WorldWideScience

Sample records for atomic-scale intracellular water

  1. Atomic-Scale Sliding Friction on Graphene in Water.

    Science.gov (United States)

    Vilhena, J G; Pimentel, Carlos; Pedraz, Patricia; Luo, Feng; Serena, Pedro A; Pina, Carlos M; Gnecco, Enrico; Pérez, Rubén

    2016-04-26

    The sliding of a sharp nanotip on graphene completely immersed in water is investigated by molecular dynamics (MD) and atomic force microscopy. MD simulations predict that the atomic-scale stick-slip is almost identical to that found in ultrahigh vacuum. Furthermore, they show that water plays a purely stochastic role in sliding (solid-to-solid) friction. These observations are substantiated by friction measurements on graphene grown on Cu and Ni, where, oppositely of the operation in air, lattice resolution is readily achieved. Our results promote friction force microscopy in water as a robust alternative to ultra-high-vacuum measurements. PMID:26982997

  2. Water near intracellular surfaces

    OpenAIRE

    Parsegian, V A; Rau, D C

    1984-01-01

    In this paper we make the following points: Water is perturbed within several angstroms of the surfaces of soluble molecules. Removal of this water can require significant amounts of work, seen as an exponentially varying "hydration force" with respect to molecular separation. The favorable and specific attractions that occur in molecular assembly or in ligand binding imply that the specific association between the molecular surfaces is stronger than the association of those surfaces with wat...

  3. Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour.

    Science.gov (United States)

    Martin, T L; Coe, C; Bagot, P A J; Morrall, P; Smith, G D W; Scott, T; Moody, M P

    2016-01-01

    Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour. PMID:27403638

  4. Atomic-scale Studies of Uranium Oxidation and Corrosion by Water Vapour

    Science.gov (United States)

    Martin, T. L.; Coe, C.; Bagot, P. A. J.; Morrall, P.; Smith, G. D. W.; Scott, T.; Moody, M. P.

    2016-07-01

    Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacial layer of uranium hydride was observed at the oxide-metal interface. Exposure to deuterated water vapour produced an equivalent deuteride signal at the metal-oxide interface, confirming the hydride as originating via the water vapour oxidation mechanism. Hydroxide ions were detected uniformly throughout the oxide, yet showed reduced prominence at the metal interface. These results support a proposed mechanism for the oxidation of uranium in water vapour environments where the transport of hydroxyl species and the formation of hydride are key to understanding the observed behaviour.

  5. Atomic Scale Plasmonic Switch

    OpenAIRE

    Emboras, A.; Niegemann, J.; Ma, P; Haffner, C; Pedersen, A.; Luisier, M.; Hafner, C; Schimmel, T.; Leuthold, J.

    2016-01-01

    The atom sets an ultimate scaling limit to Moore’s law in the electronics industry. While electronics research already explores atomic scales devices, photonics research still deals with devices at the micrometer scale. Here we demonstrate that photonic scaling, similar to electronics, is only limited by the atom. More precisely, we introduce an electrically controlled plasmonic switch operating at the atomic scale. The switch allows for fast and reproducible switching by means of the relocat...

  6. Atomic Scale Plasmonic Switch.

    Science.gov (United States)

    Emboras, Alexandros; Niegemann, Jens; Ma, Ping; Haffner, Christian; Pedersen, Andreas; Luisier, Mathieu; Hafner, Christian; Schimmel, Thomas; Leuthold, Juerg

    2016-01-13

    The atom sets an ultimate scaling limit to Moore's law in the electronics industry. While electronics research already explores atomic scales devices, photonics research still deals with devices at the micrometer scale. Here we demonstrate that photonic scaling, similar to electronics, is only limited by the atom. More precisely, we introduce an electrically controlled plasmonic switch operating at the atomic scale. The switch allows for fast and reproducible switching by means of the relocation of an individual or, at most, a few atoms in a plasmonic cavity. Depending on the location of the atom either of two distinct plasmonic cavity resonance states are supported. Experimental results show reversible digital optical switching with an extinction ratio of 9.2 dB and operation at room temperature up to MHz with femtojoule (fJ) power consumption for a single switch operation. This demonstration of an integrated quantum device allowing to control photons at the atomic level opens intriguing perspectives for a fully integrated and highly scalable chip platform, a platform where optics, electronics, and memory may be controlled at the single-atom level. PMID:26670551

  7. Visions of Atomic Scale Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, T. F. [Cameca Instruments; Miller, Michael K [ORNL; Rajan, Krishna [Iowa State University; Ringer, S. P. [University of Sydney, Australia

    2012-01-01

    A microscope, by definition, provides structural and analytical information about objects that are too small to see with the unaided eye. From the very first microscope, efforts to improve its capabilities and push them to ever-finer length scales have been pursued. In this context, it would seem that the concept of an ultimate microscope would have received much attention by now; but has it really ever been defined? Human knowledge extends to structures on a scale much finer than atoms, so it might seem that a proton-scale microscope or a quark-scale microscope would be the ultimate. However, we argue that an atomic-scale microscope is the ultimate for the following reason: the smallest building block for either synthetic structures or natural structures is the atom. Indeed, humans and nature both engineer structures with atoms, not quarks. So far as we know, all building blocks (atoms) of a given type are identical; it is the assembly of the building blocks that makes a useful structure. Thus, would a microscope that determines the position and identity of every atom in a structure with high precision and for large volumes be the ultimate microscope? We argue, yes. In this article, we consider how it could be built, and we ponder the answer to the equally important follow-on questions: who would care if it is built, and what could be achieved with it?

  8. Probing the metabolic water contribution to intracellular water using oxygen isotope ratios of PO4.

    Science.gov (United States)

    Li, Hui; Yu, Chan; Wang, Fei; Chang, Sae Jung; Yao, Jun; Blake, Ruth E

    2016-05-24

    Knowledge of the relative contributions of different water sources to intracellular fluids and body water is important for many fields of study, ranging from animal physiology to paleoclimate. The intracellular fluid environment of cells is challenging to study due to the difficulties of accessing and sampling the contents of intact cells. Previous studies of multicelled organisms, mostly mammals, have estimated body water composition-including metabolic water produced as a byproduct of metabolism-based on indirect measurements of fluids averaged over the whole organism (e.g., blood) combined with modeling calculations. In microbial cells and aquatic organisms, metabolic water is not generally considered to be a significant component of intracellular water, due to the assumed unimpeded diffusion of water across cell membranes. Here we show that the (18)O/(16)O ratio of PO4 in intracellular biomolecules (e.g., DNA) directly reflects the O isotopic composition of intracellular water and thus may serve as a probe allowing direct sampling of the intracellular environment. We present two independent lines of evidence showing a significant contribution of metabolic water to the intracellular water of three environmentally diverse strains of bacteria. Our results indicate that ∼30-40% of O in PO4 comprising DNA/biomass in early stationary phase cells is derived from metabolic water, which bolsters previous results and also further suggests a constant metabolic water value for cells grown under similar conditions. These results suggest that previous studies assuming identical isotopic compositions for intracellular/extracellular water may need to be reconsidered. PMID:27170190

  9. Probing the metabolic water contribution to intracellular water using oxygen isotope ratios of PO4

    Science.gov (United States)

    Li, Hui; Yu, Chan; Wang, Fei; Chang, Sae Jung; Yao, Jun; Blake, Ruth E.

    2016-05-01

    Knowledge of the relative contributions of different water sources to intracellular fluids and body water is important for many fields of study, ranging from animal physiology to paleoclimate. The intracellular fluid environment of cells is challenging to study due to the difficulties of accessing and sampling the contents of intact cells. Previous studies of multicelled organisms, mostly mammals, have estimated body water composition—including metabolic water produced as a byproduct of metabolism—based on indirect measurements of fluids averaged over the whole organism (e.g., blood) combined with modeling calculations. In microbial cells and aquatic organisms, metabolic water is not generally considered to be a significant component of intracellular water, due to the assumed unimpeded diffusion of water across cell membranes. Here we show that the 18O/16O ratio of PO4 in intracellular biomolecules (e.g., DNA) directly reflects the O isotopic composition of intracellular water and thus may serve as a probe allowing direct sampling of the intracellular environment. We present two independent lines of evidence showing a significant contribution of metabolic water to the intracellular water of three environmentally diverse strains of bacteria. Our results indicate that ˜30–40% of O in PO4 comprising DNA/biomass in early stationary phase cells is derived from metabolic water, which bolsters previous results and also further suggests a constant metabolic water value for cells grown under similar conditions. These results suggest that previous studies assuming identical isotopic compositions for intracellular/extracellular water may need to be reconsidered.

  10. Heat dissipation in atomic-scale junctions

    OpenAIRE

    Lee, Woochul; Kim, Kyeongtae; Jeong, Wonho; Zotti, Linda Angela; Pauly, Fabian; Cuevas, Juan Carlos; Reddy, Pramod

    2013-01-01

    Atomic and single-molecule junctions represent the ultimate limit to the miniaturization of electrical circuits. They are also ideal platforms for testing quantum transport theories that are required to describe charge and energy transfer in novel functional nanometre-scale devices. Recent work has successfully probed electric and thermoelectric phenomena in atomic-scale junctions. However, heat dissipation and transport in atomic-scale devices remain poorly characterized owing to experimenta...

  11. Defining Contact at the Atomic Scale

    OpenAIRE

    Cheng, Shengfeng; Robbins, Mark O.

    2010-01-01

    Molecular dynamics simulations are used to study different definitions of contact at the atomic scale. The roles of temperature, adhesive interactions and atomic structure are studied for simple geometries. An elastic, crystalline substrate contacts a rigid, atomically flat surface or a spherical tip. The rigid surface is formed from a commensurate or incommensurate crystal or an amorphous solid. Spherical tips are made by bending crystalline planes or removing material outside a sphere. In c...

  12. Simulations of atomic-scale sliding friction

    DEFF Research Database (Denmark)

    Sørensen, Mads Reinholdt; Jacobsen, Karsten Wedel; Stoltze, Per

    1996-01-01

    Simulation studies of atomic-scale sliding friction have been performed for a number of tip-surface and surface-surface contacts consisting of copper atoms. Both geometrically very simple tip-surface structures and more realistic interface necks formed by simulated annealing have been studied...... pinning of atoms near the boundary of the interface and is therefore more easily observed for smaller contacts. Depending on crystal orientation and load, frictional wear can also be seen in the simulations. In particular, for the annealed interface-necks which model contacts created by scanning tunneling...

  13. Atomic-scale friction : thermal effects and capillary condensation

    NARCIS (Netherlands)

    Jinesh, Kochupurackal Balakrishna Pillai

    2006-01-01

    This work entitled as "Atomic-scale friction: thermal effects and capillary condensation" is a study on the fundamental aspects of the origin of friction from the atomic-scale. We study two realistic aspects of atomic-scale friction, namely the effect of temperature and the effect of relative humidi

  14. Plasmon resonances in atomic-scale gaps

    CERN Document Server

    Kern, Johannes; Tarakina, Nadezda V; Häckel, Tim; Emmerling, Monika; Kamp, Martin; Huang, Jer-Shing; Biagioni, Paolo; Prangsma, Jord C; Hecht, Bert

    2011-01-01

    Gap modes in resonant plasmonic nanostructures exhibit optical fields whose spatial confinement and near-field enhancement strongly increases for smaller gaps[1]. In the context of augmented light-matter interaction, gap modes are of high interest for various applications such as single-emitter spectroscopy[2-4], quantum optics[5,6], extreme nonlinear optics[7,8], efficient optical switching[9], optical trapping10, and molecular opto-electronics[11]. By means of reproducible self-assembly we have obtained side-by-side aligned gold nanorod dimers with robust gaps reaching well below 0.5 nm. For such atomic-scale gaps extreme splitting of the symmetric and anti-symmetric dimer eigenmodes of more than 800 meV is observed in white-light scattering experiments. Besides providing evidence for atomic-scale gap modes at visible wavelengths with correspondingly small mode volumes and strong field enhancement, our experimental results can serve as a benchmark for electromagnetic modeling beyond local Maxwell theory[12,...

  15. Atomic scale insights into urea-peptide interactions in solution.

    Science.gov (United States)

    Steinke, Nicola; Gillams, Richard J; Pardo, Luis Carlos; Lorenz, Christian D; McLain, Sylvia E

    2016-02-01

    The mechanism by which proteins are denatured by urea is still not well understood, especially on the atomic scale where these interactions occur in vivo. In this study, the structure of the peptide GPG has been investigated in aqueous urea solutions in order to understand the combination of roles that both urea and water play in protein unfolding. Using a combination of neutron diffraction enhanced by isotopic substitution and computer simulations, it was found, in opposition with previous simulations studies, that urea is preferred over water around polar and charged portions of the peptides. Further, it appears that while urea directly replaces water around the nitrogen groups on GPG that urea and water occupy different positions around the peptide bond carbonyl groups. This suggests that urea may in fact weaken the peptide bond, disrupting the peptide backbone, thus ultimately causing denaturation. PMID:26764567

  16. Scanning Josephson spectroscopy on the atomic scale

    Science.gov (United States)

    Randeria, Mallika T.; Feldman, Benjamin E.; Drozdov, Ilya K.; Yazdani, Ali

    2016-04-01

    The Josephson effect provides a direct method to probe the strength of the pairing interaction in superconductors. By measuring the phase fluctuating Josephson current between a superconducting tip of a scanning tunneling microscope and a BCS superconductor with isolated magnetic adatoms on its surface, we demonstrate that the spatial variation of the pairing order parameter can be characterized on the atomic scale. This system provides an example where the local pairing potential suppression is not directly reflected in the spectra measured via quasiparticle tunneling. Spectroscopy with such superconducting tips also shows signatures of previously unexplored Andreev processes through individual impurity-bound Shiba states. The atomic resolution achieved here establishes scanning Josephson spectroscopy as a promising technique for the study of novel superconducting phases.

  17. Nuclear reactor materials at the atomic scale

    Directory of Open Access Journals (Sweden)

    Emmanuelle A. Marquis

    2009-11-01

    Full Text Available With the renewed interest in nuclear energy, developing new materials able to respond to the stringent requirements of the next-generation fission and future fusion reactors has become a priority. An efficient search for such materials requires detailed knowledge of material behaviour under irradiation, high temperatures and corrosive environments. Minimizing the rates of materials degradation will be possible only if the mechanisms by which it occurs are understood. Atomic-scale experimental probing as well as modelling can provide some answers and help predict in-service behaviour. This article illustrates how this approach has already improved our understanding of precipitation under irradiation, corrosion behaviour, and stress corrosion cracking. It is also now beginning to provide guidance for the development of new alloys.

  18. Tight Coupling of Metabolic Oscillations and Intracellular Water Dynamics in Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Thoke, Henrik Seir; Tobiesen, Asger; Brewer, Jonathan R.;

    2015-01-01

    We detected very strong coupling between the oscillating concentration of ATP and the dynamics of intracellular water during glycolysis in Saccharomyces cerevisiae. Our results indicate that: i) dipolar relaxation of intracellular water is heterogeneous within the cell and different from dilute c......2O in a dose-dependent manner. These results offer a new insight into the coupling of an emergent intensive physicochemical property of the cell, i.e. cell-wide water dipolar relaxation, and a central metabolite (ATP) produced by a robustly oscillating metabolic process.......We detected very strong coupling between the oscillating concentration of ATP and the dynamics of intracellular water during glycolysis in Saccharomyces cerevisiae. Our results indicate that: i) dipolar relaxation of intracellular water is heterogeneous within the cell and different from dilute...... conditions, ii) water dipolar relaxation oscillates with glycolysis and in phase with ATP concentration, iii) this phenomenon is scale-invariant from the subcellular to the ensemble of synchronized cells and, iv) the periodicity of both glycolytic oscillations and dipolar relaxation are equally affected by D...

  19. Intracellular water and the cytomatrix: some methods of study and current views

    OpenAIRE

    Clegg, J. S.

    1984-01-01

    The extent to which the properties of water in cells are like those of water in dilute aqueous solutions is a question of broad significance to cell biology. A detailed answer is not available at present, although evidence is accumulating that the properties of at least a large fraction of intracellular water are altered by interactions with cell ultrastructure, notably the cytomatrix. That and related evidence also suggests that the properties, composition, and activities of the "aqueous cyt...

  20. Cellular Metabolic Activity and the Oxygen and Hydrogen Stable Isotope Composition of Intracellular Water and Metabolites

    Science.gov (United States)

    Kreuzer-Martin, H. W.; Hegg, E. L.

    2008-12-01

    Intracellular water is an important pool of oxygen and hydrogen atoms for biosynthesis. Intracellular water is usually assumed to be isotopically identical to extracellular water, but an unexpected experimental result caused us to question this assumption. Heme O isolated from Escherichia coli cells grown in 95% H218O contained only a fraction of the theoretical value of labeled oxygen at a position where the O atom was known to be derived from water. In fact, fewer than half of the oxygen atoms were labeled. In an effort to explain this surprising result, we developed a method to determine the isotope ratios of intracellular water in cultured cells. The results of our experiments showed that during active growth, up to 70% of the oxygen atoms and 50% of the hydrogen atoms in the intracellular water of E. coli are generated during metabolism and can be isotopically distinct from extracellular water. The fraction of isotopically distinct atoms was substantially less in stationary phase and chilled cells, consistent with our hypothesis that less metabolically-generated water would be present in cells with lower metabolic activity. Our results were consistent with and explained the result of the heme O labeling experiment. Only about 40% of the O atoms on the heme O molecule were labeled because, presumably, only about 40% of the water inside the cells was 18O water that had diffused in from the culture medium. The rest of the intracellular water contained 16O atoms derived from either nutrients or atmospheric oxygen. To test whether we could also detect metabolically-derived hydrogen atoms in cellular constituents, we isolated fatty acids from log-phase and stationary phase E. coli and determined the H isotope ratios of individual fatty acids. The results of these experiments showed that environmental water contributed more H atoms to fatty acids isolated in stationary phase than to the same fatty acids isolated from log-phase cells. Stable isotope analyses of

  1. Detection of metabolic fluxes of O and H atoms into intracellular water in mammalian cells.

    Science.gov (United States)

    Kreuzer, Helen W; Quaroni, Luca; Podlesak, David W; Zlateva, Theodora; Bollinger, Nikki; McAllister, Aaron; Lott, Michael J; Hegg, Eric L

    2012-01-01

    Metabolic processes result in the release and exchange of H and O atoms from organic material as well as some inorganic salts and gases. These fluxes of H and O atoms into intracellular water result in an isotopic gradient that can be measured experimentally. Using isotope ratio mass spectroscopy, we revealed that slightly over 50% of the H and O atoms in the intracellular water of exponentially-growing cultured Rat-1 fibroblasts were isotopically distinct from growth medium water. We then employed infrared spectromicroscopy to detect in real time the flux of H atoms in these same cells. Importantly, both of these techniques indicate that the H and O fluxes are dependent on metabolic processes; cells that are in lag phase or are quiescent exhibit a much smaller flux. In addition, water extracted from the muscle tissue of rats contained a population of H and O atoms that were isotopically distinct from body water, consistent with the results obtained using the cultured Rat-1 fibroblasts. Together these data demonstrate that metabolic processes produce fluxes of H and O atoms into intracellular water, and that these fluxes can be detected and measured in both cultured mammalian cells and in mammalian tissue. PMID:22848359

  2. Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors

    OpenAIRE

    Khalilov, Umedjon; Bogaerts, Annemie; Neyts, Erik C.

    2015-01-01

    Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleat...

  3. pH in atomic scale simulations of electrochemical interfaces

    DEFF Research Database (Denmark)

    Rossmeisl, Jan; Chan, Karen; Ahmed, Rizwan;

    2013-01-01

    Electrochemical reaction rates can strongly depend on pH, and there is increasing interest in electrocatalysis in alkaline solution. To date, no method has been devised to address pH in atomic scale simulations. We present a simple method to determine the atomic structure of the metal...

  4. Intracellular water exchange for measuring the dry mass, water mass and changes in chemical composition of living cells.

    Directory of Open Access Journals (Sweden)

    Francisco Feijó Delgado

    Full Text Available We present a method for direct non-optical quantification of dry mass, dry density and water mass of single living cells in suspension. Dry mass and dry density are obtained simultaneously by measuring a cell's buoyant mass sequentially in an H2O-based fluid and a D2O-based fluid. Rapid exchange of intracellular H2O for D2O renders the cell's water content neutrally buoyant in both measurements, and thus the paired measurements yield the mass and density of the cell's dry material alone. Utilizing this same property of rapid water exchange, we also demonstrate the quantification of intracellular water mass. In a population of E. coli, we paired these measurements to estimate the percent dry weight by mass and volume. We then focused on cellular dry density - the average density of all cellular biomolecules, weighted by their relative abundances. Given that densities vary across biomolecule types (RNA, DNA, protein, we investigated whether we could detect changes in biomolecular composition in bacteria, fungi, and mammalian cells. In E. coli, and S. cerevisiae, dry density increases from stationary to exponential phase, consistent with previously known increases in the RNA/protein ratio from up-regulated ribosome production. For mammalian cells, changes in growth conditions cause substantial shifts in dry density, suggesting concurrent changes in the protein, nucleic acid and lipid content of the cell.

  5. Proteoglycans and their heterogeneous glycosaminoglycans at the atomic scale.

    Science.gov (United States)

    Sattelle, Benedict M; Shakeri, Javad; Cliff, Matthew J; Almond, Andrew

    2015-03-01

    Proteoglycan spatiotemporal organization underpins extracellular matrix biology, but atomic scale glimpses of this microarchitecture are obscured by glycosaminoglycan size and complexity. To overcome this, multimicrosecond aqueous simulations of chondroitin and dermatan sulfates were abstracted into a prior coarse-grained model, which was extended to heterogeneous glycosaminoglycans and small leucine-rich proteoglycans. Exploration of relationships between sequence and shape led to hypotheses that proteoglycan size is dependent on glycosaminoglycan unit composition but independent of sequence permutation. Uronic acid conformational equilibria were modulated by adjacent hexosamine sulfonation and iduronic acid increased glycosaminoglycan chain volume and rigidity, while glucuronic acid imparted chain plasticity. Consequently, block copolymeric glycosaminoglycans contained microarchitectures capable of multivalent binding to growth factors and collagen, with potential for interactional synergy at greater chain number. The described atomic scale views of proteoglycans and heterogeneous glycosaminoglycans provide structural routes to understanding their fundamental signaling and mechanical biological roles and development of new biomaterials. PMID:25645947

  6. Interface of transition metal oxides at the atomic scale

    Science.gov (United States)

    Shang, Tong-Tong; Liu, Xin-Yu; Gu, Lin

    2016-09-01

    Remarkable phenomena arise at well-defined heterostructures, composed of transition metal oxides, which is absent in the bulk counterpart, providing us a paradigm for exploring the various electron correlation effects. The functional properties of such heterostructures have attracted much attention in the microelectronic and renewable energy fields. Exotic and unexpected states of matter could arise from the reconstruction and coupling among lattice, charge, orbital and spin at the interfaces. Aberration-corrected scanning transmission electron microscopy (STEM) is a powerful tool to visualize the lattice structure and electronic structure at the atomic scale. In the present study some novel phenomena of oxide heterostructures at the atomic scale are summarized and pointed out from the perspective of electron microscopy.

  7. Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors

    Science.gov (United States)

    Khalilov, Umedjon; Bogaerts, Annemie; Neyts, Erik C.

    2015-12-01

    Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.

  8. Atomic scale simulation of radiation induced formation of dislocation loops

    International Nuclear Information System (INIS)

    Using the Monte Carlo technique, we have developed a model for the Atomic Scale Simulation of the formation of dislocation loops in materials under irradiation. We assume that vacancy interstitial pairs are created by particle impact and diffuse through the solid. Three types of reaction are considered: vacancy interstitial recombination, interstitial association to form a nucleus for a new dislocation loop and incorporation of interstitials into already existing dislocation loops leading to their growth. We have determined the concentration of interstitials, vacancies and dislocation loops, together with the average radius of the latter. Our results are compared with those obtained by using the chemical rate theory and with experimental data on CdTe. Moreover, Atomic Scale Simulations lead to the spatial distribution of dislocation loops, in agreement with TEM experimental observations, and to indications about the distribution of vacancies around these loops. This kind of information is totally missing in the chemical rate theory. (orig.)

  9. Atomic scale modelling of hexagonal structured metallic fission product alloys

    OpenAIRE

    Middleburgh, S. C.; King, D M; Lumpkin, G. R.

    2015-01-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)—making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperature...

  10. Atomic-scale characterization of (mostly zincblende) compound semiconductor heterostructures

    International Nuclear Information System (INIS)

    This paper provides an overview of our recent atomic-scale studies of semiconductor heterostructures, based primarily on combinations of zincblende compound materials grown by molecular beam epitaxy. Interfacial strain due to lattice mismatch inevitably causes growth defects to be introduced. Analysis of defect type and distribution using image filtering allows residual strain to be estimated. Exploratory investigations using aberration-corrected electron microscopy, which enables individual atomic columns to be resolved, are also described

  11. Contact and Alignment Marker Technology for Atomic Scale Device Fabrication

    OpenAIRE

    Zuiddam, M.R.; Rogge, S.; Van Der Drift, E.; Ilge, B; Palasantzas, G.

    1998-01-01

    This article reports on the technology to link atomic scale structures to macroscopic contact pads. Dedicated processes for electrode pattern formation in several materials have been developed and characterised. For pattern formation in CoSi2 a thermal compromise between proper silicide formation and lateral dimension loss has been established. The thermal stability of Pt and W submicron patterns (or the silicides of these) has been investigated. First results, for W in particular, show that ...

  12. Comparison of Coulter volumes with radiometrically determined intracellular water volumes for cultured cells

    Energy Technology Data Exchange (ETDEWEB)

    Burres, N.S.; Cass, C.E.

    1989-05-01

    During methotrexate-induced differentiation of cultured human choriocarcinoma (BeWo) cells, proliferation is inhibited, morphologic and biochemical changes occur, and giant, often multinucleated, cells form. We have used the increase in cell volume as a marker of the mature syncytiotrophoblastlike phenotype. Uninduced and differentiated BeWo cells are not spherical, and theoretical considerations suggested that deviations in shape could result in significant errors in Coulter volume. To determine if the values obtained by electrical pulse sizing reflected the actual mass of BeWo cells, we have evaluated the relationship between Coulter volumes and intracellular water volumes obtained using a shape-independent estimate for eight cell types. A close correlation (r2 = 0.97) was found, indicating that cell volume changes in populations of irregularly shaped cells can be accurately measured using a Coulter instrument.

  13. Understanding the Atomic-Scale World with the Molecular Workbench

    Science.gov (United States)

    Tinker, Robert F.

    2006-12-01

    The Molecular Workbench (MW) is a sophisticated system for developing and delivering interactive learning activities to teach basic concepts that govern atomic and nanoscale phenomena. The system is based on a molecular dynamics model that calculates the motion of atoms, molecules, and other objects in real time as a result of the applicable forces, including Lennard-Jones potentials, electrostatic potentials, elastic bonds, and external fields. Light-atom interactions are modeled with photons of selectable energy that interact with the excited states of atoms. The built-in authoring functions can be used to create or modify learning activities. The ease of creating MW materials has led to over 200 activities contributed by staff and collaborators. Many are housed in a database with fields that include an overview, learning objectives, a description of the central concepts addressed, textbook references, and extensions. MW has been used extensively in classrooms in grades 7-14. In several settings student learning gains have been measured using a pre-posttest design. Research results will be reported that show Overall increases in understanding of atomic scale phenomena at high school and community college levels. The ability to transfer understanding of atomic-scale phenomena to new situations and to reason about macroscopic phenomena on the basis of atomic-scale interactions. Better understanding of difficult questions that required immersive visualization and prediction MW is written in Java, so it runs under all common operating systems, including Mac OSX, Windows, and Linux. It is open source, so it can be shared and copied by any user.

  14. Towards laser-manipulated deposition for atom-scale technologies

    International Nuclear Information System (INIS)

    We have developed an apparatus for nanostructure fabrication based on direct deposition of laser-manipulated cesium vapors onto pyrolitic graphite. Key features of our apparatus are production and manipulation of a longitudinally cooled atom beam, which allows for straightforward operation in the moderate to low flux density conditions. Both unstructured and structured low surface coverage depositions have been carried out and samples carefully analyzed at the atom scale by in situ tunneling microscopy. Results represent a step forward to the realization of a novel technology for space-controlled deposition of few, eventually single, atoms.

  15. An ignition key for atomic-scale engines

    International Nuclear Information System (INIS)

    A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.

  16. Atomic scale structure investigations of epitaxial Fe/Cr multilayers

    International Nuclear Information System (INIS)

    Fe/Cr multilayers were deposited by molecular beam epitaxy on the MgO(1 0 0) substrate. Structural properties of the samples were analyzed by low energy electron diffraction, high resolution transmission electron microscopy (HRTEM), as well as by X-ray reflectivity, conversion electron Mössbauer spectroscopy (CEMS) and Auger electron spectroscopy. Investigations revealed multilayered system built of well-ordered Fe and Cr thin films with (1 0 0) orientation. A high geometrical perfection of the system, i.e. planar form of interfaces and reproducible thickness of layers, was also proven. Fe/Cr interface roughness was determined to be 2–3 atomic layers. CEMS studies allowed to analyze at atomic scale the structure of buried Fe/Cr interfaces, as well as to distinguish origin of interface roughness. Roughnesses resulting from interface corrugations and from the Fe–Cr interdiffusion at interfaces were observed. Fe/Cr multilayers showed strong antiferromagnetic coupling of Fe layers.

  17. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis of the...... hydrogen bonding network in the two bilayers. The second part deals with binary mixtures of sterols with either SM or PC. The results show how the membrane properties may vary substantially depending on the sterol and SM type available, the membrane order and interdigitation being just two of the many...

  18. Atomic-scale disproportionation in amorphous silicon monoxide.

    Science.gov (United States)

    Hirata, Akihiko; Kohara, Shinji; Asada, Toshihiro; Arao, Masazumi; Yogi, Chihiro; Imai, Hideto; Tan, Yongwen; Fujita, Takeshi; Chen, Mingwei

    2016-01-01

    Solid silicon monoxide is an amorphous material which has been commercialized for many functional applications. However, the amorphous structure of silicon monoxide is a long-standing question because of the uncommon valence state of silicon in the oxide. It has been deduced that amorphous silicon monoxide undergoes an unusual disproportionation by forming silicon- and silicon-dioxide-like regions. Nevertheless, the direct experimental observation is still missing. Here we report the amorphous structure characterized by angstrom-beam electron diffraction, supplemented by synchrotron X-ray scattering and computer simulations. In addition to the theoretically predicted amorphous silicon and silicon-dioxide clusters, suboxide-type tetrahedral coordinates are detected by angstrom-beam electron diffraction at silicon/silicon-dioxide interfaces, which provides compelling experimental evidence on the atomic-scale disproportionation of amorphous silicon monoxide. Eventually we develop a heterostructure model of the disproportionated silicon monoxide which well explains the distinctive structure and properties of the amorphous material. PMID:27172815

  19. Atomic-scale disproportionation in amorphous silicon monoxide

    Science.gov (United States)

    Hirata, Akihiko; Kohara, Shinji; Asada, Toshihiro; Arao, Masazumi; Yogi, Chihiro; Imai, Hideto; Tan, Yongwen; Fujita, Takeshi; Chen, Mingwei

    2016-01-01

    Solid silicon monoxide is an amorphous material which has been commercialized for many functional applications. However, the amorphous structure of silicon monoxide is a long-standing question because of the uncommon valence state of silicon in the oxide. It has been deduced that amorphous silicon monoxide undergoes an unusual disproportionation by forming silicon- and silicon-dioxide-like regions. Nevertheless, the direct experimental observation is still missing. Here we report the amorphous structure characterized by angstrom-beam electron diffraction, supplemented by synchrotron X-ray scattering and computer simulations. In addition to the theoretically predicted amorphous silicon and silicon-dioxide clusters, suboxide-type tetrahedral coordinates are detected by angstrom-beam electron diffraction at silicon/silicon-dioxide interfaces, which provides compelling experimental evidence on the atomic-scale disproportionation of amorphous silicon monoxide. Eventually we develop a heterostructure model of the disproportionated silicon monoxide which well explains the distinctive structure and properties of the amorphous material. PMID:27172815

  20. Directing Matter: Toward Atomic-Scale 3D Nanofabrication.

    Science.gov (United States)

    Jesse, Stephen; Borisevich, Albina Y; Fowlkes, Jason D; Lupini, Andrew R; Rack, Philip D; Unocic, Raymond R; Sumpter, Bobby G; Kalinin, Sergei V; Belianinov, Alex; Ovchinnikova, Olga S

    2016-06-28

    Enabling memristive, neuromorphic, and quantum-based computing as well as efficient mainstream energy storage and conversion technologies requires the next generation of materials customized at the atomic scale. This requires full control of atomic arrangement and bonding in three dimensions. The last two decades witnessed substantial industrial, academic, and government research efforts directed toward this goal through various lithographies and scanning-probe-based methods. These technologies emphasize 2D surface structures, with some limited 3D capability. Recently, a range of focused electron- and ion-based methods have demonstrated compelling alternative pathways to achieving atomically precise manufacturing of 3D structures in solids, liquids, and at interfaces. Electron and ion microscopies offer a platform that can simultaneously observe dynamic and static structures at the nano- and atomic scales and also induce structural rearrangements and chemical transformation. The addition of predictive modeling or rapid image analytics and feedback enables guiding these in a controlled manner. Here, we review the recent results that used focused electron and ion beams to create free-standing nanoscale 3D structures, radiolysis, and the fabrication potential with liquid precursors, epitaxial crystallization of amorphous oxides with atomic layer precision, as well as visualization and control of individual dopant motion within a 3D crystal lattice. These works lay the foundation for approaches to directing nanoscale level architectures and offer a potential roadmap to full 3D atomic control in materials. In this paper, we lay out the gaps that currently constrain the processing range of these platforms, reflect on indirect requirements, such as the integration of large-scale data analysis with theory, and discuss future prospects of these technologies. PMID:27183171

  1. The gold/ampicillin interface at the atomic scale

    Science.gov (United States)

    Tarrat, N.; Benoit, M.; Giraud, M.; Ponchet, A.; Casanove, M. J.

    2015-08-01

    In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this paper, the structure of the interface between an ampicillin molecule AMP and three flat gold facets Au(111), Au(110) and Au(100) has been investigated with numerical simulations (dispersion-corrected DFT). Adsorption energies, bond distances and electron densities indicate that the adsorption of AMP on these facets goes through multiple partially covalent bonding. The stability of the AuNP/AMP nanoconjugates is explained by large adsorption energies and their potential antibacterial activity is discussed on the basis of the constrained spatial orientation of the grafted antibiotic.In the fight against antibiotic resistance, gold nanoparticles (AuNP) with antibiotics grafted on their surfaces have been found to be potent agents. Ampicillin-conjugated AuNPs have been thus reported to overcome highly ampicillin-resistant bacteria. However, the structure at the atomic scale of these hybrid systems remains misunderstood. In this paper, the structure of the interface between an ampicillin molecule AMP and three flat gold facets Au(111), Au(110) and Au(100) has been investigated with numerical simulations (dispersion-corrected DFT). Adsorption energies, bond distances and electron densities indicate that the adsorption of AMP on these facets goes through multiple partially covalent bonding. The stability of the AuNP/AMP nanoconjugates is explained by large adsorption energies and their potential antibacterial activity is discussed on the basis of the constrained spatial orientation of the grafted antibiotic. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03318g

  2. Atomic-scale yield and dislocation nucleation in KBr

    Science.gov (United States)

    Filleter, T.; Maier, S.; Bennewitz, R.

    2006-04-01

    Atomic-scale plastic deformation on a KBr(100) surface has been produced and characterized by use of atomic force microscopy (AFM) in ultrahigh vacuum. The structure of displaced material was imaged using noncontact mode AFM after first implementing the sharp silicon tip as an indenter. After indentation the KBr(100) surface is found to exhibit monatomic terraces which are formed via dislocation nucleation and glide. Discontinuities in the force-distance curves recorded during indentation are correlated to the creation of dislocation loops in the crystal. Incipient dislocation nucleation has been characterized as the abrupt monatomic layer displacement of the tip into the sample and the corresponding creation of monatomic terraces. The indenter radius has been found to significantly influence the lateral extent of the dislocation structure and the distribution of force discontinuities during indentation. The shear stress at the yield point was experimentally determined to be 2.5GPa which is consistent with recent theoretical predictions for the ideal shear stress of KBr.

  3. The Atomic scale structure of liquid metal-electrolyte interfaces.

    Science.gov (United States)

    Murphy, B M; Festersen, S; Magnussen, O M

    2016-08-01

    Electrochemical interfaces between immiscible liquids have lately received renewed interest, both for gaining fundamental insight as well as for applications in nanomaterial synthesis. In this feature article we demonstrate that the atomic scale structure of these previously inaccessible interfaces nowadays can be explored by in situ synchrotron based X-ray scattering techniques. Exemplary studies of a prototypical electrochemical system - a liquid mercury electrode in pure NaCl solution - reveal that the liquid metal is terminated by a well-defined atomic layer. This layering decays on length scales of 0.5 nm into the Hg bulk and displays a potential and temperature dependent behaviour that can be explained by electrocapillary effects and contributions of the electronic charge distribution on the electrode. In similar studies of nanomaterial growth, performed for the electrochemical deposition of PbFBr, a complex nucleation and growth behaviour is found, involving a crystalline precursor layer prior to the 3D crystal growth. Operando X-ray scattering measurements provide detailed data on the processes of nanoscale film formation. PMID:27301317

  4. Tuning magnetotransport in a compensated semimetal at the atomic scale

    Science.gov (United States)

    Wang, Lin; Gutiérrez-Lezama, Ignacio; Barreteau, Céline; Ubrig, Nicolas; Giannini, Enrico; Morpurgo, Alberto F.

    2015-11-01

    Either in bulk form, or in atomically thin crystals, layered transition metal dichalcogenides continuously reveal new phenomena. The latest example is 1T'-WTe2, a semimetal found to exhibit the largest known magnetoresistance in the bulk, and predicted to become a topological insulator in strained monolayers. Here we show that reducing the thickness through exfoliation enables the electronic properties of WTe2 to be tuned, which allows us to identify the mechanisms responsible for the observed magnetotransport down to the atomic scale. The longitudinal resistance and the unconventional magnetic field dependence of the Hall resistance are reproduced quantitatively by a classical two-band model for crystals as thin as six monolayers, whereas a crossover to an Anderson insulator occurs for thinner crystals. Besides establishing the origin of the magnetoresistance of WTe2, our results represent a complete validation of the classical theory for two-band electron-hole transport, and indicate that atomically thin WTe2 layers remain gapless semimetals.

  5. Atomic-scale dislocation dynamics in radiation damage environment

    Energy Technology Data Exchange (ETDEWEB)

    Osetsky, Y.; Stoller, R. [Oak Ridge National Laboratory, Materials Science and Technology Div., TN (United States); Bacon, D.J. [Liverpool Univ., Dept. of Engineering Physics (United Kingdom)

    2007-07-01

    Full text of publication follows: The dynamics behavior of dislocations determines mechanical properties of crystalline materials. Long-range interactions between a moving dislocation and other defects can be treated within a continuum approach via interaction of their stress and strain fields. However, a vast contribution to mechanical properties depends on the direct interaction between dislocations and other defects and depends very much on the particular atomic scale structure of the both moving dislocation core and the obstacle. In this work we review recent progress in large-scale modeling of dislocation dynamics in metals at the atomic level by molecular dynamics and statics. We review the modem techniques used to simulate dynamics of dislocations in different lattice structures, the dependence on temperature, strain rate and obstacle size. Examples are given for bcc, fcc and hcp metals where edge and screw dislocations interact with vacancy (loops, voids, stacking fault tetrahedra, etc), self-interstitial clusters and secondary phase precipitates. Attention is paid to interpretation of atomistic results from the point of view of parameterization of continuum models. The latter is vitally necessary for further application in 3-dimensional dislocation dynamics within the multi-scale materials modeling approach. Research sponsored by the Division of Materials Sciences and Engineering and the Office of Fusion Energy Sciences, U.S. Department of Energy, under contract DE-AC0S-00OR22725 with UT-Battelle, LLC. (authors)

  6. The Atomic scale structure of liquid metal-electrolyte interfaces

    Science.gov (United States)

    Murphy, B. M.; Festersen, S.; Magnussen, O. M.

