cytoplasmic transport as well as a wide range of cellular processes. Here, we report the characterization of the first Toxoplasma gondii nuclear pore protein, named TgNup302, which appears to be the orthologue of the mammalian Nup98-96 protein. We produced a conditional knock-down mutant that expresses TgNup302 under the control of an inducible tetracycline-regulated promoter. Under ATc treatment, a substantial decrease of TgNup302 protein in inducible knock-down (iKD) parasites was observed, causing a delay in parasite proliferation. Moreover, the nuclear protein TgENO2 was trapped in the cytoplasm of ATc-treated mutants, suggesting that TgNup302 is involved in nuclear transport. Fluorescence in situ hybridization revealed that TgNup302 is essential for 18S RNA export from the nucleus to the cytoplasm, while global mRNA export remains unchanged. Using an affinity tag purification combined with mass spectrometry, we identified additional components of the nuclear pore complex, including proteins potentially interacting with chromatin. Furthermore, reverse immunoprecipitation confirmed their interaction with TgNup302, and structured illuminated microscopy confirmed the NPC localization of some of the TgNup302-interacting proteins. Intriguingly, facilitates chromatin transcription complex (FACT) components were identified, suggesting the existence of an NPC-chromatin interaction in T. gondii. Identification of TgNup302-interacting proteins also provides the first glimpse at the NPC structure in Apicomplexa, suggesting a structural conservation of the NPC components between distant eukaryotes.

  17. Pore-forming Activity of the Escherichia coli Type III Secretion System Protein EspD.

    Science.gov (United States)

    Chatterjee, Abhishek; Caballero-Franco, Celia; Bakker, Dannika; Totten, Stephanie; Jardim, Armando

    2015-10-16

    Enterohemorrhagic Escherichia coli is a causative agent of gastrointestinal and diarrheal diseases. Pathogenesis associated with enterohemorrhagic E. coli involves direct delivery of virulence factors from the bacteria into epithelial cell cytosol via a syringe-like organelle known as the type III secretion system. The type III secretion system protein EspD is a critical factor required for formation of a translocation pore on the host cell membrane. Here, we show that recombinant EspD spontaneously integrates into large unilamellar vesicle (LUV) lipid bilayers; however, pore formation required incorporation of anionic phospholipids such as phosphatidylserine and an acidic pH. Leakage assays performed with fluorescent dextrans confirmed that EspD formed a structure with an inner diameter of ∼2.5 nm. Protease mapping indicated that the two transmembrane helical hairpin of EspD penetrated the lipid layer positioning the N- and C-terminal domains on the extralumenal surface of LUVs. Finally, a combination of glutaraldehyde cross-linking and rate zonal centrifugation suggested that EspD in LUV membranes forms an ∼280-320-kDa oligomeric structure consisting of ∼6-7 subunits. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  18. 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

  19. 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.

  20. 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.

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

    International Nuclear Information System (INIS)

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

    2011-01-01

    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 odometer 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. (authors)

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

    Science.gov (United States)

    Smith, A Peyton; Bond-Lamberty, Ben; Benscoter, Brian W; Tfaily, Malak M; Hinkle, C 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-scale, core-scale, 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. Repositioning antimicrobial agent pentamidine as a disruptor of the lateral interactions of transmembrane domain 5 of EBV latent membrane protein 1.

    Directory of Open Access Journals (Sweden)

    Xiaohui Wang

    Full Text Available The lateral transmembrane protein-protein interactions (PPI have been regarded as "undruggable" despite their importance in many essential biological processes. The homo-trimerization of transmembrane domain 5 (TMD-5 of latent membrane protein 1 (LMP-1 is critical for the constitutive oncogenic activation of the Epstein-Barr virus (EBV. Herein we repurpose the antimicrobial agent pentamidine as a regulator of LMP-1 TMD-5 lateral interactions. The results of ToxR assay, tryptophan fluorescence assay, courmarin fluorescence dequenching assay, and Bis-Tris sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE consistently show pentamidine disrupts LMP-1 TMD-5 lateral interactions. Furthermore, pentamidine inhibits LMP-1 signaling, inducing cellular apoptosis and suppressing cell proliferation in the EBV infected B cells. In contrast, EBV negative cells are less susceptible to pentamidine. This study provides a novel non-peptide small molecule agent for regulating LMP-1 TMD-5 lateral interactions.

  4. 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

  5. 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.

  6. Double urine circulation: importance of pores.

    Science.gov (United States)

    Antonello, Augusto; D'Angelo, Angela; Nalesso, Federico; Capezzi, Maria; Malagoli, Andrea; Pastori, Giordano; Lazzarin, Roberta; Calò, Lorenzo; Bonfante, Luciana; Gambaro, Giovanni

    2003-01-01

    The authors examine a presentation to the Royal Academy of Sciences of Paris by L. Morin, French physician and meteorologist. In this communication the presence of "pores" in the stomach and the bladder, which would allow a quick elimination of the urines on the occasion of an abundant fluid intake.

  7. 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

  8. 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.

  9. Exploring codon optimization and response surface methodology to express biologically active transmembrane RANKL in E. coli.

    Science.gov (United States)

    Maharjan, Sushila; Singh, Bijay; Bok, Jin-Duck; Kim, Jeong-In; Jiang, Tao; Cho, Chong-Su; Kang, Sang-Kee; Choi, Yun-Jaie

    2014-01-01

    Receptor activator of nuclear factor (NF)-κB ligand (RANKL), a master cytokine that drives osteoclast differentiation, activation and survival, exists in both transmembrane and extracellular forms. To date, studies on physiological role of RANKL have been mainly carried out with extracellular RANKL probably due to difficulties in achieving high level expression of functional transmembrane RANKL (mRANKL). In the present study, we took advantage of codon optimization and response surface methodology to optimize the soluble expression of mRANKL in E. coli. We optimized the codon usage of mRANKL sequence to a preferred set of codons for E. coli changing its codon adaptation index from 0.64 to 0.76, tending to increase its expression level in E. coli. Further, we utilized central composite design to predict the optimum combination of variables (cell density before induction, lactose concentration, post-induction temperature and post-induction time) for the expression of mRANKL. Finally, we investigated the effects of various experimental parameters using response surface methodology. The best combination of response variables was 0.6 OD600, 7.5 mM lactose, 26°C post-induction temperature and 5 h post-induction time that produced 52.4 mg/L of fusion mRANKL. Prior to functional analysis of the protein, we purified mRANKL to homogeneity and confirmed the existence of trimeric form of mRANKL by native gel electrophoresis and gel filtration chromatography. Further, the biological activity of mRANKL to induce osteoclast formation on RAW264.7 cells was confirmed by tartrate resistant acid phosphatase assay and quantitative real-time polymerase chain reaction assays. Importantly, a new finding from this study was that the biological activity of mRANKL is higher than its extracellular counterpart. To the best of our knowledge, this is the first time to report heterologous expression of mRANKL in soluble form and to perform a comparative study of functional properties of both

  10. Exploring codon optimization and response surface methodology to express biologically active transmembrane RANKL in E. coli.

    Directory of Open Access Journals (Sweden)

    Sushila Maharjan

    Full Text Available Receptor activator of nuclear factor (NF-κB ligand (RANKL, a master cytokine that drives osteoclast differentiation, activation and survival, exists in both transmembrane and extracellular forms. To date, studies on physiological role of RANKL have been mainly carried out with extracellular RANKL probably due to difficulties in achieving high level expression of functional transmembrane RANKL (mRANKL. In the present study, we took advantage of codon optimization and response surface methodology to optimize the soluble expression of mRANKL in E. coli. We optimized the codon usage of mRANKL sequence to a preferred set of codons for E. coli changing its codon adaptation index from 0.64 to 0.76, tending to increase its expression level in E. coli. Further, we utilized central composite design to predict the optimum combination of variables (cell density before induction, lactose concentration, post-induction temperature and post-induction time for the expression of mRANKL. Finally, we investigated the effects of various experimental parameters using response surface methodology. The best combination of response variables was 0.6 OD600, 7.5 mM lactose, 26°C post-induction temperature and 5 h post-induction time that produced 52.4 mg/L of fusion mRANKL. Prior to functional analysis of the protein, we purified mRANKL to homogeneity and confirmed the existence of trimeric form of mRANKL by native gel electrophoresis and gel filtration chromatography. Further, the biological activity of mRANKL to induce osteoclast formation on RAW264.7 cells was confirmed by tartrate resistant acid phosphatase assay and quantitative real-time polymerase chain reaction assays. Importantly, a new finding from this study was that the biological activity of mRANKL is higher than its extracellular counterpart. To the best of our knowledge, this is the first time to report heterologous expression of mRANKL in soluble form and to perform a comparative study of functional

  11. Visualizing water molecules in transmembrane proteins using radiolytic labeling methods.

    Science.gov (United States)

    Orban, Tivadar; Gupta, Sayan; Palczewski, Krzysztof; Chance, Mark R

    2010-02-09

    Essential to cells and their organelles, water is both shuttled to where it is needed and trapped within cellular compartments and structures. Moreover, ordered waters within protein structures often colocalize with strategically placed polar or charged groups critical for protein function, yet it is unclear if these ordered water molecules provide structural stabilization, mediate conformational changes in signaling, neutralize charged residues, or carry out a combination of all these functions. Structures of many integral membrane proteins, including G protein-coupled receptors (GPCRs), reveal the presence of ordered water molecules that may act like prosthetic groups in a manner quite unlike bulk water. Identification of "ordered" waters within a crystalline protein structure requires sufficient occupancy of water to enable its detection in the protein's X-ray diffraction pattern, and thus, the observed waters likely represent a subset of tightly bound functional waters. In this review, we highlight recent studies that suggest the structures of ordered waters within GPCRs are as conserved (and thus as important) as conserved side chains. In addition, methods of radiolysis, coupled to structural mass spectrometry (protein footprinting), reveal dynamic changes in water structure that mediate transmembrane signaling. The idea of water as a prosthetic group mediating chemical reaction dynamics is not new in fields such as catalysis. However, the concept of water as a mediator of conformational dynamics in signaling is just emerging, because of advances in both crystallographic structure determination and new methods of protein footprinting. Although oil and water do not mix, understanding the roles of water is essential to understanding the function of membrane proteins.

  12. Temperature and Pressure from Collapsing Pores in HMX

    Science.gov (United States)

    Hardin, D. Barrett

    2017-06-01

    The thermal and mechanical response of collapsing voids in HMX is analyzed. In this work, the focus is simulating the temperature and pressure fields arising from isolated, idealized pores as they collapse in the presence of a shock. HMX slabs are numerically generated which contain a single pore, isolated from the boundaries to remove all wave reflections. In order to understand the primary pore characteristics leading to temperature rise, a series of 2D, plane strain simulations are conducted on HMX slabs containing both cylindrical and elliptical pores of constant size equal to the area of a circular pore with a 1 micron diameter. Each of these pore types is then subjected to shock pressures ranging from a weak shock that is unable to fully collapse the pore to a strong shock which overwhelms the tendency for localization. Results indicate that as shock strength increases, pore collapse phenomenology for a cylindrical pore transitions from a mode dominated by localized melt cracking to an idealized hydrodynamic pore collapse. For the case of elliptical pores, the orientation causing maximum temperature and pressure rise is found. The relative heating in elliptical pores is then quantified as a function of pore orientation and aspect ratio for a pore of a given area. Distribution A: Distribution unlimited. (96TW 2017-0036).

  13. 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 minimum unfavorable contact approach. S RAMAKRISHNA, SILADITYA PADHI and U DEVA PRIYAKUMAR*. Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India.

  14. Approaches to ab initio molecular replacement of α-helical transmembrane proteins

    OpenAIRE

    Thomas, Jens M. H.; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J.

    2017-01-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effe...

  15. Antigenic and immunosuppressive properties of a trimeric recombinant transmembrane envelope protein gp41 of HIV-1.

    Directory of Open Access Journals (Sweden)

    Michael Mühle

    Full Text Available The transmembrane envelope (TM protein gp41 of the human immunodeficiency virus-1 (HIV-1 plays an important role during virus infection inducing the fusion of the viral and cellular membranes. In addition, there are indications that the TM protein plays a role in the immunopathogenesis leading to the acquired immunodeficiency syndrome (AIDS. Inactivated virus particles and recombinant gp41 have been reported to inhibit lymphocyte proliferation, as well as to alter cytokine release and gene expression. The same was shown for a peptide corresponding to a highly conserved domain of all retroviral TM proteins, the immunosuppressive domain. Due to its propensity to aggregate and to be expressed at low levels, studies comprising authentic gp41 produced in eukaryotic cells are extremely rare. Here we describe the production of a secreted, soluble recombinant gp41 in 293 cells. The antigen was purified to homogeneity and characterised thoroughly by various biochemical and immunological methods. It was shown that the protein was glycosylated and assembled into trimers. Binding studies by ELISA and surface plasmon resonance using conformation-specific monoclonal antibodies implied a six-helix bundle conformation. The low binding of broadly neutralising antibodies (bnAb directed against the membrane proximal external region (MPER suggested that this gp41 is probably not suited as vaccine to induce such bnAb. Purified gp41 bound to monocytes and to a lesser extent to lymphocytes and triggered the production of specific cytokines when added to normal peripheral blood mononuclear cells. In addition, gp41 expressed on target cells inhibited the antigen-specific response of murine CD8+ T cells by drastically impairing their IFNγ production. To our knowledge, this is the first comprehensive analysis of a gp41 produced in eukaryotic cells including its immunosuppressive properties. Our data provide another line of evidence that gp41 might be directly involved in

  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. 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

  18. Tubular Unimolecular Transmembrane Channels: Construction Strategy and Transport Activities.

    Science.gov (United States)

    Si, Wen; Xin, Pengyang; Li, Zhan-Ting; Hou, Jun-Li

    2015-06-16

    Lipid bilayer membranes separate living cells from their environment. Membrane proteins are responsible for the processing of ion and molecular inputs and exports, sensing stimuli and signals across the bilayers, which may operate in a channel or carrier mechanism. Inspired by these wide-ranging functions of membrane proteins, chemists have made great efforts in constructing synthetic mimics in order to understand the transport mechanisms, create materials for separation, and develop therapeutic agents. Since the report of an alkylated cyclodextrin for transporting Cu(2+) and Co(2+) by Tabushi and co-workers in 1982, chemists have constructed a variety of artificial transmembrane channels by making use of either the multimolecular self-assembly or unimolecular strategy. In the context of the design of unimolecular channels, important advances have been made, including, among others, the tethering of natural gramicidin A or alamethicin and the modification of various macrocycles such as crown ethers, cyclodextrins, calixarenes, and cucurbiturils. Many of these unimolecular channels exhibit high transport ability for metal ions, particularly K(+) and Na(+). Concerning the development of artificial channels based on macrocyclic frameworks, one straightforward and efficient approach is to introduce discrete chains to reinforce their capability to insert into bilayers. Currently, this approach has found the widest applications in the systems of crown ethers and calixarenes. We envisioned that for macrocycle-based unimolecular channels, control of the arrangement of the appended chains in the upward and/or downward direction would favor the insertion of the molecular systems into bilayers, while the introduction of additional interactions among the chains would further stabilize a tubular conformation. Both factors should be helpful for the formation of new efficient channels. In this Account, we discuss our efforts in designing new unimolecular artificial channels from

  19. Transmembrane TNF-dependent uptake of anti-TNF antibodies.

    Science.gov (United States)

    Deora, Arun; Hegde, Subramanya; Lee, Jacqueline; Choi, Chee-Ho; Chang, Qing; Lee, Cheryl; Eaton, Lucia; Tang, Hua; Wang, Dongdong; Lee, David; Michalak, Mark; Tomlinson, Medha; Tao, Qingfeng; Gaur, Nidhi; Harvey, Bohdan; McLoughlin, Shaun; Labkovsky, Boris; Ghayur, Tariq

    TNF-α (TNF), a pro-inflammatory cytokine is synthesized as a 26 kDa protein, anchors in the plasma membrane as transmembrane TNF (TmTNF), and is subjected to proteolysis by the TNF-α converting enzyme (TACE) to release the 15 kDa form of soluble TNF (sTNF). TmTNF and sTNF interact with 2 distinct receptors, TNF-R1 (p55) and TNF-R2 (p75), to mediate the multiple biologic effects of TNF described to date. Several anti-TNF biologics that bind to both forms of TNF and block their interactions with the TNF receptors are now approved for the treatment of a variety of immune-mediated diseases. Several reports suggest that binding of anti-TNFs to TmTNF delivers an outside-to-inside 'reverse' signal that may also contribute to the efficacy of anti-TNFs. Some patients, however, develop anti-TNF drug antibody responses (ADA or immunogenicity). Here, we demonstrate biochemically that TmTNF is transiently expressed on the surface of lipopolysaccharide-stimulated primary human monocytes, macrophages, and monocyte-derived dendritic cells (DCs) and expression of TmTNF on the cell surface is enhanced following treatment of cells with TAPI-2, a TACE inhibitor. Importantly, binding of anti-TNFs to TmTNF on DCs results in rapid internalization of the anti-TNF/TmTNF complex first into early endosomes and then lysosomes. The internalized anti-TNF is processed and anti-TNF peptides can be eluted from the surface of DCs. Finally, tetanus toxin peptides fused to anti-TNFs are presented by DCs to initiate T cell recall proliferation response. Collectively, these observations may provide new insights into understanding the biology of TmTNF, mode of action of anti-TNFs, biology of ADA response to anti-TNFs, and may help with the design of the next generation of anti-TNFs.

  20. Influence of pore shape on the structure of a nanoconfined Gay-Berne liquid crystal

    Science.gov (United States)

    Ji, Qing; Lefort, Ronan; Morineau, Denis

    2009-08-01

    We present results from molecular dynamics simulations of a Gay-Berne mesogenic system GB(4.4,20,1,1) under short scale spatial confinement in a slab, a cylinder and a sphere geometry. The structure adopted by the confined phases is characterized by the density profile and the orientational order parameter as a function of temperature, and compared to the bulk. Though confinement always induces a strong surface ordering, the topological constrain introduced by the different pore shapes results in different molecular arrangements. This first study on pore shape effect on the structure of a nanoconfined Gay-Berne system is relevant to numerous experimental studies performed with different mesoporous matrices.

  1. 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

  2. Attenuation of Phosphorylation-dependent Activation of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) by Disease-causing Mutations at the Transmission Interface.