    2016-07-01

    Electrochemical interfaces between immiscible liquids have lately received renewed interest, both for gaining fundamental insight as well as for applications in nanomaterial synthesis. In this feature article we demonstrate that the atomic scale structure of these previously inaccessible interfaces nowadays can be explored by in situ synchrotron based X-ray scattering techniques. Exemplary studies of a prototypical electrochemical system - a liquid mercury electrode in pure NaCl solution - reveal that the liquid metal is terminated by a well-defined atomic layer. This layering decays on length scales of 0.5 nm into the Hg bulk and displays a potential and temperature dependent behaviour that can be explained by electrocapillary effects and contributions of the electronic charge distribution on the electrode. In similar studies of nanomaterial growth, performed for the electrochemical deposition of PbFBr, a complex nucleation and growth behaviour is found, involving a crystalline precursor layer prior to the 3D crystal growth. Operando X-ray scattering measurements provide detailed data on the processes of nanoscale film formation.

  7. The ratio total body potassium/total body water as a measure of the mean intracellular potassium concentration

    International Nuclear Information System (INIS)

    The ratios total body potassium (TBK)/total body water (TBW) and TBK/(TBW-82Br-R) are compared as a measure of the mean intracellular potassium concentration. TBK (40K), THO-distribution volume (TBW) and 82Br space (82Br-R) were measured in 28 controls, in 15 patients with cirrhosis of the liver, and in 37 rsp. 42 mechanically ventilated patients of the intensive care unit. Effects of dehydration, hyperhydration and increased membraneous permeability concerning the ratios 82Br-R/TBW, TBK/TBW and TBK/(TBW-82Br-R) are discussed and evaluated by a theoretical model. In cirrhosis of the liver we found a significantly lowered TBK and simultaneously increased values of TBW and 82Br-R. In critically ill patients TBK was lowered whereas the TBW was normal and the bromide space was increased. We believe that this was due to an increased bromide penetration into cells and to a potassium depletion. It is concluded that: a) In homeostasis of water and electrolytes TBK/TBW is a better measure of the mean intracellular potassium concentration; this is because of a lower standard error and a lower radiation dose. b) In the case of isotonic hyperhydration TBK/(TBW-82Br-R) is a better measure of the mean intracellular potassium concentration than TBK/TBW; within the next 2 weeks it is not possible to make a TBK follow-up. c) In a pathophysiological state with an increased permeability of cells to tracers of the extracellular space TBK/TBW is the better measure for the mean intracellular potassium concentration in patients with normal TBW values. (orig.)

  8. Ratio total body potassium/total body water as a measure of the mean intracellular potassium concentration

    Energy Technology Data Exchange (ETDEWEB)

    Schober, O.; Ollech, J.; Lehr, L.; Hundeshagen, H.

    1981-10-01

    The ratios total body potassium (TBK)/total body water (TBW) and TBK/(TBW-/sup 82/Br-R) are compared as a measure of the mean intracellular potassium concentration. TBK (/sup 40/K), THO-distribution volume (TBW) and /sup 82/Br space (/sup 82/Br-R) were measured in 28 controls, in 15 patients with cirrhosis of the liver, and in 37 rsp. 42 mechanically ventilated patients of the intensive care unit. Effects of dehydration, hyperhydration and increased membraneous permeability concerning the ratios /sup 82/Br-R/TBW, TBK/TBW and TBK/(TBW-/sup 82/Br-R) are discussed and evaluated by a theoretical model. In cirrhosis of the liver we found a significantly lowered TBK and simultaneously increased values of TBW and /sup 82/Br-R. In critically ill patients TBK was lowered whereas the TBW was normal and the bromide space was increased. We believe that this was due to an increased bromide penetration into cells and to a potassium depletion. It is concluded that: a) In homeostasis of water and electrolytes TBK/TBW is a better measure of the mean intracellular potassium concentration; this is because of a lower standard error and a lower radiation dose. b) In the case of isotonic hyperhydration TBK/(TBW-/sup 82/Br-R) is a better measure of the mean intracellular potassium concentration than TBK/TBW; within the next 2 weeks it is not possible to make a TBK follow-up. c) In a pathophysiological state with an increased permeability of cells to tracers of the extracellular space TBK/TBW is the better measure for the mean intracellular potassium concentration in patients with normal TBW values.

  9. EON: software for long time simulations of atomic scale systems

    International Nuclear Information System (INIS)

    The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles

  10. EON: software for long time simulations of atomic scale systems

    Science.gov (United States)

    Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

    2014-07-01

    The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

  11. Atomic-scale investigations of the struct. and dynamics of complex catalytic materials

    Energy Technology Data Exchange (ETDEWEB)

    Karl Sohlberg, Drexel University

    2007-05-16

    By some accounts, catalysis impacts ≥ 30% of GDP in developed countries [Maxwell, I. E. Nature 394, 325-326 (1998)]. Catalysis is the enabling technology for petroleum production, for control of gaseous emissions from petroleum combustion, and for the production of industrial and consumer chemicals. Future applications of catalysis are potentially even more far reaching. There is an ever-growing need to move the economy from a fossil-fuel energy base to cleaner alternatives. Hydrogen-based combustion systems and fuel cells could play a dominant role, given a plentiful and inexpensive source of hydrogen. Photocatalysis is the most promising clean technology for hydrogen production, relying solely on water and sunlight, but performance enhancements in photocatalysis are needed to make this technology economically competitive. Given the enormously wide spread utilization of catalysts, even incremental performance enhancements would have far-reaching benefits for multiple end-use sectors. In the area of fuel and chemical production, such improvements would translate into vast reductions in energy consumption. At the consumption end, improvements in the catalysts involved would yield tremendous reductions in pollution. In the area of photocatalysis, such efficiency improvements could finally render hydrogen an economically viable fuel. Prerequisite to the non-empirical design and refinement of improved catalysts is the identification of the atomic-scale structure and properties of the catalytically active sites. This has become a major industrial research priority. The focus of this research program was to combine atomic-resolution Z-contrast electron microscopy with first-principles density functional theory calculations to deliver an atomic-scale description of heterogeneous catalytic systems that could form the basis for non-empirical design of improved catalysts with greater energy efficiency.

  12. Segmental extracellular and intracellular water distribution and muscle glycogen after 72-h carbohydrate loading using spectroscopic techniques.

    Science.gov (United States)

    Shiose, Keisuke; Yamada, Yosuke; Motonaga, Keiko; Sagayama, Hiroyuki; Higaki, Yasuki; Tanaka, Hiroaki; Takahashi, Hideyuki

    2016-07-01

    Body water content increases during carbohydrate loading because 2.7-4-g water binds each 1 g of glycogen. Bioelectrical impedance spectroscopy (BIS) allows separate assessment of extracellular and intracellular water (ECW and ICW, respectively) in the whole body and each body segment. However, BIS has not been shown to detect changes in body water induced by carbohydrate loading. Here, we aimed to investigate whether BIS had sufficient sensitivity to detect changes in body water content and to determine segmental water distribution after carbohydrate loading. Eight subjects consumed a high-carbohydrate diet containing 12 g carbohydrates·kg body mass(-1)·day(-1) for 72 h after glycogen depletion cycling exercise. Changes in muscle glycogen concentration were measured by (13)C-magnetic resonance spectroscopy, and total body water (TBW) was measured by the deuterium dilution technique (TBWD2O). ICW and ECW in the whole body (wrist-to-ankle) and in each body segment (arm, trunk, and leg) were assessed by BIS. Muscle glycogen concentration [72.7 ± 10.0 (SD) to 169.4 ± 55.9 mmol/kg wet wt, P < 0.001] and TBWD2O (39.3 ± 3.2 to 40.2 ± 3.0 kg, P < 0.05) increased significantly 72 h after exercise compared with baseline, respectively. Whole-body BIS showed significant increases in ICW (P < 0.05), but not in ECW. Segmental BIS showed significant increases in ICW in the legs (P < 0.05), but not in the arms or trunk. Our results suggest that increase in body water after carbohydrate loading can be detected by BIS and is caused by segment-specific increases in ICW. PMID:27231310

  13. Understanding the Atomic-Scale Contrast in Kelvin Probe Force Microscopy

    OpenAIRE

    Nony, Laurent; Foster, Adam S.; Bocquet, Franck; Loppacher, Christian

    2009-01-01

    A numerical analysis of the origin of the atomic-scale contrast in Kelvin probe force microscopy is presented. Atomistic simulations of the tip-sample interaction force field have been combined with a noncontact atomic force microscope simulator including a Kelvin module. The implementation mimics recent experimental results on the (001) surface of a bulk alkali halide crystal for which simultaneous atomic-scale topographical and contact potential difference contrasts were reported. The local...

  14. Understanding the atomic-scale contrast in Kelvin Probe Force Microscopy

    OpenAIRE

    Nony, Laurent; Foster, Adam; Bocquet, Franck; Loppacher, Christian

    2009-01-01

    A numerical analysis of the origin of the atomic-scale contrast in Kelvin probe force microscopy (KPFM) is presented. Atomistic simulations of the tip-sample interaction force field have been combined with a non-contact Atomic Force Microscope/KPFM simulator. The implementation mimics recent experimental results on the (001) surface of a bulk alkali halide crystal for which simultaneous atomic-scale topographical and Contact Potential Difference (CPD) contrasts were reported. The local CPD do...

  15. Atomic scale imaging and spectroscopy of individual electron trap states using force detected dynamic tunnelling

    International Nuclear Information System (INIS)

    We report the first atomic scale imaging and spectroscopic measurements of electron trap states in completely non-conducting surfaces by dynamic tunnelling force microscopy/spectroscopy. Single electrons are dynamically shuttled to/from individual states in thick films of hafnium silicate and silicon dioxide. The new method opens up surfaces that are inaccessible to the scanning tunnelling microscope for imaging and spectroscopy on an atomic scale.

  16. Sensing for intracellular thiols by water-insoluble two-photon fluorescent probe incorporating nanogel

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Xudong; Zhang, Xin; Wang, Shuangqing; Li, Shayu [Beijing National Laboratory for Molecular Sciences, Key laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Hu, Rui, E-mail: hurui@iccas.ac.cn [Beijing National Laboratory for Molecular Sciences, Key laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Li, Yi, E-mail: yili@mail.ipc.ac.cn [Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190 (China); Yang, Guoqiang, E-mail: gqyang@iccas.ac.cn [Beijing National Laboratory for Molecular Sciences, Key laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190 (China)

    2015-04-15

    Highlights: • A novel “turn-on” two-photon fluorescent probe based on a π-conjugated triarylboron luminogen was designed and synthesized. • Fast, selective and sensitive detection of biothiols in 100% aqueous solution by simply loaded on a nanogel. • Single-photon and two-photon fluorescent bioimaging of biothiols in NIH/3T3 fibroblasts. - Abstract: A novel “turn-on” two-photon fluorescent probe containing a π-conjugated triarylboron luminogen and a maleimide moiety DMDP-M based on the photo-induced electron transfer (PET) mechanism for biothiol detection was designed and synthesized. By simply loading the hydrophobic DMDP-M on a cross-linked Pluronic{sup ®} F127 nanogel (CL-F127), a probing system DMDP-M/CL-F127 was established, which shows quick response, high selectivity and sensitivity to cysteine (Cys), homocysteine (Hcy) and glutathione (GSH) in aqueous phase. The DMDP-M/CL-F127 system presented the fastest response to Cys with a rate constant of 0.56 min{sup −1}, and the detection limit to Cys was calculated to be as low as 0.18 μM. The DMDP-M/CL-F127 system has been successfully applied to the fluorescence imaging of biothiols in NIH/3T3 fibroblasts either with single-photon or two-photon excitation because of its high biocompatibility and cell-membrane permeability. The present work provides a general, simple and efficient strategy for the application of hydrophobic molecules to sensing biothiols in aqueous phase, and a novel sensing system for intracellular biothiols fitted for both single-photon and two-photon fluorescence imaging.

  17. Intracellular water in Artemia cysts (brine shrimp): Investigations by deuterium and oxygen-17 nuclear magnetic resonance.

    Science.gov (United States)

    Kasturi, S R; Seitz, P K; Chang, D C; Hazlewood, C F

    1990-08-01

    The dormant cysts of Artemia undergo cycles of hydration-dehydration without losing viability. Therefore, Artemia cysts serve as an excellent intact cellular system for studying the dynamics of water-protein interactions as a function of hydration. Deuterium spin-lattice (T(1)) and spin-spin (T(2)) relaxation times of water in cysts hydrated with D(2)O have been measured for hydrations between 1.5 and 0.1 g of D(2)O per gram of dry solids. When the relaxation rates (I/T(1), I/T(2)) of (2)H and (17)O are plotted as a function of the reciprocal of hydration (1/H), an abrupt change in slope is observed near 0.6 g of D(2)O (or H(2) (17)O)/gram of dry solids, the hydration at which conventional metabolism is activated in this system. The results have been discussed in terms of the two-site and multisite exchange models for the water-protein interaction as well as protein dynamics models. The (2)H and (17)O relaxation rates as a function of hydration show striking similarities to those observed for anisotropic motion of water molecules in protein crystals.It is suggested here that although the simple two-site exchange model or n-site exchange model could be used to explain our data at high hydration levels, such models are not adequate at low hydration levels (<0.6 g H(2)O/g) where several complex interactions between water and proteins play a predominant role in the relaxation of water nuclei. We further suggest that the abrupt change in the slope of I/T(1) as a function of hydration in the vicinity of 0.6 g H(2)O/g is due to a change in water-protein interactions resulting from a variation in the dynamics of protein motion. PMID:19431762

  18. Evaluating fluorescence spectroscopy as a tool to characterize cyanobacteria intracellular organic matter upon simulated release and oxidation in natural water.

    Science.gov (United States)

    Korak, Julie A; Wert, Eric C; Rosario-Ortiz, Fernando L

    2015-01-01

    Intracellular organic matter (IOM) from cyanobacteria may be released into natural waters following cell death in aquatic ecosystems and during oxidation processes in drinking water treatment plants. Fluorescence spectroscopy was evaluated to identify the presence of IOM from three cyanobacteria species during simulated release into natural water and following oxidation processes (i.e. ozone, free chlorine, chloramine, chlorine dioxide). Peak picking and the fluorescence index (FI) were explored to determine which IOM components (e.g., pigments) provide unique and persistent fluorescence signatures with minimal interferences from the background dissolved organic matter (DOM) found in Colorado River water (CRW). When IOM was added to ultrapure water, the fluorescence signature of the three cyanobacteria species showed similarities to each other. Each IOM exhibited a strong protein-like fluorescence and fluorescence at Ex 370 nm and Em 460 nm (FDOM), where commercial fluorescence sensors monitor. All species also had strong phycobiliprotein fluorescence (i.e. phycocyanin or phycoerythrin) in the higher excitation range (500-650 nm). All three IOM isolates had FI values greater than 2. When IOM was added to CRW, phycobiliprotein fluorescence was quenched through interactions between IOM and CRW-DOM. Mixing IOM and CRW demonstrated that protein-like and FDOM intensity responses were not a simple superposition of the starting material intensities, indicating that interactions between IOM and CRW-DOM fluorescing moieties were important. Fluorescence intensity in all regions decreased with exposure to ozone, free chlorine, and chlorine dioxide, but the FI still indicated compositional differences compared to CRW-DOM. The phycobiliproteins in IOM are not promising as a surrogate for IOM release, because their fluorescence intensity is quenched by interactions with DOM and decreased during oxidation processes. Increases in both FDOM intensity and FI are viable qualitative

  19. Intracellular water in Artemia cysts (brine shrimp): Investigations by deuterium and oxygen-17 nuclear magnetic resonance

    OpenAIRE

    Kasturi, S. R.; Seitz, P. K.; Chang, D. C.; Hazlewood, C. F.

    1990-01-01

    The dormant cysts of Artemia undergo cycles of hydration-dehydration without losing viability. Therefore, Artemia cysts serve as an excellent intact cellular system for studying the dynamics of water-protein interactions as a function of hydration. Deuterium spin-lattice (T1) and spin-spin (T2) relaxation times of water in cysts hydrated with D2O have been measured for hydrations between 1.5 and 0.1 g of D2O per gram of dry solids. When the relaxation rates (I/T1, I/T2) of 2H and 17O are plot...

  20. Alterations of the intracellular water and ion concentrations in brain and liver cells during aging as revealed by energy dispersive X-ray microanalysis of bulk specimens

    Energy Technology Data Exchange (ETDEWEB)

    Lustyik, G.; Nagy, I.

    1985-01-01

    Age dependence of the intracellular concentrations of monovalent ions (Na+, K+ and Cl-) was examined in 1, 11 and 25-month-old rat brain and liver cells by using energy dispersive X-ray microanalysis. The in vivo concentrations of Na+, K+ and Cl- ions were calculated from two different measurements: The elemental concentrations were measured in freeze-dried tissue pieces, and the intracellular water content was determined by means of a recently developed X-ray microanalytic method, using frozen-hydrated and fractured bulk specimens as well as subsequent freeze-drying. All the single monovalent ion concentrations and consequently, also the total monovalent ion content showed statistically significant increases during aging in brain cortical neurons. A 3-6% loss of the intracellular water content was accompanied by a 25-45% increase of the monovalent ionic strengths by the age of 25 months. A membrane protective OH radical scavenger (centrophenoxine) reversed the dehydration in the nerve cells of old animals, resulting in a decrease of the intracellular ion concentrations. Aging has a less prominent effect on the water and ion contents of the hepatocytes. The degree of water loss of cytoplasm exceeds that of the nuclei in the liver, suggesting that dominantly the translational steps can be involved in the general age altered slowing down of the protein synthetic machinery, predicted by the membrane hypothesis of aging.

  1. Experimental atomic scale investigation of irradiation effects in CW 316SS and UFG-CW 316SS

    Science.gov (United States)

    Pareige, P.; Etienne, A.; Radiguet, B.

    2009-06-01

    Materials of the core internals of pressurized water reactor (austenitic stainless steels) are subject to neutron irradiation. To understand the ageing mechanisms associated with irradiation and propose life predictions of components or develop new materials, irradiation damage needs to be experimentally investigated. Atomic scale investigation of a neutron-irradiated CW316 SS with the laser pulsed atom probe gives a detailed description of the solute segregation in the austenitic grains. In order to understand the mechanism of solute segregation detected in the neutron-irradiated materials, ion irradiations were performed. These latest irradiations were realized on a CW 316SS as well as on a nanostructured CW 316SS. The study of irradiation effects in a nanograin material allows first, to easily analyse grain boundary segregation and second, to test the behaviour under irradiation of a new nanostructured material. The three aspects of this atomic scale investigation (neutron irradiation effect, model ion irradiation, new nanostructured CW 316 SS) are tackled in this paper.

  2. Atomic-scale structure of single-layer MoS2 nanoclusters

    DEFF Research Database (Denmark)

    Helveg, S.; Lauritsen, J. V.; Lægsgaard, E.;

    2000-01-01

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2...... nanoparticles synthesized on Au(lll), and establishes a new picture of the active edge sires of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in general....

  3. Atomic-scale structure of single-layer MoS2 nanoclusters

    OpenAIRE

    Helveg, S.; Lauritsen, J.V.; Lægsgaard, E.; Stensgaard, I.; Nørskov, Jens Kehlet; Clausen, B.S, Helveg S; Topsøe, H.; Besenbacher, Flemming

    2000-01-01

    We have studied using scanning tunneling microscopy (STM) the atomic-scale realm of molybdenum disulfide (MoS2) nanoclusters, which are of interest as a model system in hydrodesulfurization catalysis. The STM gives the first real space images of the shape and edge structure of single-layer MoS2 nanoparticles synthesized on Au(lll), and establishes a new picture of the active edge sires of the nanoclusters. The results demonstrate a way to get detailed atomic-scale information on catalysts in ...

  4. Vacuolar cytoplasmic phase separation in cultured mammalian cells involves the microfilament network and reduces motional properties of intracellular water.

    Science.gov (United States)

    Henics, T; Wheatley, D N

    1997-10-01

    Hep-2, human epithelial carcinoma cells, and human foreskin fibroblasts (FF9 and FF13) were exposed to either an ultrafiltrate (induction vacuoles were irregular and often appeared membraneless, with little in the way of electron-dense content. They started to form in the perinuclear cytoplasm and progressed towards the periphery. Osmotic stress was not involved since mitochondria remained normal throughout a vacuolization episode. Vacuoles were often seen in close contact with filamentous structures, and this association remained detectable at late stages of the phenomenon. Fluorescent visualization of F-actin confirmed that the vacuoles were frequently bordered by microfilaments. No major metabolic impairment was apparent in vacuolized cells as judged by protein synthesis measurements, but nuclear fluorescence (DNA content) and forward light scatter (nuclear volume) by flow cytometric analysis suggested late S phase and G2 retardation. 1H-nmr relaxation measurements indicated intracellular water restricted in motional characteristics in vacuolized cells. The possibility of a restricted cytoplasmic phase separation as part of a transient adaptation response is raised, and a hypothesis to explain the findings is discussed. PMID:9462232

  5. Visible Light Emission from Atomic Scale Patterns Fabricated by the Scanning Tunneling Microscope

    DEFF Research Database (Denmark)

    Thirstrup, C.; Sakurai, M.; Stokbro, Kurt; Aono, M.

    1999-01-01

    Scanning tunneling microscope (STM) induced light emission from artificial atomic scale structures comprising silicon dangling bonds on hydrogen-terminated Si(001) surfaces has been mapped spatially and analyzed spectroscopically in the visible spectral range. The light emission is based on a novel...

  6. Understanding the atomic-scale contrast in Kelvin Probe Force Microscopy

    CERN Document Server

    Nony, Laurent; Bocquet, Franck; Loppacher, Christian; 10.1103/PhysRevLett.103.036802

    2009-01-01

    A numerical analysis of the origin of the atomic-scale contrast in Kelvin probe force microscopy (KPFM) is presented. Atomistic simulations of the tip-sample interaction force field have been combined with a non-contact Atomic Force Microscope/KPFM simulator. The implementation mimics recent experimental results on the (001) surface of a bulk alkali halide crystal for which simultaneous atomic-scale topographical and Contact Potential Difference (CPD) contrasts were reported. The local CPD does reflect the periodicity of the ionic crystal, but not the magnitude of its Madelung surface potential. The imaging mechanism relies on the induced polarization of the ions at the tip-surface interface owing to the modulation of the applied bias voltage. Our findings are in excellent agreement with previous theoretical expectations and experimental observations.

  7. Atomic scale mass delivery driven by bend kink in single walled carbon nanotube

    International Nuclear Information System (INIS)

    The possibility of atomic scale mass delivery by bend kink in single walled carbon nanotube was investigated with the aid of molecular dynamics simulation. By keeping the bending angle while moving the tube end, the encapsulated atomic scale mass such as atom, molecule and atom group were successfully delivered through the nanotube. The van der Waals interaction between the encapsulated mass and the tube wall provided the driving force for the delivery. There were no dramatic changes in the van der Waals interaction, and a smooth and steady delivery was achieved when constant loading rate was applied. The influence of temperature on the atom group delivery was also analyzed. It is found raising temperature is harmful to the smooth movement of the atom group. However, the delivery rate can be promoted under higher temperature when the atom group is situated before the kink during the delivery.

  8. Is atomic-scale dissipation in NC-AFM real? Investigation using virtual atomic force microscopy

    International Nuclear Information System (INIS)

    Using a virtual dynamic atomic force microscope, that explicitly simulates the operation of a non-contact AFM experiment, we have performed calculations to investigate the formation of atomic-scale contrast in dissipation images. A non-conservative tip-surface interaction was implemented using the theory of dynamical response in scanning probe microscopy with energies and barriers derived from realistic atomistic modelling. It is shown how contrast in the damping signal is due to the hysteresis in the tip-surface force and not an artefact of the finite response of the complicated instrumentation. Topography and dissipation images of the CaO(001) surface are produced which show atomic-scale contrast in the dissipation with a corrugation of approximately 0.1 eV, which is typical of that observed in images of similar binary ionic surfaces. The effect of the fast-direction scanning speed on the image formation is also investigated and discussed

  9. Sensing and atomic-scale structure analysis of single nuclear spin clusters in diamond

    OpenAIRE

    Shi, Fazhan; Kong, Xi; Wang, Pengfei; Kong, Fei; Zhao, Nan; Liu, Ren-Bao; Du, Jiangfeng

    2013-01-01

    Single-molecule nuclear magnetic resonance (NMR) is a crown-jewel challenge in the field of magnetic resonance spectroscopy and has important applications in chemical analysis and in quantum computing. Recently, it becomes possible to tackle this grand challenge thanks to experimental advances in preserving quantum coherence of nitrogen-vacancy (NV) center spins in diamond as a sensitive probe and theoretical proposals on atomic-scale magnetometry via dynamical decoupling control. Through dec...

  10. LATERAL MAPPING OF ATOMIC SCALE INTERFACE MORPHOLOGY AND DISLOCATIONS IN QUANTUM WELLS BY CATHODOLUMINESCENCE IMAGING

    OpenAIRE

    Christen, J.; Bimberg, D.

    1989-01-01

    Our present knowledge of the atomic scale structural, chemical and electronic properties of semiconductor interfaces is inversely proportional to their importance for a whole generation of novel electronic and photonic quantum well devices. It is the purpose of this paper to demonstrate how wavelength- and time-resolved cathodoluminescence imaging (CLI) provides a one-to-one image of the crystallographic island structure of the heterointerfaces which are the boundaries of the quantum well. A ...

  11. The Atomic-scale Finite Element Method for Analyzing Mechanical Behavior of Carbon Nanotube and Quartz

    OpenAIRE

    Kim, Kyusang

    2006-01-01

    The mechanical behavior of discrete atoms has been studied with molecular dynamics whose computational time is proportional to the square of the number of atoms, O(N2). Recently, a faster algorithm, Atomic-scale Finite Element Method (AFEM) with computational time proportional to the number of atoms, O(N), had been developed. The main idea of AFEM, compared with conventional finite element method is to replace nodes with atoms and elements with electric forces between atoms. When interpreting...

  12. Dislocations and elementary processes of plasticity in FCC metals: atomic scale simulations

    International Nuclear Information System (INIS)

    We present atomic-scale simulations of two elementary processes of FCC crystal plasticity. The first study consists in the simulation by molecular dynamics, in a nickel crystal, of the interactions between an edge dislocation and glissile interstitial loops of the type that form under irradiation in displacement cascades. The simulations show various atomic-scale interaction processes leading to the absorption and drag of the loops by the dislocation. These reactions certainly contribute to the formation of the 'clear bands' observed in deformed irradiated materials. The simulations also allow to study quantitatively the role of the glissile loops in irradiation hardening. In particular, dislocation unpinning stresses for certain pinning mechanisms are evaluated from the simulations. The second study consists first in the generalization in three dimensions of the quasi-continuum method (QCM), a multi-scale simulation method which couples atomistic techniques and the finite element method. In the QCM, regions close to dislocation cores are simulated at the atomic-scale while the rest of the crystal is simulated with a lower resolution by means of a discretization of the displacement fields using the finite element method. The QCM is then tested on the simulation of the formation and breaking of dislocation junctions in an aluminum crystal. Comparison of the simulations with an elastic model of dislocation junctions shows that the structure and strength of the junctions are dominated by elastic line tension effects, as is assumed in classical theories. (author)

  13. Atomic-scale photonic hybrids for mid-infrared and terahertz nanophotonics

    Science.gov (United States)

    Caldwell, Joshua D.; Vurgaftman, Igor; Tischler, Joseph G.; Glembocki, Orest J.; Owrutsky, Jeffrey C.; Reinecke, Thomas L.

    2016-01-01

    The field of nanophotonics focuses on the ability to confine light to nanoscale dimensions, typically much smaller than the wavelength of light. The goal is to develop light-based technologies that are impossible with traditional optics. Subdiffractional confinement can be achieved using either surface plasmon polaritons (SPPs) or surface phonon polaritons (SPhPs). SPPs can provide a gate-tunable, broad-bandwidth response, but suffer from high optical losses; whereas SPhPs offer a relatively low-loss, crystal-dependent optical response, but only over a narrow spectral range, with limited opportunities for active tunability. Here, motivated by the recent results from monolayer graphene and multilayer hexagonal boron nitride heterostructures, we discuss the potential of electromagnetic hybrids -- materials incorporating mixtures of SPPs and SPhPs -- for overcoming the limitations of the individual polaritons. Furthermore, we also propose a new type of atomic-scale hybrid the crystalline hybrid -- where mixtures of two or more atomic-scale (~3 nm or less) polar dielectric materials lead to the creation of a new material resulting from hybridized optic phonon behaviour of the constituents, potentially allowing direct control over the dielectric function. These atomic-scale hybrids expand the toolkit of materials for mid-infrared to terahertz nanophotonics and could enable the creation of novel actively tunable, yet low-loss optics at the nanoscale.

  14. Atomic scale observation of oxygen delivery during silver-oxygen nanoparticle catalysed oxidation of carbon nanotubes

    Science.gov (United States)

    Yue, Yonghai; Yuchi, Datong; Guan, Pengfei; Xu, Jia; Guo, Lin; Liu, Jingyue

    2016-07-01

    To probe the nature of metal-catalysed processes and to design better metal-based catalysts, atomic scale understanding of catalytic processes is highly desirable. Here we use aberration-corrected environmental transmission electron microscopy to investigate the atomic scale processes of silver-based nanoparticles, which catalyse the oxidation of multi-wall carbon nanotubes. A direct semi-quantitative estimate of the oxidized carbon atoms by silver-based nanoparticles is achieved. A mechanism similar to the Mars-van Krevelen process is invoked to explain the catalytic oxidation process. Theoretical calculations, together with the experimental data, suggest that the oxygen molecules dissociate on the surface of silver nanoparticles and diffuse through the silver nanoparticles to reach the silver/carbon interfaces and subsequently oxidize the carbon. The lattice distortion caused by oxygen concentration gradient within the silver nanoparticles provides the direct evidence for oxygen diffusion. Such direct observation of atomic scale dynamics provides an important general methodology for investigations of catalytic processes.

  15. Atomic-scale friction modulated by potential corrugation in multi-layered graphene materials

    International Nuclear Information System (INIS)

    Friction is an important issue that has to be carefully treated for the fabrication of graphene-based nano-scale devices. So far, the friction mechanism of graphene materials on the atomic scale has not yet been clearly presented. Here, first-principles calculations were employed to unveil the friction behaviors and their atomic-scale mechanism. We found that potential corrugations on sliding surfaces dominate the friction force and the friction anisotropy of graphene materials. Higher friction forces correspond to larger corrugations of potential energy, which are tuned by the number of graphene layers. The friction anisotropy is determined by the regular distributions of potential energy. The sliding along a fold-line path (hollow-atop-hollow) has a relatively small potential energy barrier. Thus, the linear sliding observed in macroscopic friction experiments may probably be attributed to the fold-line sliding mode on the atomic scale. These findings can also be extended to other layer-structure materials, such as molybdenum disulfide (MoS2) and graphene-like BN sheets

  16. Atomic-scale friction modulated by potential corrugation in multi-layered graphene materials

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, Chunqiang, E-mail: chunqiang.zhuang@bjut.edu.cn [Beijing Key Laboratory of Microstructure and Properties of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Liu, Lei [Institute of Earthquake Science, China Earthquake Administration, Beijing 10036 (China)

    2015-03-21

    Friction is an important issue that has to be carefully treated for the fabrication of graphene-based nano-scale devices. So far, the friction mechanism of graphene materials on the atomic scale has not yet been clearly presented. Here, first-principles calculations were employed to unveil the friction behaviors and their atomic-scale mechanism. We found that potential corrugations on sliding surfaces dominate the friction force and the friction anisotropy of graphene materials. Higher friction forces correspond to larger corrugations of potential energy, which are tuned by the number of graphene layers. The friction anisotropy is determined by the regular distributions of potential energy. The sliding along a fold-line path (hollow-atop-hollow) has a relatively small potential energy barrier. Thus, the linear sliding observed in macroscopic friction experiments may probably be attributed to the fold-line sliding mode on the atomic scale. These findings can also be extended to other layer-structure materials, such as molybdenum disulfide (MoS{sub 2}) and graphene-like BN sheets.

  17. Atomic-scale observation of hydrogen-induced crack growth by atom-probe FIM

    International Nuclear Information System (INIS)

    Formation and propagation of a microcrack due to hydrogen in a Fe-0.29 wt.% Ti alloy was observed at the atomic scale by field ion microscopy. A microcrack (-20 nm in length) formed and became noticeably large when the tip was heated at 9500C in the presence of about 1 torr of Hg. Propagation was reported several times by reheating, until a portion of the tip ruptured and became detached from the tip. Compositional analysis, performed in situ using a high performance atom-probe, identified atomic hydrogen in quantity and some hydrogen molecules and FEH in the crack, but not elsewhere on the surface

  18. Spin-flip induction of Fano resonance upon electron tunneling through atomic-scale spin structures

    Energy Technology Data Exchange (ETDEWEB)

    Val' kov, V. V., E-mail: vvv@iph.krasn.ru; Aksenov, S. V., E-mail: asv86@iph.krasn.ru [Russian Academy of Sciences, Siberian Branch, Kirensky Institute of Physics (Russian Federation); Ulanov, E. A. [Siberian State Aerospace University (Russian Federation)

    2013-05-15

    The inclusion of inelastic spin-dependent electron scatterings by the potential profiles of a single magnetic impurity and a spin dimer is shown to induce resonance features due to the Fano effect in the transport characteristics of such atomic-scale spin structures. The spin-flip processes leading to a configuration interaction of the system's states play a fundamental role for the realization of Fano resonance and antiresonance. It has been established that applying an external magnetic field and a gate electric field allows the conductive properties of spin structures to be changed radically through the Fano resonance mechanism.

  19. Quantum mechanical study of the coupling of plasmon excitations to atomic-scale electron transport

    International Nuclear Information System (INIS)

    The coupling of optical excitation and electron transport through a sodium atom in a plasmonic dimer junction is investigated using time-dependent density functional theory. The optical absorption and dynamic conductance is determined as a function of gap size. Surface plasmons are found to couple to atomic-scale transport through several different channels including dipolar, multipolar, and charge transfer plasmon modes. These findings provide insight into subnanoscale couplings of plasmons and atoms, a subject of general interest in plasmonics and molecular electronics.

  20. Single atom-scale diamond defect allows a large Aharonov-Casher phase

    International Nuclear Information System (INIS)

    We propose an experiment that would produce and measure a large Aharonov-Casher (AC) phase in a solid-state system under macroscopic motion. A diamond crystal is mounted on a spinning disk in the presence of a uniform electric field. Internal magnetic states of a single nitrogen-vacancy (N-V) defect, replacing interferometer trajectories, are coherently controlled by microwave pulses. The AC phase shift is manifested as a relative phase, of up to 17 radians, between components of a superposition of magnetic substates, which is two orders of magnitude larger than that measured in any other atom-scale quantum system.

  1. Ultrafast, laser-based, x-ray science: the dawn of atomic-scale cinematography

    International Nuclear Information System (INIS)

    The characteristics of ultrafast chirped pulse amplification systems are reviewed. Application of ultrafast chirped pulse amplification to the generation of femtosecond, incoherent, 8-keV line radiation is outlined and the use of femtosecond laser-based, x-rays for novel time-resolved diffraction studies of crystalline dynamics with sub-picosecond temporal resolution and sub-picometer spatial resolution is reviewed in detail. Possible extensions of laser-based, x-ray technology and evaluation of alternative x-ray approaches for time-resolved studies of the atomic scale dynamics are given. (author)

  2. Atomic-Scale Magnetic Properties of Truly 3d-Diluted ZnO

    DEFF Research Database (Denmark)

    Mantovan, Roberto; Gunnlaugsson, Haraldur Pall; Johnston, Karl; Masenda, Hilary; Mølholt, Torben Esmann; Naidoo, Deena; Ncube, Mehluli; Shayestehaminzadeh, Seyedmohammad; Bharuth-Ram, Krish; Fanciulli, Marco; Gislason, Haflidi Petur; Langouche, Guido; Olafsson, Sveinn; Pereira, Lino M. C.; Wahl, Ulrich; Torelli, Piero; Weyer, Gerd

    In search for dilute magnetic semiconductors, the magnetic properties at the atomic-scale of Fe atoms incorporated in ZnO, in a concentration range of more than five orders of magnitude from 1 x 10(-5) to 2.2 at% have been probed using emission 57 Fe Mossbauer spectroscopy on implanted Mn-57 and Co...... any signature of magnetic ordering up to 2.2 at%. Despite the many reports of dilute magnetism in 3d-doped ZnO, this atomic level study shows no evidence of any long-range magnetic ordering between isolated Fe atoms incorporated in the ZnO lattice....

  3. Atomic-Scale Modeling of Particle Size Effects for the Oxygen Reduction Reaction of Pt

    DEFF Research Database (Denmark)

    Tritsaris, Georgios; Greeley, Jeffrey Philip; Rossmeisl, Jan;

    2011-01-01

    both the specific and mass activities for particle sizes in the range between 2 and 30 nm. The mass activity is calculated to be maximized for particles of a diameter between 2 and 4 nm. Our study demonstrates how an atomic-scale description of the surface microstructure is a key component in...... understanding particle size effects on the activity of catalytic nanoparticles.......We estimate the activity of the oxygen reduction reaction on platinum nanoparticles of sizes of practical importance. The proposed model explicitly accounts for surface irregularities and their effect on the activity of neighboring sites. The model reproduces the experimentally observed trends in...

  4. Ultrafast, laser-based, x-ray science: the dawn of atomic-scale cinematography

    Energy Technology Data Exchange (ETDEWEB)

    Barty, C.P.J. [University of California, Department of Applied Mechanics and Engineering Science, Urey Hall, Mali Code 0339, San Diego, La Jolla, CA (United States)

    2000-03-01

    The characteristics of ultrafast chirped pulse amplification systems are reviewed. Application of ultrafast chirped pulse amplification to the generation of femtosecond, incoherent, 8-keV line radiation is outlined and the use of femtosecond laser-based, x-rays for novel time-resolved diffraction studies of crystalline dynamics with sub-picosecond temporal resolution and sub-picometer spatial resolution is reviewed in detail. Possible extensions of laser-based, x-ray technology and evaluation of alternative x-ray approaches for time-resolved studies of the atomic scale dynamics are given. (author)

  5. Simulation of grain boundary sliding based on mechanics at atomic scale

    International Nuclear Information System (INIS)

    Molecular dynamics (MD) and statics simulations are being increasingly used to model the behavior of systems at the atomic scale, where atomistic details play a critical role such as in grain boundary sliding. In the last few years atomic simulations have gone beyond the realm of understanding the effects of a few atoms to that of systems of millions of atoms. Even these simulations, which demand extensive computational resources, may not be able to adequately represent the behavior of systems of interest. This necessitates a multi-scale approach to such problems. In this paper, we present the atomistic simulation studies of grain boundary sliding of symmetric tilt grain boundaries in aluminum. The simulations are in agreement with experimental results and show a clear dependence of magnitude of sliding on grain boundary energy. Asymptotic expansion homogenization (AEH) is a mathematically rigorous approach to homogenization of periodic structures, which has been used extensively in composites and porous media. We propose a methodology to adapt AEH technique to atomic scale. Refs. 2 (author)

  6. Modelling atomic scale manipulation with the non-contact atomic force microscope

    International Nuclear Information System (INIS)

    We present the results of calculations performed to model the process of lateral manipulation of an oxygen vacancy in the MgO(001) surface using the non-contact atomic force microscope (NC-AFM). The potential energy surfaces for the manipulation as a function of tip position are determined from atomistic modelling of the MgO(001) surface interacting with a Mg terminated MgO tip. These energies are then used to model the dynamical evolution of the system as the tip oscillates and at a finite temperature using a kinetic Monte Carlo method. The manipulation process is strongly dependent on the lateral position of the tip and the system temperature. It is also found that the expectation value of the point at which the vacancy jumps depends on the trajectory of the oscillating cantilever as the surface is approached. The effect of the manipulation on the operation of the NC-AFM is modelled with a virtual dynamic AFM, which explicitly simulates the entire experimental instrumentation and control loops. We show how measurable experimental signals can result from a single controlled atomic scale event and suggest the most favourable conditions for achieving successful atomic scale manipulation experimentally

  7. Compound semiconductor alloys: From atomic-scale structure to bandgap bowing

    International Nuclear Information System (INIS)

    Compound semiconductor alloys such as InxGa1−xAs, GaAsxP1−x, or CuInxGa1−xSe2 are increasingly employed in numerous electronic, optoelectronic, and photonic devices due to the possibility of tuning their properties over a wide parameter range simply by adjusting the alloy composition. Interestingly, the material properties are also determined by the atomic-scale structure of the alloys on the subnanometer scale. These local atomic arrangements exhibit a striking deviation from the average crystallographic structure featuring different element-specific bond lengths, pronounced bond angle relaxation and severe atomic displacements. The latter, in particular, have a strong influence on the bandgap energy and give rise to a significant contribution to the experimentally observed bandgap bowing. This article therefore reviews experimental and theoretical studies of the atomic-scale structure of III-V and II-VI zincblende alloys and I-III-VI2 chalcopyrite alloys and explains the characteristic findings in terms of bond length and bond angle relaxation. Different approaches to describe and predict the bandgap bowing are presented and the correlation with local structural parameters is discussed in detail. The article further highlights both similarities and differences between the cubic zincblende alloys and the more complex chalcopyrite alloys and demonstrates that similar effects can also be expected for other tetrahedrally coordinated semiconductors of the adamantine structural family

  8. Atomic-scale studies of uranium oxidation and corrosion by water vapour

    OpenAIRE

    Martin, TL; Coe, C.; Bagot, PAJ; Morrall, P; Smith, GDW; Scott, T.; Moody, MP

    2016-01-01

    Understanding the corrosion of uranium is important for its safe, long-term storage. Uranium metal corrodes rapidly in air, but the exact mechanism remains subject to debate. Atom Probe Tomography was used to investigate the surface microstructure of metallic depleted uranium specimens following polishing and exposure to moist air. A complex, corrugated metal-oxide interface was observed, with approximately 60 at.% oxygen content within the oxide. Interestingly, a very thin (~5 nm) interfacia...

  9. Osmotic and motional properties of intracellular water as influenced by osmotic swelling and shrinkage of Xenopus oocytes.

    Science.gov (United States)

    Cameron, I L; Merta, P; Fullerton, G D

    1990-03-01

    Experiments were done on fully grown Xenopus oocytes to determine the extent and the properties of cellular water of hydration. The studies involved the osmotic shrinking and swelling of the oocytes under known osmotic pressure as well as proton NMR spectral, titration, and free induction decay analyses. Studies were done both on whole oocytes and on subcellular fractions. The results show that little if any of the oocyte water in situ has the motional or osmotic properties expected of pure "bulk" water. Four distinct water of hydration compartments were found and defined on the basis of distinct hydrogen bounding mechanisms. Some of the water in yolk platelets was found not to be in fast exchange with other water compartments. Osmotic shrinkage of oocytes caused an adaptive decrease in the bound water of hydration compartments. This osmotically induced decrease is attributed to decreased surface area available for the hydrogen bounding of water molecules on cellular proteins. PMID:2312616

  10. Analysis of intracellular and extracellular microcystin variants in sediments and pore waters by accelerated solvent extraction and high performance liquid chromatography-tandem mass spectrometry

    International Nuclear Information System (INIS)

    Highlights: • First analytical method for intracellular microcystins (MCs) in sediment. • Includes a suite of variants (LR, 7dmLR, RR, YR, WR, LA, LF, LY, LW) and nodularin. • Reports the first measurements of MCs in sediment pore waters. • MCs detected in >100 year old lake sediments suggesting long-term preservation. • Sediment-pore water distribution (Kd) differed between variants suggesting differences in environmental fate. - Abstract: The fate and persistence of microcystin cyanotoxins in aquatic ecosystems remains poorly understood in part due to the lack of analytical methods for microcystins in sediments. Existing methods have been limited to the extraction of a few extracellular microcystins of similar chemistry. We developed a single analytical method, consisting of accelerated solvent extraction, hydrophilic–lipophilic balance solid phase extraction, and reversed phase high performance liquid chromatography-tandem mass spectrometry, suitable for the extraction and quantitation of both intracellular and extracellular cyanotoxins in sediments as well as pore waters. Recoveries of nine microcystins, representing the chemical diversity of microcystins, and nodularin (a marine analogue) ranged between 75 and 98% with one, microcystin-RR (MC-RR), at 50%. Chromatographic separation of these analytes was achieved within 7.5 min and the method detection limits were between 1.1 and 2.5 ng g−1 dry weight (dw). The robustness of the method was demonstrated on sediment cores collected from seven Canadian lakes of diverse geography and trophic states. Individual microcystin variants reached a maximum concentration of 829 ng g−1 dw on sediment particles and 132 ng mL−1 in pore waters and could be detected in sediments as deep as 41 cm (>100 years in age). MC-LR, -RR, and -LA were more often detected while MC-YR, -LY, -LF, and -LW were less common. The analytical method enabled us to estimate sediment-pore water distribution coefficients (Kd), MC

  11. Analysis of intracellular and extracellular microcystin variants in sediments and pore waters by accelerated solvent extraction and high performance liquid chromatography-tandem mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zastepa, Arthur, E-mail: arthur.zastepa@gmail.com; Pick, Frances R.; Blais, Jules M.; Saleem, Ammar

    2015-05-04

    Highlights: • First analytical method for intracellular microcystins (MCs) in sediment. • Includes a suite of variants (LR, {sup 7dm}LR, RR, YR, WR, LA, LF, LY, LW) and nodularin. • Reports the first measurements of MCs in sediment pore waters. • MCs detected in >100 year old lake sediments suggesting long-term preservation. • Sediment-pore water distribution (K{sub d}) differed between variants suggesting differences in environmental fate. - Abstract: The fate and persistence of microcystin cyanotoxins in aquatic ecosystems remains poorly understood in part due to the lack of analytical methods for microcystins in sediments. Existing methods have been limited to the extraction of a few extracellular microcystins of similar chemistry. We developed a single analytical method, consisting of accelerated solvent extraction, hydrophilic–lipophilic balance solid phase extraction, and reversed phase high performance liquid chromatography-tandem mass spectrometry, suitable for the extraction and quantitation of both intracellular and extracellular cyanotoxins in sediments as well as pore waters. Recoveries of nine microcystins, representing the chemical diversity of microcystins, and nodularin (a marine analogue) ranged between 75 and 98% with one, microcystin-RR (MC-RR), at 50%. Chromatographic separation of these analytes was achieved within 7.5 min and the method detection limits were between 1.1 and 2.5 ng g{sup −1} dry weight (dw). The robustness of the method was demonstrated on sediment cores collected from seven Canadian lakes of diverse geography and trophic states. Individual microcystin variants reached a maximum concentration of 829 ng g{sup −1} dw on sediment particles and 132 ng mL{sup −1} in pore waters and could be detected in sediments as deep as 41 cm (>100 years in age). MC-LR, -RR, and -LA were more often detected while MC-YR, -LY, -LF, and -LW were less common. The analytical method enabled us to estimate sediment-pore water

  12. Atomic scale properties of magnetic Mn-based alloys probed by Emission Mössbauer spectroscopy

    CERN Multimedia

    Mn-based alloys are characterized by a wealth of properties, which are of interest both from fundamental physics point of view and particularly attractive for different applications in modern technology: from magnetic storage to sensing and spin-based electronics. The possibility to tune their magnetic properties through post-growth thermal processes and/or stoichiometry engineering is highly important in order to target different applications (i.e. Mn$_{x}$Ga) or to increase their Curie temperature above room temperature (i.e. off-stoichiometric MnSi). In this project, the Mössbauer effect will be applied at $^{57}$Fe sites following implantation of radioactive $^{57}$Mn, to probe the micro-structure and magnetism of Mn-based alloys at the most atomic-scale. The proposed experimental plan is devoted to establish a direct correlation between the local structure and bulk magnetism (and other physical properties) of Mn-based alloys.

  13. Dynamic In-Situ Experimentation on Nanomaterials at the Atomic Scale.

    Science.gov (United States)

    Xu, Tao; Sun, Litao

    2015-07-15

    With the development of in situ techniques inside transmission electron microscopes (TEMs), external fields and probes can be applied to the specimen. This development transforms the TEM specimen chamber into a nanolab, in which reactions, structures, and properties can be activated or altered at the nanoscale, and all processes can be simultaneously recorded in real time with atomic resolution. Consequently, the capabilities of TEM are extended beyond static structural characterization to the dynamic observation of the changes in specimen structures or properties in response to environmental stimuli. This extension introduces new possibilities for understanding the relationships between structures, unique properties, and functions of nanomaterials at the atomic scale. Based on the idea of setting up a nanolab inside a TEM, tactics for design of in situ experiments inside the machine, as well as corresponding examples in nanomaterial research, including in situ growth, nanofabrication with atomic precision, in situ property characterization, and nanodevice construction are presented. PMID:25703228

  14. Three-dimensional atomic-scale imaging of impurity segregation to line defects

    Science.gov (United States)

    Blavette; Cadel; Fraczkiewicz; Menand

    1999-12-17

    Clouds of impurity atoms near line defects are believed to affect the plastic deformation of alloys. Three-dimensional atom probe techniques were used to image these so-called Cottrell atmospheres directly. Ordered iron-aluminum alloys (40 atomic percent aluminum) doped with boron (400 atomic parts per million) were investigated on an atomic scale along the direction. A boron enrichment was observed in the vicinity of an edge dislocation. The enriched region appeared as a three-dimensional pipe 5 nanometers in diameter, tangent to the dislocation line. The dislocation was found to be boron-enriched by a factor of 50 (2 atomic percent) relative to the bulk. The local boron enrichment is accompanied by a strong aluminum depletion of 20 atomic percent. PMID:10600736

  15. Atomic-Scale Engineering of Abrupt Interface for Direct Spin Contact of Ferromagnetic Semiconductor with Silicon

    Science.gov (United States)

    Averyanov, Dmitry V.; Karateeva, Christina G.; Karateev, Igor A.; Tokmachev, Andrey M.; Vasiliev, Alexander L.; Zolotarev, Sergey I.; Likhachev, Igor A.; Storchak, Vyacheslav G.

    2016-03-01

    Control and manipulation of the spin of conduction electrons in industrial semiconductors such as silicon are suggested as an operating principle for a new generation of spintronic devices. Coherent injection of spin-polarized carriers into Si is a key to this novel technology. It is contingent on our ability to engineer flawless interfaces of Si with a spin injector to prevent spin-flip scattering. The unique properties of the ferromagnetic semiconductor EuO make it a prospective spin injector into silicon. Recent advances in the epitaxial integration of EuO with Si bring the manufacturing of a direct spin contact within reach. Here we employ transmission electron microscopy to study the interface EuO/Si with atomic-scale resolution. We report techniques for interface control on a submonolayer scale through surface reconstruction. Thus we prevent formation of alien phases and imperfections detrimental to spin injection. This development opens a new avenue for semiconductor spintronics.

  16. Direct atomic-scale observation of layer-by-layer oxide growth during magnesium oxidation

    International Nuclear Information System (INIS)

    The atomic-scale oxide growth dynamics are directly revealed by in situ high resolution transmission electron microscopy during the oxidation of Mg surface. The oxidation process is characterized by the layer-by-layer growth of magnesium oxide (MgO) nanocrystal via the adatom process. Consistently, the nucleated MgO crystals exhibit faceted surface morphology as enclosed by (200) lattice planes. It is believed that the relatively lower surface energies of (200) lattice planes should play important roles, governing the growth mechanism. These results facilitate the understanding of the nanoscale oxide growth mechanism that will have an important impact on the development of magnesium or magnesium alloys with improved resistance to oxidation

  17. Direct atomic-scale observation of layer-by-layer oxide growth during magnesium oxidation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, He; Wu, Shujing; Sheng, Huaping; Liu, Chun; Liu, Yu; Cao, Fan; Zhou, Zhichao; Zhao, Dongshan, E-mail: wang@whu.edu.cn, E-mail: dszhao@whu.edu.cn; Wang, Jianbo, E-mail: wang@whu.edu.cn, E-mail: dszhao@whu.edu.cn [School of Physics and Technology, Center for Electron Microscopy and MOE Key Laboratory of Artificial Micro- and Nano-structures, Wuhan University, Wuhan 430072 (China); Zhao, Xingzhong [School of Physics and Technology, Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, Wuhan University, Wuhan 430072 (China)

    2014-04-07

    The atomic-scale oxide growth dynamics are directly revealed by in situ high resolution transmission electron microscopy during the oxidation of Mg surface. The oxidation process is characterized by the layer-by-layer growth of magnesium oxide (MgO) nanocrystal via the adatom process. Consistently, the nucleated MgO crystals exhibit faceted surface morphology as enclosed by (200) lattice planes. It is believed that the relatively lower surface energies of (200) lattice planes should play important roles, governing the growth mechanism. These results facilitate the understanding of the nanoscale oxide growth mechanism that will have an important impact on the development of magnesium or magnesium alloys with improved resistance to oxidation.

  18. Continuous description of a grain boundary in forsterite from atomic scale simulations: the role of disclinations

    Science.gov (United States)

    Sun, Xiao-Yu; Cordier, Patrick; Taupin, Vincent; Fressengeas, Claude; Jahn, Sandro

    2016-06-01

    We present continuous modelling at inter-atomic scale of a high-angle symmetric tilt boundary in forsterite. The model is grounded in periodic arrays of dislocation and disclination dipoles built on information gathered from discrete atomistic configurations generated by molecular dynamics simulations. The displacement, distortion (strain and rotation), curvature, dislocation and disclination density fields are determined in the boundary area using finite difference and interpolation techniques between atomic sites. The distortion fields of the O, Si and Mg sub-lattices are detailed to compare their roles in the accommodation of lattice incompatibility along the boundary. It is shown that the strain and curvature fields associated with the dislocation and disclination fields in the 'skeleton' O and Si sub-lattices accommodate the tilt incompatibility, whereas the elastic strain and rotation fields of the Mg sub-lattice are essentially compatible and induce stresses balancing the incompatibility stresses in the overall equilibrium.

  19. Atomic-scale structure of grain boundaries: Correlations to grain boundary properties

    International Nuclear Information System (INIS)

    It is generally believed that many properties of solid interfaces are ultimately determined by their structure and composition at the atomic level. We report here on work in two areas of grain boundary (GB) research in which structure-property correlations have been investigated recently. HREM observations in connection with computer modeling of GBs in fcc metals have given considerable insight into correlations between GB energy and atomic-scale GB structure. Efforts to understand and possibly control the supercurrent transport behavior across GBs in high-temperature superconductors require the combination of microstructure characterizations with investigations of electric transport properties. In both areas considerable progress is being made and has already lead to important insights concerning interfacial properties

  20. Atomic-scale observation of dynamical fluctuation and three-dimensional structure of gold clusters

    Energy Technology Data Exchange (ETDEWEB)

    Li, Junjie [Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, Department of Physics, East China Normal University, North Zhongshan Road 3663, Shanghai 200062 (China); Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Yin, Deqiang [School of Manufacturing Science and Engineering, Sichuan University, Chengdu 610064 (China); Chen, Chunlin; Lin, Liyang; Wang, Zhongchang, E-mail: zcwang@wpi-aimr.tohoku.ac.jp [Advanced Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Li, Qiang [School of Materials Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China); Sun, Rong [Institute of Engineering Innovation, The University of Tokyo, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-8656 (Japan); Huang, Sumei, E-mail: smhuang@phy.ecnu.edu.cn [Engineering Research Center for Nanophotonics and Advanced Instrument, Ministry of Education, Department of Physics, East China Normal University, North Zhongshan Road 3663, Shanghai 200062 (China)

    2015-02-28

    Unravelling three-dimensional structures and dynamical fluctuation of metal nanoclusters is critical to understanding reaction process and the origin of catalytic activity in many heterogeneous catalytic systems. We obtain three-dimensional structures of ultra-small Au clusters by combining aberration-corrected scanning transmission electron microscopy, density functional theory calculations, and imaging simulations. The configurations of unique Au clusters are revealed at the atomic scale and the corresponding electronic states are given. The sequential observations reveal a transition of ultra-small Au clusters with about 25 atoms from a near-square to an elongated structure. We also find a transition from two dimensions to three dimensions for the Au clusters. The obtained three-dimensional geometry and associated electronic states help to clarify atomistic mechanism of shape- and number-dependent catalytic activities of Au clusters.

  1. Atomic-scale imaging of surfaces and interfaces. Materials Research Society Symposium Proceedings, volume 295

    Science.gov (United States)

    Biegelsen, David K.; Smith, David J.; Tong, S. Y.

    The gap between imagining and imaging is getting ever smaller. The Atomic-Scale Imaging of Surfaces and Interfaces, Symposium W at the 1992 MRS Fall Meeting in Boston, Massachusetts, brought together researchers using state-of-the-art imaging techniques capable of resolving atomic features. Methods represented were scanning tunneling microscopy (STM), atomic force microscopy (AFM), low energy electron microscopy (LEEM), transmission (TEM) and reflection (REM) electron microscopy, scanning electron microscopy (SEM), atom probe field ion microscopy (APFIM or POSAP), high and low energy external source electron holographies, and internal source electron holographies. Some highlights from the STM papers included discussions of the limitations and future potential of STM as well as current findings. Several papers presented work with STM at elevated temperatures. Jene Golovchenko reviewed STM work showing cooperative diffusion events (Pb on Ge) involving many tens of substrate atoms. Don Eigler focused on atomic manipulation and some of its uses to enable fundamental studies of small atomic clusters.

  2. Analysis of Carbon Nanotubes on the Mechanical Properties at Atomic Scale

    Directory of Open Access Journals (Sweden)

    Xiaowen Lei

    2011-01-01

    Full Text Available This paper aims at developing a mathematic model to characterize the mechanical properties of single-walled carbon nanotubes (SWCNTs. The carbon-carbon (C–C bonds between two adjacent atoms are modeled as Euler beams. According to the relationship of Tersoff-Brenner force theory and potential energy acting on C–C bonds, material constants of beam element are determined at the atomic scale. Based on the elastic deformation energy and mechanical equilibrium of a unit in graphite sheet, simply form ED equations of calculating Young's modulus of armchair and zigzag graphite sheets are derived. Following with the geometrical relationship of SWCNTs in cylindrical coordinates and the structure mechanics approach, Young's modulus and Poisson's ratio of armchair and zigzag SWCNTs are also investigated. The results show that the approach to research mechanical properties of SWCNTs is a concise and valid method. We consider that it will be useful technique to progress on this type of investigation.

  3. Homotopy-Theoretic Study &Atomic-Scale Observation of Vortex Domains in Hexagonal Manganites.

    Science.gov (United States)

    Li, Jun; Chiang, Fu-Kuo; Chen, Zhen; Ma, Chao; Chu, Ming-Wen; Chen, Cheng-Hsuan; Tian, Huanfang; Yang, Huaixin; Li, Jianqi

    2016-01-01

    Essential structural properties of the non-trivial "string-wall-bounded" topological defects in hexagonal manganites are studied through homotopy group theory and spherical aberration-corrected scanning transmission electron microscopy. The appearance of a "string-wall-bounded" configuration in RMnO3 is shown to be strongly linked with the transformation of the degeneracy space. The defect core regions (~50 Å) mainly adopt the continuous U(1) symmetry of the high-temperature phase, which is essential for the formation and proliferation of vortices. Direct visualization of vortex strings at atomic scale provides insight into the mechanisms and macro-behavior of topological defects in crystalline materials. PMID:27324701

  4. Atomic-scale electrochemistry on the surface of a manganite by scanning tunneling microscopy

    International Nuclear Information System (INIS)

    The doped manganese oxides (manganites) have been widely studied for their colossal magnetoresistive effects, for potential applications in oxide spintronics, electroforming in resistive switching devices, and are materials of choice as cathodes in modern solid oxide fuel cells. However, little experimental knowledge of the dynamics of the surfaces of perovskite manganites at the atomic scale exists. Here, through in-situ scanning tunneling microscopy (STM), we demonstrate atomic resolution on samples of La0.625Ca0.375MnO3 grown on (001) SrTiO3 by pulsed laser deposition. Furthermore, by applying triangular DC waveforms of increasing amplitude to the STM tip, and measuring the tunneling current, we demonstrate the ability to both perform and monitor surface electrochemical processes at the atomic level, including formation of oxygen vacancies and removal and deposition of individual atomic units or clusters. Our work paves the way for better understanding of surface oxygen reactions in these systems

  5. Atomic-scale simulations of the mechanical deformation of nanocrystalline metals

    DEFF Research Database (Denmark)

    Schiøtz, Jakob; Vegge, Tejs; Di Tolla, Francesco;

    1999-01-01

    Nanocrystalline metals, i.e., metals in which the grain size is in the nanometer range, have a range of technologically interesting properties including increased hardness and yield strength. We present atomic-scale simulations of the plastic behavior of nanocrystalline copper. The simulations sh...... temperatures the material becomes softer in both the plastic and elastic regime. Porosity in the samples result in a softening of the material; this may be a significant effect in many experiments. [S0163-1829(99)05941-X]....... boundaries leads to a hardening as the grain size is increased (reverse Hall-Fetch effect), implying a maximum in hardness for a grain size above the ones studied here. We investigate the effects of varying temperature, strain rate, and porosity, and discuss the relation to recent experiments. At increasing...

  6. Atomic-scale observation of polarization switching in epitaxial ferroelectric thin films

    International Nuclear Information System (INIS)

    The thin-film x-ray standing wave (XSW) technique is used for an atomic-scale study of polarization switching in ferroelectric Pb(Zr0.3Ti0.7)O3 (PZT)/electrode heterostructures grown on SrTiO3(001). The XSW is selectively generated in the PZT by the interference between the incident x-ray wave and the weak (001) Bragg diffracted wave from the film. The XSW excites a fluorescence signal from the Pb ions in the PZT film, that is used to determine their subangstroem displacements after polarization switching has occurred. This experimental method yields unique information on the underlying atomic configurations for different polarization domain states

  7. Thin Film of Perovskite Oxide with Atomic Scale p-n Junctions

    Institute of Scientific and Technical Information of China (English)

    HU Bin; HUANG Ke-ke; HOU Chang-min; YUAN Hong-ming; PANG Guang-sheng; FENG Shou-hua

    2012-01-01

    Thin films of perovskite manganese oxide La0.66Ca0.29K0.05MnO3(LCKMO) on Au/ITO(ITO=indium tin oxide) substrates were prepared by off-axis radio frequency magnetron sputtering and characterized by X-ray diffraction(XRD),high-resolution transmission electron microscopy(HRTEM),and conductive atomic force microscopy (C-AFM) at room temperature.The thin films with thickness ranged from 100 nm to 300 nm basically show cubic structures with a=0.3886 nm,the same as that of the raw material used,but the structures are highly modulated.C-AFM results revealed that the atomic scale p-n junction feature of the thin films was the same as that of the single crystals.The preparation of the thin films thus further confirms the possibility of their application extending from micrometer-sized single crystals to macroscopic thin film.

  8. Effects of Stone-Wales and vacancy defects in atomic-scale friction on defective graphite

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xiao-Yu [Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan 430072 (China); Key Laboratory of Hubei Province for Water Jet Theory and New Technology, Wuhan University, Wuhan 430072 (China); Wu, RunNi; Xia, Re [Key Laboratory of Hubei Province for Water Jet Theory and New Technology, Wuhan University, Wuhan 430072 (China); Chu, Xi-Hua; Xu, Yuan-Jie, E-mail: yj-xu@whu.edu.cn [Department of Engineering Mechanics, School of Civil Engineering, Wuhan University, Wuhan 430072 (China)

    2014-05-05

    Graphite is an excellent solid lubricant for surface coating, but its performance is significantly weakened by the vacancy or Stone-Wales (SW) defect. This study uses molecular dynamics simulations to explore the frictional behavior of a diamond tip sliding over a graphite which contains a single defect or stacked defects. Our results suggest that the friction on defective graphite shows a strong dependence on defect location and type. The 5-7-7-5 structure of SW defect results in an effectively negative slope of friction. For defective graphite containing a defect in the surface, adding a single vacancy in the interior layer will decrease the friction coefficients, while setting a SW defect in the interior layer may increase the friction coefficients. Our obtained results may provide useful information for understanding the atomic-scale friction properties of defective graphite.

  9. Physical essence of the multibody contact-sliding at atomic scale

    Science.gov (United States)

    Han, Xuesong

    2014-01-01

    Investigation the multibody contact-sliding occurred at atomic discrete contact spot will play an important role in determine the origin of tribology behavior and evaluates the micro-mechanical property of nanomaterials and thus optimizing the design of surface texture. This paper carries out large scale parallel molecular dynamics simulation on contact-sliding at atomic scale to uncover the special physical essence. The research shows that some kind of force field exists between nanodot pair and the interaction can be expressed by the linear combination of exponential function while the effective interaction distance limited in 1 angstrom for nanodot with several tens of nanometer diameter. The variation tendency about the interaction force between nanodot array is almost the same between nanodot pairs and thus the interaction between two nanodot array can be characterized by parallel mechanical spring. Multibody effect which dominates the interaction between atoms or molecules will gradually diminish with the increasing of length scales.

  10. Atomic Scale Structure-Chemistry Relationships at Oxide Catalyst Surfaces and Interfaces

    Science.gov (United States)

    McBriarty, Martin E.

    Oxide catalysts are integral to chemical production, fuel refining, and the removal of environmental pollutants. However, the atomic-scale phenomena which lead to the useful reactive properties of catalyst materials are not sufficiently understood. In this work, the tools of surface and interface science and electronic structure theory are applied to investigate the structure and chemical properties of catalytically active particles and ultrathin films supported on oxide single crystals. These studies focus on structure-property relationships in vanadium oxide, tungsten oxide, and mixed V-W oxides on the surfaces of alpha-Al2O3 and alpha-Fe2O 3 (0001)-oriented single crystal substrates, two materials with nearly identical crystal structures but drastically different chemical properties. In situ synchrotron X-ray standing wave (XSW) measurements are sensitive to changes in the atomic-scale geometry of single crystal model catalyst surfaces through chemical reaction cycles, while X-ray photoelectron spectroscopy (XPS) reveals corresponding chemical changes. Experimental results agree with theoretical calculations of surface structures, allowing for detailed electronic structure investigations and predictions of surface chemical phenomena. The surface configurations and oxidation states of V and W are found to depend on the coverage of each, and reversible structural shifts accompany chemical state changes through reduction-oxidation cycles. Substrate-dependent effects suggest how the choice of oxide support material may affect catalytic behavior. Additionally, the structure and chemistry of W deposited on alpha-Fe 2O3 nanopowders is studied using X-ray absorption fine structure (XAFS) measurements in an attempt to bridge single crystal surface studies with real catalysts. These investigations of catalytically active material surfaces can inform the rational design of new catalysts for more efficient and sustainable chemistry.

  11. Atomic scale simulations of hydrogen implantation defects in hydrogen implanted silicon - smart Cut technology

    International Nuclear Information System (INIS)

    The topic of this thesis is related to the implantation step of the SmartCutTM technology. This technology uses hydrogen in order to transfer silicon layers on insulating substrates. The transfer is performed through a fracture induced by the formation of bidimensional defects well known in literature as 'platelets'. More exactly, we have studied within this thesis work the defects appearing in the post implant state and the evolution of the implantation damage towards a state dominated by platelets. The study is organised into two parts: in the first part we present the results obtained by atomic scale simulations while in the second part we present an infrared spectroscopy study of the evolution of defects concentrations after annealing at different temperatures. The atomic scale simulations have been performed within the density functional theory and they allowed us to compute the formation energies and the migration and recombination barriers. The defects included in our study are: the atomic and diatomic interstitials, the hydrogenated vacancies and multi-vacancies and the several platelets models. The obtained energies allowed us to build a stability hierarchy for these types of defects. This scheme has been confronted with some infrared analysis on hydrogen implanted silicon samples (37 keV) in a sub-dose regime which does not allow usually the formation of platelets during the implantation step. The analysis of the infrared data allowed the detailed description of the defects concentration based on the behaviour of peaks corresponding to the respective defects during annealing. The comparison between these evolutions and the energy scheme obtained previously allowed the validation of an evolution scenario of defects towards the platelet state. (author)

  12. 3D compositional analysis at atomic scale of InAlGaAs capped InAs/GaAs QDs

    International Nuclear Information System (INIS)

    The 3D compositional distribution at the atomic-scale of InAs/GaAs quantum dots (QDs) with an InAlGaAs capping layer has been obtained by atom probe tomography. A heterogeneous distribution of Al atoms has been revealed. An Al-rich ring around the QDs has been observed. A detailed analysis of the QDs composition evidences a high degree of In/Ga intermixing, with an increasing In gradient in the growth direction. The atomic scale analyses of these nanostructures are essential to understand their functional properties

  13. Atomic-Scale Studies of Oxides Supported Catalysts by X-ray and Imaging Methods

    Science.gov (United States)

    Feng, Zhenxing

    2011-12-01

    Oxide supported metal and metal oxide catalysts have been synthesized by molecular beam epitaxy (MBE) and atomic-layer deposition (ALD). To obtain a general idea of how a catalyst behaves chemically and structurally during reduction-oxidization (redox) reaction at atomic-scale, oxide single crystals with well-defined surfaces are used as supports to grow monolayer (ML) and sub-ML catalysts. Several model catalysis systems are investigated: Pt/SrTiO 3(001), WOX/alpha-Fe2O3(0001), VO X/alpha-TiO2(110) and mixed VOX/WOX/alpha-TiO 2(110). For purposes of comparison the catalysts include a noble metal (Pt), inert oxide (WOX) and active oxide (VOX). The oxide supports are categorized as a reducible substrate, alpha-Fe2 O3(0001), and non-reducible substrates, alpha-TiO 2(110) and SrTiO3(001). To obtain in situ information, a variety of X-ray and scanning imaging methods have been applied together to study the atomic-scale surface morphology, structure and cation dynamics during chemical reactions. These characterization techniques are: X-ray standing wave (XSW), grazing-incident small angle X-ray scattering (GISAXS), X-ray absorption fine structure (XAFS), X-ray reflectivity (XRR), X-ray fluorescence (XRF), X-ray photoelectron spectroscopy (XPS), atomic-force microscopy (AFM) and scanning electron microscopy (SEM). Our studies show that different combinations of catalysts and substrates give distinct structural and chemical state changes in redox reactions. For MBE deposited sub-monolayer (sub-ML) Pt on the 2 x 1 SrTiO 3(001) surface, AFM shows the formation of nanoparticles and XSW atomic imaging shows that these nanoparticles are composed of Pt face-centered-cubic nanocrystals with cube-on-cube epitaxy coherent to the substrate unit cell. Different Pt coverages lead to differences in the observed XSW image of the interfacial structure, which is explained by the Pt-Pt interaction becoming stronger than the Pt-substrate interaction as the coverage is increased from 0.2 to

  14. An atomic scale STM study of the Fe 3O 4(0 0 1) surface

    Science.gov (United States)

    Ceballos, S. F.; Mariotto, G.; Jordan, K.; Murphy, S.; Seoighe, C.; Shvets, I. V.

    2004-01-01

    Despite the intensive investigation into the electronic properties of magnetite, fundamental issues related to the Verwey transition and the electronic transport mechanism are not fully understood. These issues are further complicated at the surface of magnetite crystals, due to the large number of possible surface terminations. The preparation procedure plays a fundamental role in determining the O/Fe ratio, and therefore the electronic properties of a magnetite crystal. We present a detailed investigation of the influence of the preparation conditions on the morphology of Fe 3O 4(0 0 1) single crystal surfaces using AES, LEED, and STM. We show that long anneals of single crystals in UHV cause segregation of contaminants to the surface and that a series of surface reconstructions is induced. A different preparation procedure gives rise to a clean surface exhibiting a ( 2× 2)R 45° reconstruction. This surface is terminated at the octahedral plane and has been imaged down to the atomic scale. This provides a useful test system to study the Verwey transition at the surface.

  15. Point defects and irradiation in oxides: simulations at the atomic scale

    International Nuclear Information System (INIS)

    The studies done by Jean-Paul Crocombette between 1996 and 2005 in the Service de Recherches de Metallurgie Physique of the Direction de l'Energie Nucleaire in Saclay are presented in this Habilitation thesis. These works were part of the material science researches on the ageing, especially under irradiation, of oxides of interest for the nuclear industry. In this context simulation studies at the atomic scale were performed on two elementary components of ageing under irradiation : point defects and displacement cascades ; using two complementary simulation techniques : ab initio electronic structure calculations and empirical potential molecular dynamics. The first part deals with point defects : self defects (vacancies or interstitials) or hetero-atomic dopants. One first recalls the energetics of such defects in oxides, the specific features of defects calculations and the expected accuracy of these calculations. Then one presents the results obtained on uranium dioxide, oxygen in silver and amorphous silica. The second part tackles the modelling of disintegration recoil nuclei in various?displacement cascades created by crystalline matrices for actinide waste disposal. Cascade calculations give access to the amorphization mechanisms under irradiation of these materials. One thus predicts that the amorphization in zircon takes place directly in the tracks whereas in lanthanum zirconate, the amorphization proceeds through the accumulation of point defects. Finally the prospects of these studies are discussed. (author)

  16. Influence of Aromatic Residues on the Material Characteristics of Aβ Amyloid Protofibrils at the Atomic Scale.

    Science.gov (United States)

    Chang, Hyun Joon; Baek, Inchul; Lee, Myeongsang; Na, Sungsoo

    2015-08-01

    Amyloid fibrils, which cause a number of degenerative diseases, are insoluble under physiological conditions and are supported by native contacts. Recently, the effects of the aromatic residues on the Aβ amyloid protofibril were investigated in a ThT fluorescence study. However, the relationship between the material characteristics of the Aβ protofibril and its aromatic residues has not yet been investigated on the atomic scale. Here, we successfully constructed wild-type (WT) and mutated types of Aβ protofibrils by using molecular dynamics simulations. Through principle component analysis, we established the structural stability and vibrational characteristics of F20L Aβ protofibrils and compared them with WT and other mutated models such as F19L and F19LF20L. In addition, structural stability was assessed by calculating the elastic modulus, which showed that the F20L model has higher values than the other models studied. From our results, it is shown that aromatic residues influence the structural and material characteristics of Aβ protofibrils. PMID:26037071

  17. Atomic-scale magnetometry of distant nuclear spin clusters via nitrogen-vacancy spin in diamond.

    Science.gov (United States)

    Zhao, Nan; Hu, Jian-Liang; Ho, Sai-Wah; Wan, Jones T K; Liu, R B

    2011-04-01

    The detection of single nuclear spins is an important goal in magnetic resonance spectroscopy. Optically detected magnetic resonance can detect single nuclear spins that are strongly coupled to an electron spin, but the detection of distant nuclear spins that are only weakly coupled to the electron spin has not been considered feasible. Here, using the nitrogen-vacancy centre in diamond as a model system, we numerically demonstrate that it is possible to detect two or more distant nuclear spins that are weakly coupled to a centre electron spin if these nuclear spins are strongly bonded to each other in a cluster. This cluster will stand out from other nuclear spins by virtue of characteristic oscillations imprinted onto the electron spin decoherence profile, which become pronounced under dynamical decoupling control. Under many-pulse dynamical decoupling, the centre electron spin coherence can be used to measure nuclear magnetic resonances of single molecules. This atomic-scale magnetometry should improve the performance of magnetic resonance spectroscopy for applications in chemical, biological, medical and materials research, and could also have applications in solid-state quantum computing. PMID:21358646

  18. Atomic-scale decoration for improving the pitting corrosion resistance of austenitic stainless steels

    Science.gov (United States)

    Zhou, Y. T.; Zhang, B.; Zheng, S. J.; Wang, J.; San, X. Y.; Ma, X. L.

    2014-01-01

    Stainless steels are susceptible to the localized pitting corrosion that leads to a huge loss to our society. Studies in the past decades confirmed that the pitting events generally originate from the local dissolution in MnS inclusions which are more or less ubiquitous in stainless steels. Although a recent study indicated that endogenous MnCr2O4 nano-octahedra within the MnS medium give rise to local nano-galvanic cells which are responsible for the preferential dissolution of MnS, effective solutions of restraining the cells from viewpoint of electrochemistry are being tantalizingly searched. Here we report such a galvanic corrosion can be greatly resisted via bathing the steels in Cu2+-containing solutions. This chemical bath generates Cu2-δS layers on the surfaces of MnS inclusions, invalidating the nano-galvanic cells. Our study provides a low-cost approach via an atomic scale decoration to improve the pitting corrosion resistance of stainless steels in a volume-treated manner.

  19. Characterization of graphene and transition metal dichalcogenide at the atomic scale

    International Nuclear Information System (INIS)

    Edge structures and atomic defects are of fundamental importance since they can significantly affect the physical and chemical properties of low-dimensional materials, such as nanoribbons, and therefore merit thorough investigations at the atomic level. Recent developments of direct imaging and analytical techniques using an aberration-corrected scanning transmission electron microscope (STEM) have provided direct access to information on the local atomic structure and the chemical composition at the atomic scale. In this review, we report on the discrimination of single atoms including dopant atoms on a monolayered transition-metal dichalcogenide (TMD) nanoribbon and a single nitrogen adatom on graphene by time-resolved annular dark-field (ADF) imaging and spatially resolved electron energy loss spectroscopy (EELS). We also show that in situ scanning transmission electron microscopy can be used to monitor the structural transformation between semiconducting (2H) and metallic (1T) phases in monolayer MoS2, and can enable direct observation of in-plane graphene growth at a step edge of a bi-layer graphene and domain boundary formation during growth with atomic-resolution. (author)

  20. Atomic scale studies of the chemistry of the Cu/MgO {111} heterophase interface

    International Nuclear Information System (INIS)

    The Cu/MgO [111] heterophase interface is studied using a combination of transmission electron microscopy, high resolution electron microscopy and atom-probe field-ion microscopy techniques. Wire and foil specimens of a Cu-2.8 at.% Mg alloy were internally oxidized to produce MgO precipitates at a number density of 5·1015Cm-3 with a mean diameter of ∼200 Angstrom. The MgO precipitates have a semicoherent interface with the Cu matrix and they exhibit a cube-on-cube orientation relationship. The octahedral-shaped MgO precipitates were analyzed using APFIM by dissecting along a direction on an atomic scale. In this manner an MgO precipitate, with a [111] plane perpendicular to the axis of the APFIM, is uncovered after the Cu matrix has been mass analyzed. It was found that the terminating [222] plane of an MgO precipitate is pure oxygen, and the second [222] plane is pure Mg

  1. Atomic-scale properties of Ni-based FCC ternary, and quaternary alloys

    International Nuclear Information System (INIS)

    The aim of this study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. According to our study, the salient features for the ternary alloy are a negative SRO parameter between Ni–Cr and a positive between Cr–Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni–Cr and Ni–Fe pairs and positive for Cr–Cr and Fe–Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. The predicted SRO has an impact on point-defect energetics, electron–phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys

  2. Atomic-scale electrochemistry on the surface of a manganite by scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Vasudevan, Rama K., E-mail: rvv@ornl.gov; Tselev, Alexander; Baddorf, Arthur P. [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); ORNL Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Gianfrancesco, Anthony G. [UT/ORNL Bredesen Center, University of Tennessee, Knoxville, Tennessee 37996 (United States); Kalinin, Sergei V. [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); ORNL Institute for Functional Imaging of Materials, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); UT/ORNL Bredesen Center, University of Tennessee, Knoxville, Tennessee 37996 (United States)

    2015-04-06

    The doped manganese oxides (manganites) have been widely studied for their colossal magnetoresistive effects, for potential applications in oxide spintronics, electroforming in resistive switching devices, and are materials of choice as cathodes in modern solid oxide fuel cells. However, little experimental knowledge of the dynamics of the surfaces of perovskite manganites at the atomic scale exists. Here, through in-situ scanning tunneling microscopy (STM), we demonstrate atomic resolution on samples of La{sub 0.625}Ca{sub 0.375}MnO{sub 3} grown on (001) SrTiO{sub 3} by pulsed laser deposition. Furthermore, by applying triangular DC waveforms of increasing amplitude to the STM tip, and measuring the tunneling current, we demonstrate the ability to both perform and monitor surface electrochemical processes at the atomic level, including formation of oxygen vacancies and removal and deposition of individual atomic units or clusters. Our work paves the way for better understanding of surface oxygen reactions in these systems.