    Science.gov (United States)

    Chin, Stephanie; Yang, Donghe; Miles, Andrew J; Eckford, Paul D W; Molinski, Steven; Wallace, B A; Bear, Christine E

    2017-02-03

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein that functions as a phosphorylation-regulated anion channel. The interface between its two cytosolic nucleotide binding domains and coupling helices conferred by intracellular loops extending from the channel pore domains has been referred to as a transmission interface and is thought to be critical for the regulated channel activity of CFTR. Phosphorylation of the regulatory domain of CFTR by protein kinase A (PKA) is required for its channel activity. However, it was unclear if phosphorylation modifies the transmission interface. Here, we studied purified full-length CFTR protein using spectroscopic techniques to determine the consequences of PKA-mediated phosphorylation. Synchrotron radiation circular dichroism spectroscopy confirmed that purified full-length wild-type CFTR is folded and structurally responsive to phosphorylation. Intrinsic tryptophan fluorescence studies of CFTR showed that phosphorylation reduced iodide-mediated quenching, consistent with an effect of phosphorylation in burying tryptophans at the transmission interface. Importantly, the rate of phosphorylation-dependent channel activation was compromised by the introduction of disease-causing mutations in either of the two coupling helices predicted to interact with nucleotide binding domain 1 at the interface. Together, these results suggest that phosphorylation modifies the interface between the catalytic and pore domains of CFTR and that this modification facilitates CFTR channel activation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Coupling root architecture and pore network modeling - an attempt towards better understanding root-soil interactions

    Science.gov (United States)

    Leitner, Daniel; Bodner, Gernot; Raoof, Amir

    2013-04-01

    , but also improve the description of the rooting environment. Until now there have been no attempts to couple root architecture and pore network models. In our work we present a first attempt to join both types of models using the root architecture model of Leitner et al., (2010) and a pore network model presented by Raoof et al. (2010). The two main objectives of coupling both models are: (i) Representing the effect of root induced biopores on flow and transport processes: For this purpose a fixed root architecture created by the root model is superimposed as a secondary root induced pore network to the primary soil network, thus influencing the final pore topology in the network generation. (ii) Representing the influence of pre-existing pores on root branching: Using a given network of (rigid) pores, the root architecture model allocates its root axes into these preexisting pores as preferential growth paths with thereby shape the final root architecture. The main objective of our study is to reveal the potential of using a pore scale description of the plant growth medium for an improved representation of interaction processes at the interface of root and soil. References Raoof, A., Hassanizadeh, S.M. 2010. A New Method for Generating Pore-Network Models. Transp. Porous Med. 81, 391-407. Leitner, D, Klepsch, S., Bodner, G., Schnepf, S. 2010. A dynamic root system growth model based on L-Systems. Tropisms and coupling to nutrient uptake from soil. Plant Soil 332, 177-192.

  4. Pore-Scale Model for Microbial Growth

    Science.gov (United States)

    Tartakovsky, G.; Tartakovsky, A. M.; Scheibe, T. D.

    2011-12-01

    A lagrangian particle model based on smoothed particle hydrodynamics (SPH) is used to simulate pore-scale flow, reactive transport and biomass growth which is controlled by the mixing of an electron donor and acceptor, in a microfluidic porous cell. The experimental results described in Ch. Zhang et al "Effects of pore-scale heterogeneity and transverse mixing on bacterial growth in porous media" were used for this study. The model represents the homogeneous pore structure of a uniform array of cylindrical posts with microbes uniformly distributed on the grain surfaces. Each one of the two solutes (electron donor and electron acceptor) enters the domain unmixed through separate inlets. In the model, pair-wise particle-particle interactions are used to simulate interactions within the biomass, and both biomass-fluid and biomass-soil grain interactions. The biomass growth rate is described by double Monod kinetics. For the set of parameters used in the simulations the model predicts that: 1) biomass grows in the shape of bridges connecting soil grains and oriented in the direction of flow so as to minimize resistance to the fluid flow; and 2) the biomass growth occurs only in the mixing zone. Using parameters available in the literature, the biomass growth model agrees qualitatively with the experimental results. In order to achieve quantitative agreement, model calibration is required.

  5. 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...... and action of chemokines obtained through deletion of 22 amino acids from the N-terminal extension; an ORF74 with high constitutive activity but with selective elimination of stimulatory regulation by angiogenic chemokines obtained through substitution of basic residues at the extracellular ends of TM......-V or TM-VI; and an ORF74 lacking constitutive activity but with preserved ability to be stimulated by agonist chemokines obtained through introduction of an Asp residue on the hydrophobic, presumed membrane-exposed face of TM-II. It is concluded that careful molecular dissection can selectively eliminate...

  6. Real-Time Pore Pressure Detection: Indicators and Improved Methods

    OpenAIRE

    Jincai Zhang; Shangxian Yin

    2017-01-01

    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 connecti...

  7. 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

  8. NMR-based approach to measure the free energy of transmembrane helix-helix interactions.

    Science.gov (United States)

    Mineev, Konstantin S; Lesovoy, Dmitry M; Usmanova, Dinara R; Goncharuk, Sergey A; Shulepko, Mikhail A; Lyukmanova, Ekaterina N; Kirpichnikov, Mikhail P; Bocharov, Eduard V; Arseniev, Alexander S

    2014-01-01

    Knowledge of the energetic parameters of transmembrane helix-helix interactions is necessary for the establishment of a structure-energy relationship for α-helical membrane domains. A number of techniques have been developed to measure the free energies of dimerization and oligomerization of transmembrane α-helices, and all of these have their advantages and drawbacks. In this study we propose a methodology to determine the magnitudes of the free energy of interactions between transmembrane helices in detergent micelles. The suggested approach employs solution nuclear magnetic resonance (NMR) spectroscopy to determine the population of the oligomeric states of the transmembrane domains and introduces a new formalism to describe the oligomerization equilibrium, which is based on the assumption that both the dimerization of the transmembrane domains and the dissociation of the dimer can occur only upon the collision of detergent micelles. The technique has three major advantages compared with other existing approaches: it may be used to analyze both weak and relatively strong dimerization/oligomerization processes, it works well for the analysis of complex equilibria, e.g. when monomer, dimer and high-order oligomer populations are simultaneously present in the solution, and it can simultaneously yield both structural and energetic characteristics of the helix-helix interaction under study. The proposed methodology was applied to investigate the oligomerization process of transmembrane domains of fibroblast growth factor receptor 3 (FGFR3) and vascular endothelium growth factor receptor 2 (VEGFR2), and allowed the measurement of the free energy of dimerization of both of these objects. In addition the proposed method was able to describe the multi-state oligomerization process of the VEGFR2 transmembrane domain. © 2013 Elsevier B.V. All rights reserved.

  9. 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

  10. 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...

  11. 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...

  12. Coupling of voltage sensors to the channel pore: a comparative view

    Directory of Open Access Journals (Sweden)

    Vitya eVardanyan

    2012-07-01

    Full Text Available The activation of voltage-dependent ion channels is initiated by potential-induced conformational rearrangements in the voltage-sensor domains that propagates to the pore domain and finally opens the ion conduction pathway. In potassium channels voltage-sensors are covalently linked to the pore via S4-S5 linkers at the cytoplasmic site of the pore domain. Transformation of membrane electric energy into the mechanical work required for the opening or closing of the channel pore is achieved through an electromechanical coupling mechanism, which involves local interaction between residues in S4-S5 linker and pore-forming alpha helices.In this review we discuss present knowledge and open questions related to the electromechanical coupling mechanism in most intensively studied voltage-gated Shaker potassium channel and compare structure-functional aspects of coupling with those observed in distantly-related ion channels. We focus particularly on the role of electromechanical coupling in modulation of the constitutive conductance of ion channels.

  13. Synthesis of anatase mesoporous by using cyclodextrin as a pore forming template via hydrothermal treatment

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Joo Hee; An, So Young; Jang, Soe Hyun; Lee, Jun Woo; Chung, Jae Woo [Dept. of Organic Materials and Fiber Engineering, Soongsil University, Seoul (Korea, Republic of)

    2015-06-15

    Porous titanium dioxide with an average pore diameter of several nanometers and a narrow pore size distribution was prepared by using cyclodextrin (CD) in a sol–gel reaction of titanium precursor. After the reaction, a hydrothermal treatment was performed, and a WAXD analysis shows that the hydrothermal treatment successfully induces an anatase crystalline structure in TiO{sub 2} . The combined results from TGA, FT-IR, N{sub 2} adsorption–desorption isotherm, TEM, and SEM analyses show that the CD act as a pore forming template to form TiO{sub 2} with a wormhole-type pore and a large specific surface area. Furthermore, the ratio of the CD/Ti precursor affects the porosity and the morphology of the mesoporous TiO{sub 2} . In contrast, TiO{sub 2} prepared without CD does not exhibit a porous structure. The formation of these porous structures is a result of the self-assembly of Ti species around the CD molecules, TiO{sub 2} growth, and pore-forming by the removal of CD.

  14. 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

  15. Pore Pressure and Stress Distributions Around a Hydraulic Fracture in Heterogeneous Rock

    Science.gov (United States)

    Gao, Qian; Ghassemi, Ahmad

    2017-12-01

    One of the most significant characteristics of unconventional petroleum bearing formations is their heterogeneity, which affects the stress distribution, hydraulic fracture propagation and also fluid flow. This study focuses on the stress and pore pressure redistributions during hydraulic stimulation in a heterogeneous poroelastic rock. Lognormal random distributions of Young's modulus and permeability are generated to simulate the heterogeneous distributions of material properties. A 3D fully coupled poroelastic model based on the finite element method is presented utilizing a displacement-pressure formulation. In order to verify the model, numerical results are compared with analytical solutions showing excellent agreements. The effects of heterogeneities on stress and pore pressure distributions around a penny-shaped fracture in poroelastic rock are then analyzed. Results indicate that the stress and pore pressure distributions are more complex in a heterogeneous reservoir than in a homogeneous one. The spatial extent of stress reorientation during hydraulic stimulations is a function of time and is continuously changing due to the diffusion of pore pressure in the heterogeneous system. In contrast to the stress distributions in homogeneous media, irregular distributions of stresses and pore pressure are observed. Due to the change of material properties, shear stresses and nonuniform deformations are generated. The induced shear stresses in heterogeneous rock cause the initial horizontal principal stresses to rotate out of horizontal planes.

  16. Capillary pressure in a porous medium with distinct pore surface and pore volume fractal dimensions.

    Science.gov (United States)

    Deinert, M R; Dathe, A; Parlange, J-Y; Cady, K B

    2008-02-01

    The relationship between capillary pressure and saturation in a porous medium often exhibits a power-law dependence. The physical basis for this relation has been substantiated by assuming that capillary pressure is directly related to the pore radius. When the pore space of a medium exhibits fractal structure this approach results in a power-law relation with an exponent of 3-D(v), where D(v) is the pore volume fractal dimension. However, larger values of the exponent than are realistically allowed by this result have long been known to occur. Using a thermodynamic formulation for equilibrium capillary pressure we show that the standard result is a special case of the more general exponent (3-D(v))(3-D(s)) where D(s) is the surface fractal dimension of the pores. The analysis reduces to the standard result when D(s)=2, indicating a Euclidean relationship between a pore's surface area and the volume it encloses, and allows for a larger value for the exponent than the standard result when D(s)>2 .

  17. HMMpTM: improving transmembrane protein topology prediction using phosphorylation and glycosylation site prediction.

    Science.gov (United States)

    Tsaousis, Georgios N; Bagos, Pantelis G; Hamodrakas, Stavros J

    2014-02-01

    During the last two decades a large number of computational methods have been developed for predicting transmembrane protein topology. Current predictors rely on topogenic signals in the protein sequence, such as the distribution of positively charged residues in extra-membrane loops and the existence of N-terminal signals. However, phosphorylation and glycosylation are post-translational modifications (PTMs) that occur in a compartment-specific manner and therefore the presence of a phosphorylation or glycosylation site in a transmembrane protein provides topological information. We examine the combination of phosphorylation and glycosylation site prediction with transmembrane protein topology prediction. We report the development of a Hidden Markov Model based method, capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites along the protein sequence. Our method integrates a novel feature in transmembrane protein topology prediction, which results in improved performance for topology prediction and reliable prediction of phosphorylation and glycosylation sites. The method is freely available at http://bioinformatics.biol.uoa.gr/HMMpTM. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Expression of Trans-Membrane Proteins in vitro Using a Cell Free System

    Science.gov (United States)

    Weisse, Natalie; Noireaux, Vincent; Chalmeau, Jerome

    2010-10-01

    Trans-membrane proteins represent a significant portion of the proteins expressed by cells. The expression of proteins in vitro, however, remains a challenge. Numerous expression approaches have been developed with cell free expression (CFE) being one of the most promising. CFE is based on a transcription-translation system that has been extracted from E. coli bacteria. Adding the desired DNA allows expression of a selected protein, and in the presence of phospholipids the expression of trans-membrane proteins becomes possible. In order to express trans-membrane proteins in a closed native environment, the cell free system (CFS) is encapsulated with a phospholipid bilayer, creating an artificial cell. To verify protein expression, AquaporinZ (AqpZ), a well-known trans-membrane protein tagged with a green fluorescent protein (eGFP), was used so the expressed proteins could be seen under a fluorescent microscope. These artificial cells will serve as an experimental platform for testing the viability of the expressed trans-membrane proteins. Results from the manipulation of these artificial cells by attaching them to the slide surface through streptavidin-biotin bonding will be presented.

  19. Transmembrane domain quality control systems operate at the endoplasmic reticulum and Golgi apparatus.

    Science.gov (United States)

    Briant, Kit; Johnson, Nicholas; Swanton, Eileithyia

    2017-01-01

    Multiple protein quality control systems operate to ensure that misfolded proteins are efficiently cleared from the cell. While quality control systems that assess the folding status of soluble domains have been extensively studied, transmembrane domain (TMD) quality control mechanisms are poorly understood. Here, we have used chimeras based on the type I plasma membrane protein CD8 in which the endogenous TMD was substituted with transmembrane sequences derived from different polytopic membrane proteins as a mode to investigate the quality control of unassembled TMDs along the secretory pathway. We find that the three TMDs examined prevent trafficking of CD8 to the cell surface via potentially distinct mechanisms. CD8 containing two distinct non-native transmembrane sequences escape the ER and are subsequently retrieved from the Golgi, possibly via Rer1, leading to ER localisation at steady state. A third chimera, containing an altered transmembrane domain, was predominantly localised to the Golgi at steady state, indicating the existence of an additional quality control checkpoint that identifies non-native transmembrane domains that have escaped ER retention and retrieval. Preliminary experiments indicate that protein retained by quality control mechanisms at the Golgi are targeted to lysosomes for degradation.

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

    Science.gov (United States)

    Sukumwang, Neelanun; Umezawa, Kazuo

    2013-01-01

    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. PMID:23965430

  1. 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.

  2. Expression of transmembrane protein 26 (TMEM26) in breast cancer and its association with drug response

    Science.gov (United States)

    Nass, Norbert; Dittmer, Angela; Hellwig, Vicky; Lange, Theresia; Beyer, Johanna Mirjam; Leyh, Benjamin; Ignatov, Atanas; Weiβenborn, Christine; Kirkegaard, Tove; Lykkesfeldt, Anne E.; Kalinski, Thomas; Dittmer, Jürgen

    2016-01-01

    We have previously shown that stromal cells desensitize breast cancer cells to the anti-estrogen fulvestrant and, along with it, downregulate the expression of TMEM26 (transmembrane protein 26). In an effort to study the function and regulation of TMEM26 in breast cancer cells, we found that breast cancer cells express non-glycosylated and N-glycosylated isoforms of the TMEM26 protein and demonstrate that N-glycosylation is important for its retention at the plasma membrane. Fulvestrant induced significant changes in expression and in the N-glycosylation status of TMEM26. In primary breast cancer, TMEM26 protein expression was higher in ERα (estrogen receptor α)/PR (progesterone receptor)-positive cancers. These data suggest that ERα is a major regulator of TMEM26. Significant changes in TMEM26 expression and N-glycosylation were also found, when MCF-7 and T47D cells acquired fulvestrant resistance. Furthermore, patients who received aromatase inhibitor treatment tend to have a higher risk of recurrence when tumoral TMEM26 protein expression is low. In addition, TMEM26 negatively regulates the expression of integrin β1, an important factor involved in endocrine resistance. Data obtained by spheroid formation assays confirmed that TMEM26 and integrin β1 can have opposite effects in breast cancer cells. These data are consistent with the hypothesis that, in ERα-positive breast cancer, TMEM26 may function as a tumor suppressor by impeding the acquisition of endocrine resistance. In contrast, in ERα-negative breast cancer, particularly triple-negative cancer, high TMEM26 expression was found to be associated with a higher risk of recurrence. This implies that TMEM26 has different functions in ERα-positive and -negative breast cancer. PMID:27224909

  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. 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

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

    Science.gov (United States)

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

    2013-02-01

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

  6. Quantifying similarity of pore-geometry in nanoporous materials

    Science.gov (United States)

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

    2017-05-01

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

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

    DEFF Research Database (Denmark)

    Katika, Konstantina

    the mechanical or physical properties of the rock during waterflooding experiments. The phenomena include decreased pore stiffness and subsequent compaction and can be related to a variety of parameters; including precipitation and dissolution reactions, as well as adsorption reactions and changes in wettability...... to understand the potential mechanisms behind the action of ions in high concentration on the chalk surface; such as precipitation and dissolution. The effect of the divalent ions on the elasticity and pore collapse of this rock was observed and validated from the ultrasonic velocity data. Low field NMR...

  8. 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...

  9. 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

  10. 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.

  11. 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.

  12. Transmembrane topology of FRO2, a ferric chelate reductase from Arabidopsis thaliana.

    Science.gov (United States)

    Schagerlöf, Ulrika; Wilson, Greer; Hebert, Hans; Al-Karadaghi, Salam; Hägerhäll, Cecilia

    2006-09-01

    Iron uptake in Arabidopsis thaliana is mediated by ferric chelate reductase FRO2, a transmembrane protein belonging to the flavocytochrome b family. There is no high resolution structural information available for any member of this family. We have determined the transmembrane topology of FRO2 experimentally using the alkaline phosphatase fusion method. The resulting topology is different from that obtained by theoretical predictions and contains 8 transmembrane helices, 4 of which build up the highly conserved core of the protein. This core is present in the entire flavocytochrome b family. The large water soluble domain of FRO2, which contains NADPH, FAD and oxidoreductase sequence motifs, was located on the inside of the membrane.