  3. Numerical atomic scale simulations of the microstructural evolution of ferritic alloys under irradiation

    International Nuclear Information System (INIS)

    In this work, we have developed a model of point defect (vacancies and interstitials) diffusion whose aim is to simulate by kinetic Monte Carlo (KMC) the formation of solute rich clusters observed experimentally in irradiated FeCuNiMnSi model alloys and in pressure vessel steels. Electronic structure calculations have been used to characterize the interactions between point defects and the different solute atoms. Each of these solute atoms establishes an attractive bond with the vacancy. As for Mn, which is the element which has the weakest bond with the vacancy, it establishes more favourable bonds with interstitials. Binding energies, migration energies as well as other atomic scale properties, determined by ab initio calculations, have led to a parameter set for the KMC code. Firstly, these parameters have been optimised on thermal ageing experiments realised on the FeCu binary alloy and on complex alloys, described in the literature. The vacancy diffusion thermal annealing simulations show that when a vacancy is available, all the solutes migrate and form clusters, in agreement with the observed experimental tendencies. Secondly, to simulate the microstructural evolution under irradiation, we have introduced interstitials in the KMC code. Their presence leads to a more efficient transport of Mn. The first simulations of electron and neutron irradiations show that the model results are globally qualitatively coherent with the experimentally observed tendencies. (author)

  4. Polyvinylidene fluoride molecules in nanofibers, imaged at atomic scale by aberration corrected electron microscopy.

    Science.gov (United States)

    Lolla, Dinesh; Gorse, Joseph; Kisielowski, Christian; Miao, Jiayuan; Taylor, Philip L; Chase, George G; Reneker, Darrell H

    2016-01-01

    Atomic scale features of polyvinylidene fluoride molecules (PVDF) were observed with aberration corrected transmission electron microscopy. Thin, self-supporting PVDF nanofibers were used to create images that show conformations and relative locations of atoms in segments of polymer molecules, particularly segments near the surface of the nanofiber. Rows of CF2 atomic groups, at 0.25 nm intervals, which marked the paths of segments of the PVDF molecules, were seen. The fact that an electron microscope image of a segment of a PVDF molecule depended upon the particular azimuthal direction, along which the segment was viewed, enabled observation of twist around the molecular axis. The 0.2 nm side-by-side distance between the two fluorine atoms attached to the same carbon atom was clearly resolved. Morphological and chemical changes produced by energetic electrons, ranging from no change to fiber scission, over many orders of magnitude of electrons per unit area, promise quantitative new insights into radiation chemistry. Relative movements of segments of molecules were observed. Promising synergism between high resolution electron microscopy and molecular dynamic modeling was demonstrated. This paper is at the threshold of growing usefulness of electron microscopy to the science and engineering of polymer and other molecules. PMID:26369731

  5. Nuclear magnetic resonance in atomic-scale superconductor/magnet multilayered systems

    CERN Document Server

    Kanegae, Y

    2003-01-01

    We investigate the nuclear spin-lattice relaxation rate (T sub 1 T) sup - sup 1 in atomic-scale superconductor/magnet multilayered systems and discuss the discrepancy between two recent (T sub 1 T) sup - sup 1 experiments on Ru in RuSr sub 2 YCu sub 2 O sub 8. When the magnetic layers is are in the antiferromagnetic state, (T sub 1 T) sup - sup 1 in the magnetic layers is shown to decrease with decreasing due to the excitation gap associated with the magnetic ordering. The proximity effect of superconductivity on (T sub 1 T) sup - sup 1 in the magnetic layer is negligibly small. Our result indicates that the temperature dependence of (T sub 1 T) sup - sup 1 on Ru in RuSr sub 2 YCu sub 2 O sub 8 likely originates from the antiferromagnetism in the RuO sub 2 layers, but not from the superconductivity in the CuO sub 2 layers. (author)

  6. Epitaxial top-gated atomic-scale silicon wire in a three-dimensional architecture

    International Nuclear Information System (INIS)

    Three-dimensional (3D) control of dopant profiles in silicon is a critical requirement for fabricating atomically precise transistors. We demonstrate conductance modulation through an atomic scale 3 nm wide δ-doped silicon–phosphorus wire using a vertically separated epitaxial doped Si:P top-gate. We show that intrinsic crystalline silicon grown at low temperatures (∼250 °C) serves as an effective gate dielectric permitting us to achieve large gate ranges (∼2.6 V) with leakage currents below 1 pA. Combining scanning tunneling lithography for precise lateral confinement, with monolayer doping and low temperature epitaxial overgrowth for precise vertical confinement, we can realize multiple layers of nano-patterned dopants in a single crystal material. These results demonstrate the viability of highly doped, vertically separated epitaxial gates in an all-crystalline architecture with long-term implications for monolithic 3D silicon circuits and for the realization of atomically precise donor architectures for quantum computing. (paper)

  7. Characterization of Graphene and Transition Metal Dichalcogenide at the Atomic Scale

    Science.gov (United States)

    Liu, Zheng; Lin, Yung-Chang; Warner, Jamie H.; Teng, Po-Yuan; Yeh, Chao-Hui; Chiu, Po-Wen; Iijima, Sumio; Suenga, Kazu

    2015-12-01

    Edge structures and atomic defects are of fundamental importance since they can significantly affect the physical and chemical properties of low-dimensional materials, such as nanoribbons, and therefore merit thorough investigations at the atomic level. Recent developments of direct imaging and analytical techniques using an aberration-corrected scanning transmission electron microscope (STEM) have provided direct access to information on the local atomic structure and the chemical composition at the atomic scale. In this review, we report on the discrimination of single atoms including dopant atoms on a monolayered transition-metal dichalcogenide (TMD) nanoribbon and a single nitrogen adatom on graphene by time-resolved annular dark-field (ADF) imaging and spatially resolved electron energy loss spectroscopy (EELS). We also show that in situ scanning transmission electron microscopy can be used to monitor the structural transformation between semiconducting (2H) and metallic (1T) phases in monolayer MoS2, and can enable direct observation of in-plane graphene growth at a step edge of a bi-layer graphene and domain boundary formation during growth with atomic-resolution.

  8. Selective visualization of point defects in carbon nanotubes at the atomic scale by an electron-donating molecular tip.

    Science.gov (United States)

    Nishino, Tomoaki; Kanata, Satoshi; Umezawa, Yoshio

    2011-07-14

    Electron-donating molecular tips were used for the observation of single-walled carbon nanotubes (SWNTs). Defects in SWNTs were selectively visualized at the atomic scale on the basis of charge-transfer interaction with the molecular tip. PMID:21629907

  9. Atomic scale simulation of fission product trapping and migration in UO2+x and U3O8-z

    International Nuclear Information System (INIS)

    The paper discusses simulations, performed at atomic scale of fission product trapping and migration in UO2+x and U3O8-z. The solution and the migration of a range of volatile fission products including iodine, cesium, ruthenium in stoichiometric and nonstoichiometric UO2 and U3O8 are considered

  10. Bridged single-walled carbon nanotube-based atomic-scale mass sensors

    Science.gov (United States)

    Ali-Akbari, H. R.; Shaat, M.; Abdelkefi, A.

    2016-08-01

    The potentials of carbon nanotubes (CNTs) as mechanical resonators for atomic-scale mass sensing are presented. To this aim, a nonlocal continuum-based model is proposed to study the dynamic behavior of bridged single-walled carbon nanotube-based mass nanosensors. The carbon nanotube (CNT) is considered as an elastic Euler-Bernoulli beam with von Kármán type geometric nonlinearity. Eringen's nonlocal elastic field theory is utilized to model the interatomic long-range interactions within the structure of the CNT. This developed model accounts for the arbitrary position of the deposited atomic-mass. The natural frequencies and associated mode shapes are determined based on an eigenvalue problem analysis. An atom of xenon (Xe) is first considered as a specific case where the results show that the natural frequencies and mode shapes of the CNT are strongly dependent on the location of the deposited Xe and the nonlocal parameter of the CNT. It is also indicated that the first vibrational mode is the most sensitive when the mass is deposited at the middle of a single-walled carbon nanotube. However, when deposited in other locations, it is demonstrated that the second or third vibrational modes may be more sensitive. To investigate the sensitivity of bridged single-walled CNTs as mass sensors, different noble gases are considered, namely Xe, argon (Ar), and helium (He). It is shown that the sensitivity of the single-walled CNT to the Ar and He gases is much lower than the Xe gas due to the significant decrease in their masses. The derived model and performed analysis are so needed for mass sensing applications and particularly when the detected mass is randomly deposited.

  11. Atomic Scale Nanochemistry in Silicon Carbide Oxidation and H-induced Surface Metallization

    International Nuclear Information System (INIS)

    Full text: Silicon carbide (SiC) is a wide band gap IV-IV compound semiconductor having strong interest in advanced device/sensor applications, and in nanotechnology. Cubic/hexagonal SiC surfaces and interfaces are investigated by i) core level/valence band photoemission (XPS/UPS) spectroscopies and grazing incidence x-ray diffraction using 3rd generation synchrotron radiation sources, ii) atom-resolved scanning tunneling microscopy (STM) and spectroscopy (STS) and iii) multiple-reflection infrared absorption spectroscopy (MR-IRAS). Such important issues as atomic scale surface oxidation, subsequent abrupt SiO2/SiC interface formation and H-induced surface metallization will be presented and discussed. In particular, the first observation of a semiconductor surface metallization induced by atomic hydrogen will be presented. This surprising result is evidenced through band gap closing in STS, electronic states built-up at Fermi level, and Ef pinning at the conduction band minimum, reactive component at Si 2p core level and specific spectral features in MR-IRAS. In addition, SR-based CL-XPS gives fine details about interatomic charge transfers within the surface and sub-surface regions with a strong reactive component at the Si 2p core level. The metallization process results from competition between H-termination of surface dangling bonds and H-generated steric hindrance below the surface. Understanding the ingredient for H-stabilized metallization directly impacts the ability to eliminate electronic defects at semiconductor interfaces critical for microelectronics, provides means to develop electrical contacts on high band-gap chemically passive materials, particularly exciting for interfacing with biological systems, and gives control of surfaces for lubrication, e.g. for nanomechanical devices

  12. Previsions of the microstructural evolution of ferritic alloys under irradiation by numerical atomic scale simulations

    International Nuclear Information System (INIS)

    In this work, we have improved a diffusion model for point defects (vacancies and self-interstitials) by introducing hetero-interstitials. The model has been used to simulate by Kinetic Monte Carlo (KMC) the formation of solute rich clusters that are observed experimentally in irradiated ferritic model alloys of type Fe - CuMnNiSiP - C.Electronic structure calculations have been used to characterize the interactions between self-interstitials and all solute atoms, and also carbon. P interacts with vacancies and strongly with self-interstitials. Mn also interacts with self-interstitials to form mixed dumbbells. C, with occupies octahedral sites, interacts strongly with vacancies and less with self-interstitials. Binding and migration energies, as well as others atomic scale properties, obtained by ab initio calculations, have been used as parameters for the KMC code. Firstly, these parameters have been optimized over isochronal annealing experiments, in the literature, of binary alloys that have been electron-irradiated. Isochronal annealing simulations, by reproducing experimental results, have allowed us to link each mechanism to a single evolution of the resistivity during annealing. Moreover, solubility limits of all the elements have been determined by Metropolis Monte Carlo. Secondly, we have simulated the evolution at 300 C of the microstructure under irradiation of different alloys of increasing complexity: pure Fe, binary alloys, ternaries, quaternaries, and finally complex alloys which compositions are close to those of pressure vessel steels. The results show that the model globally reproduces all the experimental tendencies, what has led us to propose mechanisms to explain the behaviours observed. (author)

  13. Atomic-Scale Picture of the Composition, Decay, and Oxidation of Two-Dimensional Radioactive Films.

    Science.gov (United States)

    Pronschinske, Alex; Pedevilla, Philipp; Coughlin, Benjamin; Murphy, Colin J; Lucci, Felicia R; Payne, Matthew A; Gellman, Andrew J; Michaelides, Angelos; Sykes, E Charles H

    2016-02-23

    Two-dimensional radioactive (125)I monolayers are a recent development that combines the fields of radiochemistry and nanoscience. These Au-supported monolayers show great promise for understanding the local interaction of radiation with 2D molecular layers, offer different directions for surface patterning, and enhance the emission of chemically and biologically relevant low-energy electrons. However, the elemental composition of these monolayers is in constant flux due to the nuclear transmutation of (125)I to (125)Te, and their precise composition and stability under ambient conditions has yet to be elucidated. Unlike I, which is stable and unreactive when bound to Au, the newly formed Te atoms would be expected to be more reactive. We have used electron emission and X-ray photoelectron spectroscopy (XPS) to quantify the emitted electron energies and to track the film composition in vacuum and the effect of exposure to ambient conditions. Our results reveal that the Auger electrons emitted during the ultrafast radioactive decay process have a kinetic energy corresponding to neutral Te. By combining XPS and scanning tunneling microscopy experiments with density functional theory, we are able to identify the reaction of newly formed Te to TeO2 and its subsequent dimerization. The fact that the Te2O4 units stay intact during major lateral rearrangement of the monolayer illustrates their stability. These results provide an atomic-scale picture of the composition and mobility of surface species in a radioactive monolayer as well as an understanding of the stability of the films under ambient conditions, which is a critical aspect in their future applications. PMID:26735687

  14. Breakdown of the coral-algae symbiosis: towards formalising a linkage between warm-water bleaching thresholds and the growth rate of the intracellular zooxanthellae

    Directory of Open Access Journals (Sweden)

    S. A. Wooldridge

    2012-07-01

    Full Text Available Impairment of the photosynthetic machinery of the algal endosymbiont ("zooxanthellae" is the proximal trigger for the thermal breakdown of the coral-algae symbiosis ("coral bleaching". Yet, the primary site of thermal damage is not well resolved. In this perspective essay, I consider further a recent hypothesis which proposes an energetic disruption to the carbon-concentrating mechanisms (CCMs of the coral host, and the resultant onset of CO2-limitation within the photosynthetic "dark reactions", as a unifying cellular mechanism. The hypothesis identifies the enhanced retention of photosynthetic carbon for zooxanthellae (regrowth following an initial irradiance-driven expulsion event as the cause of the energetic disruption. If true, then it implies that the onset of the bleaching syndrome and setting of upper thermal bleaching limits are emergent attributes of the coral symbiosis that are ultimately underpinned by the characteristic growth profile of the intracellular zooxanthellae; which is known to depend not just on temperature, but also external (seawater nutrient availability and zooxanthellae genotype. Here, I review this proposed bleaching linkage at a variety of observational scales, and find it to be parsimonious with the available evidence. This provides a new standpoint to consider the future prospects of the coral symbiosis in an era of rapid environmental change, including the now crucial importance of reef water quality in co-determining thermal bleaching resistance.

  15. Analysis of intracellular and extracellular microcystin variants in sediments and pore waters by accelerated solvent extraction and high performance liquid chromatography-tandem mass spectrometry.

    Science.gov (United States)

    Zastepa, Arthur; Pick, Frances R; Blais, Jules M; Saleem, Ammar

    2015-05-01

    The fate and persistence of microcystin cyanotoxins in aquatic ecosystems remains poorly understood in part due to the lack of analytical methods for microcystins in sediments. Existing methods have been limited to the extraction of a few extracellular microcystins of similar chemistry. We developed a single analytical method, consisting of accelerated solvent extraction, hydrophilic-lipophilic balance solid phase extraction, and reversed phase high performance liquid chromatography-tandem mass spectrometry, suitable for the extraction and quantitation of both intracellular and extracellular cyanotoxins in sediments as well as pore waters. Recoveries of nine microcystins, representing the chemical diversity of microcystins, and nodularin (a marine analogue) ranged between 75 and 98% with one, microcystin-RR (MC-RR), at 50%. Chromatographic separation of these analytes was achieved within 7.5 min and the method detection limits were between 1.1 and 2.5 ng g(-1) dry weight (dw). The robustness of the method was demonstrated on sediment cores collected from seven Canadian lakes of diverse geography and trophic states. Individual microcystin variants reached a maximum concentration of 829 ng g(-1) dw on sediment particles and 132 ng mL(-1) in pore waters and could be detected in sediments as deep as 41 cm (>100 years in age). MC-LR, -RR, and -LA were more often detected while MC-YR, -LY, -LF, and -LW were less common. The analytical method enabled us to estimate sediment-pore water distribution coefficients (K(d)), MC-RR had the highest affinity for sediment particles (log K(d)=1.3) while MC-LA had the lowest affinity (log K(d)=-0.4), partitioning mainly into pore waters. Our findings confirm that sediments serve as a reservoir for microcystins but suggest that some variants may diffuse into overlying water thereby constituting a new route of exposure following the dissipation of toxic blooms. The method is well suited to determine the fate and persistence of different

  16. Atomic-scale evolution of modulated phases at the ferroelectric-antiferroelectric morphotropic phase boundary controlled by flexoelectric interaction

    Energy Technology Data Exchange (ETDEWEB)

    Borisevich, Albina Y [ORNL; Eliseev, Eugene [National Academy of Science of Ukraine, Kiev, Ukraine; Morozovska, A. N. [National Academy of Science of Ukraine, Kiev, Ukraine; Cheng, Ching-Jung [ORNL; Lin, Jiunn-Yuan [National Chiao Tung University, Hsinchu, Taiwan; Chu, Ying-Hao [National Chiao Tung University, Hsinchu, Taiwan; Kan, Daisuke [University of Maryland; Takeuchi, Ichiro [ORNL; Valanoor, Nagarajan V [ORNL; Kalinin, Sergei V [ORNL

    2012-01-01

    Physical and structural origins of morphotropic phase boundaries (MPBs) in ferroics remain elusive despite decades of studies. The leading competing theories employ either low symmetry bridging phases or adaptive phases with nanoscale textures to describe different subsets of the macroscopic data, while the decisive atomic-scale information has so far been missing. We report direct atomically-resolved mapping of polarization and structure order parameter fields in Sm-doped BiFeO3 system and their evolution as the system approaches MPB. We further show that both the experimental phase diagram and the phase evolution observed by STEM can be explained by taking into account flexoelectric interaction, which renders the effective domain wall energy negative, thus stabilizing modulated phases in the vicinity of the MPB. Our study highlights the importance of local order parameter mapping at the atomic scale and establishes a hitherto unobserved physical origin of spatially modulated phases existing in the vicinity of the MPB.

  17. First-Principles Molecular Dynamics Investigation of the Atomic-Scale Energy Transport: From Heat Conduction to Thermal Radiation

    CERN Document Server

    Ji, Pengfei

    2016-01-01

    First-principles molecular dynamics simulation based on a plane wave/pseudopotential implementation of density functional theory is adopted to investigate atomic scale energy transport for semiconductors (silicon and germanium). By imposing thermostats to keep constant temperatures of the nanoscale thin layers, initial thermal non-equilibrium between the neighboring layers is established under the vacuum condition. Models with variable gap distances with an interval of lattice constant increment of the simulated materials are set up and statistical comparisons of temperature evolution curves are made. Moreover, the equilibration time from non-equilibrium state to thermal equilibrium state of different silicon or/and germanium layers combinations are calculated. The results show significant distinctions of heat transfer under different materials and temperatures combinations. Further discussions on the equilibrium time are made to explain the simulation results. As the first work of the atomic scale energy tra...

  18. Atomic-scale observation of parallel development of super elasticity and reversible plasticity in GaAs nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Peite; Du, Sichao; Zheng, Rongkun, E-mail: rongkun.zheng@sydney.edu.au [School of Physics, The University of Sydney, Sydney, NSW 2006 (Australia); Wang, Yanbo; Liao, Xiaozhou, E-mail: xiaozhou.liao@sydney.edu.au [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006 (Australia); Cui, Xiangyuan; Yen, Hung-Wei; Kong Yeoh, Wai; Ringer, Simon P. [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, NSW 2006 (Australia); Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006 (Australia); Gao, Qiang; Hoe Tan, H.; Jagadish, Chennupati [Department of Electronic Materials Engineering, Research School of Physics and Engineering, The Australian National University, Canberra, ACT 0200 (Australia); Liu, Hongwei [Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, NSW 2006 (Australia); Zou, Jin [Materials Engineering and Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072 (Australia)

    2014-01-13

    We report the atomic-scale observation of parallel development of super elasticity and reversible dislocation-based plasticity from an early stage of bending deformation until fracture in GaAs nanowires. While this phenomenon is in sharp contrast to the textbook knowledge, it is expected to occur widely in nanostructures. This work indicates that the super recoverable deformation in nanomaterials is not simple elastic or reversible plastic deformation in nature, but the coupling of both.

  19. Atomic-scale chemical imaging and quantification of metallic alloy structures by energy-dispersive X-ray spectroscopy.

    Science.gov (United States)

    Lu, Ping; Zhou, Lin; Kramer, M J; Smith, David J

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L2(1) phase with Ni0.48Co0.52 at A-sites, Al at B(Ι)-sites and Fe0.20Ti0.80 at B(ΙΙ)-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  20. Breakdown of the coral-algae symbiosis: towards formalising a linkage between warm-water bleaching thresholds and the growth rate of the intracellular zooxanthellae

    Directory of Open Access Journals (Sweden)

    S. A. Wooldridge

    2013-03-01

    Full Text Available Impairment of the photosynthetic machinery of the algal endosymbiont ("zooxanthellae" is the proximal driver of the thermal breakdown of the coral-algae symbiosis ("coral bleaching". Yet, the initial site of damage, and early dynamics of the impairment are still not well resolved. In this perspective essay, I consider further a recent hypothesis which proposes an energetic disruption to the carbon-concentrating mechanisms (CCMs of the coral host, and the resultant onset of CO2-limitation within the photosynthetic "dark reactions" as a unifying cellular mechanism. The hypothesis identifies the enhanced retention of photosynthetic carbon for zooxanthellae (regrowth following an initial irradiance-driven expulsion event as a strong contributing cause of the energetic disruption. If true, then it implies that the onset of the bleaching syndrome and setting of upper thermal bleaching limits are emergent attributes of the coral symbiosis that are ultimately underpinned by the characteristic growth profile of the intracellular zooxanthellae; which is known to depend not just on temperature, but also external (seawater nutrient availability and zooxanthellae genotype. Here, I review this proposed bleaching linkage at a variety of observational scales, and find it to be parsimonious with the available evidence. Future experiments are suggested that can more formally test the linkage. If correct, the new cellular model delivers a valuable new perspective to consider the future prospects of the coral symbiosis in an era of rapid environmental change, including: (i the underpinning mechanics (and biological significance of observed changes in resident zooxanthellae genotypes, and (ii the now crucial importance of reef water quality in co-determining thermal bleaching resistance.

  1. Breakdown of the coral-algae symbiosis: towards formalising a linkage between warm-water bleaching thresholds and the growth rate of the intracellular zooxanthellae

    Science.gov (United States)

    Wooldridge, S. A.

    2013-03-01

    Impairment of the photosynthetic machinery of the algal endosymbiont ("zooxanthellae") is the proximal driver of the thermal breakdown of the coral-algae symbiosis ("coral bleaching"). Yet, the initial site of damage, and early dynamics of the impairment are still not well resolved. In this perspective essay, I consider further a recent hypothesis which proposes an energetic disruption to the carbon-concentrating mechanisms (CCMs) of the coral host, and the resultant onset of CO2-limitation within the photosynthetic "dark reactions" as a unifying cellular mechanism. The hypothesis identifies the enhanced retention of photosynthetic carbon for zooxanthellae (re)growth following an initial irradiance-driven expulsion event as a strong contributing cause of the energetic disruption. If true, then it implies that the onset of the bleaching syndrome and setting of upper thermal bleaching limits are emergent attributes of the coral symbiosis that are ultimately underpinned by the characteristic growth profile of the intracellular zooxanthellae; which is known to depend not just on temperature, but also external (seawater) nutrient availability and zooxanthellae genotype. Here, I review this proposed bleaching linkage at a variety of observational scales, and find it to be parsimonious with the available evidence. Future experiments are suggested that can more formally test the linkage. If correct, the new cellular model delivers a valuable new perspective to consider the future prospects of the coral symbiosis in an era of rapid environmental change, including: (i) the underpinning mechanics (and biological significance) of observed changes in resident zooxanthellae genotypes, and (ii) the now crucial importance of reef water quality in co-determining thermal bleaching resistance.

  2. Structure-Property Relationships in Atomic-Scale Junctions: Histograms and Beyond.

    Science.gov (United States)

    Hybertsen, Mark S; Venkataraman, Latha

    2016-03-15

    are pulled apart has given complementary information such as the stiffness and rupture force of the molecule-metal link bond. Overall, while the BJ technique does not produce a single molecule circuit for practical applications, it has proved remarkably versatile for fundamental studies. Measured data and analysis have been combined with atomic-scale theory and calculations, typically performed for representative junction structures, to provide fundamental physical understanding of structure-function relationships. This Account integrates across an extensive series of our specific nanoscale junction studies which were carried out with the STM- and AFM-BJ techniques and supported by theoretical analysis and density functional theory based calculations, with emphasis on the physical characteristics of the measurement process and the rich data sets that emerge. Several examples illustrate the impact of measured trends based on the most probable values for key characteristics (obtained from ensembles of order 1000-10 000 individual junctions) to build a solid picture of conductance phenomena as well as attributes of the link bond chemistry. The key forward-looking question posed here is the extent to which the full data sets represented by the individual trajectories can be analyzed to address structure-function questions at the level of individual junctions. Initial progress toward physical modeling of conductance of individual junctions indicates trends consistent with physical junction structures. Analysis of junction mechanics reveals a scaling procedure that collapses existing data onto a universal force-extension curve. This research directed to understanding the distribution of structures and physical characteristics addresses fundamental questions concerning the interplay between chemical control and stochastically driven diversity. PMID:26938931

  3. Immunity to intracellular bacteria

    OpenAIRE

    Stefan H. E. Kaufmann; Follows, George A.; Martin E. Munik

    1992-01-01

    Immunity to intracellular bacteria including Mycobacterium tuberculosis. Mycobacterium leprae, and Listeria monocytogenes depends on specific T cells. Evidence to be described suggests that CD4 (alpha/beta)T cells which interact with each other and with macrophages contribute to acquired resistence against as well as pathogenesis of intracellular bacterial infections.

  4. Immunity to intracellular bacteria

    Directory of Open Access Journals (Sweden)

    Stefan H. E. Kaufmann

    1992-01-01

    Full Text Available Immunity to intracellular bacteria including Mycobacterium tuberculosis. Mycobacterium leprae, and Listeria monocytogenes depends on specific T cells. Evidence to be described suggests that CD4 (alpha/betaT cells which interact with each other and with macrophages contribute to acquired resistence against as well as pathogenesis of intracellular bacterial infections.

  5. Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and Its Precursors on Metal Surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, George W [Columbia University

    2015-02-16

    Executive Summary of Final Report for Award DE-FG02-88ER13937 Project Title: Atomic Scale Imaging of the Electronic Structure and Chemistry of Graphene and its Precursors on Metal Surfaces Applicant/Institution: Columbia University Principal Investigator: George W. Flynn Objectives: The objectives of this project were to reveal the mechanisms and reaction processes that solid carbon materials undergo when combining with gases such as oxygen, water vapor and hydrocarbons. This research was focused on fundamental chemical events taking place on single carbon sheets of graphene, a two-dimensional, polycyclic carbon material that possesses remarkable chemical and electronic properties. Ultimately, this work is related to the role of these materials in mediating the formation of polycyclic aromatic hydrocarbons (PAH’s), their reactions at interfaces, and the growth of soot particles. Our intent has been to contribute to a fundamental understanding of carbon chemistry and the mechanisms that control the formation of PAH’s, which eventually lead to the growth of undesirable particulates. We expect increased understanding of these basic chemical mechanisms to spur development of techniques for more efficient combustion of fossil fuels and to lead to a concomitant reduction in the production of undesirable solid carbon material. Project Description: Our work treated specifically the surface chemistry aspects of carbon reactions by using proximal probe (atomic scale imaging) techniques to study model systems of graphene that have many features in common with soot forming reactions of importance in combustion flames. Scanning tunneling microscopy (STM) is the main probe technique that we used to study the interfacial structure and chemistry of graphene, mainly because of its ability to elucidate surface structure and dynamics with molecular or even atomic resolution. Scanning tunneling spectroscopy (STS), which measures the local density of quantum states over a single

  6. Atomic-Scale Characterization and Manipulation of Freestanding Graphene Using Adapted Capabilities of a Scanning Tunneling Microscope

    Science.gov (United States)

    Barber, Steven

    Graphene was the first two-dimensional material ever discovered, and it exhibits many unusual phenomena important to both pure and applied physics. To ensure the purest electronic structure, or to study graphene's elastic properties, it is often suspended over holes or trenches in a substrate. The aim of the research presented in this dissertation was to develop methods for characterizing and manipulating freestanding graphene on the atomic scale using a scanning tunneling microscope (STM). Conventional microscopy and spectroscopy techniques must be carefully reconsidered to account for movement of the extremely flexible sample. First, the acquisition of atomic-scale images of freestanding graphene using the STM and the ability to pull the graphene perpendicular to its plane by applying an electrostatic force with the STM tip are demonstrated. The atomic-scale images contained surprisingly large corrugations due to the electrostatic attractive force varying in registry with the local density of states. Meanwhile, a large range of control over the graphene height at a point was obtained by varying the tip bias voltage, and the application to strain engineering of graphene's so-called pseudomagnetic field is examined. Next, the effect of the tunneling current was investigated. With increasing current, the graphene sample moves away from the tip rather than toward it. It was determined that this must be due to local heating by the electric current, causing the graphene to contract because it has a negative coefficient of thermal expansion. Finally, by imaging a very small area, the STM can monitor the height of one location over long time intervals. Results sometimes exhibit periodic behavior, with a frequency and amplitude that depend on the tunneling current. These fluctuations are interpreted as low-frequency flexural phonon modes within elasticity theory. All of these findings set the foundation for employing a STM in the study of freestanding graphene.

  7. Atomic-scale investigation of interface-facilitated deformation twinning in severely deformed Ag-Cu nanolamellar composites

    Energy Technology Data Exchange (ETDEWEB)

    An, X. H., E-mail: anxianghai@gmail.com, E-mail: xiaozhou.liao@sydenye.edu.au; Cao, Y.; Liao, X. Z., E-mail: anxianghai@gmail.com, E-mail: xiaozhou.liao@sydenye.edu.au [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, New South Wales 2006 (Australia); Zhu, S. M.; Nie, J. F. [Department of Materials Engineering, Monash University, Melbourne, Victoria 3800 (Australia); Kawasaki, M. [Division of Materials Science and Engineering, Hanyang University, 17 Haengdang-dong, Seongdong-gu, Seoul 133-791 (Korea, Republic of); Ringer, S. P. [School of Aerospace, Mechanical and Mechatronic Engineering, The University of Sydney, Sydney, New South Wales 2006 (Australia); Australian Centre for Microscopy and Microanalysis, The University of Sydney, Sydney, New South Wales 2006 (Australia); Langdon, T. G. [Departments of Aerospace and Mechanical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1453 (United States); Materials Research Group, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ (United Kingdom); Zhu, Y. T. [Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695-7919 (United States); School of Materials Science and Engineering, Nanjing University of Science and Technology, Nanjing (China)

    2015-07-06

    We report an atomic-scale investigation of interface-facilitated deformation twinning behaviour in Ag-Cu nanolamellar composites. Profuse twinning activities in Ag supply partial dislocations to directly transmit across the Ag-Cu lamellar interface that promotes deformation twinning in the neighbouring Cu lamellae although the interface is severely deformed. The trans-interface twin bands change the local structure at the interface. Our analysis suggests that the orientation relationship and interfacial structure between neighbouring Ag-Cu lamellae play a crucial role in such special interface-facilitated twinning behaviour.

  8. Atomic-scale investigation of interface-facilitated deformation twinning in severely deformed Ag-Cu nanolamellar composites

    International Nuclear Information System (INIS)

    We report an atomic-scale investigation of interface-facilitated deformation twinning behaviour in Ag-Cu nanolamellar composites. Profuse twinning activities in Ag supply partial dislocations to directly transmit across the Ag-Cu lamellar interface that promotes deformation twinning in the neighbouring Cu lamellae although the interface is severely deformed. The trans-interface twin bands change the local structure at the interface. Our analysis suggests that the orientation relationship and interfacial structure between neighbouring Ag-Cu lamellae play a crucial role in such special interface-facilitated twinning behaviour

  9. Atomic-Scale Variations of the Mechanical Response of 2D Materials Detected by Noncontact Atomic Force Microscopy

    Science.gov (United States)

    de la Torre, B.; Ellner, M.; Pou, P.; Nicoara, N.; Pérez, Rubén; Gómez-Rodríguez, J. M.

    2016-06-01

    We show that noncontact atomic force microscopy (AFM) is sensitive to the local stiffness in the atomic-scale limit on weakly coupled 2D materials, as graphene on metals. Our large amplitude AFM topography and dissipation images under ultrahigh vacuum and low temperature resolve the atomic and moiré patterns in graphene on Pt(111), despite its extremely low geometric corrugation. The imaging mechanisms are identified with a multiscale model based on density-functional theory calculations, where the energy cost of global and local deformations of graphene competes with short-range chemical and long-range van der Waals interactions. Atomic contrast is related with short-range tip-sample interactions, while the dissipation can be understood in terms of global deformations in the weakly coupled graphene layer. Remarkably, the observed moiré modulation is linked with the subtle variations of the local interplanar graphene-substrate interaction, opening a new route to explore the local mechanical properties of 2D materials at the atomic scale.

  10. Inclusion of pH and potential in atomic-scale simulations of the electrochemical interface

    DEFF Research Database (Denmark)

    Björketun, Mårten; Rossmeisl, Jan; Chan, Karen; Zeng, Zhenhua; Ahmed, Rizwan; Tripkovic, Vladimir

    2013-01-01

    reaction intermediates. Water and electric fields are often omitted to reduce the computational resources, and the effect of potential is added a posteriori via the computational hydrogen electrode [1]. More advanced studies try to model the entire interface and focus on setting up an explicit electrode......Recent improvements in computational power and theory have allowed for density functional theory calculations on electrochemical systems. Currently, there are two main types of ab initio studies on electrochemical systems. Catalyst screening/optimization studies focus on adsorption free energies of...... potential and electric field at the interface via water layers, excess free charge, counter-ions, and counter electrodes. No existing approach addresses the effect of pH on the interfacial structure. Electrochemical reaction rates can, however, be strongly affected by solution pH, and there is increasing...

  11. A hybrid molecular dynamics/atomic-scale finite element method for quasi-static atomistic simulations at finite temperature

    CERN Document Server

    Xu, Ran

    2013-01-01

    In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some temperature effects are embedded in static AFEM simulation by applying the virtual and equivalent thermal disturbance forces extracted from MD. Alternatively performing MD and AFEM can quickly obtain a series of thermodynamic equilibrium configurations such that a quasi-static process is modeled. Moreover, a stirring-accelerated MD/AFEM fast relaxation approach is proposed, in which the atomic forces and velocities are randomly exchanged to artificially accelerate the "slow processes" such as mechanical wave propagation and thermal diffusion. The efficiency of the proposed methods is demonstrated by numerical examples on single wall carbon nanotubes.

  12. In Situ Atomic Scale Visualization Of Surface Kinetics Driven Dynamics Of Oxide Growth On A Ni–Cr Surface

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Langli; Zou, Lianfeng; Schreiber, Daniel K.; Olszta, Matthew J.; Baer, Donald R.; Bruemmer, Stephen M.; Zhou, Guangwen; Wang, Chong M.

    2016-01-20

    We report in situ atomic-scale visualization of the dynamical three-dimensional (3D) growth of NiO during initial oxidation of Ni-10at%Cr using environmental transmission electron microscopy (ETEM). Despite the thermodynamic preference for Cr2O3 formation, cubic NiO oxides nucleated and grew epitaxially as the dominating oxide phase on the Ni-Cr (100) surface during initial oxidation. The growth of NiO islands proceeds through step-by-step adatom mechanism in 3D, which is sustained by surface diffusion of Ni and O atoms. Although the shapes of oxide islands are controlled by strain energy between oxide and alloy substrate, local surface kinetic variations can lead to the change of surface planes of oxide islands. These results demonstrate that surface diffusion dominates initial oxidation of Ni-Cr in these test conditions.

  13. Atomic-scale configurations of synchroshear-induced deformation twins in the ionic MnS crystal

    Science.gov (United States)

    Zhou, Y. T.; Xue, Y. B.; Chen, D.; Wang, Y. J.; Zhang, B.; Ma, X. L.

    2014-01-01

    Deformation twinning was thought as impossible in ionic compounds with rock-salt structure due to the charge effect on {111} planes. Here we report the presence and formation mechanism of deformation {111} twins in the rock-salt manganese sulphide (MnS) inclusions embedded in a hot-rolled stainless steel. Based on the atomic-scale mapping under aberration-corrected scanning transmission electron microscopy, a dislocation-based mechanism involved two synchronized shear on adjacent atomic layers is proposed to describe the dislocation glide and consequently twinning formation. First-principles calculations of the energy barriers for twinning formation in MnS and comparing with that of PbS and MgO indicate the distinct dislocation glide scheme and deformation behaviors for the rock-salt compounds with different ionicities. This study may improve our understanding of the deformation mechanisms of rock-salt crystals and other ionic compounds. PMID:24874022

  14. Demonstration of atomic scale stick-slip events stimulated by the force versus distance mode using atomic force microscopy

    Science.gov (United States)

    Watson, Gregory S.; Dinte, Bradley P.; Blach, Jolanta A.; Myhra, Sverre

    2002-08-01

    It has been shown that longitudinal deformation of the force-sensing/imposing lever can be stimulated by the conventional force versus distance (F-d), analytical mode of a scanning force microscope. Accordingly it is possible to measure simultaneously both in-plane and out-of-plane force components acting between a tip and a surface. Discrete atomic scale stick-slip events have been observed by F-d generated friction loop analysis of cleaved WTe2, Mica and HOPG single crystals, and of a Langmuir-Blodgett film. Due to the lever geometry, the lateral resolution arising from z-stage movement is better by an order of magnitude than that obtained from translation of the x-y-stage.

  15. Role of cardiolipins in the inner mitochondrial membrane: insight gained through atom-scale simulations

    DEFF Research Database (Denmark)

    Róg, Tomasz; Martinez-Seara, Hector; Munck, Nana;

    2009-01-01

    Mitochondrial membranes are unique in many ways. Unlike other cellular membranes, they are comprised of two membranes instead of just one, and cardiolipins, one of the abundant lipid species in mitochondrial membranes, are not found in significant amounts elsewhere in the cell. Among other aspects......), phosphatidylcholines (PCs), and phosphatidylethanolamines (PEs). For comparison, we also consider pure one-component bilayers and mixed PC-PE, PC-CL, and PE-CL membranes. We find that the influence of CLs on membrane properties depends strongly on membrane composition. This is highlighted by studies of the stability...... of CL-containing membranes, which indicate that the interactions of CL in ternary lipid bilayers cannot be deduced from the corresponding ones in binary membranes. Moreover, while the membrane properties in the hydrocarbon region are only weakly affected by CLs, the changes at the membrane-water...

  16. Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments.

    Science.gov (United States)

    Gillams, Richard J; Lorenz, Christian D; McLain, Sylvia E

    2016-06-14

    Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of the lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems. PMID:27306021

  17. Comparative atomic-scale hydration of the ceramide and phosphocholine headgroup in solution and bilayer environments

    Science.gov (United States)

    Gillams, Richard J.; Lorenz, Christian D.; McLain, Sylvia E.

    2016-06-01

    Previous studies have used neutron diffraction to elucidate the hydration of the ceramide and the phosphatidylcholine headgroup in solution. These solution studies provide bond-length resolution information on the system, but are limited to liquid samples. The work presented here investigates how the hydration of ceramide and phosphatidylcholine headgroups in a solution compares with that found in a lipid bilayer. This work shows that the hydration patterns seen in the solution samples provide valuable insight into the preferential location of hydrating water molecules in the bilayer. There are certain subtle differences in the distribution, which result from a combination of the lipid conformation and the lipid-lipid interactions within the bilayer environment. The lipid-lipid interactions in the bilayer will be dependent on the composition of the bilayer, whereas the restricted exploration of conformational space is likely to be applicable in all membrane environments. The generalized description of hydration gathered from the neutron diffraction studies thus provides good initial estimation for the hydration pattern, but this can be further refined for specific systems.

  18. Enabling the measurement of in-situ, atomic scale mineral transformation rates in supercritical CO2 through development of a high pressure AFM

    Science.gov (United States)

    Lea, S.; Higgins, S. R.; Knauss, K. G.; Rosso, K. M.

    2010-12-01

    Capture and storage of carbon dioxide in deep geologic formations represents one promising scenario for minimizing the impacts of greenhouse gases on global warming. The ability to demonstrate that CO2 will remain stored in the geological formation over the long-term is needed in support of widespread implementation decisions, and knowledge of mineral-fluid chemical transformation rates is an essential aspect. The majority of previous research on mineral-fluid interactions has focused primarily on the reactivity of minerals in aqueous solutions containing various amounts of dissolved CO2. Long-term caprock integrity, however, could also be dictated by mineral transformations occurring in low-water environments dominated by the supercritical CO2 (scCO2) fluid phase, which is expected to slowly displace or dessicate residual aqueous solution at the caprock-fluid interface. Many of the mechanisms of mineral interfacial reactions with hydrated or water-saturated scCO2 are unknown and there are unique challenges to obtain kinetic and thermodynamic data for mineral transformation reactions in these fluids. We are developing a high-pressure atomic force microscope (AFM) that will enable in-situ, atomic scale measurements of metal carbonate nucleation and growth rates on mineral surfaces in contact with hydrated scCO2 fluids. This apparatus is based on the hydrothermal AFM that was developed by Higgins et al.1, but includes some enhancements and is designed to handle pressures up to 100 bar. The noise in our optically-based cantilever deflection detection scheme is subject to perturbations in the density (due to index of refraction dependence) of the compressible supercritical fluid. Consequently, variations in temperature and pressure within the fluid cell are a primary technical challenge with possible significant impact in imaging resolution. We demonstrate with our test fluid cell that the equivalent rms noise in the deflection signal is similar to (and in some cases

  19. Does the intracellular ionic concentration or the cell water content (cell volume) determine the activity of TonEBP in NIH3T3 cells?

    DEFF Research Database (Denmark)

    Rødgaard, Tina; Schou, Kenneth; Friis, Martin Barfred;

    2008-01-01

    of the present investigation was to investigate whether cell shrinkage or high intracellular ionic concentration induced the activation of TonEBP. We designed a model system for isotonically shrinking cells over a prolonged period of time. Cells swelled in hypotonic medium and performed a regulatory...... volume decrease (RVD). Upon return to the original isotonic medium, cells shrank initially followed by a regulatory volume increase (RVI). To maintain cell shrinkage, the RVI process was inhibited as follows: Ethyl-isopropyl-amiloride (EIPA) inhibited the Na(+)/H(+) antiport, Bumetanide inhibited the Na......(+)/K(+)/2Cl(-) co-transporter, and Gadolinium inhibited shrinkage-activated Na(+) channels. Cells remained shrunken for at least 4 hours (isotonically shrunken cells). The activity of TonEBP was investigated with a Luciferase assay after isotonic shrinkage and after shrinkage in a high NaCl hypertonic...

  20. Multiparameter Intracellular Cytokine Staining

    OpenAIRE

    Lovelace, Patricia; Maecker, Holden T.

    2011-01-01

    Intracellular cytokine staining (ICS) is a popular method for visualizing cellular responses, most often T-cell responses to antigenic or mitogenic stimulation. It can be coupled with staining for other functional markers, such as upregulation of CD107 or CD154, as well as phenotypic markers that define specific cellular subsets, e.g. effector and memory T-cell compartments. Recent advances in multicolor flow cytometry instrumentation and software have allowed the routine combination of 8–12 ...

  1. Intracellular Sterol Dynamics

    OpenAIRE

    Mesmin, Bruno; Maxfield, Frederick R.

    2009-01-01

    We review the cellular mechanisms implicated in cholesterol trafficking and distribution. Recent studies have provided new information about the distribution of sterols within cells, including analysis of its transbilayer distribution. The cholesterol interaction with other lipids and its engagement in various trafficking processes will determine its proper level in a specific membrane; making the cholesterol distribution uneven among the various intracellular organelles. The cholesterol cont...

  2. Measurements of intracellular calcium

    International Nuclear Information System (INIS)

    Intracellular calcium concentration ([Ca2+]i) has been measured in cultured cells by using Fura-2 load cells and a computer-controlled Perkin Elmer LS-5B spectrofluorometer. Increased [Ca2+]i in cells exposed to extracellular bilirubin was observed both with and without extracellular calcium. However, the increase was considerable larger with extracellular calcium. The enhancement of [Ca2+]i became smaller with decreasing bilirubin/BSA (bovine serum albumine) ratio. 5 refs., 5 figs

  3. In situ atomic scale mechanical microscopy discovering the atomistic mechanisms of plasticity in nano-single crystals and grain rotation in polycrystalline metals

    Energy Technology Data Exchange (ETDEWEB)

    Han, Xiaodong, E-mail: xdhan@bjut.edu.cn [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology (China); Wang, Lihua; Yue, Yonghai [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology (China); Zhang, Ze, E-mail: zezhang@zju.edu.cn [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology (China); Department of Materials Science, National Key Lab of Silicon Materials, Zhejiang University (China)

    2015-04-15

    In this review, we briefly introduce our in situ atomic-scale mechanical experimental technique (ASMET) for transmission electron microscopy (TEM), which can observe the atomic-scale deformation dynamics of materials. This in situ mechanical testing technique allows the deformation of TEM samples through a simultaneous double-tilt function, making atomic-scale mechanical microscopy feasible. This methodology is generally applicable to thin films, nanowires (NWs), tubes and regular TEM samples to allow investigation of the dynamics of mechanically stressed samples at the atomic scale. We show several examples of this technique applied to Pt and Cu single/polycrystalline specimens. The in situ atomic-scale observation revealed that when the feature size of these materials approaches the nano-scale, they often exhibit “unusual” deformation behaviours compared to their bulk counterparts. For example, in Cu single-crystalline NWs, the elastic–plastic transition is size-dependent. An ultra-large elastic strain of 7.2%, which approaches the theoretical elasticity limit, can be achieved as the diameter of the NWs decreases to ∼6 nm. The crossover plasticity transition from full dislocations to partial dislocations and twins was also discovered as the diameter of the single-crystalline Cu NWs decreased. For Pt nanocrystals (NC), the long-standing uncertainties of atomic-scale plastic deformation mechanisms in NC materials (grain size G less than 15 nm) were clarified. For larger grains with G<∼10 nm, we frequently observed movements and interactions of cross-grain full dislocations. For G between 6 and 10 nm, stacking faults resulting from partial dislocations become more frequent. For G<∼6 nm, the plasticity mechanism transforms from a mode of cross-grain dislocation to a collective grain rotation mechanism. This grain rotation process is mediated by grain boundary (GB) dislocations with the assistance of GB diffusion and shuffling. These in situ atomic-scale

  4. In situ atomic scale mechanical microscopy discovering the atomistic mechanisms of plasticity in nano-single crystals and grain rotation in polycrystalline metals

    International Nuclear Information System (INIS)

    In this review, we briefly introduce our in situ atomic-scale mechanical experimental technique (ASMET) for transmission electron microscopy (TEM), which can observe the atomic-scale deformation dynamics of materials. This in situ mechanical testing technique allows the deformation of TEM samples through a simultaneous double-tilt function, making atomic-scale mechanical microscopy feasible. This methodology is generally applicable to thin films, nanowires (NWs), tubes and regular TEM samples to allow investigation of the dynamics of mechanically stressed samples at the atomic scale. We show several examples of this technique applied to Pt and Cu single/polycrystalline specimens. The in situ atomic-scale observation revealed that when the feature size of these materials approaches the nano-scale, they often exhibit “unusual” deformation behaviours compared to their bulk counterparts. For example, in Cu single-crystalline NWs, the elastic–plastic transition is size-dependent. An ultra-large elastic strain of 7.2%, which approaches the theoretical elasticity limit, can be achieved as the diameter of the NWs decreases to ∼6 nm. The crossover plasticity transition from full dislocations to partial dislocations and twins was also discovered as the diameter of the single-crystalline Cu NWs decreased. For Pt nanocrystals (NC), the long-standing uncertainties of atomic-scale plastic deformation mechanisms in NC materials (grain size G less than 15 nm) were clarified. For larger grains with G<∼10 nm, we frequently observed movements and interactions of cross-grain full dislocations. For G between 6 and 10 nm, stacking faults resulting from partial dislocations become more frequent. For G<∼6 nm, the plasticity mechanism transforms from a mode of cross-grain dislocation to a collective grain rotation mechanism. This grain rotation process is mediated by grain boundary (GB) dislocations with the assistance of GB diffusion and shuffling. These in situ atomic-scale

  5. Direct methods for the determination of atomic-scale structure of amorphous solids (X-ray, electron, and neutron scattering)

    International Nuclear Information System (INIS)

    The atomic-scale structure of amorphous solids can be determined from the X-ray, electron or neutron scattering pattern. The atomic distribution function rho(r) or the pair correlation function g(r)=rho(r)/rho0, where rho0 is the average atomic density, is related to the interference function or structure factor I(K) by a Fourier transformation. Unfortunately, I(K) is not directly accessible from the scattering experiment, but can be deduced from the scattering pattern after suitable corrections for polarization, absorption, inelastic scattering, multiple scattering, and static approximation, and after normalization to absolute units. The latest developments in the experimental techniques for the determination of the interference function I(K) are presented, and examples of the scattering patterns of metallic glasses are given, which were obtained by the conventional, variable 2theta technique, and by the variable lambda technique. Attempts are discussed to deduce the partial interference functions in binary systems from several experiments, and to determine concentration fluctuations in binary alloys. (Auth.)

  6. Atomic-scale intergranular crack-tip plasticity in tilt grain boundaries acting as an effective dislocation source

    International Nuclear Information System (INIS)

    The intergranular fracture toughness of plastic deformable crystalline materials is strongly controlled by the plastic work ahead of the intergranular crack tip. Therefore, in studies of intergranular fracture toughness, the grain boundaries (GBs) should be regarded as both a cleavage plane and dislocation source. Combining continuum analyses and atomic simulations, this study investigates the atomic-scale mechanism of intergranular crack tip plasticity in aluminum 〈1 1 2〉 tilt GBs as an effective dislocation source. To quantitatively predict the first plastic deformation near the intergranular crack tip, we first model the dislocation emission from the GBs ahead of the intergranular crack tip and analytically derive the critical stress intensity factor. If the predicted first plastic phenomenon is dislocation emission from the GBs, the resulting wedge disclination can shield the stress field near the crack. Dislocation emissions from the crack tip are accompanied by dislocation emissions from the GBs, despite the predicted difficulty of the latter. The lattice defect evolution nucleates a nanograin with a disclination at the triple-junction ahead of the crack tip, which can weaken the mechanical field near the crack tip. Consequently, when improving the intergranular fracture toughness of materials, the role of GBs as dislocation sources cannot be ignored

  7. Crystallization, phase evolution and corrosion of Fe-based metallic glasses: An atomic-scale structural and chemical characterization study

    International Nuclear Information System (INIS)

    Understanding phase changes, including their formation and evolution, is critical for the performance of functional as well as structural materials. We analyze in detail microstructural and chemical transformations of the amorphous steel Fe50Cr15Mo14C15B6 during isothermal treatments at temperatures ranging from 550 to 800 °C. By combining high-resolution transmission electron microscopy and Rietveld analyses of X-ray diffraction patterns together with the local chemical data obtained by atom probe tomography, this research provides relevant information at the atomic scale about the mechanisms of crystallization and the subsequent phases evolution. During the initial stages of crystallization a stable (Fe,Cr)23(C,B)6 precipitates as well as two metastable intermediates of M3(C,B) and the intermetallic χ-phase. When full crystallization is reached, only a percolated nano-scale Cr-rich (Fe,Cr)23(C,B)6 and Mo-rich η-Fe3Mo3C structure is detected, with no evidence to suggest that other phases appear at any subsequent time. Finally, the corrosion behavior of the developed phases is discussed from considerations of the obtained atomic information

  8. Phase Transitions and Atomic-Scale Migration During the Preoxidation of a Titania/Ferrous Oxide Solution

    Science.gov (United States)

    Wang, Zhen-Yang; Zhang, Jian-Liang; Xing, Xiang-Dong; Liu, Zheng-Jian; Zhang, Ya-Peng; Liu, Xing-Le; Liu, Yi-Ran

    2016-02-01

    The non-isothermal preoxidation of the titania/ferrous oxide solution (TFOS) was investigated between 300°C and 1200°C. To explore the TFOS preoxidation mechanism, the phase transitions, crystal structure behavior, subreactions, and atomic-scale migration and enrichment of the TFOS during preoxidation were studied. Two different titanium and iron solutions were distinguished by scanning electron microscopy analysis. The phase transitions from titanomagnetite (TTM) to titanohematite to pseudobrookite (PSB) were indicated by the separation and enrichment of Ti and Fe, which migrated into PSB and hematite, respectively. This occurred alongside the generation and destruction of FeTiO3. Multiple local maxima and shoulders were observed in the double-derivative thermogravimetric curves during the preoxidation process, indicating the existence and initial reaction temperatures of five stages of subreactions. Compared with the theoretical mass gain (3.28 wt.%), only 80.8 at.% of the Fe2+ was oxidized to Fe3+, leaving unoxidized TTM in the solid solution during non-isothermal oxidation at 1200°C. The concentration of Ti gradually increased in the lamellar structures. However, Fe, Al, and O were mostly restricted to the homogeneous regions. The segregation of Mg only became obvious when TFOS was oxidized at high temperatures. The enrichment reduced the impact of Ti when O migrated during the reduction process, thus, enhancing the reducibility of the TFOS after preoxidation.

  9. Inhomogeneous thermal expansion of metallic glasses in atomic-scale studied by in-situ synchrotron X-ray diffraction

    Science.gov (United States)

    Taghvaei, Amir Hossein; Shakur Shahabi, Hamed; Bednarčik, Jozef; Eckert, Jürgen

    2015-01-01

    Numerous investigations have demonstrated that the elastic strain in metallic glasses subjected to mechanical loading could be inhomogeneous in the atomic-scale and it increases with distance from an average atom and eventually reaches the macroscopic strain at larger inter-atomic distances. We have observed a similar behavior for the thermal strain imposed by heating of Co40Fe22Ta8B30 glassy particles below the glass transition temperature by analysis of the scattering data obtained by in-situ high-energy synchrotron X-ray diffraction (XRD). The results imply that the volumetric thermal strains calculated from the shift in position of the principal diffraction maximum and reduced pair correlation function (PDF) peaks are in good agreement for the length scales beyond 0.6 nm, corresponding to the atoms located over the third near-neighbor shell. However, smaller and even negative volumetric thermal strains have been calculated based on the shifts in the positions of the second and first PDF peaks, respectively. The structural changes of Co40Fe22Ta8B30 glassy particles are accompanied by decreasing the average coordination number of the first near-neighbor shell, which manifests the occurrence of local changes in the short-range order upon heating. It is believed that the detected length-scale dependence of the volumetric thermal strain is correlated with the local atomic rearrangements taking place in the topologically unstable regions of the glass governed by variations in the atomic-level stresses.

  10. Nanomechanics analysis of perfect and defected graphene sheets via a novel atomic-scale finite element method

    Science.gov (United States)

    Malakouti, M.; Montazeri, A.

    2016-06-01

    Due to their accuracy and reliability, atomistic-based methods such as molecular dynamics (MD) simulations have played an essential role in the field of predictive modeling of single layered graphene sheets (SLGSs) at the nanoscale. However, their applications are limited due to the computational costs. Additionally, consistent with the discrete nature of SLGSs, conventional continuum-based methods cannot be utilized to study the mechanical characteristics of these nanostructures. To overcome these issues, a new Atomic-scale Finite Element Method (AFEM) based on the Tersoff-Brenner potential has been developed in this study. Efficiency of the proposed method is demonstrated employing several numerical examples and its applicability is carefully testified in the case of perfect and defected SLGSs. To facilitate a better comparison, the mechanical behavior obtained by this method is compared with the one determined via MD simulation in various case studies. The results reveal that the proposed method has the accuracy of MD simulations and the speed of continuum-based approaches, simultaneously.

  11. Quantitative Z-Contrast Imaging of Supported Metal Complexes and Clusters - A Gateway to Understanding Catalysis on the Atomic Scale

    Energy Technology Data Exchange (ETDEWEB)

    Browning, Nigel D.; Aydin, C.; Lu, Jing; Kulkarni, Apoorva; Okamoto, Norihiko L.; Ortalan, V.; Reed, Bryan W.; Uzun, Alper; Gates, Bruce C.

    2013-09-01

    Z-contrast imaging in an aberration-corrected scanning transmission electron microscope can be used to observe and quantify the sizes, shapes, and compositions of the metal frames in supported mono-, bi-, and multimetallic metal clusters and can even detect the metal atoms in single-metal-atom complexes, as well as providing direct structural information characterizing the metal-support interface. Herein, we assess the major experimental challenges associated with obtaining atomic resolution Z-contrast images of the materials that are highly beam-sensitive, that is, the clusters readily migrate and sinter on support surfaces, and the support itself can drastically change in structure if the experiment is not properly controlled. Calibrated and quantified Z-contrast images are used in conjunction with exsitu analytical measurements and larger-scale characterization methods such as extended X-ray absorption fine structure spectroscopy to generate an atomic-scale understanding of supported catalysts and their function. Examples of the application of these methods include the characterization of a wide range of sizes and compositions of supported clusters, primarily those incorporating Ir, Os, and Au, on highly crystalline supports (zeolites and MgO).

  12. Atomic Scale Interface Manipulation, Structural Engineering, and Their Impact on Ultrathin Carbon Films in Controlling Wear, Friction, and Corrosion.

    Science.gov (United States)

    Dwivedi, Neeraj; Yeo, Reuben J; Yak, Leonard J K; Satyanarayana, Nalam; Dhand, Chetna; Bhat, Thirumaleshwara N; Zhang, Zheng; Tripathy, Sudhiranjan; Bhatia, Charanjit S

    2016-07-13

    Reducing friction, wear, and corrosion of diverse materials/devices using systems. Here, we present a novel approach based on atomic scale interface manipulation to engineer and control the friction, wear, corrosion, and structural characteristics of 0.7-1.7 nm carbon-based films on CoCrPt:oxide-based magnetic media. We demonstrate that when an atomically thin (∼0.5 nm) chromium nitride (CrNx) layer is sandwiched between the magnetic media and an ultrathin carbon overlayer (1.2 nm), it modifies the film-substrate interface, creates various types of interfacial bonding, increases the interfacial adhesion, and tunes the structure of carbon in terms of its sp(3) bonding. These contribute to its remarkable functional properties, such as stable and lowest coefficient of friction (∼0.15-0.2), highest wear resistance and better corrosion resistance despite being only ∼1.7 nm thick, surpassing those of ∼2.7 nm thick current commercial carbon overcoat (COC) and other overcoats in this work. While this approach has direct implications for advancing current magnetic storage technology with its ultralow thickness, it can also be applied to advance the protective and barrier capabilities of other ultrathin materials for associated technologies. PMID:27267790

  13. Atomic-scale study of the adsorption of calcium fluoride on Si(100) at low-coverage regime

    International Nuclear Information System (INIS)

    We investigate, experimentally and theoretically, the initial stage of the formation of Ca/Si and Si/F structures that occurs during the adsorption of CaF2 molecules onto a bare Si(100) surface heated to 1000 K in a low-coverage regime (0.3 monolayer). A low-temperature (5 K) scanning tunneling microscope (STM) is used to observe the topographies and the electronic properties of the exposed silicon surfaces. Our atomic-scale study reveals that several chemical reactions arise during CaF2 deposition, such as dissociation of the CaF2 molecules and etching of the surface silicon dimers. The experimental and calculated STM topographies are compared using the density functional theory, and this comparison enables us to identify two types of reacted structures on the Si(100) surface. The first type of observed complex surface structure consists of large islands formed with a semiperiodic sequence of 3 x 2 unit cells. The second one is made of isolated Ca adatoms adsorbed at specific sites on the Si(100)-2 x 1 surface.

  14. Nanovehicular intracellular delivery systems.

    Science.gov (United States)

    Prokop, Ales; Davidson, Jeffrey M

    2008-09-01

    This article provides an overview of principles and barriers relevant to intracellular drug and gene transport, accumulation and retention (collectively called as drug delivery) by means of nanovehicles (NV). The aim is to deliver a cargo to a particular intracellular site, if possible, to exert a local action. Some of the principles discussed in this article apply to noncolloidal drugs that are not permeable to the plasma membrane or to the blood-brain barrier. NV are defined as a wide range of nanosized particles leading to colloidal objects which are capable of entering cells and tissues and delivering a cargo intracelullarly. Different localization and targeting means are discussed. Limited discussion on pharmacokinetics and pharmacodynamics is also presented. NVs are contrasted to micro-delivery and current nanotechnologies which are already in commercial use. Newer developments in NV technologies are outlined and future applications are stressed. We also briefly review the existing modeling tools and approaches to quantitatively describe the behavior of targeted NV within the vascular and tumor compartments, an area of particular importance. While we list "elementary" phenomena related to different level of complexity of delivery to cancer, we also stress importance of multi-scale modeling and bottom-up systems biology approach. PMID:18200527

  15. Atomic scale study of phase transformation in long term thermally aged duplex stainless steels: relation between microstructure and properties

    International Nuclear Information System (INIS)

    In this paper, the ferrite of thermally aged CF3M duplex stainless steels is studied at the atomic scale. Accelerated ageing was performed at 350 C. Ingots of CF3M steel were aged in laboratory at 350 C up to 200 000 h (> 20 years). Spatial and chemical evolution of the microstructure of ferrite, characterised by 3D atom probe and micro-hardness values were compared to microstructural and mechanical characteristics of ferrite of the same ingots aged at 325 C (service temperature) and to ferrite of actual steel aged on site. This work has shown that: -) Accelerating the ageing at 350 C anticipates the on-site ageing at 323 C; -) The linear relation between micro-hardness and variation V is still valid after 200.000 h of ageing at 350 C (this corresponds to an equivalent ageing time of 190 years at 323 C); -) Activation energy is the same for both spinodal decomposition and G-phase precipitation: a value of 243 kJ/mol has been obtained; -) Time evolution of the wave length of the α/α' decomposition still follows a law proportional to t0.16 after 200.000 h of ageing (no increase of the effective time exponent is observed); -) After 30.000 h of ageing, coarsening of G-phase particles starts, the equilibrium volume fraction of G-phase is estimated to 8.5% and no modification of the time evolution of the radius of precipitates is observed; -) G-phase particles have no direct influence on the evolution of the ferrite micro-hardness. This does not exclude indirect effect due to synergetic precipitation of G-phase which leads to the decrease of the amount of Ni in ferrite matrix. Later could slower kinetics and then explain the absence of increase in the time exponent. (authors)

  16. Inhomogeneous thermal expansion of metallic glasses in atomic-scale studied by in-situ synchrotron X-ray diffraction

    International Nuclear Information System (INIS)

    Numerous investigations have demonstrated that the elastic strain in metallic glasses subjected to mechanical loading could be inhomogeneous in the atomic-scale and it increases with distance from an average atom and eventually reaches the macroscopic strain at larger inter-atomic distances. We have observed a similar behavior for the thermal strain imposed by heating of Co40Fe22Ta8B30 glassy particles below the glass transition temperature by analysis of the scattering data obtained by in-situ high-energy synchrotron X-ray diffraction (XRD). The results imply that the volumetric thermal strains calculated from the shift in position of the principal diffraction maximum and reduced pair correlation function (PDF) peaks are in good agreement for the length scales beyond 0.6 nm, corresponding to the atoms located over the third near-neighbor shell. However, smaller and even negative volumetric thermal strains have been calculated based on the shifts in the positions of the second and first PDF peaks, respectively. The structural changes of Co40Fe22Ta8B30 glassy particles are accompanied by decreasing the average coordination number of the first near-neighbor shell, which manifests the occurrence of local changes in the short-range order upon heating. It is believed that the detected length-scale dependence of the volumetric thermal strain is correlated with the local atomic rearrangements taking place in the topologically unstable regions of the glass governed by variations in the atomic-level stresses

  17. Validation of Force Fields of Rubber through Glass-Transition Temperature Calculation by Microsecond Atomic-Scale Molecular Dynamics Simulation.

    Science.gov (United States)

    Sharma, Pragati; Roy, Sudip; Karimi-Varzaneh, Hossein Ali

    2016-02-25

    Microsecond atomic-scale molecular dynamics simulation has been employed to calculate the glass-transition temperature (Tg) of cis- and trans-1,4-polybutadiene (PB) and 1,4-polyisoprene (PI). Both all-atomistic and united-atom models have been simulated using force fields, already available in literature. The accuracy of these decade old force fields has been tested by comparing calculated glass-transition temperatures to the corresponding experimental values. Tg depicts the phase transition in elastomers and substantially affects various physical properties of polymers, and hence the reproducibility of Tg becomes very crucial from a thermodynamic point of view. Such validation using Tg also evaluates the ability of these force fields to be used for advanced materials like rubber nanocomposites, where Tg is greatly affected by the presence of fillers. We have calculated Tg for a total of eight systems, featuring all-atom and united-atom models of cis- and trans-PI and -PB, which are the major constituents of natural and synthetic rubber. Tuning and refinement of the force fields has also been done using quantum-chemical calculations to obtain desirable density and Tg. Thus, a set of properly validated force fields, capable of reproducing various macroscopic properties of rubber, has been provided. A novel polymer equilibration protocol, involving potential energy convergence as the equilibration criterion, has been proposed. We demonstrate that not only macroscopic polymer properties like density, thermal expansion coefficient, and Tg but also local structural characteristics like end-to-end distance (R) and radius of gyration (Rg) and mechanical properties like bulk modulus have also been equilibrated using our strategy. Complete decay of end-to-end vector autocorrelation function with time also supports proper equilibration using our strategy. PMID:26836395

  18. Inversion boundary induced grain growth in ZnO ceramics: from atomic-scale investigations to microstructural engineering

    International Nuclear Information System (INIS)

    In semiconducting materials special boundaries play the key role in crystal growth. They introduce an abrupt structural and chemical anisotropy, which is readily reflected in an unusual microstructure evolution, whereas their local structure affects the physical properties of semiconducting materials. These effects, however, can be exploited to tailor the electronic and optical properties of the materials, as demonstrated in this review. The presented topic fits in the field of preparatory stage of phase transformations, manifested through evolution of chemically induced structural faults. In the noncentrosymmetric structure of ZnO, inversion boundaries (IBs) are the most common type of planar faults that can be triggered by the addition of specific spinel-forming dopants (Sb2O3, SnO2, TiO2). In addition to conventional HRTEM techniques several new methods were developed to resolve crystallography and atomic-scale chemistry of IBs. The absolute orientation of the polar c-axes on both sides of the IB was determined by a novel quantitative microdiffraction method, providing a reliable identification of crystal polarity in noncentrosymmetric crystals. To determine sub-monolayer quantities of dopants on the IB, we developed a special technique of analytical electron microscopy using concentric electron probe (CEP) in EDS or EELS mode, providing more accurate and precise results than any other available technique. Knowing the local crystal chemistry of IBs we were able to design experiments to identify their formation mechanism. IBs nucleate in the early stage of grain growth as a dopant-rich topotaxial 2D reaction product on Zn-terminated surfaces of ZnO grains. Soon after their nucleation, ZnO is epitaxially grown on the inherent 2D phase in an inverted orientation, which effectively starts to dictate anisotropic growth of the infected crystallite. In very short time the grains with IBs dominate the entire microstructure in ZnO ceramics via IB-induced exaggerated

  19. Dynamic and atomic-scale understanding of the twin thickness effect on dislocation nucleation and propagation activities by in situ bending of Ni nanowires

    International Nuclear Information System (INIS)

    Although their mechanical behavior has been extensively studied, the atomic-scale deformation mechanisms of metallic nanowires (NWs) with growth twins are not completely understood. Using our own atomic-scale and dynamic mechanical testing techniques, bending experiments were conducted on single-crystalline and twin-structural Ni NWs (D = ∼40 nm) using a high-resolution transmission electron microscope (HRTEM). Atomic-scale and time-resolved dislocation nucleation and propagation activities were captured in situ. A large number of in situ HRTEM observations indicated strong effects from the twin thickness (TT) on dislocation type and glide system. In thick twin lamella (TT > ∼12 nm) and single-crystalline NWs, the plasticity was controlled by full dislocation nucleation. For NWs with twin thicknesses of ∼9 nm < TT < ∼12 nm, full and partial dislocation nucleation occurred from the free surface, and the dislocations glided on multiple systems and interacted with each other during plastic deformation. For NWs with twin thicknesses of ∼6 nm < TT < ∼9 nm, partial dislocation nucleation from the free surface and the gliding of those dislocations on the plane that intersected the twin boundaries (TBs) were the dominant plasticity events. For the NWs with twin thicknesses of ∼1 nm < TT < ∼6 nm, the plasticity was accommodated by a partial dislocation nucleation process and glide parallel to the TBs. When TT < ∼1 nm, TB migration and detwinning processes resulting from partial dislocation nucleation and glide adjacent to the TBs were frequently observed

  20. Atomic scale effects of alloying, partitioning, solute drag and austempering on the mechanical properties of high-carbon bainitic–austenitic TRIP steels

    International Nuclear Information System (INIS)

    Understanding alloying and thermal processing at an atomic scale is essential for the optimal design of high-carbon (0.71 wt.%) bainitic–austenitic transformation-induced plasticity (TRIP) steels. We investigate the influence of the austempering temperature, chemical composition (especially the Si:Al ratio) and partitioning on the nanostructure and mechanical behavior of these steels by atom probe tomography. The effects of the austempering temperature and of Si and Al on the compositional gradients across the phase boundaries between retained austenite and bainitic ferrite are studied. We observe that controlling these parameters (i.e. Si, Al content and austempering temperature) can be used to tune the stability of the retained austenite and hence the mechanical behavior of these steels. We also study the atomic scale redistribution of Mn and Si at the bainitic ferrite/austenite interface. The observations suggest that either para-equilibrium or local equilibrium-negligible partitioning conditions prevail depending on the Si:Al ratio during bainite transformation.

  1. A biexponential DWI study in rat brain intracellular oedema

    Energy Technology Data Exchange (ETDEWEB)

    Steier, Roy, E-mail: roy.steier@gmail.com [Department of Neurosurgery, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Pecs Diagnostic Center, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Aradi, Mihaly [Department of Neurosurgery, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Pecs Diagnostic Center, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Pal, Jozsef [Department of Neurosurgery, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Perlaki, Gabor; Orsi, Gergely; Bogner, Peter [Pecs Diagnostic Center, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); Galyas, Ferenc [Department of Neurosurgery, Faculty of Medicine University of Pecs, H-7623 Pecs, Ret street 2 (Hungary); and others

    2012-08-15

    Purpose: To examine the changes in MR parameters derived from diffusion weighted imaging (DWI) biexponential analysis in an in vivo intracellular brain oedema model, and to apply electron microscopy (EM) to shed more light on the morphological background of MR-related observations. Materials and methods: Intracellular oedema was induced in ten male Wistar rats (380-450 g) by way of water load, using a 20% body weight intraperitoneal injection of 140 mmol/L dextrose solution. A 3T MRI instrument was used to perform serial DWI, and MR specroscopy (water signal) measurements. Following the MR examination the brains of the animals were analyzed for EM. Results: Following the water load induction, apparent diffusion coefficient (ADC) values started declining from 724 {+-} 43 {mu}m{sup 2}/s to 682 {+-} 26 {mu}m{sup 2}/s (p < 0.0001). ADC-fast values dropped from 948 {+-} 122 to 840 {+-} 66 {mu}m{sup 2}/s (p < 0.001). ADC-slow showed a decrease from 226 {+-} 66 to 191 {+-} 74 {mu}m{sup 2}/s (p < 0.05). There was a shift from the slow to the fast component at 110 min time point. The percentage of the fast component demonstrated moderate, yet significant increase from 76.56 {+-} 7.79% to 81.2 {+-} 7.47% (p < 0.05). The water signal was increasing by 4.98 {+-} 3.52% compared to the base line (p < 0.01). The results of the E.M. revealed that water was detected intracellularly, within astrocytic preivascular end-feet and cell bodies. Conclusion: The unexpected volume fraction changes (i.e. increase in fast component) detected in hypotonic oedema appear to be substantially different from those observed in stroke. It may suggest that ADC decrease in stroke, in contrast to general presumptions, cannot be explained only by water shift from extra to intracellular space (i.e. intracellular oedema).

  2. A biexponential DWI study in rat brain intracellular oedema

    International Nuclear Information System (INIS)

    Purpose: To examine the changes in MR parameters derived from diffusion weighted imaging (DWI) biexponential analysis in an in vivo intracellular brain oedema model, and to apply electron microscopy (EM) to shed more light on the morphological background of MR-related observations. Materials and methods: Intracellular oedema was induced in ten male Wistar rats (380–450 g) by way of water load, using a 20% body weight intraperitoneal injection of 140 mmol/L dextrose solution. A 3T MRI instrument was used to perform serial DWI, and MR specroscopy (water signal) measurements. Following the MR examination the brains of the animals were analyzed for EM. Results: Following the water load induction, apparent diffusion coefficient (ADC) values started declining from 724 ± 43 μm2/s to 682 ± 26 μm2/s (p 2/s (p 2/s (p < 0.05). There was a shift from the slow to the fast component at 110 min time point. The percentage of the fast component demonstrated moderate, yet significant increase from 76.56 ± 7.79% to 81.2 ± 7.47% (p < 0.05). The water signal was increasing by 4.98 ± 3.52% compared to the base line (p < 0.01). The results of the E.M. revealed that water was detected intracellularly, within astrocytic preivascular end-feet and cell bodies. Conclusion: The unexpected volume fraction changes (i.e. increase in fast component) detected in hypotonic oedema appear to be substantially different from those observed in stroke. It may suggest that ADC decrease in stroke, in contrast to general presumptions, cannot be explained only by water shift from extra to intracellular space (i.e. intracellular oedema).

  3. Palladium-mediated intracellular chemistry

    OpenAIRE

    Rahimi M. Yusop; Unciti-Broceta, Asier; Johansson, Emma M. V.; Rosario M. Sanchez-Martin; Bradley, Mark

    2011-01-01

    Many important intracellular biochemical reactions are modulated by transition metals, typically in the form of metalloproteins. The ability to carry out selective transformations inside a cell would allow researchers to manipulate or interrogate innumerable biological processes. Here, we show that palladium nanoparticles trapped within polystyrene microspheres can enter cells and mediate a variety of Pd-0-catalysed reactions, such as allylcarbamate cleavage and Suzuki-Miyaura cross-coupling....

  4. Stochastic models of intracellular transport

    KAUST Repository

    Bressloff, Paul C.

    2013-01-09

    The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.

  5. SNARE protein mimicry by an intracellular bacterium

    OpenAIRE

    DELEVOYE, Cédric; Nilges, Michael; Dehoux, Pierre; Paumet, Fabienne; Perrinet, Stéphanie; Dautry-Varsat, Alice; Subtil, Agathe

    2008-01-01

    Many intracellular pathogens rely on host cell membrane compartments for their survival. The strategies they have developed to subvert intracellular trafficking are often unknown, and SNARE proteins, which are essential for membrane fusion, are possible targets. The obligate intracellular bacteria Chlamydia replicate within an intracellular vacuole, termed an inclusion. A large family of bacterial proteins is inserted in the inclusion membrane, and the role of these inclusion proteins is most...

  6. Intracellular parcel service: current issues in intracellular membrane trafficking.

    Science.gov (United States)

    Herrmann, Johannes M; Spang, Anne

    2015-01-01

    Eukaryotic cells contain a multitude of membrane structures that are connected through a highly dynamic and complex exchange of their constituents. The vibrant instability of these structures challenges the classical view of defined, static compartments that are connected by different types of vesicles. Despite this astonishing complexity, proteins and lipids are accurately transported into the different intracellular membrane systems. Over the past few decades many factors have been identified that either mediate or regulate intracellular membrane trafficking. Like in a modern parcel sorting system of a logistics center, the cargo typically passes through several sequential sorting stations until it finally reaches the location that is specified by its individual address label. While each membrane system employs specific sets of factors, the transport processes typically operate on common principles. With the advent of genome- and proteome-wide screens, the availability of mutant collections, exciting new developments in microscope technology and sophisticated methods to study their dynamics, the future promises a broad and comprehensive picture of the processes by which eukaryotic cells sort their proteins. PMID:25702105

  7. Atomic-scale insight into the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field

    Science.gov (United States)

    Verlackt, C. C. W.; Neyts, E. C.; Jacob, T.; Fantauzzi, D.; Golkaram, M.; Shin, Y.-K.; van Duin, A. C. T.; Bogaerts, A.

    2015-10-01

    Cold atmospheric pressure plasmas have proven to provide an alternative treatment of cancer by targeting tumorous cells while leaving their healthy counterparts unharmed. However, the underlying mechanisms of the plasma-cell interactions are not yet fully understood. Reactive oxygen species, and in particular hydroxyl radicals (OH), are known to play a crucial role in plasma driven apoptosis of malignant cells. In this paper we investigate the interaction of OH radicals, as well as H2O2 molecules and HO2 radicals, with DNA by means of reactive molecular dynamics simulations using the ReaxFF force field. Our results provide atomic-scale insight into the dynamics of oxidative stress on DNA caused by the OH radicals, while H2O2 molecules appear not reactive within the considered time-scale. Among the observed processes are the formation of 8-OH-adduct radicals, forming the first stages towards the formation of 8-oxoGua and 8-oxoAde, H-abstraction reactions of the amines, and the partial opening of loose DNA ends in aqueous solution.

  8. A comprehensive picture in the view of atomic scale on piezoelectricity of ZnO tunnel junctions: The first principles simulation

    Directory of Open Access Journals (Sweden)

    Genghong Zhang

    2016-06-01

    Full Text Available Piezoelectricity is closely related with the performance and application of piezoelectric devices. It is a crucial issue to understand its detailed fundamental for designing functional devices with more peculiar performances. Basing on the first principles simulations, the ZnO piezoelectric tunnel junction is taken as an example to systematically investigate its piezoelectricity (including the piezopotential energy, piezoelectric field, piezoelectric polarization and piezocharge and explore their correlation. The comprehensive picture of the piezoelectricity in the ZnO tunnel junction is revealed at atomic scale and it is verified to be the intrinsic characteristic of ZnO barrier, independent of its terminated surface but dependent on its c axis orientation and the applied strain. In the case of the ZnO c axis pointing from right to left, an in-plane compressive strain will induce piezocharges (and a piezopotential energy drop with positive and negative signs (negative and positive signs emerging respectively at the left and right terminated surfaces of the ZnO barrier. Meanwhile a piezoelectric polarization (and a piezoelectric field pointing from right to left (from left to right are also induced throughout the ZnO barrier. All these piezoelectric physical quantities would reverse when the applied strain switches from compressive to tensile. This study provides an atomic level insight into the fundamental behavior of the piezoelectricity of the piezoelectric tunnel junction and should have very useful information for future designs of piezoelectric devices.

  9. Atomic scale modelling of nanosize Ni sub 3 Al cluster beam deposition on Al, Ni and Ni sub 3 Al (1 1 1) surfaces

    CERN Document Server

    Kharlamov, V S; Hou, M

    2002-01-01

    The slowing down of Ni sub 3 Al clusters on a Al, Ni and Ni sub 3 Al (1 1 1) surfaces is studied by atomic scale modelling. The semi-grand canonical metropolis Monte Carlo is used for the preparation of isolated clusters at thermodynamic equilibrium. The cluster deposition on the surface is studied in detail by classical Molecular Dynamics simulations that include a model to account for electron-phonon coupling. Long- and short-range orders in the cluster are evaluated as functions of temperature in an impact energy range between 0 and 1.5 eV/atom. The interaction between the Ni sub 3 Al cluster and an Al surface is characterised low short range (chemical) disorder. No sizeable epitaxy is found, subsequent to the impact. In contrast, in the case of Ni and Ni sub 3 Al substrates, which are harder materials than aluminium, the chemical disorder is higher and epitaxial accommodation is possible. With these substrates, chemical disorder in the cluster is an increasing function of the impact energy, as well as of ...

  10. Atomic-Scale Theoretical Studies of Fundamental Properties and Processes in CHNO Plastic-Bonded Explosive Constituent Materials under Static and Dynamic Compression

    Science.gov (United States)

    Sewell, Thomas

    2013-06-01

    The results of recent theoretical atomic-scale studies of CHNO plastic-bonded explosive constituent materials will be presented, emphasizing the effects of static and dynamic compression on structure, vibrational spectroscopy, energy redistribution, and dynamic deformation processes. Among the chemical compounds to be discussed are pentaerythritol tetranitrate (PETN), hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX), nitromethane, and hydroxyl-terminated polybutadiene (HTPB). Specific topics to be discussed include pressure-dependent terahertz IR absorption spectra in crystalline PETN and RDX, microscopic material flow characteristics and energy localization during and after pore collapse in shocked (100)-oriented RDX, establishment of local thermodynamic temperature and the approach to thermal equilibrium in shocked (100)-oriented nitromethane, and structural changes and relaxation phenomena that occur in shocked amorphous cis-HTPB. In the case of shocked HTPB, comparisons will be made between results obtained using fully-atomic and coarse-grained (united atom) molecular dynamics force field models. Rather than attempting to discuss any given topic in extended detail, 3-4 vignettes will be presented that highlight outstanding scientific questions and the predictive methods and tools we are developing to answer them. The U.S. Defense Threat Reduction Agency and Office of Naval Research supported this research.