  13. Photosensitized electron transport across lipid vesicle walls: Enhancement of quantum yield by ionophores and transmembrane potentials

    Science.gov (United States)

    Laane, Colja; Ford, William E.; Otvos, John W.; Calvin, Melvin

    1981-01-01

    The photosensitized reduction of heptylviologen in the bulk aqueous phase of phosphatidylcholine vesicles containing EDTA inside and a membrane-bound tris(2,2′-bipyridine)ruthenium(2+) derivative is enhanced by a factor of 6.5 by the addition of valinomycin in the presence of K+. A 3-fold stimulation by gramicidin and carbonyl cyanide m-chlorophenylhydrazone is observed. The results suggest that, under these conditions, the rate of photoinduced electron transfer across vesicle walls in the absence of ion carriers is limited by cotransport of cations. The rate of electron transfer across vesicle walls could be influenced further by generating transmembrane potentials with K+ gradients in the presence of valinomycin. When vesicles are made with transmembrane potentials, interior more negative, the quantum yield of heptylviologen reduction is doubled, and, conversely, when vesicles are made with transmembrane potentials, interior more positive, the quantum yield is decreased and approaches the value found in the absence of valinomycin. PMID:16593002

  14. Membrane-Pore Forming Characteristics of the Bordetella pertussis CyaA-Hemolysin Domain

    Directory of Open Access Journals (Sweden)

    Chattip Kurehong

    2015-04-01

    Full Text Available Previously, the 126-kDa Bordetella pertussis CyaA pore-forming/hemolysin (CyaA-Hly domain was shown to retain its hemolytic activity causing lysis of susceptible erythrocytes. Here, we have succeeded in producing, at large quantity and high purity, the His-tagged CyaA-Hly domain over-expressed in Escherichia coli as a soluble hemolytically-active form. Quantitative assays of hemolysis against sheep erythrocytes revealed that the purified CyaA-Hly domain could function cooperatively by forming an oligomeric pore in the target cell membrane with a Hill coefficient of ~3. When the CyaA-Hly toxin was incorporated into planar lipid bilayers (PLBs under symmetrical conditions at 1.0 M KCl, 10 mM HEPES buffer (pH 7.4, it produced a clearly resolved single channel with a maximum conductance of ~35 pS. PLB results also revealed that the CyaA-Hly induced channel was unidirectional and opened more frequently at higher negative membrane potentials. Altogether, our results first provide more insights into pore-forming characteristics of the CyaA-Hly domain as being the major pore-forming determinant of which the ability to induce such ion channels in receptor-free membranes could account for its cooperative hemolytic action on the target erythrocytes.

  15. Facile fabrication of BiVO4 nanofilms with controlled pore size and their photoelectrochemical performances

    Science.gov (United States)

    Feng, Chenchen; Jiao, Zhengbo; Li, Shaopeng; Zhang, Yan; Bi, Yingpu

    2015-12-01

    We demonstrate a facile method for the rational fabrication of pore-size controlled nanoporous BiVO4 photoanodes, and confirmed that the optimum pore-size distributions could effectively absorb visible light through light diffraction and confinement functions. Furthermore, in situ X-ray photoelectron spectroscopy (XPS) reveals more efficient photoexcited electron-hole separation than conventional particle films, induced by light confinement and rapid charge transfer in the inter-crossed worm-like structures.We demonstrate a facile method for the rational fabrication of pore-size controlled nanoporous BiVO4 photoanodes, and confirmed that the optimum pore-size distributions could effectively absorb visible light through light diffraction and confinement functions. Furthermore, in situ X-ray photoelectron spectroscopy (XPS) reveals more efficient photoexcited electron-hole separation than conventional particle films, induced by light confinement and rapid charge transfer in the inter-crossed worm-like structures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr06584d

  16. 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.

  17. Combined Effects of Surface Charge and Pore Size on Co-enhanced Permeability and Ion Selectivity through RGO-OCNT Nanofiltration Membranes.

    Science.gov (United States)

    Zhang, Haiguang; Quan, Xie; Chen, Shuo; Fan, Xinfei; Wei, Gaoliang; Yu, Hongtao

    2018-04-04

    Nanofiltration (NF) has received much attention for wastewater treatment and desalination. However, NF membranes generally suffer from the trade-off between permeability and selectivity. In this work, the co-enhancement of permeability and ion selectivity was achieved through tuning the surface charge and pore size of oxidized carbon nanotube (OCNT) intercalated reduced graphene oxide (RGO) membranes. With the increase of OCNT content from 0 to 83%, the surface charge and the pore size are increased. The permeability increased to 10.6 L m-2 h-1 bar-1 and rejection rate reached 78.1% for Na2SO4 filtration at a transmembrane pressure of 2 bar, which were 11.8 and 1.3 times higher than those of pristine RGO membrane. The composite membrane also showed 11.1 times higher permeability (11.1 L m-2 h-1 bar-1) and 2.9 times higher rejection rate (35.3%) for NaCl filtration. The analyses based on Donnan steric pore model suggest that the increased permeability is attributed to the combined effects of enlarged pore size and increased surface charge, while the enhanced ion selectivity is mainly dependent on the electrostatic interaction between the membrane and target ions. This finding provides a new insight for the development of high-performance NF membranes in water treatment and desalination.

  18. [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.

  19. 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.

  20. The influence of allosteric modulators and transmembrane mutations on desensitisation and activation of α7 nicotinic acetylcholine receptors.

    Science.gov (United States)

    Chatzidaki, Anna; D'Oyley, Jarryl M; Gill-Thind, JasKiran K; Sheppard, Tom D; Millar, Neil S

    2015-10-01

    Acetylcholine activates nicotinic acetylcholine receptors (nAChRs) by binding at an extracellular orthosteric site. Previous studies have described several positive allosteric modulators (PAMs) that are selective for homomeric α7 nAChRs. These include type I PAMs, which exert little or no effect on the rate of receptor desensitisation, and type II PAMs, which cause a dramatic loss of agonist-induced desensitisation. Here we report evidence that transmembrane mutations in α7 nAChRs have diverse effects on receptor activation and desensitisation by allosteric ligands. It has been reported previously that the L247T mutation, located toward the middle of the second transmembrane domain (at the 9' position), confers reduced levels of desensitisation. In contrast, the M260L mutation, located higher up in the TM2 domain (at the 22' position), does not show any difference in desensitisation compared to wild-type receptors. We have found that in receptors containing the L247T mutation, both type I PAMs and type II PAMs are converted into non-desensitising agonists. In contrast, in receptors containing the M260L mutation, this effect is seen only with type II PAMs. These findings, indicating that the M260L mutation has a selective effect on type II PAMs, have been confirmed both with previously described PAMs and also with a series of novel α7-selective PAMs. The novel PAMs examined in this study have close chemical similarity but diverse pharmacological properties. For example, they include compounds displaying effects on receptor desensitisation that are typical of classical type I and type II PAMs but, in addition, they include compounds with intermediate properties. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Use of Membrane Potential to Achieve Transmembrane Modification with an Artificial Receptor.

    Science.gov (United States)

    Hatanaka, Wataru; Kawaguchi, Miki; Sun, Xizheng; Nagao, Yusuke; Ohshima, Hiroyuki; Hashida, Mitsuru; Higuchi, Yuriko; Kishimura, Akihiro; Katayama, Yoshiki; Mori, Takeshi

    2017-02-15

    We developed a strategy to modify cell membranes with an artificial transmembrane receptor. Coulomb force on the receptor, caused by the membrane potential, was used to achieve membrane penetration. A hydrophobically modified cationic peptide was used as a membrane potential sensitive region that was connected to biotin through a transmembrane oligoethylene glycol (OEG) chain. This artificial receptor gradually disappeared from the cell membrane via penetration despite the presence of a hydrophilic OEG chain. However, when the receptor was bound to streptavidin (SA), it remained on the cell membrane because of the large and hydrophilic nature of SA.

  2. The transmembrane domain and acidic lipid flip-flop regulates voltage-dependent fusion mediated by class II and III viral proteins.

    Directory of Open Access Journals (Sweden)

    Ruben M Markosyan

    Full Text Available Voltage dependence of fusion induced by class II and class III viral fusion proteins was investigated. Class II proteins from Ross River and Sindbus virus and a mutant class III protein from Epstein Barr virus were found to induce cell-cell fusion that is voltage dependent. Combined with previous studies, in all, four class II and two class III protein have now been shown to exhibit voltage-dependent fusion, demonstrating that this is probably a general phenomenon for these two classes of viral fusion proteins. In the present study, monitoring fusion of pseudovirus expressing Vesicular Stomatitis virus (VSV G within endosomes shows that here, too, fusion is voltage dependent. This supports the claim that voltage dependence of fusion is biologically relevant and that cell-cell fusion reliably models the voltage dependence. Fusion induced by class I viral proteins is independent of voltage; chimeras expressing the ectodomain of a class I fusion protein and the transmembrane domain of VSV G could therefore be used to explore the location within the protein responsible for voltage dependence. Results showed that the transmembrane domain is the region associated with voltage dependence. Experiments in which cells were enriched with acidic lipids led to the conclusion that it is the flip-flop of acidic lipids that carries the charge responsible for the observed voltage dependence of fusion. This flip-flop occurred downstream of hemifusion, in accord with previous findings that the voltage dependent steps of fusion occur at a stage subsequent to hemifusion.

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Maarten G. K. Ghequire

    2017-02-01

    Full Text Available 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.

  5. 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

  6. Competitive binding at a nicotinic receptor transmembrane site of two α7-selective positive allosteric modulators with differing effects on agonist-evoked desensitization.

    Science.gov (United States)

    Collins, Toby; Young, Gareth T; Millar, Neil S

    2011-12-01

    Positive allosteric modulators (PAMs) of nicotinic acetylcholine receptors (nAChRs) have attracted considerable interest as a novel area of therapeutic drug discovery. Two types of α7-selective PAMs have been identified (type I and type II). Whilst both potentiate peak agonist-induced responses, they have different effects on the rate of agonist-induced receptor desensitization. Type I PAMs have little or no effect on the rapid rate of desensitization that is characteristic of α7 nAChRs, whereas type II PAMs cause dramatic slowing of receptor desensitization. Previously, we have obtained evidence indicating that PNU-120596, a type II PAM, causes potentiation by interacting with an allosteric transmembrane site. In contrast, other studies have demonstrated the importance of the 'M2-M3 segment' in modulating the effects of the type I PAM NS1738 and have led to the proposal that NS1738 may interact with the extracellular N-terminal domain. Here, our aim has been to compare the mechanism of allosteric potentiation of α7 nAChRs by NS1738 and PNU-120596. Functional characterization of a series of mutated α7 nAChRs indicates that mutation of amino acids within a proposed intrasubunit transmembrane cavity have a broadly similar effect on these two PAMs. In addition, we have employed a functional assay designed to examine the ability of ligands to act competitively at either the orthosteric or allosteric binding site of α7 nAChRs. These data, together with computer docking simulations, lead us to conclude that both the type I PAM NS1738 and the type II PAM PNU-120596 bind competitively at a mutually exclusive intrasubunit transmembrane site. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. A Stereolithography Pore-Throat Model

    Science.gov (United States)

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

    2007-12-01

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

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

    Science.gov (United States)

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

    2016-06-01

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

  9. 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...... the printing ink. The extent to which the pore structure is modified by changing several parameters in the membrane electrode assembly MEA manufacturing process is discussed. The pore structure of the printed layers is found to be invariant with respect to changes in powder loading or in choice of printing...... substrate, and is relatively undisturbed by MEA hot-pressing. Changing the source of the primer powder and adding a pore-forming agent to the catalyst ink are found to be successful methods of creating a more open pore structure in the printed layers....

  10. 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)

  11. Factors Determining the Pore Shape in Polycarbonate Track Membranes

    CERN Document Server

    Apel, P Yu; Orelovich, O L; Akimenko, S N; Sartowska, B; Dmitriev, S N

    2004-01-01

    The process of pore formation in ion-irradiated polycarbonate films on treatment with alkali solutions in the presence of a surfactant is studied. It is found that the pore shape depends on both the structure of the initial films and the peculiarities of the interaction of the surfactant with the polymer surface and the transport of the surfactant into tracks. Due to heterogeneity of the films the cross-section of a track pore channel changes along its length. The presence of the surfactant results in a further effect. Surfactant molecules adsorb on the polymer surface at the pore entries and reduce the etch rate which leads to formation of cigar-like pore channels. The use of surfactant as a component of chemical etchant enables one to control the pore shape in track membranes thus optimizing their retention and permeation characteristics.

  12. 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

  13. Deciphering pore-level precipitation mechanisms.

    Science.gov (United States)

    Prasianakis, N I; Curti, E; Kosakowski, G; Poonoosamy, J; Churakov, S V

    2017-10-23

    Mineral precipitation and dissolution in aqueous solutions has a significant effect on solute transport and structural properties of porous media. The understanding of the involved physical mechanisms, which cover a large range of spatial and temporal scales, plays a key role in several geochemical and industrial processes. Here, by coupling pore scale reactive transport simulations with classical nucleation theory, we demonstrate how the interplay between homogeneous and heterogeneous precipitation kinetics along with the non-linear dependence on solute concentration affects the evolution of the system. Such phenomena are usually neglected in pure macroscopic modelling. Comprehensive parametric analysis and comparison with laboratory experiments confirm that incorporation of detailed microscale physical processes in the models is compulsory. This sheds light on the inherent coupling mechanisms and bridges the gap between atomistic processes and macroscopic observations.

  14. Ion track pores in intelligent films

    International Nuclear Information System (INIS)

    Asano, Masaharu; Yoshida, Masaru; Omichi, Hideki; Nagaoka, Noriyasu; Kubota, Hitoshi; Katakai, Ryoichi; Reber, N.; Spohr, R.

    1996-01-01

    To create an intelligent chemical valve which behaves to biological membranes, we combined the following technologies: (1) creation of intelligent gels based on pendant α-amino acids or their oligomers, (2) preparation of nuclear track films by etching chemically after heavy ion irradiation, especially preparation of cylindrical pores passed through the film, and (3) a combination of (1) and (2). The two factors, REL (Restricted Energy Loss) and radiation sensitivity [(V t /V b )-1] play an important role in formation of such cylindrical track films. In the case of CR-39 film, there were found to be REL>1.6x10 4 MeV cm 2 g -1 and (V t /V b )-1>100, respectively. The cylindrical tracks films with intelligent functions, which consist of a combination of (1) and (2), can be fabricated by two techniques, copolymerization and grafting. (author)

  15. Evolution of Deformation, Pore Pressure, and Coulomb Stress Following the M9 Sumatra- Andaman Earthquake.

    Science.gov (United States)

    Masterlark, T.; Hughes, K. L.

    2007-12-01

    The M9 Sumatra-Andaman Earthquake of 2004 ruptured the interface of the subducting Indo-Australian plate and overriding Burma microplate. Near-field GPS measurements of the coseismic deformation are on the order of several meters. This deformation induced a devastating tsunami and generated transient stress and pore pressure changes that triggered numerous aftershocks, including the M8.7 Nias earthquake. Finite element models (FEMs) are uniquely capable of simulating the coseismic load and induced evolution of postseismic deformation, pore pressure, and Coulomb stress; while simultaneously honoring the known geologic complexity of the subduction zone. We construct FEMs that simulate deformation of the earthquake for a three-dimensional problem domain partitioned to account for the distribution of material properties of the subducting slab, mantle wedge, forearc, volcanic arc, and backarc. The coseismic slip distribution is estimated from the near-field GPS data via standard inverse methods and FEM-generated Green's functions. Forward models, driven by this slip distribution, predict the evolution of poroelastic and viscoelastic deformation, stress, and pore pressure following the earthquake. Preliminary results suggest poroelastic deformation may be up to several tens-of-centimeters in offshore regions, although predicted poroelastic displacements for near-field GPS sites are generally a few centimeters. Initial pore pressure magnitudes, due to the load of the coseismic slip, exceed 1 MPa in the near- field region. Predicted postseismic pore pressure recovery correlates to the observed spatial and temporal distribution of aftershock swarms, in accord with the poroelastic formulation of Coulomb failure theory. Although the predicted poroelastic displacements are resolvable by GPS measurements in the near-field region, more than a meter of viscoelastic deformation is expected for near-field GPS sites over the next decade.

  16. 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).

  17. The role of transmembrane segment II in 7TM receptor activation

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, M M

    2009-01-01

    During the two past decades tremendous effort has been put into uncovering the activation mechanism of 7TM receptors. The majority of such studies have focused on the major binding pocket, comprised of transmembrane segments (TM) -III through -VII, as most non-peptide and peptide ligands, in addi...

  18. Role of Side-Chain Conformational Entropy in Transmembrane Helix Dimerization of Glycophorin A

    Science.gov (United States)

    Liu, Wei; Crocker, Evan; Siminovitch, David J.; Smith, Steven O.

    2003-01-01

    Dimerization of the transmembrane domain of glycophorin A is mediated by a seven residue motif LIxxGVxxGVxxT through a combination of van der Waals and hydrogen bonding interactions. One of the unusual features of the motif is the large number of β-branched amino acids that may limit the entropic cost of dimerization by restricting side-chain motion in the monomeric transmembrane helix. Deuterium NMR spectroscopy is used to characterize the dynamics of fully deuterated Val80 and Val84, two essential amino acids of the dimerization motif. Deuterium spectra of the glycophorin A transmembrane dimer were obtained using synthetic peptides corresponding to the transmembrane sequence containing either perdeuterated Val80 or Val84. These data were compared with spectra of monomeric glycophorin A peptides deuterated at Val84. In all cases, the deuterium line shapes are characterized by fast methyl group rotation with virtually no motion about the Cα-Cβ bond. This is consistent with restriction of the side chain in both the monomer and dimer due to intrahelical packing interactions involving the β-methyl groups, and indicates that there is no energy cost associated with dimerization due to loss of conformational entropy. In contrast, deuterium NMR spectra of Met81 and Val82, in the lipid interface, reflected greater motional averaging and fast exchange between different side-chain conformers. PMID:12547806

  19. 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

  20. Self-assembly of small-molecule fumaramides allows transmembrane chloride channel formation.

    Science.gov (United States)

    Roy, Arundhati; Gautam, Amitosh; Malla, Javid Ahmad; Sarkar, Sohini; Mukherjee, Arnab; Talukdar, Pinaki

    2018-02-20

    This study reports the formation of self-assembled transmembrane anion channels by small-molecule fumaramides. Such artificial ion channel formation was confirmed by ion transport across liposomes and by planar bilayer conductance measurements. The geometry-optimized model of the channel and Cl - ion selectivity within the channel lumen was also illustrated.