  11. Point defects and irradiation in oxides: simulations at the atomic scale; Defauts ponctuels et irradiation dans les oxydes: simulation a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Crocombette, J.P

    2005-12-15

    The studies done by Jean-Paul Crocombette between 1996 and 2005 in the Service de Recherches de Metallurgie Physique of the Direction de l'Energie Nucleaire in Saclay are presented in this Habilitation thesis. These works were part of the material science researches on the ageing, especially under irradiation, of oxides of interest for the nuclear industry. In this context simulation studies at the atomic scale were performed on two elementary components of ageing under irradiation : point defects and displacement cascades ; using two complementary simulation techniques : ab initio electronic structure calculations and empirical potential molecular dynamics. The first part deals with point defects : self defects (vacancies or interstitials) or hetero-atomic dopants. One first recalls the energetics of such defects in oxides, the specific features of defects calculations and the expected accuracy of these calculations. Then one presents the results obtained on uranium dioxide, oxygen in silver and amorphous silica. The second part tackles the modelling of disintegration recoil nuclei in various?displacement cascades created by crystalline matrices for actinide waste disposal. Cascade calculations give access to the amorphization mechanisms under irradiation of these materials. One thus predicts that the amorphization in zircon takes place directly in the tracks whereas in lanthanum zirconate, the amorphization proceeds through the accumulation of point defects. Finally the prospects of these studies are discussed. (author)

  12. Molecular dynamics investigation on the atomic-scale friction behaviors between copper(0 0 1) and diamond(1 1 1) surfaces

    International Nuclear Information System (INIS)

    Classical molecular dynamics (MD) simulations are conducted to examine the atomic-scale friction behavior of an infinite flat-flat contact between copper(0 0 1) and diamond(1 1 1) surfaces. Two types of diamond surface, namely H-free and hydrogenated, are constructed and on each of them the copper counterface is brought to slide along the [1 1 -2] and [1 -1 0] crystallographic directions with a variety of loads. The simulation results demonstrate that the hydrogen atoms chemisorbed to the diamond surface can to large extent eliminate the directional dependency of its friction behavior with copper. Under pressures less than 30 GPa, the sliding between copper and hydrogenated is wearless. In this period, the shear stress of them just slightly increases to 0.6 GPa. Between 30 GPa and 32 GPa, copper atoms near the interface begin to be worn and incorporate into the diamond substrate and this causes a sharp shift from 0.6 GPa to 2.7 GPa in their shear stress. In contrast, the sliding process between copper and H-free diamond is always wearless even under pressure beyond 40 GPa. The H-free [1 -1 0] model exhibits much higher shear stress than H-free [1 1 -2] under pressures less than 35 GPa. Beyond 35 GPa, they present nearly consistent shear stress evolution. Moreover, the simulations for hydrogenated diamond models suggest that their friction behavior is independent on sliding velocity only under wearless sliding regime.

  13. A low temperature ultrahigh vacuum scanning tunneling microscope with high-NA optics to probe optical interactions at the atomic scale

    Science.gov (United States)

    Zhang, Haigang; Smerdon, Joseph; Suzer, Ozgun; Kersell, Heath; Guest, Jeffrey

    2015-03-01

    The optical and photophysical properties of single molecules/atoms, defects, and nanoscale structures at surfaces hinge on structure at the atomic scale. In order to characterize and control this structure and unravel these correlations, we are developing a low temperature (LT) laser-coupled ultrahigh vacuum (UHV) scanning tunneling microscope (LT Laser UHV STM) based on the Pan-style STM scanner with integrated high-numerical-aperture (NA) optics for single particle spectroscopy measurements under the STM tip. Using slip-stick inertial piezo steppers, the sample stage can be coarsely translated in X and Y directions. For optical measurements, high-NA optics behind and above the sample focus laser excitation on and collect photons emitted from the tip-sample junction. The STM is cooled by a liquid helium bath surrounded by a liquid nitrogen jacket for operation near 5 K; two separate ultrahigh vacuum chambers are used for sample preparation and STM measurements, respectively. We will describe our progress in demonstrating this instrument and plans for experiments studying the correlation between structure and optical function in nanoscale systems. U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences.

  14. Atomic scale structure of the 5-fold surface of an AlPdMn quasicrystal: A quantitative X-Ray photoelectron diffraction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Jin-Cheng; Huan, C.H.A.; Wee, A.T.S.; Van Hove, M.A.; Fadley, C.S.; Shi, F.J.; Rotenberg, E.; Barman, S.R.; Paggel, J.J.; Horn, K.; Ebert, Ph.; Urban, K.

    2004-02-11

    The atomic scale structure of the 5-fold symmetric surface of an AlPdMn quasicrystal is investigated quantitatively by comparing x-ray photoelectron diffraction (XPD) simulations to experiment. The observed 5-fold symmetry of the diffraction patterns indicates that the surface is quasicrystalline with no hint of a reconstruction from the bulk structure. In analyzing the experimental data, many possible bulk terminations have been tested. Those few that fit best to the data have in common that they contain an Al-rich surface layer followed by a dense mixed Al/Pd/Mn layer. These best terminations, while not identical to each other, are suggested to form terraces coexisting on a real surface. Structural relaxations of the quasicrystal surface are also analyzed: mixing several best-fit terminations gives average best-fit interlayer spacing changes of Dd12 = -0.057 Angstrom, Dd24 = +0.159 Angstrom. These results are in good agreement with a prior structure determination by LEED on a sample that was prepared in a different manner.

  15. An atomic scale study of surface termination and digital alloy growth in InGaAs/AlAsSb multi-quantum wells.

    Science.gov (United States)

    Mauger, S J C; Bozkurt, M; Koenraad, P M; Zhao, Y; Folliot, H; Bertru, N

    2016-07-20

    An atomic scale study has been performed to understand the influence of the (As,Sb) shutter sequences during interface formation on the optical properties of InGaAs/AlAsSb quantum wells. Our cross-sectional scanning tunneling microscopy results show that the onset of the Sb profile is steep in the Sb-containing layers whereas an appreciable segregation of Sb in the subsequently grown Sb free layers is observed. The steep rise of the Sb profile is due to extra Sb that is supplied to the surface prior to the growth of the Sb-containing layers. No relation is found between the (As,Sb) termination conditions of the Sb-containing layers and the resulting Sb profiles in the capping layers. Correspondingly we see that the optical properties of these quantum wells are also nearly independent on the (As,Sb) shutter sequences at the interface. Digital alloy growth in comparison to conventional molecular beam epitaxy growth was also explored. X-ray results suggest that the structural properties of the quantum well structures grown by conventional molecular beam epitaxy techniques are slightly better than those formed by digital alloy growth. However photoluminescence studies indicate that the digital alloy samples give rise to a more intense and broader photoluminescence emission. Cross-sectional scanning tunneling microscopy measurements reveal that lateral composition modulations present in the digital alloys are responsible for the enhancement of the photoluminescence intensity and inhomogeneous broadening. PMID:27228395

  16. Atomic scale modelling of nanosize Ni3Al cluster beam deposition on Al, Ni and Ni3Al (1 1 1) surfaces

    International Nuclear Information System (INIS)

    The slowing down of Ni3Al clusters on a Al, Ni and Ni3Al (1 1 1) surfaces is studied by atomic scale modelling. The semi-grand canonical metropolis Monte Carlo is used for the preparation of isolated clusters at thermodynamic equilibrium. The cluster deposition on the surface is studied in detail by classical Molecular Dynamics simulations that include a model to account for electron-phonon coupling. Long- and short-range orders in the cluster are evaluated as functions of temperature in an impact energy range between 0 and 1.5 eV/atom. The interaction between the Ni3Al cluster and an Al surface is characterised low short range (chemical) disorder. No sizeable epitaxy is found, subsequent to the impact. In contrast, in the case of Ni and Ni3Al substrates, which are harder materials than aluminium, the chemical disorder is higher and epitaxial accommodation is possible. With these substrates, chemical disorder in the cluster is an increasing function of the impact energy, as well as of temperature when the impact energy is low enough. The cluster epitaxy is enhanced by both the temperature and the impact energy. A direct correlation between epitaxy and chemical disordering is found during the accommodation of the cluster with the surface

  17. Atomic-scale structure of η-phase Mn 3N 2(0 1 0) studied by scanning tunneling microscopy and first-principles theory

    Science.gov (United States)

    Yang, Haiqiang; Yang, Rong; Smith, Arthur R.; Lambrecht, Walter R. L.

    2004-01-01

    The (0 1 0) surface of η-phase Mn 3N 2 grown on MgO(0 0 1) by molecular beam epitaxy is studied using scanning tunneling microscopy. The images show that the surface is composed of rows with spacing of 6.07 Å. Two types of domains with their c-planes perpendicular are observed in which the domain boundary is oriented at ˜45° to the c-planes. In other cases, the angle between the c-planes of the two domains is closer to 87°, consistent with a twin model in which the two domains meet along a (1 0 1) plane. Atomic resolution images vary with the sample bias. At lower sample bias, primarily Mn1 atoms are observed. At higher sample bias, both Mn1 and Mn2 atoms can be resolved. The dependence of the atomic resolution image on sample bias is explained by the ratio of the integrated local density of states of Mn1 to that of Mn2, which are based on first-principles theory. Simulations of the STM atomic-scale height profiles using the integrated local densities of states vs. sample bias voltage are in excellent agreement with the experimental line profiles.

  18. Peculiarities of intracellular reparation of irradiated keratinocytes

    International Nuclear Information System (INIS)

    The processes of intracellular reparation and possibility of their modification, using certain known radioprotectors and new chemical compounds in the process of local X-radiation rat limb skin in the dose 7.74x10sup(-1)Ci/kg, have been investigated. Mitochondrias, and internal mitochondrical membrane in particular as well as intracellular are referred to the slowest repaired intracellular formations. Using modifiers, it is possible to a considerable degree to normalize intracellular reparation processes and intercellular interactions, physiological regeneration of ultrastructures

  19. Diversity of sub-bandgap states in lead-sulfide nanocrystals: real-space spectroscopy and mapping at the atomic-scale

    Science.gov (United States)

    Gervasi, Christian F.; Kislitsyn, Dmitry A.; Allen, Thomas L.; Hackley, Jason D.; Maruyama, Ryuichiro; Nazin, George V.

    2015-11-01

    Colloidal semiconductor nanocrystals have emerged as a promising class of technological materials with optoelectronic properties controllable through quantum-confinement effects. Despite recent successes in this field, an important factor that remains difficult to control is the impact of the nanocrystal surface structure on the photophysics and electron transport in nanocrystal-based materials. In particular, the presence of surface defects and irregularities can result in the formation of localized sub-bandgap states that can dramatically affect the dynamics of charge carriers and electronic excitations. Here we use Scanning Tunneling Spectroscopy (STS) to investigate, in real space, sub-bandgap states in individual ligand-free PbS nanocrystals. In the majority of studied PbS nanocrystals, spatial mapping of electronic density of states with STS shows atomic-scale variations attributable to the presence of surface reconstructions. STS spectra show that the presence of surface reconstructions results in formation of surface-bound sub-bandgap electronic states. The nature of the surface reconstruction varies depending on the surface stoichiometry, with lead-rich surfaces producing unoccupied sub-bandgap states, and sulfur-rich areas producing occupied sub-bandgap states. Highly off-stoichiometric areas produce both occupied and unoccupied states showing dramatically reduced bandgaps. Different reconstruction patterns associated with specific crystallographic directions are also found for different nanocrystals. This study provides insight into the mechanisms of sub-bandgap state formation that, in a modified form, are likely to be applicable to ligand-passivated nanocrystal surfaces, where steric hindrance between ligands can result in under-coordination of surface atoms.Colloidal semiconductor nanocrystals have emerged as a promising class of technological materials with optoelectronic properties controllable through quantum-confinement effects. Despite recent

  20. Chemical inhomogeneity in In{sub x}Ga{sub 1-x}N and ZnO. A HRTEM study on atomic scale clustering

    Energy Technology Data Exchange (ETDEWEB)

    Bartel, T.P.

    2008-10-08

    Nanostructuration as well as the nucleation and growth of nanoparticles pervades the development of modern materials and devices. Quantitative high resolution transmission electron microscopy (HRTEM) is currently being developed for a structural and chemical analysis at an atomic scale. It is used in this thesis to study the chemical inhomogeneity and clustering in In{sub x}Ga{sub 1-x}N, InN and ZnO. A methodology for reliable quantitative HRTEM is rst de ned: it necessitates a damage free sample, the avoidance of electron beam damage and the control of microscope instabilities. With these conditions satis ed, the reliability of quantitative HRTEM is demonstrated by an accurate measurement of lattice relaxation in a thin TEM sample. Clustering in an alloy can then be distinguished from a random distribution of atoms. In In{sub x}Ga{sub 1-x}N for instance, clustering is detected for concentrations x>0.1. The sensitivity is insufficient to determine whether clustering is present for lower concentrations. HRTEM allows to identify the amplitude and the spatial distribution of the decomposition which is attributed to a spinodal decomposition. In InN, nanometer scale metallic indium inclusions are detected. With decreasing size of the metallic clusters, the photoluminescence of the sample shifts towards the infrared. This indicates that the inclusions may be responsible for the infrared activity of InN. Finally, ZnO grown homoepitaxially on zinc-face and oxygen-face substrates is studied. The O-face epilayer is strained whereas the Zn-face epilayer is almost strain free and has a higher crystalline quality. Quantitative analysis of exit wave phases is in good agreement with simulations, but the signal to noise ratio needs to be improved for the detection of single point defects. (orig.)

  1. Chemical inhomogeneity in InxGa1-xN and ZnO. A HRTEM study on atomic scale clustering

    International Nuclear Information System (INIS)

    Nanostructuration as well as the nucleation and growth of nanoparticles pervades the development of modern materials and devices. Quantitative high resolution transmission electron microscopy (HRTEM) is currently being developed for a structural and chemical analysis at an atomic scale. It is used in this thesis to study the chemical inhomogeneity and clustering in InxGa1-xN, InN and ZnO. A methodology for reliable quantitative HRTEM is rst de ned: it necessitates a damage free sample, the avoidance of electron beam damage and the control of microscope instabilities. With these conditions satis ed, the reliability of quantitative HRTEM is demonstrated by an accurate measurement of lattice relaxation in a thin TEM sample. Clustering in an alloy can then be distinguished from a random distribution of atoms. In InxGa1-xN for instance, clustering is detected for concentrations x>0.1. The sensitivity is insufficient to determine whether clustering is present for lower concentrations. HRTEM allows to identify the amplitude and the spatial distribution of the decomposition which is attributed to a spinodal decomposition. In InN, nanometer scale metallic indium inclusions are detected. With decreasing size of the metallic clusters, the photoluminescence of the sample shifts towards the infrared. This indicates that the inclusions may be responsible for the infrared activity of InN. Finally, ZnO grown homoepitaxially on zinc-face and oxygen-face substrates is studied. The O-face epilayer is strained whereas the Zn-face epilayer is almost strain free and has a higher crystalline quality. Quantitative analysis of exit wave phases is in good agreement with simulations, but the signal to noise ratio needs to be improved for the detection of single point defects. (orig.)

  2. Exploring Anti-Bacterial Compounds against Intracellular Legionella

    OpenAIRE

    Christopher F Harrison; Sébastien Kicka; Valentin Trofimov; Kathrin Berschl; Hajer Ouertatani-Sakouhi; Nikolaus Ackermann; Christian Hedberg; Pierre Cosson; Thierry Soldati; Hubert Hilbi

    2013-01-01

    Legionella pneumophila is a ubiquitous fresh-water bacterium which reproduces within its erstwhile predators, environmental amoeba, by subverting the normal pathway of phagocytosis and degradation. The molecular mechanisms which confer resistance to amoeba are apparently conserved and also allow replication within macrophages. Thus, L. pneumophila can act as an ‘accidental’ human pathogen and cause a severe pneumonia known as Legionnaires’ disease. The intracellular localisation of L. pneumop...

  3. HYPERTHERMIA, INTRACELLULAR FREE CALCIUM AND CALCIUM IONOPHORES

    NARCIS (Netherlands)

    STEGE, GJJ; WIERENGA, PK; KAMPINGA, HH; KONINGS, AWT

    1993-01-01

    It is shown that heat-induced increase of intracellular calcium does not correlate with hyperthermic cell killing. Six different cell lines were investigated; in four (EAT, HeLa S3, L5178Y-R and L5178Y-S) heat treatments killing 90% of the cells did not affect the levels of intracellular free calciu

  4. Dynamics of intracellular information decoding

    International Nuclear Information System (INIS)

    A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity

  5. Dynamics of intracellular information decoding

    Science.gov (United States)

    Kobayashi, Tetsuya J.; Kamimura, Atsushi

    2011-10-01

    A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.

  6. Efficient plasma-enhanced method for layered LiNi1/3Co1/3Mn1/3O2 cathodes with sulfur atom-scale modification for superior-performance Li-ion batteries

    Science.gov (United States)

    Jiang, Qianqian; Chen, Ning; Liu, Dongdong; Wang, Shuangyin; Zhang, Han

    2016-05-01

    In order to improve the electrochemical performance of LiNi1/3Co1/3Mn1/3O2 as a lithium insertion positive electrode material, atom-scale modification was realized to obtain the layered oxysulfide LiNi1/3Co1/3Mn1/3O2-xSx using a novel plasma-enhanced doping strategy. The structure and electrochemical performance of LiNi1/3Co1/3Mn1/3O2-xSx are investigated systematically, which confirms that the S doping can make the structure stable and benefit the electrochemical performance. The phys-chemical characterizations indicate that oxygen atoms in the initial LiNi1/3Co1/3Mn1/3O2 have been partially replaced by S atoms. It should be pointed out that the atom-scale modification does not significantly alter the intrinsic structure of the cathode. Compared to the pristine material, the LiNi1/3Co1/3Mn1/3O2-xSx shows a superior performance with a higher capacity (200.4 mA h g-1) and a significantly improved cycling stability (maintaining 94.46% of its initial discharge capacity after 100 cycles). Moreover, it has an excellent rate performance especially at elevated performance, which is probably due to the faster Li+ transportation after S doping into the layered structure. All the results show that the atom-scale modification with sulfur atoms on LiNi1/3Co1/3Mn1/3O2, which significantly improved the electrochemical performance, offers a novel anionic doping strategy to realize the atom-scale modification of electrode materials to improve their electrochemical performance.In order to improve the electrochemical performance of LiNi1/3Co1/3Mn1/3O2 as a lithium insertion positive electrode material, atom-scale modification was realized to obtain the layered oxysulfide LiNi1/3Co1/3Mn1/3O2-xSx using a novel plasma-enhanced doping strategy. The structure and electrochemical performance of LiNi1/3Co1/3Mn1/3O2-xSx are investigated systematically, which confirms that the S doping can make the structure stable and benefit the electrochemical performance. The phys

  7. Atomic-scale microstructures, Raman spectra and dielectric properties of cubic pyrochlore-typed Bi1.5MgNb1.5O7 dielectric ceramics

    KAUST Repository

    Li, Yangyang

    2014-07-01

    Single-phase cubic pyrochlore-typed Bi1.5MgNb 1.5O7 (BMN) dielectric ceramics were synthesized at temperatures of 1050-1200 °C by solid-state reaction method. Their atomic-scale microstructures and dielectric properties were investigated. X-ray diffraction patterns revealed that the BMN ceramics had an average cubic pyrochlore structure, whereas the Raman spectra indicated that they had an essentially cubic symmetry with small local deviations at the A and O\\' sites of the cubic pyrochlore structure. This was confirmed by selected electron area diffraction (SAED) patterns, where the reflections of {442} (not allowed in the cubic pyrochlore with Fd3̄m symmetry) were clearly observed. SEM and TEM images revealed that the average grain size was increased with the sintering temperature, and an un-homogeneous grain growth was observed at high temperatures. HRTEM images and SAED patterns revealed the single-crystalline nature of the BMN ceramic grains. Energy dispersive spectroscopy (EDS) elemental mapping studies indicated that the compositional distributions of Bi, Mg, Nb and O elements in the ceramic grains were homogenous, and no elemental precipitation was observed at the grain boundary. Quantitative EDS data on ceramic grains revealed the expected cationic stoichiometry based on the initial composition of Bi1.5MgNb1.5O7. Dielectric constants of all the BMN samples exhibited almost frequency independent characteristic in the frequency range of 102-106 Hz, and the highest value was 195 for the BMN ceramics sintered at sintered at 1150 °C with the highest bulk density. The dielectric losses were stable and less than 0.002 in the frequency range of 102-105 Hz. The high dielectric constants of the present BMN samples can be ascribed to the local atomic deviations at the A and O\\' sites from the ideal atomic positions of the pyrochlore structure, which affect the different polarization mechanisms in the BMN ceramics, and which in turn enhance the dielectric

  8. Efficient plasma-enhanced method for layered LiNi1/3Co1/3Mn1/3O2 cathodes with sulfur atom-scale modification for superior-performance Li-ion batteries.

    Science.gov (United States)

    Jiang, Qianqian; Chen, Ning; Liu, Dongdong; Wang, Shuangyin; Zhang, Han

    2016-06-01

    In order to improve the electrochemical performance of LiNi1/3Co1/3Mn1/3O2 as a lithium insertion positive electrode material, atom-scale modification was realized to obtain the layered oxysulfide LiNi1/3Co1/3Mn1/3O2-xSx using a novel plasma-enhanced doping strategy. The structure and electrochemical performance of LiNi1/3Co1/3Mn1/3O2-xSx are investigated systematically, which confirms that the S doping can make the structure stable and benefit the electrochemical performance. The phys-chemical characterizations indicate that oxygen atoms in the initial LiNi1/3Co1/3Mn1/3O2 have been partially replaced by S atoms. It should be pointed out that the atom-scale modification does not significantly alter the intrinsic structure of the cathode. Compared to the pristine material, the LiNi1/3Co1/3Mn1/3O2-xSx shows a superior performance with a higher capacity (200.4 mA h g(-1)) and a significantly improved cycling stability (maintaining 94.46% of its initial discharge capacity after 100 cycles). Moreover, it has an excellent rate performance especially at elevated performance, which is probably due to the faster Li(+) transportation after S doping into the layered structure. All the results show that the atom-scale modification with sulfur atoms on LiNi1/3Co1/3Mn1/3O2, which significantly improved the electrochemical performance, offers a novel anionic doping strategy to realize the atom-scale modification of electrode materials to improve their electrochemical performance. PMID:27189799

  9. Dislocations and elementary processes of plasticity in FCC metals: atomic scale simulations; Dislocations et processus elementaires de la plasticite dans les metaux CFC: apports des simulations a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Rodney, D

    2000-07-01

    We present atomic-scale simulations of two elementary processes of FCC crystal plasticity. The first study consists in the simulation by molecular dynamics, in a nickel crystal, of the interactions between an edge dislocation and glissile interstitial loops of the type that form under irradiation in displacement cascades. The simulations show various atomic-scale interaction processes leading to the absorption and drag of the loops by the dislocation. These reactions certainly contribute to the formation of the 'clear bands' observed in deformed irradiated materials. The simulations also allow to study quantitatively the role of the glissile loops in irradiation hardening. In particular, dislocation unpinning stresses for certain pinning mechanisms are evaluated from the simulations. The second study consists first in the generalization in three dimensions of the quasi-continuum method (QCM), a multi-scale simulation method which couples atomistic techniques and the finite element method. In the QCM, regions close to dislocation cores are simulated at the atomic-scale while the rest of the crystal is simulated with a lower resolution by means of a discretization of the displacement fields using the finite element method. The QCM is then tested on the simulation of the formation and breaking of dislocation junctions in an aluminum crystal. Comparison of the simulations with an elastic model of dislocation junctions shows that the structure and strength of the junctions are dominated by elastic line tension effects, as is assumed in classical theories. (author)

  10. Effect of growth in biofilms upon antibiotic and chlorine susceptibility of Mycobacterium avium and Mycobacterium intracellulare

    OpenAIRE

    Steed, Keesha

    2003-01-01

    ABSTRACT Mycobacterium avium and Mycobacterium intracellulare are environmental opportunistic pathogens whose source for human infection is water and soil. M. avium and M. intracellulare cause pulmonary infections (tuberculosis) in immunocompetent individuals and bacteremia in immunodeficient individuals (e.g. AIDS). One factor likely influencing the lack of success of antibiotic therapy in patients would be their ability to form biofilms. Growth in biofilms might result in antimicrob...

  11. Differentiating Intracellular from Extracellular Alkaline Phosphatase Activity in Soil by Sonication

    OpenAIRE

    2013-01-01

    Differentiating intracellular from extracellular enzyme activity is important in soil enzymology, but not easy. Here, we report on an adjusted sonication method for the separation of intracellular from extracellular phosphatase activity in soil. Under optimal sonication conditions [soil:water ratio  =  1/8 (w/v) and power density  =  15 watt ml-1], the activity of alkaline phosphomonoesterase (phosphatase) in a Haplic Cambisol soil increased with sonication time in two distinct steps. A first...

  12. Differentiating Intracellular from Extracellular Alkaline Phosphatase Activity in Soil by Sonication

    OpenAIRE

    Qin, S.P.; C. S. Hu; Oenema, O.

    2013-01-01

    Differentiating intracellular from extracellular enzyme activity is important in soil enzymology, but not easy. Here, we report on an adjusted sonication method for the separation of intracellular from extracellular phosphatase activity in soil. Under optimal sonication conditions [soil:water ratio = 1/8 (w/v) and power density = 15 watt ml(-1)], the activity of alkaline phosphomonoesterase (phosphatase) in a Haplic Cambisol soil increased with sonication time in two distinct steps. A first p...

  13. Water

    Science.gov (United States)

    ... www.girlshealth.gov/ Home Nutrition Nutrition basics Water Water Did you know that water makes up more ... to drink more water Other drinks How much water do you need? top Water is very important, ...

  14. Nanoparticles for intracellular-targeted drug delivery

    International Nuclear Information System (INIS)

    Nanoparticles (NPs) are very promising for the intracellular delivery of anticancer and immunomodulatory drugs, stem cell differentiation biomolecules and cell activity modulators. Although initial studies in the area of intracellular drug delivery have been performed in the delivery of DNA, there is an increasing interest in the use of other molecules to modulate cell activity. Herein, we review the latest advances in the intracellular-targeted delivery of short interference RNA, proteins and small molecules using NPs. In most cases, the drugs act at different cellular organelles and therefore the drug-containing NPs should be directed to precise locations within the cell. This will lead to the desired magnitude and duration of the drug effects. The spatial control in the intracellular delivery might open new avenues to modulate cell activity while avoiding side-effects.

  15. Intracellular trafficking of P-glycoprotein

    OpenAIRE

    Fu, Dong; Arias, Irwin M.

    2011-01-01

    Overexpression of P-glycoprotein (P-gp) is a major cause of multidrug resistance in cancer. P-gp is mainly localized in the plasma membrane and can efflux structurally and chemically unrelated substrates, including anticancer drugs. P-gp is also localized in intracellular compartments, such as ER, Golgi, endosomes and lysosomes, and cycles between endosomal compartments and the plasma membrane in a microtubular-actin dependent manner. Intracellular trafficking pathways for P-gp and participat...

  16. Adaptor protein complexes and intracellular transport

    OpenAIRE

    2014-01-01

    The AP (adaptor protein) complexes are heterotetrameric protein complexes that mediate intracellular membrane trafficking along endocytic and secretory transport pathways. There are five different AP complexes: AP-1, AP-2 and AP-3 are clathrin-associated complexes; whereas AP-4 and AP-5 are not. These five AP complexes localize to different intracellular compartments and mediate membrane trafficking in distinct pathways. They recognize and concentrate cargo proteins into vesicular carriers th...

  17. Tracking hantavirus nucleocapsid protein using intracellular antibodies

    Directory of Open Access Journals (Sweden)

    Liang Mifang

    2010-11-01

    Full Text Available Abstract Background Hantavirus nucleocapsid (N protein is a multifunctional viral macromolecule involved in multiple stages of the viral replication cycle. The intracellular trafficking of N protein during virus assembly remains unclear. Methods We used N protein-specific intracellular expressed antibodies to track the localization and distribution of Hantaan virus and Seoul virus N protein. The N protein-specific antibody single-chain variable antibody fragments (scFvs, which bind an N-terminal linear epitope (L13F3 and C-terminal conformational domain (H34, were intracellularly expressed in the endoplasmic reticulum (ER by fusion of the SEKDEL retention signal peptide at the carboxyl terminus, and in the cytoplasm (Cyto by deletion of the ER membrane target signal peptide. Stable Vero-E6 cell lines expressing intracellular scFvs were either infected with hantavirus or transfected with an N protein expression plasmid; virus replication and N protein intracellular localization were determined. Result N protein co-localized with scFvs in the ER and cytoplasm with or without viral membrane glycoproteins. Hantavirus replication was inhibited in both the scFvs-ER- and scFvs-Cyto-expressing stable cell lines. Conclusion N protein may be expressed in the ER retention signal peptide of KDEL circulating region (ER/cis-Golgi without the assistance of G protein, and so expression of N protein in both the cytoplasm and within the ER/cis-Golgi plays an important role in virus replication.

  18. Real-time atomic-resolution imaging of crystal growth process in water by phase modulation atomic force microscopy at one frame per second

    International Nuclear Information System (INIS)

    Recent advancement in dynamic-mode atomic force microscopy (AFM) has enabled its operation in liquid with atomic-scale resolution. However, its imaging speed has often been too slow to visualize atomic-scale dynamic processes. Here, we propose a method for making a significant improvement in the operation speed of dynamic-mode AFM. In this method, we use a wideband and low-latency phase detector with an improved algorithm for the signal complexification. We demonstrate atomic-scale imaging of a calcite crystal growth process in water at one frame per second. The significant improvement in the imaging speed should enable various studies on unexplored atomic-scale interfacial processes

  19. Multiplexed imaging of intracellular protein networks.

    Science.gov (United States)

    Grecco, Hernán E; Imtiaz, Sarah; Zamir, Eli

    2016-08-01

    Cellular functions emerge from the collective action of a large number of different proteins. Understanding how these protein networks operate requires monitoring their components in intact cells. Due to intercellular and intracellular molecular variability, it is important to monitor simultaneously multiple components at high spatiotemporal resolution. However, inherent trade-offs narrow the boundaries of achievable multiplexed imaging. Pushing these boundaries is essential for a better understanding of cellular processes. Here the motivations, challenges and approaches for multiplexed imaging of intracellular protein networks are discussed. © 2016 International Society for Advancement of Cytometry. PMID:27183498

  20. Peroxisome is a reservoir of intracellular calcium.

    Science.gov (United States)

    Raychaudhury, Bikramjit; Gupta, Shreedhara; Banerjee, Shouvik; Datta, Salil C

    2006-07-01

    We have examined fura 2-loaded purified peroxisomes under confocal microscope to prove that this mammalian organelle is a store of intracellular calcium pool. Presence of calcium channel and vanadate sensitive Ca(2+)-ATPase in the purified peroxisomal membrane has been demonstrated. We have further observed that machineries to maintain calcium pool in this mammalian organelle are impaired during infection caused by Leishmania donovani. Results reveal that peroxisomes have a merit to play a significant role in the metabolism of intracellular calcium. PMID:16713100

  1. Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

    OpenAIRE

    Meng Shen; Ali Han; Xijun Wang; Yun Goo Ro; Alireza Kargar; Yue Lin; Hua Guo; Pingwu Du; Jun Jiang; Jingyu Zhang; Dayeh, Shadi A.; Bin Xiang

    2015-01-01

    Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synth...

  2. Stochastic Kinetics of Intracellular Calcium Oscillations

    Institute of Scientific and Technical Information of China (English)

    陈昌胜; 曾仁端

    2003-01-01

    A stochastic model of intracellular calcium oscillations is put forward by taking into account the random opening-closing of Ca2+ channels in endoplasmic reticulum (ER) membrane. The numerical results of the stochastic model show simple and complex calcium oscillations, which accord with the experiment results.

  3. Histoplasma capsulatum surmounts obstacles to intracellular pathogenesis.

    Science.gov (United States)

    Garfoot, Andrew L; Rappleye, Chad A

    2016-02-01

    The fungal pathogen Histoplasma capsulatum causes respiratory and disseminated disease, even in immunocompetent hosts. In contrast to opportunistic pathogens, which are readily controlled by phagocytic cells, H. capsulatum yeasts are able to infect macrophages, survive antimicrobial defenses, and proliferate as an intracellular pathogen. In this review, we discuss some of the molecular mechanisms that enable H. capsulatum yeasts to overcome obstacles to intracellular pathogenesis. H. capsulatum yeasts gain refuge from extracellular obstacles such as antimicrobial lung surfactant proteins by engaging the β-integrin family of phagocytic receptors to promote entry into macrophages. In addition, H. capsulatum yeasts conceal immunostimulatory β-glucans to avoid triggering signaling receptors such as the β-glucan receptor Dectin-1. H. capsulatum yeasts counteract phagocyte-produced reactive oxygen species by expression of oxidative stress defense enzymes including an extracellular superoxide dismutase and an extracellular catalase. Within the phagosome, H. capsulatum yeasts block phagosome acidification, acquire essential metals such as iron and zinc, and utilize de novo biosynthesis pathways to overcome nutritional limitations. These mechanisms explain how H. capsulatum yeasts avoid and negate macrophage defense strategies and establish a hospitable intracellular niche, making H. capsulatum a successful intracellular pathogen of macrophages. PMID:26235362

  4. Intracellular aspartic protease of Candida albicans

    Czech Academy of Sciences Publication Activity Database

    Bauerová, Václava; Pichová, Iva; Hrušková-Heidingsfeldová, Olga

    Mátraháza : -, 2007. s. 43. [Alexander Von Humboldt Workshop on Structure Based Approaches Towards Disease Control. 22.05.2007-27.05.2007, Mátraháza] Institutional research plan: CEZ:AV0Z40550506 Keywords : Candida parapsilosis * intracellular * aspartic protease Subject RIV: CE - Biochemistry

  5. Dynamics of gradient formation by intracellular shuttling

    Energy Technology Data Exchange (ETDEWEB)

    Berezhkovskii, Alexander M. [Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892 (United States); Shvartsman, Stanislav Y. [Department of Chemical and Biological Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544 (United States)

    2015-08-21

    A number of important cellular functions rely on the formation of intracellular protein concentration gradients. Experimental studies discovered a number of mechanisms for the formation of such gradients. One of the mechanisms relies on the intracellular shuttling of a protein that interconverts between the two states with different diffusivities, under the action of two enzymes, one of which is localized to the plasma membrane, whereas the second is uniformly distributed in the cytoplasm. Recent work reported an analytical solution for the steady state gradient in this mechanism, obtained in the framework of a one-dimensional reaction-diffusion model. Here, we study the dynamics in this model and derive analytical expressions for the Laplace transforms of the time-dependent concentration profiles in terms of elementary transcendental functions. Inverting these transforms numerically, one can obtain time-dependent concentration profiles of the two forms of the protein.

  6. Biology and intracellular life of chlamydia

    Directory of Open Access Journals (Sweden)

    Ranin Lazar

    2011-01-01

    Full Text Available Introduction. Chlamydiae are Gram-negative obligate intracellular bacteria. The developmental cycle of Chlamydiae is specific and different from other bacteria. The elementary body is the infectious form of the organism, responsible for attaching to the target host cell and promoting its entry. The reticulate body is the larger, metabolically active form of the organism, synthesizing deoxyribonucleic acid, ribonucleic acid and proteins. The elementary body and reticulate body represent evolutionary adaptations to extracellular and intracellular environments. Intracellular persistence of Chlamydia. Predisposition of Chlamydia to persist within the host cell has been recognized as a major factor in the pathogenesis of chlamydial disease. The persistence implies a long-term association between chlamydiae and their host cell that may not manifest as clinically recognizable disease. The ability of chlamydia to remain within one morphological state for a long time in response to exogenous factors suggests an innate ability of these organisms to persist intracellulary in a unique developmental form. Chlamydiae induce interferon γ and exhibit growth inhibition in their presence. While the high levels of interferon γ completely restrict the development of chlamydia, its low levels induce the development of morphologically aberrant intracellular forms. The persistent forms contain reduced levels of major outer membrane protein but high levels of chlamydial heat shock protein. Conclusion. Immunopathogenesis of chlamydial infection is one of the main focal points of current research into Chlamydia. Chlamydial infections are highly prevalent, usually asymptomatic and associated with serious sequelae. Screening programmes are the most important in the prevention of a long-term sequele.

  7. A practical approach for intracellular protein delivery

    OpenAIRE

    Weill, Claire O; Biri, Stéphanie; Adib, Abdennaji; Erbacher, Patrick

    2007-01-01

    Protein delivery represents a powerful tool for experiments in live cells including studies of protein-protein interactions, protein interference with blocking antibodies, intracellular trafficking and protein or peptide biological functions. Most available reagents dedicated to the protein delivery allow efficient crossing of the plasma membrane. Nevertheless, the major disadvantage for these reagents is a weak release of the delivered protein into the cytoplasm. In this publication we demon...

  8. Paclitaxel Arrests Growth of Intracellular Toxoplasma gondii

    OpenAIRE

    Estes, Randee; Vogel, Nicolas; Mack, Douglas; McLeod, Rima

    1998-01-01

    Addition of paclitaxel (Taxol) at a concentration of 1 μM to Toxoplasma gondii-infected human foreskin fibroblasts arrested parasite multiplication. Division of the T. gondii tachyzoite nucleus was inhibited, leading to syncytium-like parasite structures within the fibroblasts by 24 h after infection and treatment of the cultures. By 4 days after infection and treatment of the cultures with paclitaxel, this inhibition was irreversible, since the arrested intracellular form was incapable of le...

  9. Error Propagation Analysis for Quantitative Intracellular Metabolomics

    Directory of Open Access Journals (Sweden)

    Jana Tillack

    2012-11-01

    Full Text Available Model-based analyses have become an integral part of modern metabolic engineering and systems biology in order to gain knowledge about complex and not directly observable cellular processes. For quantitative analyses, not only experimental data, but also measurement errors, play a crucial role. The total measurement error of any analytical protocol is the result of an accumulation of single errors introduced by several processing steps. Here, we present a framework for the quantification of intracellular metabolites, including error propagation during metabolome sample processing. Focusing on one specific protocol, we comprehensively investigate all currently known and accessible factors that ultimately impact the accuracy of intracellular metabolite concentration data. All intermediate steps are modeled, and their uncertainty with respect to the final concentration data is rigorously quantified. Finally, on the basis of a comprehensive metabolome dataset of Corynebacterium glutamicum, an integrated error propagation analysis for all parts of the model is conducted, and the most critical steps for intracellular metabolite quantification are detected.

  10. Fluorescent nanoparticles for intracellular sensing: A review

    Energy Technology Data Exchange (ETDEWEB)

    Ruedas-Rama, Maria J., E-mail: mjruedas@ugr.esmailto [Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071, Granada (Spain); Walters, Jamie D. [Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, UK CB2 1QT (United Kingdom); Orte, Angel [Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, 18071, Granada (Spain); Hall, Elizabeth A.H., E-mail: lisa.hall@biotech.cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT (United Kingdom)

    2012-11-02

    Highlights: Black-Right-Pointing-Pointer Analytical applications of fluorescent nanoparticles (NPs) in intracellular sensing. Black-Right-Pointing-Pointer Critical review on performance of QDots, metal NPs, silica NPs, and polymer NPs. Black-Right-Pointing-Pointer Highlighted potential of fluorescence lifetime imaging microscopy (FLIM). - Abstract: Fluorescent nanoparticles (NPs), including semiconductor NPs (Quantum Dots), metal NPs, silica NPs, polymer NPs, etc., have been a major focus of research and development during the past decade. The fluorescent nanoparticles show unique chemical and optical properties, such as brighter fluorescence, higher photostability and higher biocompatibility, compared to classical fluorescent organic dyes. Moreover, the nanoparticles can also act as multivalent scaffolds for the realization of supramolecular assemblies, since their high surface to volume ratio allow distinct spatial domains to be functionalized, which can provide a versatile synthetic platform for the implementation of different sensing schemes. Their excellent properties make them one of the most useful tools that chemistry has supplied to biomedical research, enabling the intracellular monitoring of many different species for medical and biological purposes. In this review, we focus on the developments and analytical applications of fluorescent nanoparticles in chemical and biological sensing within the intracellular environment. The review also points out the great potential of fluorescent NPs for fluorescence lifetime imaging microscopy (FLIM). Finally, we also give an overview of the current methods for delivering of fluorescent NPs into cells, where critically examine the benefits and liabilities of each strategy.

  11. Atomic Scale Analysis of the Enhanced Electro- and Photo-Catalytic Activity in High-Index Faceted Porous NiO Nanowires

    Science.gov (United States)

    Shen, Meng; Han, Ali; Wang, Xijun; Ro, Yun Goo; Kargar, Alireza; Lin, Yue; Guo, Hua; Du, Pingwu; Jiang, Jun; Zhang, Jingyu; Dayeh, Shadi A.; Xiang, Bin

    2015-02-01

    Catalysts play a significant role in clean renewable hydrogen fuel generation through water splitting reaction as the surface of most semiconductors proper for water splitting has poor performance for hydrogen gas evolution. The catalytic performance strongly depends on the atomic arrangement at the surface, which necessitates the correlation of the surface structure to the catalytic activity in well-controlled catalyst surfaces. Herein, we report a novel catalytic performance of simple-synthesized porous NiO nanowires (NWs) as catalyst/co-catalyst for the hydrogen evolution reaction (HER). The correlation of catalytic activity and atomic/surface structure is investigated by detailed high resolution transmission electron microscopy (HRTEM) exhibiting a strong dependence of NiO NW photo- and electrocatalytic HER performance on the density of exposed high-index-facet (HIF) atoms, which corroborates with theoretical calculations. Significantly, the optimized porous NiO NWs offer long-term electrocatalytic stability of over one day and 45 times higher photocatalytic hydrogen production compared to commercial NiO nanoparticles. Our results open new perspectives in the search for the development of structurally stable and chemically active semiconductor-based catalysts for cost-effective and efficient hydrogen fuel production at large scale.

  12. Intracellular ethanol accumulation in Saccharomyces cerevisiae during fermentation.

    OpenAIRE

    D'Amore, T; C.J. Panchal; Stewart, G G

    1988-01-01

    An intracellular accumulation of ethanol in Saccharomyces cerevisiae was observed during the early stages of fermentation (3 h). However, after 12 h of fermentation, the intracellular and extracellular ethanol concentrations were similar. Increasing the osmotic pressure of the medium caused an increase in the ratio of intracellular to extracellular ethanol concentrations at 3 h of fermentation. As in the previous case, the intracellular and extracellular ethanol concentrations were similar af...

  13. Curcumin protects against intracellular amyloid toxicity in rat primary neurons

    OpenAIRE

    Ye, Jelina; Zhang, Yan

    2012-01-01

    To investigate whether curcumin is protective against intracellular amyloid β (Aβ) toxicity, different concentrations of curcumin were applied to with intracellular Aβ in rat primary hippocampal neurons in culture. We find that at low dosages, curcumin effectively inhibits intracellular Aβ toxicity. Reactive oxidative species (ROS) is involved in mediating intracellular Aβ toxicity and possibly curcumin protection. Our results indicate that oxidative stress may mediate cell death induced by i...

  14. Proton-dependent zinc release from intracellular ligands

    OpenAIRE

    Kiedrowski, Lech

    2014-01-01

    In cultured cortical and hippocampal neurons when intracellular pH drops from 6.6 to 6.1, yet unclear intracellular stores release micromolar amounts of Zn2+ into the cytosol. Mitochondria, acidic organelles, and/or intracellular ligands could release this Zn2+. Although exposure to the protonophore FCCP precludes re-loading of the mitochondria and acidic organelles with Zn2+, FCCP failed to compromise the ability of the intracellular stores to repeatedly release Zn2+. There...

  15. Two complementary approaches for intracellular delivery of exogenous enzymes.

    Science.gov (United States)

    Rust, Aleksander; Hassan, Hazirah H A; Sedelnikova, Svetlana; Niranjan, Dhevahi; Hautbergue, Guillaume; Abbas, Shaymaa A; Partridge, Lynda; Rice, David; Binz, Thomas; Davletov, Bazbek

    2015-01-01

    Intracellular delivery of biologically active proteins remains a formidable challenge in biomedical research. Here we show that biomedically relevant enzymes can be delivered into cells using a new DNA transfection reagent, lipofectamine 3000, allowing assessment of their intracellular functions. We also show that the J774.2 macrophage cell line exhibits unusual intracellular uptake of structurally and functionally distinct enzymes providing a convenient, reagent-free approach for evaluation of intracellular activities of enzymes. PMID:26207613

  16. Water

    International Nuclear Information System (INIS)

    An up-date overview of the situation of the Austrian waters is given by analyzing the status of the water quality (groundwater, surface waters) and water protection measures. Maps containing information of nitrate and atrazine in groundwaters (analyses at monitoring stations), nitrate contents and biological water quality of running waters are included. Finally, pollutants (nitrate, orthophosphate, ammonium, nitrite, atrazine etc.) trends in annual mean values and median values for the whole country for the years 1992-1999 are presented in tables. Figs. 5. (nevyjel)

  17. Curcumin protects against intracellular amyloid toxicity in rat primary neurons

    NARCIS (Netherlands)

    Ye, Jelina; Zhang, Yan

    2012-01-01

    To investigate whether curcumin is protective against intracellular amyloid beta (A beta) toxicity, different concentrations of curcumin were applied to with intracellular A beta in rat primary hippocampal neurons in culture. We find that at low dosages, curcumin effectively inhibits intracellular A

  18. Use of magnetic nanobeads to study intracellular antigen processing

    International Nuclear Information System (INIS)

    Magnetic nanobeads were covalently linked to antigens and used as a tool to simultaneously follow their intracellular transport into the cells and specifically purify the intracellular compartments implicated in antigen processing. The protein content of these vesicles was analysed by 2D-electrophoresis. Furthermore, nanobeads allowed intracellular localisation of the antigen in electron and fluorescence microscopy

  19. Use of magnetic nanobeads to study intracellular antigen processing

    Energy Technology Data Exchange (ETDEWEB)

    Perrin-Cocon, Laure A.; Chesne, Serge; Pignot-Paintrand, Isabelle; Marche, Patrice N.; Villiers, Christian L. E-mail: christian.villiers@cea.fr

    2001-07-01

    Magnetic nanobeads were covalently linked to antigens and used as a tool to simultaneously follow their intracellular transport into the cells and specifically purify the intracellular compartments implicated in antigen processing. The protein content of these vesicles was analysed by 2D-electrophoresis. Furthermore, nanobeads allowed intracellular localisation of the antigen in electron and fluorescence microscopy.

  20. Solvent properties of ground substance studied by cryomicrodissection and intracellular reference-phase techniques

    OpenAIRE

    Horowitz, S. B.; Miller, D S

    1984-01-01

    Water, sodium, potassium, ATP, amino acids, and sugars are not uniformly distributed in Rana pipiens oocytes. Concentration differences exist between nucleus (germinal vesicle) and ooplasm and between animal and vegetal ooplasmic regions. The mechanisms responsible for these differences were investigated using intracellular reference-phase (iRP) analysis. The iRP is an artificial "organelle" that has the solvent properties of a dilute salt solution and is in diffusional equilibrium with water...

  1. Evidence that downregulation of hexose transport limits intracellular glucose in 3T3-L1 fibroblasts

    International Nuclear Information System (INIS)

    Measurements of initial glucose entry rate and intracellular glucose concentration in cultured cells are difficult because of rapid transport relative to intracellular volume and a substantial extracellular space from which glucose cannot be completely removed by quick exchanges of medium. In 3T3-L1 cells, we obtained good estimates of initial entry of [14C]methylglucose and D-[14C]glucose with (1) L-[3H]glucose as an extracellular marker together with the [14C]glucose or [14C]methylglucose in the substrate mixture, (2) sampling times as short as 2 s, (3) ice-cold phloretin-containing medium to stop uptake and rinse away the extracellular label, and (4) nonlinear regression of time courses. Methylglucose equilibrated in two phases--the first with a half-time of 1.7 s and the second with a half-time of 23 s; it eventually equilibrated in an intracellular space of 8 microliters/mg protein. Entry of glucose remained almost linear for 10 s, making its transport kinetics easier to study (Km = 5.7 mM, Vmax = 590 nmol.s-1.ml-1 cell water). Steady-state intracellular glucose concentration was 75-90% of extracellular glucose concentration. Cells grown in a high-glucose medium (24 mM) exhibited a 67% reduction of glucose-transport activity and a 50% reduction of steady-state ratio of intracellular glucose to extracellular glucose

  2. Intracellular α-Amylase of Streptococcus mutans

    OpenAIRE

    Simpson, Christine L.; Russell, Roy R. B.

    1998-01-01

    Sequencing upstream of the Streptococcus mutans gene for a CcpA gene homolog, regM, revealed an open reading frame, named amy, with homology to genes encoding α-amylases. The deduced amino acid sequence showed a strong similarity (60% amino acid identity) to the intracellular α-amylase of Streptococcus bovis and, in common with this enzyme, lacked a signal sequence. Amylase activity was found only in S. mutans cell extracts, with no activity detected in culture supernatants. Inactivation of a...

  3. Stochastic models of intracellular calcium signals

    International Nuclear Information System (INIS)

    Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed

  4. Stochastic models of intracellular calcium signals

    Energy Technology Data Exchange (ETDEWEB)

    Rüdiger, Sten, E-mail: sten.ruediger@physik.hu-berlin.de

    2014-01-10

    Cellular signaling operates in a noisy environment shaped by low molecular concentrations and cellular heterogeneity. For calcium release through intracellular channels–one of the most important cellular signaling mechanisms–feedback by liberated calcium endows fluctuations with critical functions in signal generation and formation. In this review it is first described, under which general conditions the environment makes stochasticity relevant, and which conditions allow approximating or deterministic equations. This analysis provides a framework, in which one can deduce an efficient hybrid description combining stochastic and deterministic evolution laws. Within the hybrid approach, Markov chains model gating of channels, while the concentrations of calcium and calcium binding molecules (buffers) are described by reaction–diffusion equations. The article further focuses on the spatial representation of subcellular calcium domains related to intracellular calcium channels. It presents analysis for single channels and clusters of channels and reviews the effects of buffers on the calcium release. For clustered channels, we discuss the application and validity of coarse-graining as well as approaches based on continuous gating variables (Fokker–Planck and chemical Langevin equations). Comparison with recent experiments substantiates the stochastic and spatial approach, identifies minimal requirements for a realistic modeling, and facilitates an understanding of collective channel behavior. At the end of the review, implications of stochastic and local modeling for the generation and properties of cell-wide release and the integration of calcium dynamics into cellular signaling models are discussed.

  5. Strategies for Intracellular Survival of Burkholderia pseudomallei.

    Science.gov (United States)

    Allwood, Elizabeth M; Devenish, Rodney J; Prescott, Mark; Adler, Ben; Boyce, John D

    2011-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a disease with high mortality that is prevalent in tropical regions of the world. A key component of the pathogenesis of melioidosis is the ability of B. pseudomallei to enter, survive, and replicate within mammalian host cells. For non-phagocytic cells, bacterial adhesins have been identified both on the bacterial surface and associated with Type 4 pili. Cell invasion involves components of one or more of the three Type 3 Secretion System clusters, which also mediate, at least in part, the escape of bacteria from the endosome into the cytoplasm, where bacteria move by actin-based motility. The mechanism of actin-based motility is not clearly understood, but appears to differ from characterized mechanisms in other bacterial species. A small proportion of intracellular bacteria is targeted by host cell autophagy, involving direct recruitment of LC3 to endosomes rather than through uptake by canonical autophagosomes. However, the majority of bacterial cells are able to circumvent autophagy and other intracellular defense mechanisms such as the induction of inducible nitric oxide synthase, and then replicate in the cytoplasm and spread to adjacent cells via membrane fusion, resulting in the formation of multi-nucleated giant cells. A potential role for host cell ubiquitin in the autophagic response to bacterial infection has recently been proposed. PMID:22007185

  6. Intracellular alpha-amylase of Streptococcus mutans.

    Science.gov (United States)

    Simpson, C L; Russell, R R

    1998-09-01

    Sequencing upstream of the Streptococcus mutans gene for a CcpA gene homolog, regM, revealed an open reading frame, named amy, with homology to genes encoding alpha-amylases. The deduced amino acid sequence showed a strong similarity (60% amino acid identity) to the intracellular alpha-amylase of Streptococcus bovis and, in common with this enzyme, lacked a signal sequence. Amylase activity was found only in S. mutans cell extracts, with no activity detected in culture supernatants. Inactivation of amy by insertion of an antibiotic resistance marker confirmed that S. mutans has a single alpha-amylase activity. The amylase activity was induced by maltose but not by starch, and no acid was produced from starch. S. mutans can, however, transport limit dextrins and maltooligosaccharides generated by salivary amylase, but inactivation of amy did not affect growth on these substrates or acid production. The amylase digested the glycogen-like intracellular polysaccharide (IPS) purified from S. mutans, but the amy mutant was able to digest and produce acid from IPS; thus, amylase does not appear to be essential for IPS breakdown. However, when grown on excess maltose, the amy mutant produced nearly threefold the amount of IPS produced by the parent strain. The role of Amy has not been established, but Amy appears to be important in the accumulation of IPS in S. mutans grown on maltose. PMID:9721315

  7. Intracellular ice and cell survival in cryo-exposed embryonic axes of recalcitrant seeds of Acer saccharinum: an ultrastructural study of factors affecting cell and ice structures

    Science.gov (United States)

    Cryogenic technologies are required to preserve embryonic axes of recalcitrant seeds. Formation of potentially lethal intracellular ice limits successful cryopreservation; thus, it is important to understand the relationships among cryo-exposure techniques, water content and survival. In this pap...

  8. Intracellular signalling by C-peptide.

    Science.gov (United States)

    Hills, Claire E; Brunskill, Nigel J

    2008-01-01

    C-peptide, a cleavage product of the proinsulin molecule, has long been regarded as biologically inert, serving merely as a surrogate marker for insulin release. Recent findings demonstrate both a physiological and protective role of C-peptide when administered to individuals with type I diabetes. Data indicate that C-peptide appears to bind in nanomolar concentrations to a cell surface receptor which is most likely to be G-protein coupled. Binding of C-peptide initiates multiple cellular effects, evoking a rise in intracellular calcium, increased PI-3-kinase activity, stimulation of the Na(+)/K(+) ATPase, increased eNOS transcription, and activation of the MAPK signalling pathway. These cell signalling effects have been studied in multiple cell types from multiple tissues. Overall these observations raise the possibility that C-peptide may serve as a potential therapeutic agent for the treatment or prevention of long-term complications associated with diabetes. PMID:18382618

  9. Intracellular Signalling by C-Peptide

    Directory of Open Access Journals (Sweden)

    Claire E. Hills

    2008-01-01

    Full Text Available C-peptide, a cleavage product of the proinsulin molecule, has long been regarded as biologically inert, serving merely as a surrogate marker for insulin release. Recent findings demonstrate both a physiological and protective role of C-peptide when administered to individuals with type I diabetes. Data indicate that C-peptide appears to bind in nanomolar concentrations to a cell surface receptor which is most likely to be G-protein coupled. Binding of C-peptide initiates multiple cellular effects, evoking a rise in intracellular calcium, increased PI-3-kinase activity, stimulation of the Na+/K+ ATPase, increased eNOS transcription, and activation of the MAPK signalling pathway. These cell signalling effects have been studied in multiple cell types from multiple tissues. Overall these observations raise the possibility that C-peptide may serve as a potential therapeutic agent for the treatment or prevention of long-term complications associated with diabetes.

  10. Cytoskeletal network morphology regulates intracellular transport dynamics

    CERN Document Server

    Ando, David; Huang, Kerwyn Casey; Gopinathan, Ajay

    2016-01-01

    Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific locations is accomplished through a combination of passive diffusion and active transport by molecular motors that ballistically move along a network of cytoskeletal filaments. Although motor-based transport is known to be necessary to overcome cytoplasmic crowding and the limited range of diffusion within reasonable time scales, the topological features of the cytoskeletal network that regulate transport efficiency and robustness have not been established. Using a continuum diffusion model, we observed that the time required for cellular transport was minimized when the network was localized near the nucleus. In simulations that explicitly incorporated network spatial architectures, total filament mass was the primary driver of network transit times. However, filament traps that r...

  11. Intracellular calcium release modulates polycystin-2 trafficking

    Directory of Open Access Journals (Sweden)

    Miyakawa Ayako

    2013-02-01

    Full Text Available Abstract Background Polycystin-2 (PC2, encoded by the gene that is mutated in autosomal dominant polycystic kidney disease (ADPKD, functions as a calcium (Ca2+ permeable ion channel. Considerable controversy remains regarding the subcellular localization and signaling function of PC2 in kidney cells. Methods We investigated the subcellular PC2 localization by immunocytochemistry and confocal microscopy in primary cultures of human and rat proximal tubule cells after stimulating cytosolic Ca2+ signaling. Plasma membrane (PM Ca2+ permeability was evaluated by Fura-2 manganese quenching using time-lapse fluorescence microscopy. Results We demonstrated that PC2 exhibits a dynamic subcellular localization pattern. In unstimulated human or rat proximal tubule cells, PC2 exhibited a cytosolic/reticular distribution. Treatments with agents that in various ways affect the Ca2+ signaling machinery, those being ATP, bradykinin, ionomycin, CPA or thapsigargin, resulted in increased PC2 immunostaining in the PM. Exposing cells to the steroid hormone ouabain, known to trigger Ca2+ oscillations in kidney cells, caused increased PC2 in the PM and increased PM Ca2+ permeability. Intracellular Ca2+ buffering with BAPTA, inositol 1,4,5-trisphosphate receptor (InsP3R inhibition with 2-aminoethoxydiphenyl borate (2-APB or Ca2+/Calmodulin-dependent kinase inhibition with KN-93 completely abolished ouabain-stimulated PC2 translocation to the PM. Conclusions These novel findings demonstrate intracellular Ca2+-dependent PC2 trafficking in human and rat kidney cells, which may provide new insight into cyst formations in ADPKD.

  12. Strategies to improve intracellular drug delivery by targeted liposomes

    OpenAIRE

    Fretz, M.M.

    2007-01-01

    Biotechnological advances increased the number of novel macromolecular drugs and new drug targets. The latter are mostly found intracellular. Unfortunately, most of the new macromolecular drugs rely on drug delivery tools for their intracellular delivery because their unfavourable physicochemical properties hamper them to cross cellular barriers, like the plasma and endosomal membranes. The work described in this thesis aims to improve intracellular drug delivery by applying targeted liposome...

  13. Biosensor Scheme for the Determination of Intracellular Pressure of Erythrocyte

    Directory of Open Access Journals (Sweden)

    Yu.S. Nagornov

    2016-03-01

    Full Text Available The paper presents a scheme of the biosensor for determining the intracellular pressure of erythrocytes. The possibility of measuring of the volume and area of the erythrocyte is provided in a biosensor to determine the value intracellular pressure. In MEMS this creates flow that enters into Coulter capacitive sensor through the rate control system and then in the system of signal transmitting. The definition of erythrocyte volume and calculation of intracellular pressure occur in the computer system.

  14. Neuronal calcium sparks and intracellular calcium “noise”

    OpenAIRE

    Melamed-Book, Naomi; Kachalsky, Sylvia G.; Kaiserman, Igor; Rahamimoff, Rami

    1999-01-01

    Intracellular calcium ions are involved in many forms of cellular function. To accommodate so many control functions, a complex spatiotemporal organization of calcium signaling has developed. In both excitable and nonexcitable cells, calcium signaling was found to fluctuate. Sudden localized increases in the intracellular calcium concentration—or calcium sparks—were found in heart, striated and smooth muscle, Xenopus Laevis oocytes, and HeLa and P12 cells. In the nervous system, intracellular...

  15. Resistance to Sliding on Atomic Scales

    Science.gov (United States)

    Dominik, C.; Tielens, A.; Cuzzi, Jeffrey (Technical Monitor)

    1995-01-01

    The structure and stability of agglomerates of micron-sized particles is determined by the mechanical properties of the individual contacts between the constituent particles. In this paper we study the possibility of aggregate rearrangements by sliding. Since the contacts between (sub)micron particles are only a few hundred atoms in diameter, processes on atomic levels will play the dominating roll. We study a theoretical model of sliding friction for surfaces that are either flat or contain steps in their grids. The results show that sliding over flat surfaces may produce a large range of friction coefficients, including zero if the adhesive forces are small compared to the binding forces inside a body. However, both grid alignment and steps in the surface will lead to high values for friction. These processes combined virtually eliminate the possibility of sliding in a collision of two (sub)micron sized particles at velocities low enough for sticking to occur. On the other hand we show that in collisions between aggregates sliding may be an important factor for energy dissipation and compaction.

  16. Zirconium oxidation on the atomic scale

    OpenAIRE

    Hudson, Daniel; Smith, George D. W.

    2011-01-01

    This work was produced as part of a multidisciplinary study of the corrosion of zirconium alloys undertaken by a consortium of universities working in the MUZIC program; Oxford, Manchester and The Open University. The objective of the project as a whole was to further the understanding of the mechanisms of the breakaway oxidation process and to characterise these corrosion processes within a number of fuel rod cladding materials. This thesis describes laser 3D atom probe characterisation of t...

  17. Zirconium oxidation on the atomic scale.

    Science.gov (United States)

    Hudson, Daniel; Cerezo, Alfred; Smith, George D W

    2009-04-01

    Zirconium alloys are used in the nuclear industry as fuel rod cladding. They are chosen for this role because of their good mechanical properties and low thermal neutron absorption. Oxidation of these alloys by coolant is one of the chief limiting factors of the fuel burn-up efficiency. The aim of the present study is to understand these oxidation mechanisms. As a first step, a fundamental study of the oxidation of commercially pure zirconium has been conducted using the 3D atom probe (3DAP). The current generation of 3DAPs allows both voltage and laser pulsing, providing data sets of many millions of ions. According to the literature the only stable oxide of zirconium is ZrO(2). However, the 3DAP shows that an initial layer a few nanometres thick forms with a composition of ZrO(1-)(x) when subjected to light oxidation. This result confirms and extends the work of Wadman et al. [Colloque de Physique 50 (1989) C8 303; Journal de Physique, 11 (1988) C6 49] and Wadman and Andrén [in: C.M. Euchen, A.M. Garde (Eds.), Zirconium in the Nuclear Industry: Ninth Symposium, ASTM STP 1132, ASTM, USA, 1991, p. 461], who used 1DAP techniques, obtaining reduced data sets. Segregation of hydrogen to the metal-oxide interface and a distinct ZrH phase were observed in this study. A novel kinetics study of the room temperature oxidation of zirconium showed the ZrO layer to be non-protective over the time period investigated (up to 1h). PMID:19101084

  18. Assessment of Methods for the Intracellular Blockade of GABAA Receptors.

    Science.gov (United States)

    Atherton, Laura A; Burnell, Erica S; Mellor, Jack R

    2016-01-01

    Selective blockade of inhibitory synaptic transmission onto specific neurons is a useful tool for dissecting the excitatory and inhibitory synaptic components of ongoing network activity. To achieve this, intracellular recording with a patch solution capable of blocking GABAA receptors has advantages over other manipulations, such as pharmacological application of GABAergic antagonists or optogenetic inhibition of populations of interneurones, in that the majority of inhibitory transmission is unaffected and hence the remaining network activity preserved. Here, we assess three previously described methods to block inhibition: intracellular application of the molecules picrotoxin, 4,4'-dinitro-stilbene-2,2'-disulphonic acid (DNDS) and 4,4'-diisothiocyanostilbene-2,2'-disulphonic acid (DIDS). DNDS and picrotoxin were both found to be ineffective at blocking evoked, monosynaptic inhibitory postsynaptic currents (IPSCs) onto mouse CA1 pyramidal cells. An intracellular solution containing DIDS and caesium fluoride, but lacking nucleotides ATP and GTP, was effective at decreasing the amplitude of IPSCs. However, this effect was found to be independent of DIDS, and the absence of intracellular nucleotides, and was instead due to the presence of fluoride ions in this intracellular solution, which also blocked spontaneously occurring IPSCs during hippocampal sharp waves. Critically, intracellular fluoride ions also caused a decrease in both spontaneous and evoked excitatory synaptic currents and precluded the inclusion of nucleotides in the intracellular solution. Therefore, of the methods tested, only fluoride ions were effective for intracellular blockade of IPSCs but this approach has additional cellular effects reducing its selectivity and utility. PMID:27501143

  19. Modeling HIV-1 intracellular replication: two simulation approaches

    NARCIS (Netherlands)

    N. Zarrabi; E. Mancini; J. Tay; S. Shahand; P.M.A. Sloot

    2010-01-01

    Many mathematical and computational models have been developed to investigate the complexity of HIV dynamics, immune response and drug therapy. However, there are not many models which consider the dynamics of virus intracellular replication at a single level. We propose a model of HIV intracellular

  20. Intracellular Shuttle: The Lactate Aerobic Metabolism

    Directory of Open Access Journals (Sweden)

    Rogério Santos de Oliveira Cruz

    2012-01-01

    Full Text Available Lactate is a highly dynamic metabolite that can be used as a fuel by several cells of the human body, particularly during physical exercise. Traditionally, it has been believed that the first step of lactate oxidation occurs in cytosol; however, this idea was recently challenged. A new hypothesis has been presented based on the fact that lactate-to-pyruvate conversion cannot occur in cytosol, because the LDH enzyme characteristics and cytosolic environment do not allow the reaction in this way. Instead, the Intracellular Lactate Shuttle hypothesis states that lactate first enters in mitochondria and only then is metabolized. In several tissues of the human body this idea is well accepted but is quite resistant in skeletal muscle. In this paper, we will present not only the studies which are protagonists in this discussion, but the potential mechanism by which this oxidation occurs and also a link between lactate and mitochondrial proliferation. This new perspective brings some implications and comes to change our understanding of the interaction between the energy systems, because the product of one serves as a substrate for the other.

  1. Duodenal Intracellular Bicarbonate and the 'CF Paradox'

    Directory of Open Access Journals (Sweden)

    Kaunitz JD

    2001-07-01

    Full Text Available HCO(3(- secretion, which is believed to neutralize acid within the mucus gel, is the most studied duodenal defense mechanism. In general, HCO(3(- secretion rate and mucosal injury susceptibility correlate closely. Recent studies suggest that luminal acid can lower intracellular pH (pH(i of duodenal epithelial cells and that HCO(3(- secretion is unchanged during acid stress. Furthermore, peptic ulcers are rare in cystic fibrosis (CF, although, with impaired HCO(3(- secretion, increased ulcer prevalence is predicted, giving rise to the 'CF Paradox'. We thus tested the hypothesis that duodenal epithelial cell protection occurs as the result of pH(i regulation rather than by neutralization of acid by HCO(3(- in the pre-epithelial mucus. Cellular acidification during luminal acid perfusion, and unchanged HCO(3(- secretion during acid stress are inconsistent with pre-epithelial acid neutralization by secreted HCO(3(-. Furthermore, inhibition of HCO(3(- secretion by 5-nitro-2-(3-phenylpropylamino benzoic acid (NPPB despite preservation of pH(i and protection from acid-induced injury further question the pre-epithelial acid neutralization hypothesis. This decoupling of HCO(3(- secretion and injury susceptibility by NPPB (and possibly by CF further suggest that cellular buffering, rather than HCO(3(- exit into the mucus, is of primary importance for duodenal mucosal protection, and may account for the lack of peptic ulceration in CF patients.

  2. Intracellular Signals of T Cell Costimulation

    Institute of Scientific and Technical Information of China (English)

    Jianxun Song; Fengyang Tylan Lei; Xiaofang Xiong; Rizwanul Haque

    2008-01-01

    Ligation of T cell receptor (TCR) alone is insufficient to induce full activation of T lymphocytes. Additional ligand-receptor interactions (costimulation) on antigen presenting cells (APCs) and T cells are required. T cell costimulation has been shown to be essential for eliciting efficient T cell responses, involving all phases during T cell development. However, the mechanisms by which costimulation affects the function of T cells still need to be elucidated. In recent years, advances have been made in studies of costimulation as potential therapies in cancer, infectious disease as well as autoimmune disease. In this review, we discussed intracellular costimulation signals that regulate T cell proliferation, cell cycle progression, cytokine production, survival, and memory development. In general, the pathway of phosphoinositide-3 kinase (PBK)/protein kinase B (PKB, also known as Akt)/nuclear factor κB (NF-κB) might be central to many costimulatory effects. Through these pathways, costimulation controls T-cell expansion and proliferation by maintenance of survivin and aurora B expression, and sustains long-term T-cell survival and memory development by regulating the expression of bci-2 family members. Cellular & Molecular Immunology.2008;5(4):239-247.

  3. On the Computing Potential of Intracellular Vesicles.

    Directory of Open Access Journals (Sweden)

    Richard Mayne

    Full Text Available Collision-based computing (CBC is a form of unconventional computing in which travelling localisations represent data and conditional routing of signals determines the output state; collisions between localisations represent logical operations. We investigated patterns of Ca2+-containing vesicle distribution within a live organism, slime mould Physarum polycephalum, with confocal microscopy and observed them colliding regularly. Vesicles travel down cytoskeletal 'circuitry' and their collisions may result in reflection, fusion or annihilation. We demonstrate through experimental observations that naturally-occurring vesicle dynamics may be characterised as a computationally-universal set of Boolean logical operations and present a 'vesicle modification' of the archetypal CBC 'billiard ball model' of computation. We proceed to discuss the viability of intracellular vesicles as an unconventional computing substrate in which we delineate practical considerations for reliable vesicle 'programming' in both in vivo and in vitro vesicle computing architectures and present optimised designs for both single logical gates and combinatorial logic circuits based on cytoskeletal network conformations. The results presented here demonstrate the first characterisation of intracelluar phenomena as collision-based computing and hence the viability of biological substrates for computing.

  4. Atomic-scale microstructural characterization and dielectric properties of crystalline cubic pyrochlore Bi1.5MgNb1.5O7 nanoparticles synthesized by sol-gel method

    KAUST Repository

    Zhang, Yuan

    2013-12-24

    Here, we report the atomic-scale microstructural characterization and dielectric properties of crystalline cubic pyrochlore Bi1.5MgNb 1.5O7 (BMN) nanoparticles with mean size of 70 nm, which were synthesized by sol-gel method. The crystallinity, phase formation, morphology, and surface microstructure of the BMN nanoparticles were characterized by X-ray diffraction (XRD), Raman spectra, transmission electron microscopy (TEM), and high-resolution transmission electron microscopy (HRTEM), respectively. The phase evolution of the BMN nanoparticles investigated by XRD patterns showed that uniform cubic pyrochlore BMN nanoparticles were obtained after calcination at temperature of 800 C, and their structural information was revealed by Raman spectrum. TEM images demonstrated that the BMN nanoparticles had a spherical morphology with an average particle size of 70 nm, and their crystalline nature was revealed by HRTEM images. In addition, HRTEM images also demonstrate a terrace-ledge-kink (TLK) surface structure at the edges of rough BMN nanoparticles, where the terrace was on the (100) plane, and the ledge on the (001) plane. The formation of such a TLK surface structure can be well explained by a theory of periodic bond chains. Due to the surface structural reconstruction in the BMN nanoparticles, the formation of a tetragonal structure in a rough BMN nanoparticle was also revealed by HRTEM image. The BMN nanoparticles exhibited dielectric constants of 50 at 100 kHz and 30 at 1 MHz, and the dielectric loss of 0.19 at 1 MHz. © 2013 Springer Science+Business Media Dordrecht.

  5. Average and local atomic-scale structure in BaZrxTi1−xO3 (x = 0.10, 0.20, 0.40) ceramics by high-energy x-ray diffraction and Raman spectroscopy

    International Nuclear Information System (INIS)

    High-resolution x-ray diffraction (XRD), Raman spectroscopy and total scattering XRD coupled to atomic pair distribution function (PDF) analysis studies of the atomic-scale structure of archetypal BaZrxTi1−xO3 (x = 0.10, 0.20, 0.40) ceramics are presented over a wide temperature range (100–450 K). For x = 0.1 and 0.2 the results reveal, well above the Curie temperature, the presence of Ti-rich polar clusters which are precursors of a long-range ferroelectric order observed below TC. Polar nanoregions (PNRs) and relaxor behaviour are observed over the whole temperature range for x = 0.4. Irrespective of ceramic composition, the polar clusters are due to locally correlated off-centre displacement of Zr/Ti cations compatible with local rhombohedral symmetry. Formation of Zr-rich clusters is indicated by Raman spectroscopy for all compositions. Considering the isovalent substitution of Ti with Zr in BaZrxTi1−xO3, the mechanism of formation and growth of the PNRs is not due to charge ordering and random fields, but rather to a reduction of the local strain promoted by the large difference in ion size between Zr4+ and Ti4+. As a result, non-polar or weakly polar Zr-rich clusters and polar Ti-rich clusters are randomly distributed in a paraelectric lattice and the long-range ferroelectric order is disrupted with increasing Zr concentration. (paper)

  6. Systematic study of structural, electronic, and optical properties of atomic-scale defects in the two-dimensional transition metal dichalcogenides M X2 (M = Mo , W; X = S , Se, Te)

    Science.gov (United States)

    Haldar, Soumyajyoti; Vovusha, Hakkim; Yadav, Manoj Kumar; Eriksson, Olle; Sanyal, Biplab

    2015-12-01

    In this work, we have systematically studied structural, electronic, and magnetic properties of atomic-scale defects in 2D transition metal dichalcogenides M X2 (M = Mo and W; X = S , Se, and Te) by density functional theory. Various types of defects, e.g., X vacancy, X interstitial, M vacancy, M interstitial, and M X and X X double vacancies, have been considered. It has been found that the X interstitial has the lowest formation energy (˜1 eV) for all the systems in the X -rich condition, whereas for the M -rich condition, X vacancy has the lowest formation energy except for M Te2 systems. Both these defects have very high equilibrium defect concentrations at growth temperatures (1000-1200 K) reported in literature. A pair of defects, e.g., two X vacancies or one M and one X vacancies, tend to occupy the nearest possible distance. No trace of magnetism has been found for any one of the defects considered. Apart from X interstitial, all other defects have defect states appearing in the band gap, which can greatly affect the electronic and optical properties of the pristine systems. Our calculated optical properties show that the defect states cause optical transitions at ˜1.0 eV, which can be beneficial for light emitting devices. The results of our systematic study are expected to guide the experimental nanoengineering of defects to achieve suitable properties related to band gap modifications and characterization of defect fingerprints via optical absorption measurements.

  7. Modelling at the atomic scale of the irradiation effects in SiC: example of the stability of the Frenkel pairs and of the swelling due to the amorphization

    International Nuclear Information System (INIS)

    The evolution of the structural and mechanical properties due to the defects induced by irradiation is an important problem for nuclear materials. The modelling at the atomic scale can bring pertinent data difficult to obtain experimentally on the implied processes. Several atomistic modelling studies on the behaviour of silicon carbide under irradiation have been carried out. Here are presented two examples of these studies. The first example is the study by the density functional method of the stability and of the recombination of the Frenkel pairs in the cubic silicon carbide. The use of this method called 'ab initio' allows to determine the energies and the geometries of these defects with a very good accuracy. The thermodynamic stability of the Frenkel pairs has been determined and compared to those of the intrinsic point defects. The recombination kinetics has then been studied by the calculation of the implied activation energies. With the migration mechanisms, the recombination processes plays indeed an essential role in the annealing of materials during and after irradiation. The second example is the study by classical molecular dynamics of the swelling due to amorphization in silicon carbide. The irradiation is modelled in two successive steps: (a)creation at a constant volume of an amorphous zone of structure, of variable size and shape (b)relaxation in volume allowing the swelling. The swelling is then determined in terms of the amorphous material fraction, and an elaborated analysis of the created disorder is carried out. These results are compared in one part to the RBS analyses results of implanted materials available in literature, and in another part with an elastic model. For that, two different definitions of the amorphous fraction are used. (O.M.)

  8. Imaging and controlling intracellular reactions: Lysosome transport as a function of diameter and the intracellular synthesis of conducting polymers

    Science.gov (United States)

    Payne, Christine

    2014-03-01

    Eukaryotic cells are the ultimate complex environment with intracellular chemical reactions regulated by the local cellular environment. For example, reactants are sequestered into specific organelles to control local concentration and pH, motor proteins transport reactants within the cell, and intracellular vesicles undergo fusion to bring reactants together. Current research in the Payne Lab in the School of Chemistry and Biochemistry at Georgia Tech is aimed at understanding and utilizing this complex environment to control intracellular chemical reactions. This will be illustrated using two examples, intracellular transport as a function of organelle diameter and the intracellular synthesis of conducting polymers. Using single particle tracking fluorescence microscopy, we measured the intracellular transport of lysosomes, membrane-bound organelles, as a function of diameter as they underwent transport in living cells. Both ATP-dependent active transport and diffusion were examined. As expected, diffusion scales with the diameter of the lysosome. However, active transport is unaffected suggesting that motor proteins are insensitive to cytosolic drag. In a second example, we utilize intracellular complexity, specifically the distinct micro-environments of different organelles, to carry out chemical reactions. We show that catalase, found in the peroxisomes of cells, can be used to catalyze the polymerization of the conducting polymer PEDOT:PSS. More importantly, we have found that a range of iron-containing biomolecules are suitable catalysts with different iron-containing biomolecules leading to different polymer properties. These experiments illustrate the advantage of intracellular complexity for the synthesis of novel materials.

  9. Intracellular signaling by diffusion: can waves of hydrogen peroxide transmit intracellular information in plant cells?

    DEFF Research Database (Denmark)

    Vestergaard, Christian L.; Flyvbjerg, Henrik; Møller, Ian Max

    2012-01-01

    Amplitude- and frequency-modulated waves of Ca(2+) ions transmit information inside cells. Reactive Oxygen Species (ROS), specifically hydrogen peroxide, have been proposed to have a similar role in plant cells. We consider the feasibility of such an intracellular communication system in view of...... the physical and biochemical conditions in plant cells. As model system, we use a H(2)O(2) signal originating at the plasma membrane (PM) and spreading through the cytosol. We consider two maximally simple types of signals, isolated pulses and harmonic oscillations. First we consider the basic limits...

  10. Intracellular signaling by diffusion: can waves of hydrogen peroxide transmit intracellular information in plant cells?

    DEFF Research Database (Denmark)

    Vestergaard, Christian Lyngby; Flyvbjerg, Henrik; Møller, Ian Max

    2012-01-01

    Amplitude- and frequency-modulated waves of Ca2+ ions transmit information inside cells. Reactive Oxygen Species (ROS), specifically hydrogen peroxide, have been proposed to have a similar role in plant cells. We consider the feasibility of such an intracellular communication system in view of the...... physical and biochemical conditions in plant cells. As model system, we use a H2O2 signal originating at the plasma membrane (PM) and spreading through the cytosol. We consider two maximally simple types of signals, isolated pulses and harmonic oscillations. First we consider the basic limits on such...

  11. 31P nuclear magnetic resonance measurements of intracellular pH in giant barnacle muscle

    International Nuclear Information System (INIS)

    The accuracy of intracellular pH (pH/sub i/) measurements by 31P nuclear magnetic resonance (NMR) spectroscopy was examined in single muscle fibers from the giant barnacle, Balanus nubilis. The pH/sub i/ was derived from the chemical shifts of 2-deoxy-D-glucose-6-phosphate and inorganic phosphate. In fibers superfused with sea water at pH 7.7, pH/sub i/ = 7.30 +/- 0.02 at 200C. Experimentally induced pH/sub i/ changes were followed with a time resolution of 3 min. Intracellular alkalinization was induced by exposure to NH3Cl and intracellular acidification followed when NH3 was removed. Then acid extrusion was stimulated by exposure to bicarbonate containing sea water. In single muscle fibers 31P NMR results were in excellent agreement with microelectrode studies over the pH range of 6.5 to 8.0. The initial acid extrusion rate was 1.7 +/- 0.3 mmol x 1-1 x min-1 at pH/sub i/ 6.75. The authors results showed that 31P NMR is a reliable in vivo pH probe

  12. Vesicular demyelination induced by raised intracellular calcium.

    Science.gov (United States)

    Smith, K J; Hall, S M; Schauf, C L

    1985-11-01

    myelin vesiculation. We conclude that vesicular demyelination can be initiated in vital Schwann cells by a raised intracellular Ca2+ concentration. Such demyelination does not necessarily lead to Schwann cell death. The possible relevance of the findings to vesicular demyelinating neuropathies is discussed, and a hypothesis regarding the mechanism of demyelination is advanced. PMID:3003255

  13. The Structural Pathway for Water Permeation through Sodium-Glucose Cotransporters

    OpenAIRE

    Sasseville, Louis J.; Cuervo, Javier E.; Lapointe, Jean-Yves; Noskov, Sergei Y.

    2011-01-01

    Although water permeation across cell membranes occurs through several types of membrane proteins, the only permeation mechanism resolved at atomic scale is that through aquaporins. Crystallization of the Vibrio parahaemolyticus sodium-galactose transporter (vSGLT) allows investigation of putative water permeation pathways through both vSGLT and the homologous human Na-glucose cotransporter (hSGLT1) using computational methods. Grand canonical Monte Carlo and molecular dynamics simulations we...