  1. 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......-s1 and NCAM-s2 and the function of soluble NCAM forms were investigated. It was shown that all three soluble forms could be released from brain membranes with M(r) values identical to the three major membrane-associated forms: the large transmembrane 190,000-M(r) form (NCAM-A), the smaller...... intact soluble form from membranes of cells transfected with this isoform. Thus, NCAM-s1 and NCAM-s2 probably represent intact released transmembrane NCAM-A and NCAM-B. The soluble transmembrane forms are likely to exist in vivo, as NCAM-s1 and NCAM-s2 were readily demonstrated in cerebrospinal fluid...

  2. CoPreTHi: a Web tool which combines transmembrane protein segment prediction methods

    OpenAIRE

    Promponas, Vasilis; Palaios, Giorgos; Pasquier, Claude; Hamodrakas, Ioannis; Hamodrakas, Stavros

    2009-01-01

    International audience; CoPreTHi is a Java based web application, which combines the results of methods that predict the location of transmembrane segments in protein sequences into a joint prediction histogram. Clearly, the joint prediction algorithm, produces superior quality results than individual prediction schemes. The program is available at http://o2.db.uoa.gr/CoPreTHi.

  3. 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

  4. Detergent properties influence the stability of the glycophorin A transmembrane helix dimer in lysophosphatidylcholine micelles.

    Science.gov (United States)

    Stangl, Michael; Veerappan, Anbazhagan; Kroeger, Anja; Vogel, Peter; Schneider, Dirk

    2012-12-19

    Detergents might affect membrane protein structures by promoting intramolecular interactions that are different from those found in native membrane bilayers, and fine-tuning detergent properties can be crucial for obtaining structural information of intact and functional transmembrane proteins. To systematically investigate the influence of the detergent concentration and acyl-chain length on the stability of a transmembrane protein structure, the stability of the human glycophorin A transmembrane helix dimer has been analyzed in lyso-phosphatidylcholine micelles of different acyl-chain length. While our results indicate that the transmembrane protein is destabilized in detergents with increasing chain-length, the diameter of the hydrophobic micelle core was found to be less crucial. Thus, hydrophobic mismatch appears to be less important in detergent micelles than in lipid bilayers and individual detergent molecules appear to be able to stretch within a micelle to match the hydrophobic thickness of the peptide. However, the stability of the GpA TM helix dimer linearly depends on the aggregation number of the lyso-PC detergents, indicating that not only is the chemistry of the detergent headgroup and acyl-chain region central for classifying a detergent as harsh or mild, but the detergent aggregation number might also be important. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. The trans-membrane potential of biological membranes in computer simulation

    Czech Academy of Sciences Publication Activity Database

    Melcr, Josef; Timr, Štěpán; Jungwirth, Pavel

    2015-01-01

    Roč. 44, Suppl 1 (2015), S170 ISSN 0175-7571. [EBSA European Biophysics Congress /10./. 18.07.2015-22.07.2015, Dresden] Institutional support: RVO:61388963 Keywords : molecular dynamics * trans-membrane potential Subject RIV: CF - Physical ; Theoretical Chemistry

  6. 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

  7. 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

  8. Transmembrane Helices Are an Overlooked Source of Major Histocompatibility Complex Class I Epitopes

    NARCIS (Netherlands)

    Bianchi, F.; Textor, J.C.; Bogaart, G. van den

    2017-01-01

    About a fourth of the human proteome is anchored by transmembrane helices (TMHs) to lipid membranes. TMHs require multiple hydrophobic residues for spanning membranes, and this shows a striking resemblance with the requirements for peptide binding to major histocompatibility complex (MHC) class I.

  9. 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

    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 al...

  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...

  11. 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

  12. Modeling the structure of SARS 3a transmembrane protein using a ...

    Indian Academy of Sciences (India)

    Abstract. 3a is an accessory protein from SARS coronavirus that is known to play a significant role in the proliferation of the virus by forming tetrameric ion channels. Although the monomeric units are known to consist of three transmembrane (TM) domains, there are no solved structures available for the complete monomer.

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

    NARCIS (Netherlands)

    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

  14. 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®.

  15. Cytolytic pore-forming protein associated with the surface membrane of Naegleria fowleri

    Energy Technology Data Exchange (ETDEWEB)

    Lowrey, D.M.

    1985-01-01

    Whole cell homogenates of Naegleria fowleri were examined by hemolytic and /sup 51/Cr-release assays for the presence of cytolytic molecules which may participate in the cytopathogenic action of this amoeba. Two distinct cytolytic activities were found. A surface membrane cytolysin was identified which was found to be avidly associated with membranes possessing an equilibrium density of 1.135 g/cm/sup 3/ in isopycnic sucrose gradients. The activity of the surface membrane cytolysin was not affected by heating at 75/sup 0/C for 30 min. The second cytolytic activity was found in putative lysosomes possessing an equilibrium density of 1.162 g/cm/sup 3/ and was completely inactivated by heating at 75/sup 0/C for 30 min. Cytolysis produced in the presence of both cytolysins was consistently synergistic with respect to the activity of either cytolysin alone. The lesions produced on erythrocytes by this cooperative process were characterized by electron microscopy as transmembrane pores resembling a number of other cytolytic effector molecules including the ninth component of complement, perforins of cytolytic T lymphocytes, and the alphatoxin of Staphylococcus aureus.

  16. 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.

  17. 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.

  18. 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.

  19. Experimental study on pore structure and performance of sintered porous wick

    Science.gov (United States)

    He, Da; Wang, Shufan; Liu, Rutie; Wang, Zhubo; Xiong, Xiang; Zou, Jianpeng

    2018-02-01

    Porous wicks were prepared via powder metallurgy using NH4HCO3 powders as pore-forming agent. The pore-forming agent particle size was varied to control the pore structure and equivalent pore size distribution feature of porous wick. The effect of pore-forming agent particle size on the porosity, pore structures, equivalent pore size distribution and capillary pumping performance were investigated. Results show that with the particle size of pore-forming agent decrease, the green density and the volume shrinkage of the porous wicks gradually increase and the porosity reduces slightly. There are two types of pores inside the porous wick, large-sized prefabricated pores and small-sized gap pores. With the particle size of pore-forming agent decrease, the size of the prefabricated pores becomes smaller and the distribution tends to be uniform. Gap pores and prefabricated pores inside the wick can make up different types of pore channels. The equivalent pore size of wick is closely related to the structure of pore channels. Furthermore, the equivalent pore size distribution of wick shows an obvious double-peak feature when the pore-forming agent particle size is large. With the particle size of pore-forming agent decrease, the two peaks of equivalent pore size distribution approach gradually to each other, resulting in a single-peak feature. Porous wick with single-peak feature equivalent pore size distribution possesses the better capillary pumping performances.

  20. Electrochemical Platform for the Detection of Transmembrane Proteins Reconstituted into Liposomes.

    Science.gov (United States)

    Vacek, Jan; Zatloukalova, Martina; Geleticova, Jaroslava; Kubala, Martin; Modriansky, Martin; Fekete, Ladislav; Masek, Josef; Hubatka, Frantisek; Turanek, Jaroslav

    2016-04-19

    The development of new methods and strategies for the investigation of membrane proteins is limited by poor solubility of these proteins in an aqueous environment and hindered by a number of other problems linked to the instability of the proteins outside lipid bilayers. Therefore, current research focuses on an analysis of membrane proteins incorporated into model lipid membrane, most frequently liposomes. In this work, we introduce a new electrochemical methodology for the analysis of transmembrane proteins reconstituted into a liposomal system. The proposed analytical approach is based on proteoliposomal sample adsorption on the surface of working electrodes followed by analysis of the anodic and cathodic signals of the reconstituted proteins. It works based on the fact that proteins are electroactive species, in contrast to the lipid components of the membranes under the given experimental conditions. Electroanalytical experiments were performed with two transmembrane proteins; the Na(+)/K(+)ATPase that contains transmembrane as well as large extramembraneous segments and the mitochondrial uncoupling protein 1, which is a transmembrane protein essentially lacking extramembraneous segments. Electrochemical analyses of proteoliposomes were compared with analyses of both proteins solubilized with detergents (C12E8 and octyl-PoE) and supported by the following complementary methods: microscopy techniques, protein activity testing, molecular model visualizations, and immunochemical identification of both proteins. The label-free electrochemical platform presented here enables studies of reconstituted transmembrane proteins at the nanomolar level. Our results may contribute to the development of new electrochemical sensors and microarray systems applicable within the field of poorly water-soluble proteins.

  1. 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.

  2. Entropy of Shortest Distance (ESD as Pore Detector and Pore-Shape Classifier

    Directory of Open Access Journals (Sweden)

    Klaudia Oleschko

    2013-06-01

    Full Text Available The entropy of shortest distance (ESD between geographic elements (“elliptical intrusions”, “lineaments”, “points” on a map, or between "vugs", "fractures" and "pores" in the macro- or microscopic images of triple porosity naturally fractured vuggy carbonates provides a powerful new tool for the digital processing, analysis, classification and space/time distribution prognostic of mineral resources as well as the void space in carbonates, and in other rocks. The procedure is applicable at all scales, from outcrop photos, FMI, UBI, USI (geophysical imaging techniques to micrographs, as we shall illustrate through some examples. Out of the possible applications of the ESD concept, we discuss in details the sliding window entropy filtering for nonlinear pore boundary enhancement, and propose this procedure as unbiased thresholding technique.

  3. Membrane pore architecture of the CslF6 protein controls (1-3,1-4)-β-glucan structure.

    Science.gov (United States)

    Jobling, Stephen A

    2015-06-01

    The cereal cell wall polysaccharide (1-3,1-4)-β-glucan is a linear polymer of glucose containing both β1-3 and β1-4 bonds. The structure of (1-3,1-4)-β-glucan varies between different cereals and during plant growth and development, but little is known about how this is controlled. The cellulose synthase-like CslF6 protein is an integral membrane protein and a major component of the (1-3,1-4)-β-glucan synthase. I show that a single amino acid within the predicted transmembrane pore domain of CslF6 controls (1-3,1-4)-β-glucan structure. A new mechanism for the control of the polysaccharide structure is proposed where membrane pore architecture and the translocation of the growing polysaccharide across the membrane control how the acceptor glucan is coordinated at the active site and thus the proportion of β1-3 and β1-4 bonds within the polysaccharide.

  4. Pore-Filled Scintillating Membrane as Sensing Matrix for α-Emitting Actinides.

    Science.gov (United States)

    Chavan, Vivek; Agarwal, Chhavi; Pandey, A K

    2016-04-05

    Pore-filled membranes with scintillating properties have been synthesized for sensing α-emitting radionuclides. The membranes have been prepared by in situ UV-initiator-induced polymerization of monomer bis[2-(methacryloxy)ethyl] phosphate in pores of the host membranes, poly(propylene) and poly(ethersulfone). The polymerization has been carried out in the presence of scintillating molecules, 2,5-diphenyloxazole. These scintillating molecules are physically trapped in the thus formed microgel in the membrane. Much higher α-scintillation efficiency has been obtained for the (241)Am-loaded poly(ethersulfone)-based grafted membrane compared to poly(propylene)-based membrane. This was attributed to the aromatic backbone of the poly(ethersulfone) membrane. The scintillation response of poly(ethersulfone)-based membranes has been found to be linear over the range of (241)Am activity studied. The pore-filled scintillating membranes have been found to be selective toward Pu(4+) ions at higher HNO3 concentration compared to Am(3+). The analytical performance of the pore-filled scintillating membranes has been evaluated. The membranes have been found to be stable and reusable. The scintillating membrane with optimized composition has been applied for quantification of Pu in a soil sample.

  5. 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.

  6. 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

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

    Science.gov (United States)

    Reuven, Eliran Moshe; Ali, Mohammad; Rotem, Etai; Schwarzer, Roland; Schwarzter, Roland; Gramatica, Andrea; Futerman, Anthony H; Shai, Yechiel

    2014-08-01

    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 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.

  10. 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.

  11. Transmembrane Helix-helix Association: Relative Stabilities at Low pH†

    Science.gov (United States)

    Valluru, Neelima; Silva, Frances; Dhage, Manmath; Rodriguez, Gustavo; Alloor, Srinivas R.; Renthal, Robert

    2008-01-01

    We have previously studied the unfolding equilibrium of bacterio-opsin in a single phase solvent, using Förster mechanism fluorescence resonance energy transfer (FRET) as a probe, from tryptophan donors to a dansyl acceptor. We observed an apparent unfolding transition in bacterio-opsin perturbed by increasing ethanol concentrations [Nannepaga et al.(2004) Biochemistry 43, 50–59]. We have further investigated this transition and find the unfolding is pH-dependent. We have now measured the apparent pK of acid-induced unfolding of bacterio-opsin in 90% ethanol. When the acceptor is on helix B (Lys 41), the apparent pK for unfolding is 4.75; on the EF connecting loop (Cys 163), 5.15; and on helix G (Cys 222), 5.75. Five-helix proteolytic fragments are less stable. The apparent unfolding pKs are, for residues 72-248 (Cys 163), 5.46; and 1-166 (Lys 41), 7.36. When interpreted in terms of a simple equilibrium model for unfolding, the apparent pKs give relative free energies of unfolding, in the range of −0.54 to −3.5 kcal/mol. The results suggest that the C-terminal helix of bacterio-opsin is less stably folded than the N-terminal helices. We analyzed the pair-wise helix-helix interaction surfaces of bacteriorhodopsin and three other 7-transmembrane helix proteins, based on crystal structures. The results show that the interaction surfaces are smoother and the helix axis separations are closer in the amino-terminal two-thirds of the proteins compared with the carboxyl terminal one-third. However, the F helix is important in stabilizing the folded structure, as shown by the instability of the 1-166 fragment. Considering the high resolution crystal structure of bacteriorhodopsin, there are no obvious helix-helix interactions involving protein side chains which would be destabilized by protonation at the estimated pH of the unfolding transitions. However, a number of helix-bridging water molecules could become protonated, thereby weakening the helix

  12. Transmembrane helix-helix association: relative stabilities at low pH.

    Science.gov (United States)

    Valluru, Neelima; Silva, Frances; Dhage, Manmath; Rodriguez, Gustavo; Alloor, Srinivas R; Renthal, Robert

    2006-04-11

    We have previously studied the unfolding equilibrium of bacterioopsin in a single phase solvent, using Förster mechanism fluorescence resonance energy transfer (FRET) as a probe, from tryptophan donors to a dansyl acceptor. We observed an apparent unfolding transition in bacterioopsin perturbed by increasing ethanol concentrations [Nannepaga et al. (2004) Biochemistry 43, 50-59]. We have further investigated this transition and find that the unfolding is pH-dependent. We have now measured the apparent pK of acid-induced unfolding of bacterioopsin in 90% ethanol. When the acceptor is on helix B (Lys 41), the apparent pK for unfolding is 4.75; on the EF connecting loop (Cys 163), 5.15; and on helix G (Cys 222), 5.75. Five-helix proteolytic fragments are less stable. The apparent unfolding pKs are 5.46 for residues 72-248 (Cys 163) and 7.36 for residues 1-166 (Lys 41). When interpreted in terms of a simple equilibrium model for unfolding, the apparent pKs give relative free energies of unfolding in the range of -0.54 to -3.5 kcal/mol. The results suggest that the C-terminal helix of bacterioopsin is less stably folded than the N-terminal helices. We analyzed the pairwise helix-helix interaction surfaces of bacteriorhodopsin and three other seven-transmembrane-helix proteins on the basis of crystal structures. The results show that the interaction surfaces are smoother and the helix axis separations are closer in the amino-terminal two-thirds of the proteins compared with the carboxyl-terminal one-third. However, the F helix is important in stabilizing the folded structure, as shown by the instability of the 1-166 fragment. Considering the high-resolution crystal structure of bacteriorhodopsin, there are no obvious helix-helix interactions involving protein side chains which would be destabilized by protonation at the estimated pH of the unfolding transitions. However, a number of helix-bridging water molecules could become protonated, thereby weakening the helix

  13. 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

    M, and its inhibitory efficacy was 75%. In addition, we show that EBI2 constitutively activated extracellular signal-regulated kinase (ERK) in a pertussis toxin-insensitive manner. Intriguingly, GSK682753A inhibited ERK phosphorylation, GTPγS binding, and cAMP-response element-binding protein activation...

  14. The Antibodies against the Computationally Designed Mimic of the Glycoprotein Hormone Receptor Transmembrane Domain Provide Insights into Receptor Activation and Suppress the Constitutively Activated Receptor Mutants*

    Science.gov (United States)

    Majumdar, Ritankar; Railkar, Reema; Dighe, Rajan R.

    2012-01-01

    The exoloops of glycoprotein hormone receptors (GpHRs) transduce the signal generated by the ligand-ectodomain interactions to the transmembrane helices either through direct hormonal contact and/or by modulating the interdomain interactions between the hinge region (HinR) and the transmembrane domain (TMD). The ligand-induced conformational alterations in the HinRs and the interhelical loops of luteinizing hormone receptor/follicle stimulating hormone receptor/thyroid stimulating hormone receptor were mapped using exoloop-specific antibodies generated against a mini-TMD protein designed to mimic the native exoloop conformations that were created by joining the thyroid stimulating hormone receptor exoloops constrained through helical tethers and library-derived linkers. The antibody against the mini-TMD specifically recognized all three GpHRs and inhibited the basal and hormone-stimulated cAMP production without affecting hormone binding. Interestingly, binding of the antibody to all three receptors was abolished by prior incubation of the receptors with the respective hormones, suggesting that the exoloops are buried in the hormone-receptor complexes. The antibody also suppressed the high basal activities of gain-of-function mutations in the HinRs, exoloops, and TMDs such as those involved in precocious puberty and thyroid toxic adenomas. Using the antibody and point/deletion/chimeric receptor mutants, we demonstrate that changes in the HinR-exoloop interactions play an important role in receptor activation. Computational analysis suggests that the mini-TMD antibodies act by conformationally locking the transmembrane helices by means of restraining the exoloops and the juxta-membrane regions. Using GpHRs as a model, we describe a novel computational approach of generating soluble TMD mimics that can be used to explain the role of exoloops during receptor activation and their interplay with TMDs. PMID:22904318

  15. 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

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

    Indian Academy of Sciences (India)

    Two kinds of channels, straight channels made of cylindrical capillaries and curved channels made of slit-shaped pores, exist in the bulk materials. The influence of the pore structure of mesoporous TiO2 on its photocatalytic performance was studied. The sample with higher porosity, better textural properties and straight ...

  17. Significant improvement in the pore properties of SBA-15 brought ...

    Indian Academy of Sciences (India)

    WINTEC

    Presence of carboxylic acids as well as hydrothermal treatment improves the pore properties of SBA-15. Keywords. SBA-15; mesoporous; carboxylic acids; adsorption; hydrothermal treatment; morphology. 1. Introduction. Molecular sieves with large pores have been of great use in carrying out reactions and separation proc-.

  18. 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)

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

    Indian Academy of Sciences (India)

    Administrator

    Abstract. Mesoporous titania was synthesized by a sol–gel method using the surfactants Span85 and. X114 as the template. 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 formed through.

  20. 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.)

  1. Bacteriocins : mechanism of membrane insertion and pore formation

    NARCIS (Netherlands)

    Moll, G.N.; Konings, W.N; Driessen, A.J.M.

    1999-01-01

    Lactic acid bacteria produce several types of pore forming peptides. Class I bacteriocins are lantibiotics that contain (methyl)lanthionine residues that may form intramolecular thioether rings. These peptides generally have a broad spectrum of activity and form unstable pores. Class II bacteriocins

  2. Small angle neutron scattering study of pore microstructure in ceria ...

    Indian Academy of Sciences (India)

    fractal morphology of the pore space with fractal dimensionality lying between 2.70 and. 2.76. Keywords. Ceria; sintering ... This paper deals with SANS investigation of internal pore microstructure of sintered compacts of ceria over ... compaction pressure of 200 MPa and sintered at 1250◦C for 2 h. Pramana – J. Phys., Vol.

  3. Analysis Of Pore Pressure Using Geophysical Methods | Dosumnu ...

    African Journals Online (AJOL)

    Many methods have been devised for predicting and evaluating the values of pore pressure in oil and gas formations. The present work employs geophysical approach for prediction of formation pore pressure in Niger Delta. This involved the use of seismic derived data before drilling operation, which was correlated with ...

  4. Pore structure and growth kinetics in carbon materials

    Energy Technology Data Exchange (ETDEWEB)

    Bose, S.

    1978-04-01

    Pore structure of glassy carbon (GC) and pyrolytic graphite (PG) have been investigated. GC is one of the most impervious of solids finding applications in prosthetic devices and fuel cells while PG is used extensively in the aerospace industry. One third of the microstructure of GC consists of closed pores inaccessible to fluids. The microstructure of this material has been characterized using x-ray diffraction (XRD) and high resolution electron microscopy. Small angle x-ray scattering (SAXS) has been used to measure the angstrom sized pores and to follow the evolution of pore surface area as a function of heat treatment temperature (HTT) and heat treatment time (HTt) at constant temperature. From these measurements an analysis of the surface area kinetics was made to find out if rate processes are involved and to locate graphitization occurring at pore surfaces. PG on the other hand has been found to have larger sized pores that comprise five percent of its volume. In addition to being closed these pores are oriented. Some pore models are proposed for PG and the existing scattering theory from oriented ellipsoids is modified to include the proposed shapes.

  5. 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.

  6. 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.

  7. Water nanodroplets confined in zeolite pores.

    Science.gov (United States)

    Coudert, François-Xavier; Cailliez, Fabien; Vuilleumier, Rodolphe; Fuchs, Alain H; Boutin, Anne

    2009-01-01

    We provide a comprehensive depiction of the behaviour of a nanodroplet of approximately equal to 20 water molecules confined in the pores of a series of 3D-connected isostructural zeolites with varying acidity, by means of molecular simulations. Both grand canonical Monte Carlo simulations using classical interatomic forcefields and first-principles Car-Parrinello molecular dynamics were used in order to characterise the behaviour of confined water by computing a range of properties, from thermodynamic quantities to electronic properties such as dipole moment, including structural and dynamical information. From the thermodynamic point of view, we have identified the all-silica zeolite as hydrophobic, and the cationic zeolites as hydrophilic; the condensation transition in the first case was demonstrated to be of first order. Furthermore, in-depth analysis of the dynamical and electronic properties of water showed that water in the hydrophobic zeolite behaves as a nanodroplet trying to close its hydrogen-bond network onto itself, with a few short-lived dangling OH groups, while water in hydrophilic zeolites "opens up" to form weak hydrogen bonds with the zeolite oxygen atoms. Finally, the dipole moment of confined water is studied and the contributions of water self-polarisation and the zeolite electric field are discussed.

  8. 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

  9. 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.

  10. Characterization of pore volume of cumulative water injection distribution

    Directory of Open Access Journals (Sweden)

    Guoqing Feng

    2015-06-01

    Full Text Available Pore volume of Cumulative water injection is one of the factors for evaluating water flood effect in a water flood oil field. In previous study, there were limited lab studies for evaluating oil displacement efficiency. A method to characterize the distribution of pore volume of cumulative water injection is proposed in this paper, and it is verified by a five-spot water flooding streamline simulation model. The logarithmic relation between pore volume of cumulative water injection and water saturation is established by regression. An inflection point and limit point of cumulative water injection pore volume are identified. Current simulation model indicates inflection point appears after 2–5 pore volume (PV injection, and limit point appears after 15–25 PV injection. Both inflection and limit point vary in different regions of reservoir.

  11. 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.

  12. 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.

  13. 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

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

    Science.gov (United States)

    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 CaI2 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 CaI2 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.

  15. 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.

  16. 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

  17. 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

  18. Effects of pore size on the adsorption of hydrogen in slit pores of constant width and varying height

    Energy Technology Data Exchange (ETDEWEB)

    Culp, J.T.; Natesakhawat, S.; Smith, M.R.; Bittner, E.W.; Matranga, C.S.; Bockrath, B.C.

    2007-08-01

    The effects of pore size on the hydrogen storage properties of a series of pillared layered solids were investigated at 77 K and 87 K up to a pressure of 1 atm. The isotherms were fit to the Langmuir-Freundlich equation and extrapolated to determine saturation values. The materials studied are based on the M(L)[M'(CN)4] structural motif, where M = Co or Ni, L = pyrazine (pyz), 4,4'bipyridine (bpy) or 4,4'-dipyridylacetylene (dpac), and M' = Ni, Pd or Pt. The compounds all possess slit like pores with constant inplane dimensions and pore heights that vary as a function of (L). The pyz pillared materials with the smallest pore dimensions store hydrogen at a pore density similar to the bulk liquid. The adsorbed hydrogen density drops by a factor of two as the relative pore size is tripled in the dpac material. The decreased storage efficiency diminishes the expected gravimetric gain in capacity for the larger pore materials. The heats of adsorption were found to range from 6 to 8 kJ/mol in the series, and weakly correlate with pore size.

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

    Science.gov (United States)

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

  20. Transmembrane proteoglycans control stretch-activated channels to set cytosolic calcium levels

    DEFF Research Database (Denmark)

    Gopal, Sandeep; Søgaard, Pernille; Multhaupt, Hinke A B

    2015-01-01

    Transmembrane heparan sulfate proteoglycans regulate multiple aspects of cell behavior, but the molecular basis of their signaling is unresolved. The major family of transmembrane proteoglycans is the syndecans, present in virtually all nucleated cells, but with mostly unknown functions. Here, we...... show that syndecans regulate transient receptor potential canonical (TRPCs) channels to control cytosolic calcium equilibria and consequent cell behavior. In fibroblasts, ligand interactions with heparan sulfate of syndecan-4 recruit cytoplasmic protein kinase C to target serine714 of TRPC7...... the loss of syndecan by suppressing neuronal guidance and locomotory defects related to increases in neuronal calcium levels. The widespread and conserved syndecan-TRPC axis therefore fine tunes cytoskeletal organization and cell behavior....

  1. Buried lysine, but not arginine, titrates and alters transmembrane helix tilt.

    Science.gov (United States)

    Gleason, Nicholas J; Vostrikov, Vitaly V; Greathouse, Denise V; Koeppe, Roger E

    2013-01-29

    The ionization states of individual amino acid residues of membrane proteins are difficult to decipher or assign directly in the lipid-bilayer membrane environment. We address this issue for lysines and arginines in designed transmembrane helices. For lysines (but not arginines) at two locations within dioleoyl-phosphatidylcholine bilayer membranes, we measure pK(a) values below 7.0. We find that buried charged lysine, in fashion similar to arginine, will modulate helix orientation to maximize its own access to the aqueous interface or, if occluded by aromatic rings, may cause a transmembrane helix to exit the lipid bilayer. Interestingly, the influence of neutral lysine (vis-à-vis leucine) upon helix orientation also depends upon its aqueous access. Our results suggest that changes in the ionization states of particular residues will regulate membrane protein function and furthermore illustrate the subtle complexity of ionization behavior with respect to the detailed lipid and protein environment.

  2. Metal ion site engineering indicates a global toggle switch model for seven-transmembrane receptor activation

    DEFF Research Database (Denmark)

    Elling, Christian E; Frimurer, Thomas M; Gerlach, Lars-Ole

    2006-01-01

    Much evidence indicates that, during activation of seven-transmembrane (7TM) receptors, the intracellular segments of the transmembrane helices (TMs) move apart with large amplitude, rigid body movements of especially TM-VI and TM-VII. In this study, AspIII:08 (Asp113), the anchor point...... in sites constructed between positions III:08 (Asp or His), VI:16 (preferentially Cys), and/or VII:06 (preferentially Cys). In molecular models built over the backbone conformation of the inactive rhodopsin structure, the heavy atoms that coordinate the metal ion were located too far away from each other...... ion sites, we propose a global toggle switch mechanism for 7TM receptor activation in which inward movement of the extracellular segments of especially TM-VI and, to some extent, TM-VII is coupled to the well established outward movement of the intracellular segments of these helices. We suggest...

  3. A Dimeric Bis(melamine)-Substituted Bispidine for Efficient Transmembrane H+/Cl-Cotransport.

    Science.gov (United States)

    Shinde, Sopan Valiba; Talukdar, Pinaki

    2017-04-03

    A 3,7-diazabicyclo[3.3.1]nonane linking to two melamines is a unique transmembrane H + /Cl - carrier. In the solid state, the V-shaped compound forms a HCl-bound zig-zag network through cooperative protonation and hydrogen bond interactions. In the lipid membrane, the receptor forms a dimeric self-assembly involving multiple H + and Cl - leading to the efficient transport of the acid. The pH-dependent Cl - efflux observed for the compound was rationalized based on a gradual protonation model that confers an active transmembrane carrier at physiological pH. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. 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...... 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.......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...

  5. 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.

  6. 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.

  7. [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.

  8. 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.

  9. 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 MySQL and Apache, with all major browsers supported.

  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. Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

    Science.gov (United States)

    Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

    2017-12-01

    α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

  12. Agonist activation of α7 nicotinic acetylcholine receptors via an allosteric transmembrane site

    Science.gov (United States)

    Gill, JasKiran K.; Savolainen, Mari; Young, Gareth T.; Zwart, Ruud; Sher, Emanuele; Millar, Neil S.

    2011-01-01

    Conventional nicotinic acetylcholine receptor (nAChR) agonists, such as acetylcholine, act at an extracellular “orthosteric” binding site located at the interface between two adjacent subunits. Here, we present evidence of potent activation of α7 nAChRs via an allosteric transmembrane site. Previous studies have identified a series of nAChR-positive allosteric modulators (PAMs) that lack agonist activity but are able to potentiate responses to orthosteric agonists, such as acetylcholine. It has been shown, for example, that TQS acts as a conventional α7 nAChR PAM. In contrast, we have found that a compound with close chemical similarity to TQS (4BP-TQS) is a potent allosteric agonist of α7 nAChRs. Whereas the α7 nAChR antagonist metyllycaconitine acts competitively with conventional nicotinic agonists, metyllycaconitine is a noncompetitive antagonist of 4BP-TQS. Mutation of an amino acid (M253L), located in a transmembrane cavity that has been proposed as being the binding site for PAMs, completely blocks agonist activation by 4BP-TQS. In contrast, this mutation had no significant effect on agonist activation by acetylcholine. Conversely, mutation of an amino acid located within the known orthosteric binding site (W148F) has a profound effect on agonist potency of acetylcholine (resulting in a shift of ∼200-fold in the acetylcholine dose-response curve), but had little effect on the agonist dose-response curve for 4BP-TQS. Computer docking studies with an α7 homology model provides evidence that both TQS and 4BP-TQS bind within an intrasubunit transmembrane cavity. Taken together, these findings provide evidence that agonist activation of nAChRs can occur via an allosteric transmembrane site. PMID:21436053

  13. Comparative genomic sequence analysis of the human and mouse cystic fibrosis transmembrane conductance regulator genes

    OpenAIRE

    Ellsworth, Rachel E.; Jamison, D. Curtis; Touchman, Jeffrey W.; Chissoe, Stephanie L.; Braden Maduro, Valerie V.; Bouffard, Gerard G.; Dietrich, Nicole L.; Beckstrom-Sternberg, Stephen M.; Iyer, Leslie M.; Weintraub, Lauren A.; Cotton, Marc; Courtney, Laura; Edwards, Jennifer; Maupin, Rachel; Ozersky, Philip

    2000-01-01

    The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous advances in elucidating the function of the encoded protein and the physiological basis of cystic fibrosis. However, numerous areas of cystic fibrosis biology require additional investigation, some of which would be facilitated by information about the long-range sequence context of the CFTR gene. Fo...

  14. 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 - Neurology Impact factor: 3.999, year: 2009

  15. The PEST sequence does not contribute to the stability of the cystic fibrosis transmembrane conductance regulator

    OpenAIRE

    Chen, Eva Y; Clarke, David M

    2002-01-01

    Abstract Background Endoplasmic reticulum retention of misfolded cystic fibrosis transmembrane conductance regulator (CFTR) mutants and their rapid degradation is the major cause of cystic fibrosis (CF). An important goal is to understand the mechanism of how the misfolded proteins are recognized, retained, and targeted for degradation. Results Using a web-based algorithm, PESTFind, we found a PEST sequence in the regulatory (R) domain of CFTR. The PEST sequence is found in many short-lived e...

  16. 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

  17. 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

  18. Impact of pore and pore-throat distributions on porosity-permeability evolution in heterogeneous mineral dissolution and precipitation scenarios

    Science.gov (United States)

    Beckingham, L. E.; Bensinger, J.; Steinwinder, J.

    2017-12-01

    Porosity and permeability in porous media can be altered by mineral dissolution and precipitation reactions, such as those following CO2 injection in saline aquifers. While the extent of reaction controls changes in porosity, the spatial location of geochemical reactions in individual pores and throats and in the greater pore network controls the evolution of permeability. Geochemical reactions have been observed to occur uniformly on all grain surfaces and non-uniformly, controlled by pore size, PeDa, or mineral distribution, for example. These discrete reaction patterns result in variations in pore scale porosity and corresponding differences in permeability. Macroscopic porosity-permeability relationships are often used to predict the evolution of permeability. These relationships, however, are unable to reflect non-uniform structure modifications. Using pore network modeling simulations, the permeability evolution for a range of uniform and non-uniform mineral reaction scenarios and the applicability of common macroscopic porosity—permeability relationships is investigated. The impact of variations in pore and pore-throat size distributions is evaluated using distributions for real sandstone samples complemented with synthetic distributions. Simulated permeability varies greatly for different reaction patterns. For an Alberta basin sandstone sample, macroscopic relationships are only able to reflect permeability alteration given a uniform reaction scenario where the extent of reaction is related to pore and pore-throat size. For this same sample, simulated permeability for uniform reactions with a fixed reaction thickness and all non-uniform reaction scenarios are unable to be captured using common porosity-permeability relationships. Size-dependent reaction scenarios, where reactions initiate in small or large pores, have the largest disagreement with the porosity-permeability relationships. In these scenarios, porosity-permeability resembles a step function

  19. Transmembrane activator and CAML interactor (TACI) haploinsufficiency results in B-cell dysfunction in patients with Smith-Magenis syndrome.

    Science.gov (United States)

    Chinen, Javier; Martinez-Gallo, Monica; Gu, Wenli; Cols, Montserrat; Cerutti, Andrea; Radigan, Lin; Zhang, Li; Potocki, Lorraine; Withers, Marjorie; Lupski, James R; Cunningham-Rundles, Charlotte

    2011-06-01

    Heterozygous deleterious mutations in the gene encoding the tumor necrosis factor receptor superfamily member 13b (TNFRSF13B), or transmembrane activator and CAML interactor (TACI), have been associated with the development of common variable immunodeficiency. Smith-Magenis syndrome (SMS) is a genetic disorder characterized by developmental delay, behavioral disturbances, craniofacial anomalies, and recurrent respiratory tract infections. Eighty percent of subjects have a chromosome 17p11.2 microdeletion, which includes TACI. The remaining subjects have mutations sparing this gene. We examined TACI protein expression and function in patients with SMS to define the role of TACI haploinsufficiency in B-cell function. We studied TACI expression and function in a cohort of 29 patients with SMS. In patients with SMS with only 1 TACI allele, we found decreased B-cell extracellular and intracellular expression of TACI, reduced binding of a proliferation-inducing ligand, and decreased TACI-induced expression of activation-induced cytidine deaminase mRNA, but these were normal for cells from patients with SMS and 2 TACI alleles. Impaired upregulation of B-cell surface TACI expression by a Toll-like receptor 9 agonist was also observed in cells from patients with 1 TACI allele. Gene sequence analysis of the remaining TACI allele revealed common polymorphisms, with the exception of 1 patient with an amino acid change of uncertain significance. Patients with SMS with the lowest TACI expression had significantly reduced antibody responses to pneumococcal vaccine serotypes. Our findings suggest that haploinsufficiency of the TACI gene results in humoral immune dysfunction, highlighting the role of genomic copy number variants in complex traits. Copyright © 2011 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

  20. Formation of highly efficient dye-sensitized solar cells by hierarchical pore generation with nanoporous TiO{sub 2} spheres

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yong Joo; Lee, Mi Hyeon; Kim, Hark Jin; Lim, Gooil; Choi, Young Sik; Lee, Wan In [Nano Materials and Devices Lab., Department of Chemistry, Inha University Incheon 402-751 (Korea); Park, Nam-Gyu; Kim, Kyungkon [Center for Energy Materials Materials Science and Technology Division, Korea Institute Science and Technology (KIST) Seoul 136-791 (Korea)

    2009-09-25

    Nanoporous TiO{sub 2} structures were successfully applied for the fabrication of DSC electrodes, providing high surface areas and large pore sizes at the same time. High photocurrent was induced in these DSCs by great adsorption of dye molecules and efficient electrolyte diffusion, caused by the generated hierarchical pore structures in the TiO{sub 2} layer. (Abstract Copyright [2009], Wiley Periodicals, Inc.)

  1. Cystic fibrosis transmembrane conductance regulator protein expression in the male excretory duct system during development.

    Science.gov (United States)

    Marcorelles, Pascale; Gillet, Danièle; Friocourt, Gaëlle; Ledé, Françoise; Samaison, Laura; Huguen, Geneviève; Ferec, Claude

    2012-03-01

    Sterility due to bilateral destruction in utero or in early infancy resulting in congenital absence of the vas deferens is the rule in male patients with cystic fibrosis. To understand the developmental pattern of this anomaly, the microscopic morphology of the male excretory system was analyzed during development and the expression of the cystic fibrosis transmembrane conductance regulator protein was explored by immunohistochemistry. We observed that cystic fibrosis fetuses had no excretory ducts agenesis or obstruction until 22 weeks of gestation. However, a focal inflammatory pattern and mucinous plugs in the oldest cystic fibrosis case suggested a disruptive mechanism. Immunolabeling of cytoplasmic epithelial cystic fibrosis transmembrane conductance regulator protein was demonstrated in all cystic fibrosis and control cases with a similar pattern of expression of the protein between age-matched controls and cystic fibrosis cases. At midgestation, an apical intensification appeared in both cystic fibrosis and control cases and was stable during the remainder of fetal life. No gradient of intensity could be detected between the different segments of the excretory tract. These findings are different from those reported in adults. The absence of any morphologic anomaly until 22 weeks of gestation, the focal destruction of the epithelial structures during the second trimester, and the chronological pattern of expression of cystic fibrosis transmembrane conductance regulator are of interest for a better understanding of the pathophysiology of this disease. Copyright © 2012 Elsevier Inc. All rights reserved.

  2. Regulated Erlin-dependent release of the B12 transmembrane J-protein promotes ER membrane penetration of a non-enveloped virus.

    Directory of Open Access Journals (Sweden)

    Takamasa Inoue

    2017-06-01

    Full Text Available The molecular mechanism by which non-enveloped viruses penetrate biological membranes remains enigmatic. The non-enveloped polyomavirus SV40 penetrates the endoplasmic reticulum (ER membrane to reach the cytosol and cause infection. We previously demonstrated that SV40 creates its own membrane penetration structure by mobilizing select transmembrane proteins to distinct puncta in the ER membrane called foci that likely function as the cytosol entry sites. How these ER membrane proteins reorganize into the foci is unknown. B12 is a transmembrane J-protein that mobilizes into the foci to promote cytosol entry of SV40. Here we identify two closely related ER membrane proteins Erlin1 and Erlin2 (Erlin1/2 as B12-interaction partners. Strikingly, SV40 recruits B12 to the foci by inducing release of this J-protein from Erlin1/2. Our data thus reveal how a non-enveloped virus promotes its own membrane translocation by triggering the release and recruitment of a critical transport factor to the membrane penetration site.

  3. 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.

  4. 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.

  5. Imaging Slit Pores Under Delaminated Splats by White Light Interference

    Science.gov (United States)

    Chen, Lin; Gao, Li-li; Yang, Guan-Jun

    2018-01-01

    The slit pores under delaminated films significantly contribute to the properties of the film and the coating. In the present study, a novel and practical technique, the white light interference method, is proposed to characterize the slit pores covered by the 8YSZ and LZ splats. In this method, only an ordinary optical microscopy (OM) is used. Interestingly, colorful Newton's rings and parabolic shapes of the slit pores were clearly observed by OM. The crack spacing and the shapes of the slit pores captured by OM were in good agreement with those obtained by scanning electron microscopy and focus ion beam. Moreover, this is the first time when successful quantitative imaging of the slit pores under the thermal spray splats is achieved. Besides, mechanical analyses were carried out, and the results were consistent with those obtained by OM. In addition, the essential fact that the slit pores were mainly caused by transverse cracking/delamination in the thermal spray coatings was clarified. These results indicate that white light interference is an excellent method to characterize the slit pores under smooth and transparent films.

  6. Imaging Slit Pores Under Delaminated Splats by White Light Interference

    Science.gov (United States)

    Chen, Lin; Gao, Li-li; Yang, Guan-Jun

    2018-02-01

    The slit pores under delaminated films significantly contribute to the properties of the film and the coating. In the present study, a novel and practical technique, the white light interference method, is proposed to characterize the slit pores covered by the 8YSZ and LZ splats. In this method, only an ordinary optical microscopy (OM) is used. Interestingly, colorful Newton's rings and parabolic shapes of the slit pores were clearly observed by OM. The crack spacing and the shapes of the slit pores captured by OM were in good agreement with those obtained by scanning electron microscopy and focus ion beam. Moreover, this is the first time when successful quantitative imaging of the slit pores under the thermal spray splats is achieved. Besides, mechanical analyses were carried out, and the results were consistent with those obtained by OM. In addition, the essential fact that the slit pores were mainly caused by transverse cracking/delamination in the thermal spray coatings was clarified. These results indicate that white light interference is an excellent method to characterize the slit pores under smooth and transparent films.

  7. 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.

  8. Production of disulfide bond-rich peptides by fusion expression using small transmembrane proteins of Escherichia coli.

    Science.gov (United States)

    Chang, Ziwei; Lu, Ming; Ma, Yunqi; Kwag, Dong-Geon; Kim, Seo-Hyun; Park, Ji-Min; Nam, Bo-Hye; Kim, Young-Ok; An, Cheul-Min; Li, Huayue; Jung, Jee H; Park, Jang-Su

    2015-03-01

    Recombinant expression in Escherichia coli allows the simple, economical, and effective production of bioactive peptides. On the other hand, the production of native peptides, particularly those rich in disulfide bonds, is a major problem. Previous studies have reported that the use of carrier proteins for fusion expression can result in good peptide yields, but few are folded correctly. In this study, two transmembrane small proteins in E. coli, YoaJ and YkgR, which both orientate with their N-termini in cytoplasm and their C-termini in periplasm, were used for fusion expression. The recombinant production of two peptides, asteropsin A (ASPA) and β-defensin (BD), was induced in the periplasm of E. coli using a selected carrier protein. Both peptides were expressed at high levels, at yields of approximately 5-10 mg/L of culture. Mass spectrometry showed that the resulting peptide had the same molecular weight as their natural forms. After purification, single peaks were observed by reversed phase high-performance liquid chromatography (RP-HPLC), demonstrating the absence of isoforms. Furthermore, cytoplasmically expressed fusion proteins with a carrier at their C-termini did not contain disulfide bonds. This study provides new carrier proteins for fusion expression of disulfide bond-rich peptides in E. coli.

  9. ER-associated complexes (ERACs) containing aggregated cystic fibrosis transmembrane conductance regulator (CFTR) are degraded by autophagy.

    Science.gov (United States)

    Fu, Lianwu; Sztul, Elizabeth

    2009-04-01

    The ubiquitin-proteasome pathway and autophagy are the two major mechanisms responsible for the clearance of cellular proteins. We have used the yeast Saccharomyces cerevisiae as a model system and the cystic fibrosis transmembrane conductance regulator (CFTR) as a model substrate to study the interactive function of these two pathways in the degradation of misfolded proteins. EGFP-tagged human CFTR was introduced into yeast and expressed under a copper-inducible promoter. The localization and degradation of EGFP-CFTR in live cells were monitored by time-lapse imaging following its de novo synthesis. EGFP-CFTR first appears within the perinuclear and sub-cortical ER and is mobile within the plane of the membrane as assessed by fluorescence recovery after photobleaching (FRAP). This pool of EGFP-CFTR is subsequently degraded through a proteasome-dependent pathway that is inhibited in the pre1-1 yeast strain defective in proteasomal degradation. Prolonged expression of EGFP-CFTR leads to the sequestration of EGFP-CFTR molecules into ER structures called ER-associated complexes (ERACs). The sequestration of EGFP-CFTR into ERACs appears to be driven by aggregation since EGFP-CFTR molecules present within ERACs are immobile as measured by FRAP. Individual ERACs are cleared from cells through the autophagic pathway that is blocked in the atg6Delta and atg1Delta yeast strains defective in autophagy. Our results suggest that the proteasomal and the autophagic pathways function together to clear misfolded proteins from the ER.

  10. 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.

  11. Multiple transmembrane binding sites for p-trifluoromethyldiazirinyl-etomidate, a photoreactive Torpedo nicotinic acetylcholine receptor allosteric inhibitor.

    Science.gov (United States)

    Hamouda, Ayman K; Stewart, Deirdre S; Husain, S Shaukat; Cohen, Jonathan B

    2011-06-10

    Photoreactive derivatives of the general anesthetic etomidate have been developed to identify their binding sites in γ-aminobutyric acid, type A and nicotinic acetylcholine receptors. One such drug, [(3)H]TDBzl-etomidate (4-[3-(trifluoromethyl)-3H-diazirin-3-yl]benzyl-[(3)H]1-(1-phenylethyl)-1H-imidazole-5-carboxylate), acts as a positive allosteric potentiator of Torpedo nACh receptor (nAChR) and binds to a novel site in the transmembrane domain at the γ-α subunit interface. To extend our understanding of the locations of allosteric modulator binding sites in the nAChR, we now characterize the interactions of a second aryl diazirine etomidate derivative, TFD-etomidate (ethyl-1-(1-(4-(3-trifluoromethyl)-3H-diazirin-3-yl)phenylethyl)-1H-imidazole-5-carboxylate). TFD-etomidate inhibited acetylcholine-induced currents with an IC(50) = 4 μM, whereas it inhibited the binding of [(3)H]phencyclidine to the Torpedo nAChR ion channel in the resting and desensitized states with IC(50) values of 2.5 and 0.7 mm, respectively. Similar to [(3)H]TDBzl-etomidate, [(3)H]TFD-etomidate bound to a site at the γ-α subunit interface, photolabeling αM2-10 (αSer-252) and γMet-295 and γMet-299 within γM3, and to a site in the ion channel, photolabeling amino acids within each subunit M2 helix that line the lumen of the ion channel. In addition, [(3)H]TFD-etomidate photolabeled in an agonist-dependent manner amino acids within the δ subunit M2-M3 loop (δIle-288) and the δ subunit transmembrane helix bundle (δPhe-232 and δCys-236 within δM1). The fact that TFD-etomidate does not compete with ion channel blockers at concentrations that inhibit acetylcholine responses indicates that binding to sites at the γ-α subunit interface and/or within δ subunit helix bundle mediates the TFD-etomidate inhibitory effect. These results also suggest that the γ-α subunit interface is a binding site for Torpedo nAChR negative allosteric modulators (TFD-etomidate) and for positive

  12. Multiple Transmembrane Binding Sites for p-Trifluoromethyldiazirinyl-etomidate, a Photoreactive Torpedo Nicotinic Acetylcholine Receptor Allosteric Inhibitor*

    Science.gov (United States)

    Hamouda, Ayman K.; Stewart, Deirdre S.; Husain, S. Shaukat; Cohen, Jonathan B.

    2011-01-01

    Photoreactive derivatives of the general anesthetic etomidate have been developed to identify their binding sites in γ-aminobutyric acid, type A and nicotinic acetylcholine receptors. One such drug, [3H]TDBzl-etomidate (4-[3-(trifluoromethyl)-3H-diazirin-3-yl]benzyl-[3H]1-(1-phenylethyl)-1H-imidazole-5-carboxylate), acts as a positive allosteric potentiator of Torpedo nACh receptor (nAChR) and binds to a novel site in the transmembrane domain at the γ-α subunit interface. To extend our understanding of the locations of allosteric modulator binding sites in the nAChR, we now characterize the interactions of a second aryl diazirine etomidate derivative, TFD-etomidate (ethyl-1-(1-(4-(3-trifluoromethyl)-3H-diazirin-3-yl)phenylethyl)-1H-imidazole-5-carboxylate). TFD-etomidate inhibited acetylcholine-induced currents with an IC50 = 4 μm, whereas it inhibited the binding of [3H]phencyclidine to the Torpedo nAChR ion channel in the resting and desensitized states with IC50 values of 2.5 and 0.7 mm, respectively. Similar to [3H]TDBzl-etomidate, [3H]TFD-etomidate bound to a site at the γ-α subunit interface, photolabeling αM2-10 (αSer-252) and γMet-295 and γMet-299 within γM3, and to a site in the ion channel, photolabeling amino acids within each subunit M2 helix that line the lumen of the ion channel. In addition, [3H]TFD-etomidate photolabeled in an agonist-dependent manner amino acids within the δ subunit M2-M3 loop (δIle-288) and the δ subunit transmembrane helix bundle (δPhe-232 and δCys-236 within δM1). The fact that TFD-etomidate does not compete with ion channel blockers at concentrations that inhibit acetylcholine responses indicates that binding to sites at the γ-α subunit interface and/or within δ subunit helix bundle mediates the TFD-etomidate inhibitory effect. These results also suggest that the γ-α subunit interface is a binding site for Torpedo nAChR negative allosteric modulators (TFD-etomidate) and for positive modulators (TDBzl

  13. 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.

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

    Science.gov (United States)

    Sachtler, Wolfgang M. H.; Huang, Yin-Yan

    1998-01-01

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

  15. 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...... permeability for the medium covered with a filter (3) and furthermore having at least one' channel in fluid contact with the pores of the surface. A pressure difference is established across the filter (3) and both, the filter (3) and the filter cake is passed through the rollers (2,7), whereby the medium...

  16. Scaling theory of pore growth in a reactive solid

    International Nuclear Information System (INIS)

    Kerstein, A.R.; Bug, A.L.R.

    1986-01-01

    Pores in a reactive solid are modeled as a randomly selected fraction p of the bonds of a lattice. Solid bonds adjacent to the open porosity are consumed, leading to the opening of previously closed pores. Just above the pore percolation threshold p/sub c/, exact analysis of the Bethe lattice indicates that the solid is consumed in a time t 0 --ln[ln(1/epsilon)], where epsilon = p-p/sub c/. A scaling argument, supported by computational results, gives t 0 --ln(1/epsilon) for finite-dimensional lattices. Aspects of the time-varying morphology of the solid are examined analytically and computationally

  17. Formation of conical fractures in sedimentary basins: Experiments involving pore fluids and implications for sandstone intrusion mechanisms

    Science.gov (United States)

    Mourgues, R.; Bureau, D.; Bodet, L.; Gay, A.; Gressier, J. B.

    2012-01-01

    Large sand intrusions often exhibit conical morphologies analogous to magmatic intrusions such as saucer-shaped or cup-shaped sills. Whereas some physical processes may be similar, we show with scaled experiments that the formation of conical sand intrusions may be favoured by the pore-pressure gradients prevailing in the host rock before sand injection. Our experiments involve injecting air into a permeable and cohesive analogue material to produce hydraulic fractures while controlling the pore pressure field. We control the state of overpressure in the overburden by applying homogeneous basal pore pressure, and then adding a second local pore pressure field by injecting air via a central injector to initiate hydraulic fractures near the injection point. In experiments involving small vertical effective stresses (small overburden, or high pore fluid overpressure), the fracturing pressure ( λfract) is supralithostatic and two dipping fractures are initiated at the injection point forming a conical structure. From theoretical considerations, we predict that high values of λfract are due to strong cohesion or high pore fluid overpressure distributed in the overburden. Such conditions are favoured by the pore pressure/stress coupling induced by both pore pressure fields. The dips of cones can be accounted for elastic-stress rotation occurring around the source. Contrary to magmatic chamber models, the aqueous fluid overpressure developed in a parent sandbody (and prevailing before the formation of injectites) may diffuse into the surrounding overburden, thus favouring stress rotation and the formation of inclined sheets far from the parent source. For experiments involving higher vertical effective stresses (thick overburden or low pore fluid overpressure), the fracturing pressure is lower than the lithostatic stress, and a single fracture is opened in mode I which then grows vertically. At a critical depth, the fracture separates into two dilatant branches forming

  18. Effect of pore water velocities and solute input methods on chloride transport in the undisturbed soil columns of Loess Plateau

    Science.gov (United States)

    Zhou, BeiBei; Wang, QuanJiu

    2017-09-01

    Studies on solute transport under different pore water velocity and solute input methods in undisturbed soil could play instructive roles for crop production. Based on the experiments in the laboratory, the effect of solute input methods with small pulse input and large pulse input, as well as four pore water velocities, on chloride transport in the undisturbed soil columns obtained from the Loess Plateau under controlled condition was studied. Chloride breakthrough curves (BTCs) were generated using the miscible displacement method under water-saturated, steady flow conditions. Using the 0.15 mol L-1 CaCl2 solution as a tracer, a small pulse (0.1 pore volumes) was first induced, and then, after all the solution was wash off, a large pulse (0.5 pore volumes) was conducted. The convection-dispersion equation (CDE) and the two-region model (T-R) were used to describe the BTCs, and their prediction accuracies and fitted parameters were compared as well. All the BTCs obtained for the different input methods and the four pore water velocities were all smooth. However, the shapes of the BTCs varied greatly; small pulse inputs resulted in more rapid attainment of peak values that appeared earlier with increases in pore water velocity, whereas large pulse inputs resulted in an opposite trend. Both models could fit the experimental data well, but the prediction accuracy of the T-R was better. The values of the dispersivity, λ, calculated from the dispersion coefficient obtained from the CDE were about one order of magnitude larger than those calculated from the dispersion coefficient given by the T-R, but the calculated Peclet number, Pe, was lower. The mobile-immobile partition coefficient, β, decreased, while the mass exchange coefficient increased with increases in pore water velocity.

  19. The impact of kaolin dehydroxylation on the porosity and mechanical integrity of kaolin based ceramics using different pore formers

    Directory of Open Access Journals (Sweden)

    David O. Obada

    Full Text Available Thermally induced lattice defects in kaolin play a key role in the mechanical integrity of kaolin based ceramics during heat treatment due to their phase transformations. The effects of three types of pore formers (sawdust, styrofoam and powdery high density polyethylene on the porosity and mechanical integrity of kaolin based ceramics have been studied based on their batch formulations. The porosity of the ceramic bodies was experimentally determined, while the structure and chemistry of the materials were elucidated via X-ray diffraction (XRD, scanning electron microscopy (SEM, FTIR, DSC/TG/DTA, and zeta potential. The kaolin-based porous samples sintered at 1150 °C exhibited mullite phase transformation attributed to recrystallization effects. Morphologically, open pores were distributed on the sample surfaces due to larger pathways and available channels of eviction of the pore formers. Compressive strength decreased linearly as apparent porosity increased signifying its correlation. The compressive strength showed to be much more sensitive to defects created by dehydroxylation as micro cracks were observed on the sample with HDPE as pore former which could be as a result of large volume change accompanying phase transformations and sensitivity to the dehydroxylation phase. It is noted that the new pore former (HDPE used in this study produced ceramic bodies with porosity as high as 67% and hence the least compressive strength. Keywords: Porosity, Kaolin clay, Mechanical property, Lattice defects, Calcination

  20. Vertical structure of pore pressure under surface gravity waves on a steep, megatidal, mixed sand-gravel-cobble beach

    Science.gov (United States)

    Guest, Tristan B.; Hay, Alex E.

    2017-01-01

    The vertical structure of surface gravity wave-induced pore pressure is investigated within the intertidal zone of a natural, steeply sloping, megatidal, mixed sand-gravel-cobble beach. Results from a coherent vertical array of buried pore pressure sensors are presented in terms of signal phase lag and attenuation as functions of oscillatory forcing frequency and burial depth. Comparison of the observations with the predictions of a theoretical poro-elastic bed response model indicates that the large observed phase lags and attenuation are attributable to interstitial trapped air. In addition to the dependence on entrapped air volume, the pore pressure phase and attenuation are shown to be sensitive to the hydraulic conductivity of the sediment, to the changing mean water depth during the tidal cycle, and to the redistribution/rearrangement of beach face material by energetic wave action during storm events. The latter result indicates that the effects on pore pressure of sediment column disturbance during instrument burial can persist for days to weeks, depending upon wave forcing conditions. Taken together, these results raise serious questions as to the practicality of using pore pressure measurements to estimate the kinematic properties of surface gravity waves on steep, mixed sand-gravel beaches.

  1. 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.

  2. Relationship between pore structure and compressive strength of ...

    Indian Academy of Sciences (India)

    Keywords. Pore structure; compressive strength; concrete; statistical model; mercury intrusion porosimetry (MIP) ... Author Affiliations. J BU1 Z TIAN. College of Water Conservancy and Hydropower Engineering, Hohai University, Nanjing, Jiangsu 210098, People's Republic of China ...

  3. 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.

  4. Straight Pore Microfilter with Efficient Regeneration, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase I project is directed toward development of a novel microfiltration filter that has distinctively narrow pore size...

  5. Straight Pore Microfilter with Efficient Regeneration, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — This Small Business Innovation Research Phase II project is directed toward development of a novel microfiltration filter that has distinctively narrow pore size...

  6. 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

  7. Pore shapes, volume distribution and orientations in monodisperse granular assemblies

    OpenAIRE

    Sufian, Adnan; Russell, Adrian R.; Saadatfar, Mohammad; Whittle, Andrew

    2015-01-01

    The complex mechanical behaviour of granular materials is commonly studied by considering the evolving particle contact network. An often overlooked feature is the influence of micro-scale geometric configuration of pores on the macroscopic response. This paper presents a series of tools to quantify the shape, volume distribution and orientation characteristics of the pore space. The proposed approach is compared against data extracted from physical and numerical experiments with monodisperse...

  8. Relationship between pore structure and compressive strength of ...

    Indian Academy of Sciences (India)

    J BU

    [16] Shi C 1996 Strength, pore structure and permeability of alkali-activated slag mortars. Cem. Concr. Res. 26(10): 1789–. 1799. [17] O'Farrell M, Wild S and Sabir B B 2001 Pore size distribution and compressive strength of waste clay brick mortar. Cem. Concr. Res. 23(1): 81–91. [18] Wen C E, Yamada Y, Shimojima K, ...

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

    Science.gov (United States)

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

    2012-04-13

    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. Copyright © 2012 Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. The lamellar structure of reactive mixtures in porous media: Pore scale experimental imaging and upscaling

    Science.gov (United States)

    Le Borgne, T.; De Anna, P.; Turuban, R.; Jimenez-Martinez, J.; Tabuteau, H.; Meheust, Y.; Ginn, T. R.; Dentz, M.

    2014-12-01

    Effective reaction rates in porous media are controlled by the spatial organization of chemical species concentrations at the pore scale. From high resolution millifluidic pore scale imaging of reactive tracers we report experimental evidence of the formation of well-developed lamellar structures in reactive mixtures transported through porous media (de Anna et al., Environ. Sci. Technol., 2014). The latter are highlighted by a chemioluminescent reaction producing photons that localize along spatially coherent lines, representing hotspots of mixing and reaction at pore scale. These elongated spatial structures are naturally created by the stretching action of the pore scale velocity field, which induces a dynamic deformation of the material elements carrying solutes (Le Borgne et al., Phys. Rev. Lett., 2013). This particular spatial organization is shown to have a major impact on global reactivity by increasing the surface available for reactive mixing and by enhancing local chemical gradients (de Anna et al., Geophys. Res. Lett. 2014). We quantify this phenomenon for different flow topologies using a reactive lamella representation, which links fluid deformation, diffusion and reaction at the elementary scale. The upscaled reaction rates, estimated by integrating the distribution of local deformation rates, are shown to follow different temporal behavior depending on the distribution of local velocity gradients. This approach allows for the systematic evaluation of the temporal evolution of upscaled reaction rates, and establishes a direct link between the global reaction efficiency and the spatial characteristics of the underlying pore scale flow field.References:[1] P. de Anna, J. Jimenez-Martinez, H. Tabuteau, R. Turuban, T. Le Borgne, M. Derrien,and Yves Méheust, Mixing and reaction kinetics in porous media : an experimental pore scale quantification, Environ. Sci. Technol.48, 508-516, 2014. [2] de Anna, P., Dentz, M., Tartakovsky A. and Le Borgne, T., The

  16. Novel molecular determinants in the pore region of sodium channels regulate local anesthetic binding.

    Science.gov (United States)

    Yamagishi, Toshio; Xiong, Wei; Kondratiev, Andre; Vélez, Patricio; Méndez-Fitzwilliam, Ailsa; Balser, Jeffrey R; Marbán, Eduardo; Tomaselli, Gordon F

    2009-10-01

    The pore of the Na+ channel is lined by asymmetric loops formed by the linkers between the fifth and sixth transmembrane segments (S5-S6). We investigated the role of the N-terminal portion (SS1) of the S5-S6 linkers in channel gating and local anesthetic (LA) block using site-directed cysteine mutagenesis of the rat skeletal muscle (Na(V)1.4) channel. The mutants examined have variable effects on voltage dependence and kinetics of fast inactivation. Of the cysteine mutants immediately N-terminal to the putative DEKA selectivity filter in four domains, only Q399C in domain I and F1236C in domain III exhibit reduced use-dependent block. These two mutations also markedly accelerated the recovery from use-dependent block. Moreover, F1236C and Q399C significantly decreased the affinity of QX-314 for binding to its channel receptor by 8.5- and 3.3-fold, respectively. Oddly enough, F1236C enhanced stabilization of slow inactivation by both hastening entry into and delaying recovery from slow inactivation states. It is noteworthy that symmetric applications of QX-314 on both external and internal sides of F1236C mutant channels reduced recovery from use-dependent block, indicating an allosteric effect of external QX-314 binding on the recovery of availability of F1236C. These observations suggest that cysteine mutation in the SS1 region, particularly immediate adjacent to the DEKA ring, may lead to a structural rearrangement that alters binding of permanently charged QX-314 to its receptor. The results lend further support for a role for the selectivity filter region as a structural determinant for local anesthetic block.

  17. 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

  18. Calcitonin Forms Oligomeric Pore-Like Structures in Lipid Membranes

    Science.gov (United States)

    Diociaiuti, Marco; Polzi, Laura Zanetti; Valvo, Luisa; Malchiodi-Albedi, Fiorella; Bombelli, Cecilia; Gaudiano, Maria Cristina

    2006-01-01

    Calcitonin is a polypeptidic hormone involved in calcium metabolism in the bone. It belongs to the amyloid protein family, which is characterized by the common propensity to aggregate acquiring a β-sheet conformation and include proteins associated with important neurodegenerative diseases. Here we show for the first time, to our knowledge, by transmission electron microscopy (TEM) that salmon-calcitonin (sCT) forms annular oligomers similar to those observed for β-amyloid and α-sinuclein (Alzheimer's and Parkinson's diseases). We also investigated the interaction between sCT and model membranes, such as liposomes, with particular attention to the effect induced by lipid “rafts” made of cholesterol and GM1. We observed, by TEM immunogold labeling of sCT, that protein binding is favored by the presence of rafts. In addition, we found by TEM that sCT oligomers inserted in the membrane have the characteristic pore-like morphology of the amyloid proteins. Circular dichroism experiments revealed an increase in β-content in sCT secondary structure when the protein was reconstituted in rafts mimicking liposomes. Finally, we showed, by spectrofluorimetry experiments, that the presence of sCT allowed Ca2+ entry in rafts mimicking liposomes loaded with the Ca2+-specific fluorophore Fluo-4. This demonstrates that sCT oligomers have ion-channel activity. Our results are in good agreement with recent electrophysiological studies reporting that sCT forms Ca2+-permeable ion channels in planar model membranes. It has been proposed that, beyond the well-known interaction of the monomer with the specific receptor, the formation of Ca2+ channels due to sCT oligomers could represent an extra source of Ca2+ entry in osteoblasts. Structural and functional data reported here support this hypothesis. PMID:16940475

  19. The pore-forming toxin listeriolysin O mediates a novel entry pathway of L. monocytogenes into human hepatocytes.

    Directory of Open Access Journals (Sweden)

    Stephen Vadia

    2011-11-01

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

  20. The pore-forming toxin listeriolysin O mediates a novel entry pathway of L. monocytogenes into human hepatocytes.

    Science.gov (United States)

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

    2011-11-01

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

  1. Transgenic nematodes as biosensors for metal stress in soil pore water samples.

    Science.gov (United States)

    Anbalagan, Charumathi; Lafayette, Ivan; Antoniou-Kourounioti, Melissa; Haque, Mainul; King, John; Johnsen, Bob; Baillie, David; Gutierrez, Carmen; Martin, Jose A Rodriguez; de Pomerai, David

    2012-03-01

    Caenorhabditis elegans strains carrying stress-reporter green fluorescent protein transgenes were used to explore patterns of response to metals. Multiple stress pathways were induced at high doses by most metals tested, including members of the heat shock, oxidative stress, metallothionein (mtl) and xenobiotic response gene families. A mathematical model (to be published separately) of the gene regulatory circuit controlling mtl production predicted that chemically similar divalent metals (classic inducers) should show additive effects on mtl gene induction, whereas chemically dissimilar metals should show interference. These predictions were verified experimentally; thus cadmium and mercury showed additive effects, whereas ferric iron (a weak inducer) significantly reduced the effect of mercury. We applied a similar battery of tests to diluted samples of soil pore water extracted centrifugally after mixing 20% w/w ultrapure water with air-dried soil from an abandoned lead/zinc mine in the Murcia region of Spain. In addition, metal contents of both soil and soil pore water were determined by ICP-MS, and simplified mixtures of soluble metal salts were tested at equivalent final concentrations. The effects of extracted soil pore water (after tenfold dilution) were closely mimicked by mixtures of its principal component ions, and even by the single most prevalent contaminant (zinc) alone, though other metals modulated its effects both positively and negatively. In general, mixtures containing similar (divalent) metal ions exhibited mainly additive effects, whereas admixture of dissimilar (e.g. trivalent) ions often resulted in interference, reducing overall levels of stress-gene induction. These findings were also consistent with model predictions.

  2. F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling

    Science.gov (United States)

    Heemskerk, Niels; Schimmel, Lilian; Oort, Chantal; van Rijssel, Jos; Yin, Taofei; Ma, Bin; van Unen, Jakobus; Pitter, Bettina; Huveneers, Stephan; Goedhart, Joachim; Wu, Yi; Montanez, Eloi; Woodfin, Abigail; van Buul, Jaap D.

    2016-01-01

    During immune surveillance and inflammation, leukocytes exit the vasculature through transient openings in the endothelium without causing plasma leakage. However, the exact mechanisms behind this intriguing phenomenon are still unknown. Here we report that maintenance of endothelial barrier integrity during leukocyte diapedesis requires local endothelial RhoA cycling. Endothelial RhoA depletion in vitro or Rho inhibition in vivo provokes neutrophil-induced vascular leakage that manifests during the physical movement of neutrophils through the endothelial layer. Local RhoA activation initiates the formation of contractile F-actin structures that surround emigrating neutrophils. These structures that surround neutrophil-induced endothelial pores prevent plasma leakage through actomyosin-based pore confinement. Mechanistically, we found that the initiation of RhoA activity involves ICAM-1 and the Rho GEFs Ect2 and LARG. In addition, regulation of actomyosin-based endothelial pore confinement involves ROCK2b, but not ROCK1. Thus, endothelial cells assemble RhoA-controlled contractile F-actin structures around endothelial pores that prevent vascular leakage during leukocyte extravasation. PMID:26814335

  3. 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.

  4. 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.

  5. The activation energy for insertion of transmembrane alpha-helices is dependent on membrane composition.

    Science.gov (United States)

    Meijberg, Wim; Booth, Paula J

    2002-06-07

    The physical mechanisms that govern the folding and assembly of integral membrane proteins are poorly understood. It appears that certain properties of the lipid bilayer affect membrane protein folding in vitro, either by modulating helix insertion or packing. In order to begin to understand the origin of this effect, we investigate the effect of lipid forces on the insertion of a transmembrane alpha-helix using a water-soluble, alanine-based peptide, KKAAAIAAAAAIAAWAAIAAAKKKK-amide. This peptide binds to preformed 1,2-dioleoyl-l-alpha-phosphatidylcholine (DOPC) vesicles at neutral pH, but spontaneous transmembrane helix insertion directly from the aqueous phase only occurs at high pH when the Lys residues are de-protonated. These results suggest that the translocation of charge is a major determinant of the activation energy for insertion. Time-resolved measurements of the insertion process at high pH indicate biphasic kinetics with time constants of ca 30 and 430 seconds. The slower phase seems to correlate with formation of a predominantly transmembrane alpha-helical conformation, as determined from the transfer of the tryptophan residue to the hydrocarbon region of the membrane. Temperature-dependent measurements showed that insertion can proceed only above a certain threshold temperature and that the Arrhenius activation energy is of the order of 90 kJ mol(-1). The kinetics, threshold temperature and the activation energy change with the mole fraction of 1,2-dioleoyl-l-alpha-phosphatidylethanolamine (DOPE) introduced into the DOPC membrane. The activation energy increases with increasing DOPE content, which could reflect the fact that this lipid drives the bilayer towards a non-bilayer transition and increases the lateral pressure in the lipid chain region. This suggests that folding events involving the insertion of helical segments across the bilayer can be controlled by lipid forces. (c) 2002 Elsevier Science Ltd.

  6. 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.

  7. Probing the interaction mechanisms between transmembrane peptides and the chaperonin GroEL with fluorescence anisotropy

    Science.gov (United States)

    Wang, Xiaoqiang; Chen, Han; Lu, Xinwei; Chi, Haixia; Li, Shixin; Huang, Fang

    2018-04-01

    Proper translocation, membrane insertion and folding are crucial biophysical steps in the biogenesis of functional transmembrane peptides/proteins (TMPs). ATP-dependent chaperonins are able to regulate each of these processes, but the underlying mechanisms remain unclear. In this work, interaction between the bacterial chaperonin GroEL and a synthetic fluorescent transmembrane peptide was investigated by fluorescence anisotropy. Binding of the peptide with GroEL resulted in increased fluorescence anisotropy and intensity. The dissociation constant and binding stoichiometry, as assessed by titration of the peptide with GroEL, were estimated to be 0.6 ± 0.2 μM and 2.96 ± 0.35, respectively. Complementary study with the single-ring version of GroEL confirmed the high-affinity peptide binding, and indicates that the two GroEL rings may function alternatively in binding the peptides. The co-chaperonin GroES was found to be effective at releasing the peptides initially bound to GroEL with the help of ATP. Moreover, our observation with the single-ring GroEL mutant demonstrated that during the encapsulation of GroEL by GroES, the bound peptides may either be confined in the cage thus formed, or escape outside. Competitive binding experiments indicated that the peptides studied interact with GroEL through the paired helices H and I on its apical domain. Our spectroscopic studies revealed some basic mechanisms of interaction between transmembrane peptides and GroEL, which would be instrumental for deciphering the chaperonin-mediated TMP biogenesis.

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. 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...

  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. 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...

  15. 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.

  16. 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

  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. Three-Dimensional Quantification of Pore Space in Flocculated Sediments

    Science.gov (United States)

    Lawrence, Tom; Spencer, Kate; Bushby, Andy; Manning, Andrew

    2017-04-01

    Flocculated sediment structure plays a vital role in determining sediment dynamics within the water column in fresh and saline water bodies. The porosity of flocs contributes to their specific density and therefore their settling characteristics, and can also affect settling characteristics via through-flow. The process of settling and resuspension of flocculated material causes the formation of larger and more complex individual flocs, about which little is known quantitatively of the internal micro-structure and therefore porosity. Hydrological and sedimentological modelling software currently uses estimations of porosity, because it is difficult to capture and analyse flocs. To combat this, we use a novel microscopy method usually performed on biological material to scan the flocs, the output of which can be used to quantify the dimensions and arrangement of pores. This involves capturing flocculated sediment, staining the sample with heavy metal elements to highlight organic content in the Scanning Electron Microscope later, and finally setting the sample in resin. The overall research aim is to quantitatively characterise the dimensions and distribution of pore space in flocs in three dimensions. In order to gather data, Scanning Electron Microscopy and micro-Computed Tomography have been utilised to produce the necessary images to identify and quantify the pore space. The first objective is to determine the dimensional limits of pores in the structure (i.e. what area do they encapsulate? Are they interconnected or discreet?). This requires a repeatable definition to be established, so that all floc pore spaces can be quantified using the same parameters. The LabSFLOC settling column and dyes will be used as one possible method of determining the outer limits of the discreet pore space. LabSFLOC is a sediment settling column that uses a camera to record the flocs, enabling analysis of settling characteristics. The second objective is to develop a reliable

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

    Science.gov (United States)

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

    2014-12-01

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

  20. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Ewing, R P

    2009-02-25

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

  2. Calcium influx rescues adenylate cyclase-hemolysin from rapid cell membrane removal and enables phagocyte permeabilization by toxin pores.

    Directory of Open Access Journals (Sweden)

    Radovan Fiser

    Full Text Available Bordetella adenylate cyclase toxin-hemolysin (CyaA penetrates the cytoplasmic membrane of phagocytes and employs two distinct conformers to exert its multiple activities. One conformer forms cation-selective pores that permeabilize phagocyte membrane for efflux of cytosolic potassium. The other conformer conducts extracellular calcium ions across cytoplasmic membrane of cells, relocates into lipid rafts, translocates the adenylate cyclase enzyme (AC domain into cells and converts cytosolic ATP to cAMP. We show that the calcium-conducting activity of CyaA controls the path and kinetics of endocytic removal of toxin pores from phagocyte membrane. The enzymatically inactive but calcium-conducting CyaA-AC⁻ toxoid was endocytosed via a clathrin-dependent pathway. In contrast, a doubly mutated (E570K+E581P toxoid, unable to conduct Ca²⁺ into cells, was rapidly internalized by membrane macropinocytosis, unless rescued by Ca²⁺ influx promoted in trans by ionomycin or intact toxoid. Moreover, a fully pore-forming CyaA-ΔAC hemolysin failed to permeabilize phagocytes, unless endocytic removal of its pores from cell membrane was decelerated through Ca²⁺ influx promoted by molecules locked in a Ca²⁺-conducting conformation by the 3D1 antibody. Inhibition of endocytosis also enabled the native B. pertussis-produced CyaA to induce lysis of J774A.1 macrophages at concentrations starting from 100 ng/ml. Hence, by mediating calcium influx into cells, the translocating conformer of CyaA controls the removal of bystander toxin pores from phagocyte membrane. This triggers a positive feedback loop of exacerbated cell permeabilization, where the efflux of cellular potassium yields further decreased toxin pore removal from cell membrane and this further enhances cell permeabilization and potassium efflux.

  3. Multifractal Characteristics of Bimodal Mercury Pore Size Distribution Curves

    Science.gov (United States)

    dos Santos Bonini, C.; Alves, M. C.; Paz González, A.

    2012-04-01

    Characterization of Hg pore size distribution (PSDs) curves by monofractal or multifractal analysis has been demonstrated to be an useful tool, which allows a better understanding of the organization of the soil pore space. There are also evidences that multiscale analysis of different segments found in bimodal pore size distributions measured by Hg intrusion can provide further valuable information. In this study we selected bimodal PSDs from samples taken from an experimental area in São Paulo state, Brazil, where a revegetation trial was set up over saprolitic material. The saprolite was left abandoned after decapitation of an Oxisol for building purposes. The field trial consisted of various treatments with different grass species and amendments. Pore size distribution of the sampled aggregates was measured in the equivalent diameter range from 0.005 to about 50 μm and it was characterized by a bimodal pattern, so that two compartments, i.e. 0.005 to 0.2 μm and 0.2 to 50 μm, could be distinguished. The multifractal theory was used to analyse both segments. The scaling properties of these two segments could be fitted reasonably well with multifractal models. Multifractal parameters obtained for equivalent diameters for the segments > 0.2 and pore size distributions studied.

  4. The Bicomponent Pore-Forming Leucocidins of Staphylococcus aureus

    Science.gov (United States)

    Alonzo, Francis

    2014-01-01

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

  5. Darier disease mutation E917K of SERCA2b relieves the inhibitory influence of the 11th transmembrane segment

    DEFF Research Database (Denmark)

    Mikkelsen, Stine; Holdensen, Anne Nyholm; Vangheluwe, Peter

    partners located in M5, M7 and M10. Hence, mutation of the glutamate to lysine could interfere with these bonds and lead to disturbance of the stabilization of the cytoplasmic loop L8-9. It is believed that the 11th transmembrane segment of SERCA2b is located in the groove between transmembrane segments M7...... to the proteins SERCA1, SERCA2 and SERCA3. SERCA2 is spliced into three variants SERCA2a, SERCA2b and SERCA2c, the only difference between SERCA2a and SERCA2b is the extended C-terminus of SERCA2b (49 amino acids) which forms an extra 11th transmembrane segment (compared with the 10 transmembrane segments of all...... loop between transmembrane segments M8 and M9 (L8-9) and mutation E917K leads to decreased Ca2+ affinity and increased catalytic turnover rate. Our kinetic analysis demonstrates that the increased turnover rate is caused by an increase of the rates of the partial reaction steps E1PE2P, E2PE2 and E2E...

  6. Metal bridges between the PhoQ sensor domain and the membrane regulate transmembrane signaling.

    Science.gov (United States)

    Cho, Uhn Soo; Bader, Martin W; Amaya, Maria F; Daley, Margaret E; Klevit, Rachel E; Miller, Samuel I; Xu, Wenqing

    2006-03-10

    Bacterial histidine kinases respond to environmental stimuli by transducing a signal from an extracytosolic sensor domain to a cytosolic catalytic domain. Among them, PhoQ promotes bacterial virulence and is tightly repressed by the divalent cations such as calcium and magnesium. We have determined the crystal structure of the PhoQ sensor domain from Salmonella typhimurium in the Ca2+-bound state, which reveals a highly negatively charged surface that is in close proximity to the inner membrane. This acidic surface binds at least three Ca2+, which mediate the PhoQ-membrane interaction. Mutagenesis analysis indicates that structural integrity at the membrane proximal region of the PhoQ sensor domain promotes metal-mediated repression. We propose that depletion or displacement of divalent cations leads to charge repulsion between PhoQ and the membrane, which initiates transmembrane signaling through a change in orientation between the PhoQ sensor domain and membrane. Therefore, both PhoQ and the membrane are required for extracytosolic sensing and transmembrane signaling.

  7. Dissecting the functions of conserved prolines within transmembrane helices of the D2 dopamine receptor.

    Science.gov (United States)

    Van Arnam, Ethan B; Lester, Henry A; Dougherty, Dennis A

    2011-10-21

    G protein-coupled receptors (GPCRs) contain a number of conserved proline residues in their transmembrane helices, and it is generally assumed these play important functional and/or structural roles. Here we use unnatural amino acid mutagenesis, employing α-hydroxy acids and proline analogues, to examine the functional roles of five proline residues in the transmembrane helices of the D2 dopamine receptor. The well-known tendency of proline to disrupt helical structure is important at all sites, while we find no evidence for a functional role for backbone amide cis-trans isomerization, another feature associated with proline. At most proline sites, the loss of the backbone NH is sufficient to explain the role of the proline. However, at one site, P210(5.50), a substituent on the backbone N appears to be essential for proper function. Interestingly, the pattern in functional consequences that we see is mirrored in the pattern of structural distortions seen in recent GPCR crystal structures.

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

    Science.gov (United States)

    Culhane, Kelly J; Liu, Yuting; Cai, Yingying; Yan, Elsa C Y

    2015-01-01

    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.

  9. 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.

  10. Structural Organization of a Full-Length Gp130/LIF-R Cytokine Receptor Transmembrane Complex

    Energy Technology Data Exchange (ETDEWEB)

    Skiniotis, G.; Lupardus, P.J.; Martick, M.; Walz, T.; Garcia, K.C.

    2009-05-26

    gp130 is a shared receptor for at least nine cytokines, and can signal either as a homodimer, or as a heterodimer with Leukemia Inhibitory Factor Receptor (LIF-R). Here we biophysically and structurally characterize the full-length, transmembrane form of a quaternary cytokine receptor complex consisting of gp130, LIF-R, the cytokine Ciliary Neurotrophic Factor (CNTF), and its alpha receptor (CNTF-R{alpha}). Thermodynamic analysis indicates that, unlike the cooperative assembly of the symmetric gp130/Interleukin-6/IL-6R{alpha} hexameric complex, CNTF/CNTF-R{alpha} heterodimerizes gp130 and LIF-R via non-cooperative energetics to form an asymmetric 1:1:1:1 complex. Single particle electron microscopic (EM) analysis of the full-length gp130/LIF-R/CNTF-R{alpha}/CNTF quaternary complex elucidates an asymmetric structural arrangement, in which the receptor extracellular and transmembrane segments join as a continuous, rigid unit, poised to sensitively transduce ligand engagement to the membrane-proximal intracellular signaling regions. These studies also enumerate the organizing principles for assembly of the 'tall' class of gp130-family cytokine receptor complexes including LIF, IL-27, IL-12, and others.

  11. 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.

  12. Channel Gating Regulation by the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) First Cytosolic Loop.

    Science.gov (United States)

    Ehrhardt, Annette; Chung, W Joon; Pyle, Louise C; Wang, Wei; Nowotarski, Krzysztof; Mulvihill, Cory M; Ramjeesingh, Mohabir; Hong, Jeong; Velu, Sadanandan E; Lewis, Hal A; Atwell, Shane; Aller, Steve; Bear, Christine E; Lukacs, Gergely L; Kirk, Kevin L; Sorscher, Eric J

    2016-01-22

    In this study, we present data indicating a robust and specific domain interaction between the cystic fibrosis transmembrane conductance regulator (CFTR) first cytosolic loop (CL1) and nucleotide binding domain 1 (NBD1) that allows ion transport to proceed in a regulated fashion. We used co-precipitation and ELISA to establish the molecular contact and showed that binding kinetics were not altered by the common clinical mutation F508del. Both intrinsic ATPase activity and CFTR channel gating were inhibited severely by CL1 peptide, suggesting that NBD1/CL1 binding is a crucial requirement for ATP hydrolysis and channel function. In addition to cystic fibrosis, CFTR dysregulation has been implicated in the pathogenesis of prevalent diseases such as chronic obstructive pulmonary disease, acquired rhinosinusitis, pancreatitis, and lethal secretory diarrhea (e.g. cholera). On the basis of clinical relevance of the CFTR as a therapeutic target, a cell-free drug screen was established to identify modulators of NBD1/CL1 channel activity independent of F508del CFTR and pharmacologic rescue. Our findings support a targetable mechanism of CFTR regulation in which conformational changes in the NBDs cause reorientation of transmembrane domains via interactions with CL1 and result in channel gating. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Construction and genetic selection of small transmembrane proteins that activate the human erythropoietin receptor.

    Science.gov (United States)

    Cammett, Tobin J; Jun, Susan J; Cohen, Emily B; Barrera, Francisco N; Engelman, Donald M; Dimaio, Daniel

    2010-02-23

    This work describes a genetic approach to isolate small, artificial transmembrane (TM) proteins with biological activity. The bovine papillomavirus E5 protein is a dimeric, 44-amino acid TM protein that transforms cells by specifically binding and activating the platelet-derived growth factor beta receptor (PDGFbetaR). We used the E5 protein as a scaffold to construct a retrovirus library expressing approximately 500,000 unique 44-amino acid proteins with randomized TM domains. We screened this library to select small, dimeric TM proteins that were structurally unrelated to erythropoietin (EPO), but specifically activated the human EPO receptor (hEPOR). These proteins did not activate the murine EPOR or the PDGFbetaR. Genetic studies with one of these activators suggested that it interacted with the TM domain of the hEPOR. Furthermore, this TM activator supported erythroid differentiation of primary human hematopoietic progenitor cells in vitro in the absence of EPO. Thus, we have changed the specificity of a protein so that it no longer recognizes its natural target but, instead, modulates an entirely different protein. This represents a novel strategy to isolate small artificial proteins that affect diverse membrane proteins. We suggest the word "traptamer" for these transmembrane aptamers.

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

    Science.gov (United States)

    Sjöstedt, Noora; van den Heuvel, Jeroen J M W; Koenderink, Jan B; Kidron, Heidi

    2017-08-01

    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. The transport activity of the variants was tested in inside-out membrane vesicles from Sf9 insect and human derived HEK293 cells overexpressing ABCG2. Lucifer Yellow and estrone sulfate were used as probe substrates of activity. The expression levels and cellular localization of the variants was compared to the wild-type ABCG2 by western blotting and immunofluorescence microscopy. All studied variants of ABCG2 displayed markedly decreased transport in both Sf9-ABCG2 and HEK293-ABCG2 vesicles. Impaired transport could be explained for some variants by altered expression levels and cellular localization. Moreover, the destructive effect on transport activity of variants G406R, P480L, M515R and T542A is, to our knowledge, reported for the first time. These results indicate that the transmembrane region of ABCG2 is sensitive to amino acid substitution and that patients harboring these ABCG2 variant forms could suffer from unexpected pharmacokinetic events of ABCG2 substrate drugs or have an increased risk for diseases such as gout where ABCG2 is implicated.

  15. HMM_RA: An Improved Method for Alpha-Helical Transmembrane Protein Topology Prediction

    Directory of Open Access Journals (Sweden)

    Changhui Yan

    2008-01-01

    Full Text Available α-helical transmembrane (TM proteins play important and diverse functional roles in cells. The ability to predict the topology of these proteins is important for identifying functional sites and inferring function of membrane proteins. This paper presents a Hidden Markov Model (referred to as HMM_RA that can predict the topology of α-helical transmembrane proteins with improved performance. HMM_RA adopts the same structure as the HMMTOP method, which has five modules: inside loop, inside helix tail, membrane helix, outside helix tail and outside loop. Each module consists of one or multiple states. HMM_RA allows using reduced alphabets to encode protein sequences. Thus, each state of HMM_RA is associated with n emission probabilities, where n is the size of the reduced alphabet set. Direct comparisons using two standard data sets show that HMM_RA consistently outperforms HMMTOP and TMHMM in topology prediction. Specifically, on a high-quality data set of 83 proteins, HMM_RA outperforms HMMTOP by up to 7.6% in topology accuracy and 6.4% in α-helices location accuracy. On the same data set, HMM_RA outperforms TMHMM by up to 6.4% in topology accuracy and 2.9% in location accuracy. Comparison also shows that HMM_RA achieves comparable performance as Phobius, a recently published method.

  16. 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.

  17. ER-mediated control for abundance, quality, and signaling of transmembrane immune receptors in plants

    Directory of Open Access Journals (Sweden)

    Nico eTintor

    2014-02-01

    Full Text Available Plants recognize a wide range of microbes with cell-surface and intracellular immune receptors. Transmembrane pattern recognition receptors (PRRs initiate immune responses upon recognition of cognate ligands characteristic of microbes or aberrant cellular states, designated microbe-associated molecular patterns (MAMPs or danger-associated molecular patterns (DAMPs, respectively. Pattern-triggered immunity (PTI provides a first line of defense that restricts the invasion and propagation of both adapted and non-adapted pathogens. Receptor kinases (RKs and receptor-like proteins (RLPs with an extracellular leucine-rich repeat (LRR or lysine-motif (LysM domain are extensively used as PRRs. The correct folding of the extracellular domain of these receptors is under quality control (QC in the endoplasmic reticulum (ER, which thus provides a critical step in plant immunity. Genetic and structural insight suggests that ERQC regulates not only the abundance and quality of transmembrane receptors but also affects signal sorting between multi-branched pathways downstream of the receptor. However, ERQC dysfunction can also positively stimulate plant immunity, possibly through cell death and DAMP signaling pathways.

  18. Multifunctional Transmembrane Protein Ligands for Cell-Specific Targeting of Plasma Membrane-Derived Vesicles.

    Science.gov (United States)

    Zhao, Chi; Busch, David J; Vershel, Connor P; Stachowiak, Jeanne C

    2016-07-01

    Liposomes and nanoparticles that bind selectively to cell-surface receptors can target specific populations of cells. However, chemical conjugation of ligands to these particles is difficult to control, frequently limiting ligand uniformity and complexity. In contrast, the surfaces of living cells are decorated with highly uniform populations of sophisticated transmembrane proteins. Toward harnessing cellular capabilities, here it is demonstrated that plasma membrane vesicles (PMVs) derived from donor cells can display engineered transmembrane protein ligands that precisely target cells on the basis of receptor expression. These multifunctional targeting proteins incorporate (i) a protein ligand, (ii) an intrinsically disordered protein spacer to make the ligand sterically accessible, and (iii) a fluorescent protein domain that enables quantification of the ligand density on the PMV surface. PMVs that display targeting proteins with affinity for the epidermal growth factor receptor (EGFR) bind at increasing concentrations to breast cancer cells that express increasing levels of EGFR. Further, as an example of the generality of this approach, PMVs expressing a single-domain antibody against green fluorescence protein (eGFP) bind to cells expressing eGFP-tagged receptors with a selectivity of ≈50:1. The results demonstrate the versatility of PMVs as cell targeting systems, suggesting diverse applications from drug delivery to tissue engineering. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Differential transmembrane domain GXXXG motif pairing impacts major histocompatibility complex (MHC) class II structure.

    Science.gov (United States)

    Dixon, Ann M; Drake, Lisa; Hughes, Kelly T; Sargent, Elizabeth; Hunt, Danielle; Harton, Jonathan A; Drake, James R

    2014-04-25

    Major histocompatibility complex (MHC) class II molecules exhibit conformational heterogeneity, which influences their ability to stimulate CD4 T cells and drive immune responses. Previous studies suggest a role for the transmembrane domain of the class II αβ heterodimer in determining molecular structure and function. Our previous studies identified an MHC class II conformer that is marked by the Ia.2 epitope. These Ia.2(+) class II conformers are lipid raft-associated and able to drive both tyrosine kinase signaling and efficient antigen presentation to CD4 T cells. Here, we establish that the Ia.2(+) I-A(k) conformer is formed early in the class II biosynthetic pathway and that differential pairing of highly conserved transmembrane domain GXXXG dimerization motifs is responsible for formation of Ia.2(+) versus Ia.2(-) I-A(k) class II conformers and controlling lipid raft partitioning. These findings provide a molecular explanation for the formation of two distinct MHC class II conformers that differ in their inherent ability to signal and drive robust T cell activation, providing new insight into the role of MHC class II in regulating antigen-presenting cell-T cell interactions critical to the initiation and control of multiple aspects of the immune response.

  20. 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