  14. The interferon response to intracellular DNA: why so many receptors?

    Science.gov (United States)

    Unterholzner, Leonie

    2013-11-01

    The detection of intracellular DNA has emerged to be a key event in the innate immune response to viruses and intracellular bacteria, and during conditions of sterile inflammation and autoimmunity. One of the consequences of the detection of DNA as a 'stranger' and a 'danger' signal is the production of type I interferons and pro-inflammatory cytokines. Much work has been dedicated to the elucidation of the signalling cascades that activate this DNA-induced gene expression programme. However, while many proteins have been proposed to act as sensors for intracellular DNA in recent years, none has been met with universal acceptance, and a theory linking all the recent observations is, as yet, lacking. This review presents the evidence for the various interferon-inducing DNA receptors proposed to date, and examines the hypotheses that might explain why so many different receptors appear to be involved in the innate immune recognition of intracellular DNA. PMID:23962476

  15. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

    Science.gov (United States)

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungalrelated parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and...

  16. Genome degeneration affects both extracellular and intracellular bacterial endosymbionts

    OpenAIRE

    Feldhaar, Heike; Gross, Roy

    2009-01-01

    The obligate intracellular bacterial endosymbionts of insects are a paradigm for reductive genome evolution. A study published recently in BMC Biology demonstrates that similar evolutionary forces shaping genome structure may also apply to extracellular endosymbionts.

  17. Intracellular calcium ions as regulators of renal tubular sodium transport.

    Science.gov (United States)

    Windhager, E; Frindt, G; Yang, J M; Lee, C O

    1986-09-15

    This review addresses the putative role of intracellular calcium ions in the regulation of sodium transport by renal tubules. Cytoplasmic calcium-ion activities in proximal tubules of Necturus are less than 10(-7) M and can be increased by lowering the electrochemical potential gradient for sodium ions across the peritubular cell membrane, or by addition of quinidine or ionomycin to peritubular fluid. Whereas lowering of the peritubular Na concentration increases cytosolic [Ca++] and [H+], ionomycin, a calcium ionophore, raises intracellular [Ca++] without decreasing pHi. The intracellular calcium-ion level is maintained by transport processes in the plasma membrane and membranes of intracellular organelles, as well as by calcium-binding proteins. Calcium ions inhibit net transport of sodium by reducing the rate of sodium entry across the luminal cell membrane. In the collecting tubule this inhibition is caused, at least in part, by an indirect reduction in the activity of the amiloride-sensitive sodium channel. PMID:2430134

  18. Acquisition of an animal gene by microsporidian intracellular parasites

    OpenAIRE

    Selman, Mohammed; Pombert, Jean-François; Solter, Leellen; Farinelli, Laurent; Weiss, Louis M.; Keeling, Patrick; Corradi, Nicolas

    2011-01-01

    Parasites have adapted to their specialised way of life by a number of means, including the acquisition of genes by horizontal gene transfer. These newly acquired genes seem to come from a variety of sources, but seldom from the host, even in the most intimate associations between obligate intracellular parasite and host [1]. Microsporidian intracellular parasites have acquired a handful of genes, mostly from bacteria, that help them take energy from their hosts or protect them from the envir...

  19. Parkin promotes intracellular Aβ1–42 clearance

    OpenAIRE

    Burns, Mark P.; Zhang, Lihua; Rebeck, G. William; Querfurth, Henry W.; Moussa, Charbel E.-H.

    2009-01-01

    Alzheimer's disease and Parkinson's disease are common neurodegenerative diseases that may share some underlying mechanisms of pathogenesis. Aβ1–42 fragments are found intracellularly, and extracellularly as amyloid plaques, in Alzheimer's disease and in dementia with Lewy Bodies. Parkin is an E3-ubiquitin ligase involved in proteasomal degradation of intracellular proteins. Mutations in parkin, which result in loss of parkin function, lead to early onset Parkinsonism. Here we tested whether ...

  20. Intracellular life of Coxiella burnetii in acrophages : an update

    OpenAIRE

    E. Ghigo; Pretat, L.; Desnues, B.; Capo, C.; Raoult, Didier; Mege, J L

    2009-01-01

    Coxiella burnetii, the agent of Q fever, is an obligate intracellular bacterium that is considered a potential biological weapon of category B. C. burnetii survives within myeloid cells by subverting receptor-mediated phagocytosis and preventing phagosome maturation. The intracellular fate of C. burnetii also depends on the functional state of myeloid cells. This review describes the mechanisms used by C. burnetii to circumvent uptake and trafficking events, and the role of cytokines on C. bu...

  1. Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria.

    OpenAIRE

    Benzerara, Karim; Skouri-Panet, Feriel; Li, Jinhua; Férard, Céline; Gugger, Muriel; Laurent, Thierry; Couradeau, Estelle; Ragon, Marie; Cosmidis, Julie; Menguy, N.; Margaret-Oliver, Isabel; Tavera, Rosaluz; López-García, Purificación; Moreira, David

    2014-01-01

    Cyanobacteria have played a significant role in the formation of past and modern carbonate deposits at the surface of the Earth using a biomineralization process that has been almost systematically considered induced and extracellular. Recently, a deep-branching cyanobacterial species, Candidatus Gloeomargarita lithophora, was reported to form intracellular amorphous Ca-rich carbonates. However, the significance and diversity of the cyanobacteria in which intracellular biomineralization occur...

  2. Intra-cellular Staphylococcus aureus alone causes infection in vivo

    Directory of Open Access Journals (Sweden)

    T Hamza

    2013-07-01

    Full Text Available Chronic and recurrent bone infections occur frequently but have not been explained. Staphylococcus aureus (S. aureus is often found among chronic and recurrent infections and may be responsible for such infections. One possible reason is that S. aureus can internalize and survive within host cells and by doing so, S. aureus can evade both host defense mechanisms and most conventional antibiotic treatments. In this study, we hypothesized that intra-cellular S. aureus could induce infections in vivo. Osteoblasts were infected with S. aureus and, after eliminating extra-cellular S. aureus, inoculated into an open fracture rat model. Bacterial cultures and radiographic observations at post-operative day 21 confirmed local bone infections in animals inoculated with intra-cellular S. aureus within osteoblasts alone. We present direct in vivo evidence that intra-cellular S. aureus could be sufficient to induce bone infection in animals; we found that intra-cellular S. aureus inoculation of as low as 102 colony forming units could induce severe bone infections. Our data may suggest that intra-cellular S. aureus can “hide” in host cells during symptom-free periods and, under certain conditions, they may escape and lead to infection recurrence. Intra-cellular S. aureus therefore could play an important role in the pathogenesis of S. aureus infections, especially those chronic and recurrent infections in which disease episodes may be separated by weeks, months, or even years.

  3. Intracellular accumulation of potent amiloride analogues by human neutrophils

    International Nuclear Information System (INIS)

    The mechanism of uptake of a series of amiloride derivatives by human neutrophils was investigated using [14C]amiloride and the 14C-labeled 5-(1-hexahydroazepinyl)-6-bromo analogue (BrMM) which is approximately 500-fold more potent than the parent compound at inhibiting Na+/H+ exchange. At an external concentration of 2 microM, the influx of BrMM at 37 degrees C was rapid, reaching a steady state by approximately 20 min. The rate of BrMM uptake (approximately 25 mumol/liter.min) was approximately 90-fold faster than for the same concentration of amiloride, a finding which correlates with differences in lipid partitioning of the two compounds. Uptake was unrelated to specific binding to Na+/H+ exchange transport sites: influx of either drug was nonsaturable whereas amiloride- and BrMM-mediated inhibition of Na+/H+ countertransport obeyed Michaelis-Menten kinetics with apparent Ki values of approximately 75 and approximately 0.2 microM. Entry occurred exclusively via the neutral (uncharged) forms (pK'a 8.40-8.55). Influx was markedly pH-dependent: it was enhanced by extracellular alkalinization and reduced by acidification. Influx was, however, insensitive to large changes in membrane voltage, thereby implying the protonated (charged) species to be impermeant. About 75% of the total intracellular pool of amiloride, but only approximately 25% of BrMM, is contained within the lysosomes, an expected consequence of the partitioning and subsequent trapping of a weak base within this strongly acidic subcellular compartment. With BrMM, there was a relative approximately 60-fold enrichment in the internal/external water concentration ratio of the drug; the value for amiloride was much less, approximately 4. This disparity is consistent with substantial binding of BrMM to internal constituents, presumably to proteins and/or nucleic acids

  4. An Intracellular Nanotrap Redirects Proteins and Organelles in Live Bacteria

    Science.gov (United States)

    Borg, Sarah; Popp, Felix; Hofmann, Julia; Leonhardt, Heinrich; Rothbauer, Ulrich

    2015-01-01

    ABSTRACT  Owing to their small size and enhanced stability, nanobodies derived from camelids have previously been used for the construction of intracellular “nanotraps,” which enable redirection and manipulation of green fluorescent protein (GFP)-tagged targets within living plant and animal cells. By taking advantage of intracellular compartmentalization in the magnetic bacterium Magnetospirillum gryphiswaldense, we demonstrate that proteins and even entire organelles can be retargeted also within prokaryotic cells by versatile nanotrap technology. Expression of multivalent GFP-binding nanobodies on magnetosomes ectopically recruited the chemotaxis protein CheW1-GFP from polar chemoreceptor clusters to the midcell, resulting in a gradual knockdown of aerotaxis. Conversely, entire magnetosome chains could be redirected from the midcell and tethered to one of the cell poles. Similar approaches could potentially be used for building synthetic cellular structures and targeted protein knockdowns in other bacteria. Importance   Intrabodies are commonly used in eukaryotic systems for intracellular analysis and manipulation of proteins within distinct subcellular compartments. In particular, so-called nanobodies have great potential for synthetic biology approaches because they can be expressed easily in heterologous hosts and actively interact with intracellular targets, for instance, by the construction of intracellular “nanotraps” in living animal and plant cells. Although prokaryotic cells also exhibit a considerable degree of intracellular organization, there are few tools available equivalent to the well-established methods used in eukaryotes. Here, we demonstrate the ectopic retargeting and depletion of polar membrane proteins and entire organelles to distinct compartments in a magnetotactic bacterium, resulting in a gradual knockdown of magneto-aerotaxis. This intracellular nanotrap approach has the potential to be applied in other bacteria for

  5. Characterization of intracellular pteroylpolyglutamate hydrolase (PPH) from human intestinal mucosa

    Energy Technology Data Exchange (ETDEWEB)

    Wang, T.T.Y.; Chandler, C.J.; Halsted, C.H.

    1986-03-01

    There are two forms of pteroylpolyglutamate hydrolase (PPH) in the human intestinal mucosa, one in the brush border membrane and the other intracellular; brush border PPH is an exopeptidase with optimal activity at pH 6.5 and a requirement for zinc. The presence study characterized human intracellular PPH and compared its properties to those of brush border PPH. Intracellular PPH was purified 30-fold. The enzyme had a MW of 75,000 by gel filtration, was optimally active at pH 4.5, and had an isoelectric point at pH 8.0. In contrast to brush border PPH, intracellular PPH was unstable at increasing temperatures, was unaffected by dialysis against chelating agents and showed no requirement for Zn/sup 2 +/. Using PteGlu/sub 2/(/sup 14/C)Glu as substrate, they demonstrated a K/sub m/ of 1.2 ..mu..M and increasing affinity for folates with longer glutamate chains. Intracellular PPH required the complete folic acid (PteGlu) moiety and a ..gamma..-glutamyl linkage for activity. Using ion exchange chromatography and an HPLC method to determine the hydrolytic products of the reaction, they found intracellular PPH could cleave both internal and terminal ..gamma..-glutamyl linkages, with PteGlu as an end product. After subcellular fractionation of the mucosa, PPH was found in the lysosomes. In summary, the distinct characteristics of brush border and intracellular PPH suggest that the two hydrolases serve different roles in folate metabolism.

  6. Factors influencing intracellular uptake and radiosensitization by 2-nitroimidazoles in vitro

    International Nuclear Information System (INIS)

    In this study it is shown that the radiosensitization of hypoxic Chinese hamster ovary (HA-1) cells in vitro by misonidazole (MIS) and other 1-substituted 2-nitroimidazoles depends on the rate and extent of intracellular uptake of these radiosensitizers, which in turn is governed by their lipophilicity [expressed as the octanol:water partition coefficient (P)]. As the lipophilicity of the compounds decreased, the rate of drug entry into the cells was slower, and below P values of approximately 0.05, peak intracellular drug concentrations were found to be lower than that of MIS (P=0.43). In addition, the number of hydroxyl groups on the side chain of the nitroimidazole molecule influenced the uptake of drug into the cells. For compounds of similar P, but differing in the number of side-chain hydroxyl groups, the addition of a single hydroxyl group to the molecule decreased the amount of drug entering the cell by a factor of approximately 2. These compounds enter the cell by nonmediated passive diffusion since altering the energy (ATP) capacity of the cell by 2-deoxyglucose did not affect uptake. It is also shown that increases in temperature or decreases in pH can increase the intracellular uptake of MIS. For example, equal intracellular and extracellular concentrations (100% uptake) of MIS were obtained if cells were heated to 44-450C for 15 min compared to 20-40% uptake at 370C. Increases in MIS uptake by factors of 2 to 3 could be demonstrated within 30 min when cells were incubated in Hanks' balanced salt solution at pH between 6.0 and 6.3 without loss of cell viability. In addition, MIS uptake in aerobic cultured cells varied from 15 to 60% depending on the cell line and culure conditions used

  7. Proton-dependent zinc release from intracellular ligands.

    Science.gov (United States)

    Kiedrowski, Lech

    2014-07-01

    In cultured cortical and hippocampal neurons when intracellular pH drops from 6.6 to 6.1, yet unclear intracellular stores release micromolar amounts of Zn(2+) into the cytosol. Mitochondria, acidic organelles, and/or intracellular ligands could release this Zn(2+) . Although exposure to the protonophore FCCP precludes reloading of the mitochondria and acidic organelles with Zn(2+) , FCCP failed to compromise the ability of the intracellular stores to repeatedly release Zn(2+) . Therefore, Zn(2+) -releasing stores were not mitochondria or acidic organelles but rather intracellular Zn(2+) ligands. To test which ligands might be involved, the rate of acid-induced Zn(2+) release from complexes with cysteine, glutathione, histidine, aspartate, glutamate, glycine, and carnosine was investigated; [Zn(2+) ] was monitored in vitro using the ratiometric Zn(2+) -sensitive fluorescent probe FuraZin-1. Carnosine failed to chelate Zn(2+) but did chelate Cu(2+) ; the remaining ligands chelated Zn(2+) and upon acidification were releasing it into the medium. However, when pH was decreasing from 6.6 to 6.1, only zinc-cysteine complexes rapidly accelerated the rate of Zn(2+) release. The zinc-cysteine complexes also released Zn(2+) when a histidine-modifying agent, diethylpyrocarbonate, was applied at pH 7.2. Since the cytosolic zinc-cysteine complexes can contain micromolar amounts of Zn(2+) , these complexes may represent the stores responsible for an acid-induced intracellular Zn(2+) release. This study aimed at identifying intracellular stores which release Zn(2+) when pHi drops from 6.6 to 6.1. It was found that these stores are not mitochondria or acidic organelles, but rather intracellular Zn(2+) ligands. When the pH was decreasing from 6.6 to 6.1, only zinc-cysteine complexes showed a rapid acceleration in the rate of Zn(2+) release. Therefore, the stores responsible for an acid-induced intracellular Zn(2+) release in neurons may be the cytosolic zinc-cysteine complexes

  8. Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates

    Directory of Open Access Journals (Sweden)

    Singhal Neelja

    2012-03-01

    Full Text Available Abstract Background Tuberculosis (TB is the most threatening infectious disease globally. Although progress has been made to reduce global incidence of TB, emergence of multidrug resistant (MDR TB threatens to undermine these advances. To combat the disease, novel intervention strategies effective against drug resistant and sensitive subpopulations of M. tuberculosis are urgently required as adducts in the present treatment regimen. Using THP-1 cells we have analyzed and compared the global protein expression profile of broth-cultured and intraphagosomally grown drug resistant and sensitive M.tuberculosis clinical isolates. Results On comparing the two dimensional (2-DE gels, many proteins were found to be upregulated/expressed during intracellular state which were identified by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS. Four proteins (adenosylhomocysteinase, aspartate carbomyltransferase, putatitive thiosulfate sulfurtransferase and universal stress protein were present in both intracellular MDR and sensitive isolates and three of these belonged to intermediary metabolism and respiration category. Two proteins (alanine dehydrogenase and adenosine kinase of intracellular MDR isolate and two (glucose-6-phosphate isomerase and ATP synthase epsilon chain of intracellular sensitive isolate belonged to intermediary metabolism and respiration category. One protein (Peroxidase/Catalase of intracellular MDR and three (HSPX, 14 kDa antigen and 10 kDa chaperonin of sensitive isolate belonged to virulence, detoxification and adaptation category. ESAT-6 of intracellular MDR belonged to cell wall and cell processes category. Two proteins (Antigen 85-C and Antigen 85-A of intracellular sensitive isolate were involved in lipid metabolism while probable peptidyl-prolyl cis-trans isomerase A was involved in information pathways. Four (Rv0635, Rv1827, Rv0036c and Rv2032 of intracellular MDR and two proteins (Rv2896c and Rv2558c of

  9. Advances in genetic manipulation of obligate intracellular bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Paul eBeare

    2011-05-01

    Full Text Available Infections by obligate intracellular bacterial pathogens result in significant morbidity and mortality worldwide. These bacteria include Chlamydia spp., which causes millions of cases of sexually transmitted disease and blinding trachoma annually, and members of the α-proteobacterial genera Anaplasma, Ehrlichia, Orientia and Rickettsia, agents of serious human illnesses including epidemic typhus. Coxiella burnetii, the agent of human Q fever, has also been considered a prototypical obligate intracellular bacterium, but recent host cell-free (axenic growth has rescued it from obligatism. The historic genetic intractability of obligate intracellular bacteria has severely limited molecular dissection of their unique lifestyles and virulence factors involved in pathogenesis. Host cell restricted growth is a significant barrier to genetic transformation that can make simple procedures for free-living bacteria, such as cloning, exceedingly difficult. Low transformation efficiency requiring long term culture in host cells to expand small transformant populations is another obstacle. Despite numerous technical limitations, the last decade has witnessed significant gains in genetic manipulation of obligate intracellular bacteria including allelic exchange. Continued development of genetic tools should soon enable routine mutation and complementation strategies for virulence factor discovery and stimulate renewed interest in these refractory pathogens. In this review, we discuss the technical challenges associated with genetic transformation of obligate intracellular bacteria and highlight advances made with individual genera.

  10. High-Throughput Intracellular Antimicrobial Susceptibility Testing of Legionella pneumophila.

    Science.gov (United States)

    Chiaraviglio, Lucius; Kirby, James E

    2015-12-01

    Legionella pneumophila is a Gram-negative opportunistic human pathogen that causes a severe pneumonia known as Legionnaires' disease. Notably, in the human host, the organism is believed to replicate solely within an intracellular compartment, predominantly within pulmonary macrophages. Consequently, successful therapy is predicated on antimicrobials penetrating into this intracellular growth niche. However, standard antimicrobial susceptibility testing methods test solely for extracellular growth inhibition. Here, we make use of a high-throughput assay to characterize intracellular growth inhibition activity of known antimicrobials. For select antimicrobials, high-resolution dose-response analysis was then performed to characterize and compare activity levels in both macrophage infection and axenic growth assays. Results support the superiority of several classes of nonpolar antimicrobials in abrogating intracellular growth. Importantly, our assay results show excellent correlations with prior clinical observations of antimicrobial efficacy. Furthermore, we also show the applicability of high-throughput automation to two- and three-dimensional synergy testing. High-resolution isocontour isobolograms provide in vitro support for specific combination antimicrobial therapy. Taken together, findings suggest that high-throughput screening technology may be successfully applied to identify and characterize antimicrobials that target bacterial pathogens that make use of an intracellular growth niche. PMID:26392509

  11. High-Throughput Intracellular Antimicrobial Susceptibility Testing of Legionella pneumophila

    Science.gov (United States)

    Chiaraviglio, Lucius

    2015-01-01

    Legionella pneumophila is a Gram-negative opportunistic human pathogen that causes a severe pneumonia known as Legionnaires' disease. Notably, in the human host, the organism is believed to replicate solely within an intracellular compartment, predominantly within pulmonary macrophages. Consequently, successful therapy is predicated on antimicrobials penetrating into this intracellular growth niche. However, standard antimicrobial susceptibility testing methods test solely for extracellular growth inhibition. Here, we make use of a high-throughput assay to characterize intracellular growth inhibition activity of known antimicrobials. For select antimicrobials, high-resolution dose-response analysis was then performed to characterize and compare activity levels in both macrophage infection and axenic growth assays. Results support the superiority of several classes of nonpolar antimicrobials in abrogating intracellular growth. Importantly, our assay results show excellent correlations with prior clinical observations of antimicrobial efficacy. Furthermore, we also show the applicability of high-throughput automation to two- and three-dimensional synergy testing. High-resolution isocontour isobolograms provide in vitro support for specific combination antimicrobial therapy. Taken together, findings suggest that high-throughput screening technology may be successfully applied to identify and characterize antimicrobials that target bacterial pathogens that make use of an intracellular growth niche. PMID:26392509

  12. Intracellular biology and virulence determinants of Francisella tularensis revealed by transcriptional profiling inside macrophages

    OpenAIRE

    Wehrly, Tara D.; Chong, Audrey; Virtaneva, Kimmo; Sturdevant, Dan E.; Child, Robert; Edwards, Jessica A.; Brouwer, Dedeke; Nair, Vinod; Fischer, Elizabeth R.; Wicke, Luke; Curda, Alissa J.; Kupko, John J.; Martens, Craig; Crane, Deborah D.; Bosio, Catharine M.

    2009-01-01

    The highly infectious bacterium Francisella tularensis is a facultative intracellular pathogen, whose virulence requires proliferation inside host cells, including macrophages. Here we have performed a global transcriptional profiling of the highly virulent F. tularensis subsp. tularensis Schu S4 strain during its intracellular cycle within primary murine macrophages, to characterize its intracellular biology and identify pathogenic determinants based on their intracellular expression profile...

  13. Quantifying intracellular hydrogen peroxide perturbations in terms of concentration

    Directory of Open Access Journals (Sweden)

    Beijing K. Huang

    2014-01-01

    Full Text Available Molecular level, mechanistic understanding of the roles of reactive oxygen species (ROS in a variety of pathological conditions is hindered by the difficulties associated with determining the concentration of various ROS species. Here, we present an approach that converts fold-change in the signal from an intracellular sensor of hydrogen peroxide into changes in absolute concentration. The method uses extracellular additions of peroxide and an improved biochemical measurement of the gradient between extracellular and intracellular peroxide concentrations to calibrate the intracellular sensor. By measuring peroxiredoxin activity, we found that this gradient is 650-fold rather than the 7–10-fold that is widely cited. The resulting calibration is important for understanding the mass-action kinetics of complex networks of redox reactions, and it enables meaningful characterization and comparison of outputs from endogenous peroxide generating tools and therapeutics across studies.

  14. EFFECT OF TETRACYCLINES ON THE INTRACELLULAR AMINO ACIDS OF MOLDS.

    Science.gov (United States)

    FREEMAN, B A; CIRCO, R

    1963-07-01

    Freeman, Bob A. (University of Chicago, Chicago, Ill.) and Richard Circo. Effect of tetracyclines on the intracellular amino acids of molds. J. Bacteriol. 86:38-44. 1963.-The tetracycline antibiotics were shown to alter the amino acid metabolism of molds whose growth is not markedly affected. Eight molds were grown in the presence of these antiobiotics; four exhibited a general reduction in the concentration of the intracellular amino acids, except for glutamic acid and alanine. In most of these four cultures, the tetracyclines also caused the complete disappearance of arginine, lysine, proline, phenylalanine, and tyrosine from the intracellular amino acid pool. The significance of these observations and the usefulness of the method in the study of the mechanisms of antibiotic action are discussed. PMID:14051820

  15. Direct determination of the intracellular oxidation state of plutonium.

    Science.gov (United States)

    Gorman-Lewis, Drew; Aryal, Baikuntha P; Paunesku, Tatjana; Vogt, Stefan; Lai, Barry; Woloschak, Gayle E; Jensen, Mark P

    2011-08-15

    Microprobe X-ray absorption near edge structure (μ-XANES) measurements were used to determine directly, for the first time, the oxidation state of intracellular plutonium in individual 0.1-μm(2) areas within single rat pheochromocytoma cells (PC12). The living cells were incubated in vitro for 3 h in the presence of Pu added to the media in different oxidation states (Pu(III), Pu(IV), and Pu(VI)) and in different chemical forms. Regardless of the initial oxidation state or chemical form of Pu presented to the cells, the XANES spectra of the intracellular Pu deposits were always consistent with tetravalent Pu even though the intracellular milieu is generally reducing. PMID:21755934

  16. Mobilization of intracellular calcium by intracellular flash photolysis of caged dihydrosphingosine in cultured neonatal rat sensory neurones.

    Science.gov (United States)

    Ayar, A; Thatcher, N M; Zehavi, U; Trentham, D R; Scott, R H

    1998-01-01

    The ability of dihydrosphingosine to release Ca2+ from intracellular stores in neurones was investigated by combining the whole cell patch clamp technique with intracellular flash photolysis of caged, N-(2-nitrobenzyl)dihydrosphingosine. The caged dihydrosphingosine (100 microM) was applied to the intracellular environment via the CsCl-based patch pipette solution which also contained 0.3% dimethylformamide and 2 mM dithiothreitol. Cultured dorsal root ganglion neurones from neonatal rats were voltage clamped at -90 mV and inward whole cell Ca2+-activated currents were recorded in response to intracellular photorelease of dihydrosphingosine. Intracellular photorelease of dihydrosphingosine (about 5 microM) was achieved using a Xenon flash lamp. Inward Ca2+-activated currents were evoked in 50 out of 57 neurones, the mean delay to current activation following photolysis was 82+/-13 s. The responses were variable with neurones showing transient, oscillating or sustained inward currents. High voltage-activated Ca2+ currents evoked by 100 ms voltage step commands to 0 mV were not attenuated by photorelease of dihydrosphingosine. Controls showed that alone a flash from the Xenon lamp did not activate currents, and that the unphotolysed caged dihydrosphingosine, and intracellular photolysis of 2-(2-nitrobenzylamino) propanediol also did not evoke responses. The dihydrosphingosine current had a reversal potential of -11+/-3 mV (n = 11), and was carried by two distinct Cl- and cation currents which were reduced by 85% and about 20% following replacement of monovalent cations with N-methyl-D-glucamine or application of the Cl- channel blocker niflumic acid (10 microM) respectively. The responses to photoreleased dihydrosphingosine were inhibited by intracellular application of 20 mM EGTA, 10 microM ryanodine or extracellular application of 10 microM dantrolene, but persisted when Ca2+ free saline was applied to the extracellular environment. Intracellular application of

  17. Role of intracellular calcium in contraction of internal anal sphincter

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    @@ INTRODUCTION Internal anal sphincter (IAS) is a continuation of the smooth circular muscle layer thickened at the rectum, innervated by vegetative nerve. IAS is a special smooth muscle, which is different from colonic smooth muscle in physiology and pharmaology[1]. It was found that contraction of gastric smooth muscle depends on the influx of extracellular calcium and release of intracellular calcium[2]. In present study, we observed and compared the effects of extra- and intracellular calcium on the contraction of IAS and colonic smooth muscle.

  18. Intracellular accumulation of azithromycin by cultured human fibroblasts.

    OpenAIRE

    Gladue, R P; Snider, M E

    1990-01-01

    Azithromycin was shown to achieve high concentrations in human skin fibroblasts. Intracellular penetration occurred rapidly (10 micrograms/mg of cellular protein after 3 h) and then increased progressively over a 3-day period; azithromycin accumulated up to 21 times more than erythromycin (61.1 versus 2.9 micrograms/mg of protein). Uptake was dependent on the extracellular concentration, was inhibited at 4 degrees C, did not occur in nonviable cells, and was reduced by a low pH. Intracellular...

  19. Intracellular pH of acid-tolerant ruminal bacteria.

    OpenAIRE

    Russell, J B

    1991-01-01

    Acid-tolerant ruminal bacteria (Bacteroides ruminicola B1(4), Selenomonas ruminantium HD4, Streptococcus bovis JB1, Megasphaera elsdenii B159, and strain F) allowed their intracellular pH to decline as a function of extracellular pH and did not generate a large pH gradient across the cell membrane until the extracellular pH was low (less than 5.2). This decline in intracellular pH prevented an accumulation of volatile fatty acid anions inside the cells.

  20. Intracellular proliferation of S. aureus in osteoblasts and effects of rifampicin and gentamicin on S. aureus intracellular proliferation and survival

    Directory of Open Access Journals (Sweden)

    W Mohamed

    2014-10-01

    Full Text Available Staphylococcus aureus is the most clinically relevant pathogen regarding implant-associated bone infection and its capability to invade osteoblasts is well known. The aim of this study was to investigate firstly whether S. aureus is not only able to invade but also to proliferate within osteoblasts, secondly to delineate the mechanism of invasion and thirdly to clarify whether rifampicin or gentamicin can inhibit intracellular proliferation and survival of S. aureus. The SAOS-2 osteoblast-like cell line and human primary osteoblasts were infected with S. aureus EDCC5055 and S. aureus Rosenbach 1884. Both S. aureus strains were able to invade efficiently and to proliferate within human osteoblasts. Immunofluorescence microscopy showed intracellular invasion of S. aureus and transmission electron microscopy images could demonstrate bacterial division as a sign of intracellular proliferation as well as cytosolic bacterial persistence. Cytochalasin D, the major actin depolymerisation agent, was able to significantly reduce S. aureus invasion, suggesting that invasion was enabled by promoting actin rearrangement at the cell surface. 7.5 μg/mL of rifampicin was able to inhibit bacterial survival in SAOS-2 cells with almost complete elimination of bacteria after 4 h. Gentamicin could also kill intracellular S. aureus in a dose-dependent manner, an effect that was significantly lower than that observed using rifampicin. In conclusion, S. aureus is not only able to invade but also to proliferate in osteoblasts. Invasion seems to be associated with actin rearrangement at the cell surface. Rifampicin is effective in intracellular eradication of S. aureus whereas gentamicin only poorly eliminates intracellularly replicating bacteria.

  1. Correlation of Cell Strain in Single Osteocytes with Intracellular Calcium, but not Intracellular Nitric Oxide, in Response to Fluid Flow

    OpenAIRE

    Rath, Amber L.; Bonewald, Lynda F.; Ling, Jian; Jiang, Jean X.; VAN DYKE, MARK E.; Nicolella, Daniel P

    2010-01-01

    Osteocytes compose 90–95% of all bone cells and are the mechanosensors of bone. In this study, the strain experienced by individual osteocytes resulting from an applied fluid flow shear stress was quantified and correlated to two biological responses measured in real-time within the same individual osteocytes: 1) the upregulation of intracellular calcium and 2) changes in intracellular nitric oxide. Osteocyte-like MLO-Y4 cells were loaded with Fluo-4 AM and DAR-4M and exposed to uniform lamin...

  2. In vitro testing of agents to remove intracellular transuranic elements

    International Nuclear Information System (INIS)

    An in vitro test system to study biological mechanisms of particulate radionuclide uptake, intracellular solubilization and mobilization of these particulates is being developed. In vitro cultures of essentially pure rabbit-lung macrophases have been maintained for 2 weeks without cell turnover or alteration. Suspensions of freshly harvested cells have been shown to phagocytize 239PuO2 particles

  3. Nanodiamonds as Intracellular Probes for Imaging in Biology and Medicine

    Czech Academy of Sciences Publication Activity Database

    Šlegerová, Jitka; Řehoř, Ivan; Havlík, Jan; Raabová, Helena; Muchová, Eva; Cígler, Petr

    Dordrecht : Springer, 2014 - (Prokop, A.; Iwasaki, Y.; Harada, A.), s. 363-401 ISBN 978-94-017-8895-3. - (Fundamental Biomedical Technologies. 7) Institutional support: RVO:61388963 Keywords : nanodiamond * fluorescence * nitrogen-vacancy center * intracellular probe * bioimaging * biocompatibility Subject RIV: EI - Biotechnology ; Bionics

  4. FLIPR assays of intracellular calcium in GPCR drug discovery

    DEFF Research Database (Denmark)

    Hansen, Kasper Bø; Bräuner-Osborne, Hans

    Fluorescent dyes sensitive to changes in intracellular calcium have become increasingly popular in G protein-coupled receptor (GPCR) drug discovery for several reasons. First of all, the assays using the dyes are easy to perform and are of low cost compared to other assays. Second, most non-Galph...

  5. Galectin-3 guides intracellular trafficking of some human serotransferrin glycoforms

    DEFF Research Database (Denmark)

    Carlsson, Carl Michael; Bengtson, Per; Cucak, Helena;

    2013-01-01

    these transferrin glycoforms differently after preloading with exogenously added galectin-3. In all, this study provides the first evidence of a functional role for transferrin glycans, in intracellular trafficking after uptake. Moreover, the galectin-3 bound glycoform increased in cancer, suggesting a...

  6. The proteome targets of intracellular targeting antimicrobial peptides.

    Science.gov (United States)

    Shah, Pramod; Hsiao, Felix Shih-Hsiang; Ho, Yu-Hsuan; Chen, Chien-Sheng

    2016-04-01

    Antimicrobial peptides have been considered well-deserving candidates to fight the battle against microorganisms due to their broad-spectrum antimicrobial activities. Several studies have suggested that membrane disruption is the basic mechanism of AMPs that leads to killing or inhibiting microorganisms. Also, AMPs have been reported to interact with macromolecules inside the microbial cells such as nucleic acids (DNA/RNA), protein synthesis, essential enzymes, membrane septum formation and cell wall synthesis. Proteins are associated with many intracellular mechanisms of cells, thus protein targets may be specifically involved in mechanisms of action of AMPs. AMPs like pyrrhocoricin, drosocin, apidecin and Bac 7 are documented to have protein targets, DnaK and GroEL. Moreover, the intracellular targeting AMPs are reported to influence more than one protein targets inside the cell, suggesting for the multiple modes of actions. This complex mechanism of intracellular targeting AMPs makes them more difficult for the development of resistance. Herein, we have summarized the current status of AMPs in terms of their mode of actions, entry to cytoplasm and inhibition of macromolecules. To reveal the mechanism of action, we have focused on AMPs with intracellular protein targets. We have also included the use of high-throughput proteome microarray to determine the unidentified AMP protein targets in this review. PMID:26648572

  7. Deciphering the Intracellular Fate of Propionibacterium acnes in Macrophages

    Directory of Open Access Journals (Sweden)

    Natalie Fischer

    2013-01-01

    Full Text Available Propionibacterium acnes is a Gram-positive bacterium that colonizes various niches of the human body, particularly the sebaceous follicles of the skin. Over the last years a role of this common skin bacterium as an opportunistic pathogen has been explored. Persistence of P. acnes in host tissue has been associated with chronic inflammation and disease development, for example, in prostate pathologies. This study investigated the intracellular fate of P. acnes in macrophages after phagocytosis. In a mouse model of P. acnes-induced chronic prostatic inflammation, the bacterium could be detected in prostate-infiltrating macrophages at 2 weeks postinfection. Further studies performed in the human macrophage cell line THP-1 revealed intracellular survival and persistence of P. acnes but no intracellular replication or escape from the host cell. Confocal analyses of phagosome acidification and maturation were performed. Acidification of P. acnes-containing phagosomes was observed at 6 h postinfection but then lost again, indicative of cytosolic escape of P. acnes or intraphagosomal pH neutralization. No colocalization with the lysosomal markers LAMP1 and cathepsin D was observed, implying that the P. acnes-containing phagosome does not fuse with lysosomes. Our findings give first insights into the intracellular fate of P. acnes; its persistency is likely to be important for the development of P. acnes-associated inflammatory diseases.

  8. Molecular phylogeny of intracellular symbiotic Gammaproteobacteria in insects

    OpenAIRE

    HUSNÍK, Filip

    2010-01-01

    Many groups of insects harbor mutualistic intracellular bacteria. These bacteria originated mainly from two bacterial phyla: Bacteroidetes and Proteobacteria. The thesis is focused on phylogeny of Enterobacteriaceae - the most diverse group of endosymbiotic bacteria within Gammaproteobacteria. The study brings new phylogenetical data on "primary" symbionts and summarizes the current state of knowledge on their phylogeny, evolution and diversity.

  9. Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Emily R Troemel

    2008-12-01

    Full Text Available For decades the soil nematode Caenorhabditis elegans has been an important model system for biology, but little is known about its natural ecology. Recently, C. elegans has become the focus of studies of innate immunity and several pathogens have been shown to cause lethal intestinal infections in C. elegans. However none of these pathogens has been shown to invade nematode intestinal cells, and no pathogen has been isolated from wild-caught C. elegans. Here we describe an intracellular pathogen isolated from wild-caught C. elegans that we show is a new species of microsporidia. Microsporidia comprise a large class of eukaryotic intracellular parasites that are medically and agriculturally important, but poorly understood. We show that microsporidian infection of the C. elegans intestine proceeds through distinct stages and is transmitted horizontally. Disruption of a conserved cytoskeletal structure in the intestine called the terminal web correlates with the release of microsporidian spores from infected cells, and appears to be part of a novel mechanism by which intracellular pathogens exit from infected cells. Unlike in bacterial intestinal infections, the p38 MAPK and insulin/insulin-like growth factor (IGF signaling pathways do not appear to play substantial roles in resistance to microsporidian infection in C. elegans. We found microsporidia in multiple wild-caught isolates of Caenorhabditis nematodes from diverse geographic locations. These results indicate that microsporidia are common parasites of C. elegans in the wild. In addition, the interaction between C. elegans and its natural microsporidian parasites provides a system in which to dissect intracellular intestinal infection in vivo and insight into the diversity of pathogenic mechanisms used by intracellular microbes.

  10. Intracellular recording of action potentials by nanopillar electroporation

    Science.gov (United States)

    Xie, Chong; Lin, Ziliang; Hanson, Lindsey; Cui, Yi; Cui, Bianxiao

    2012-03-01

    Action potentials have a central role in the nervous system and in many cellular processes, notably those involving ion channels. The accurate measurement of action potentials requires efficient coupling between the cell membrane and the measuring electrodes. Intracellular recording methods such as patch clamping involve measuring the voltage or current across the cell membrane by accessing the cell interior with an electrode, allowing both the amplitude and shape of the action potentials to be recorded faithfully with high signal-to-noise ratios. However, the invasive nature of intracellular methods usually limits the recording time to a few hours, and their complexity makes it difficult to simultaneously record more than a few cells. Extracellular recording methods, such as multielectrode arrays and multitransistor arrays, are non-invasive and allow long-term and multiplexed measurements. However, extracellular recording sacrifices the one-to-one correspondence between the cells and electrodes, and also suffers from significantly reduced signal strength and quality. Extracellular techniques are not, therefore, able to record action potentials with the accuracy needed to explore the properties of ion channels. As a result, the pharmacological screening of ion-channel drugs is usually performed by low-throughput intracellular recording methods. The use of nanowire transistors, nanotube-coupled transistors and micro gold-spine and related electrodes can significantly improve the signal strength of recorded action potentials. Here, we show that vertical nanopillar electrodes can record both the extracellular and intracellular action potentials of cultured cardiomyocytes over a long period of time with excellent signal strength and quality. Moreover, it is possible to repeatedly switch between extracellular and intracellular recording by nanoscale electroporation and resealing processes. Furthermore, vertical nanopillar electrodes can detect subtle changes in action

  11. Comparative studies of intracellular transport of secretory proteins.

    Science.gov (United States)

    Tartakoff, A; Vassalli, P; Détraz, M

    1978-12-01

    The physiology of protein intracellular transport and secretion by cell types thought to be free from short-term control has been compared with that of the pancreatic acinar cell, using pulse-chase protocols to follow biosynthetically-labeled secretory products. Data previously obtained (Tartakoff, A.M., and P. Vassalli. J. Exp. Med. 146:1332-1345) has shown that plasma-cell immunoglobulin (Ig) secretion is inhibited by respiratory inhibitors, by partial Na/K equilibration effected by the carboxylic ionophore monensin, and by calcium withdrawal effected by the carboxylic ionophore A 23187 in the presence of ethylene glycol bis (beta-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) and absence of calcium. We report here that both inhibition of respiration and treatment with monensin slow secretion by fibroblasts, and also macrophages and slow intracellular transport (though not discharge per se) by the exocrine pancreatic cells. Attempted calcium withdrawal is inhibitory for fibroblasts but not for macrophages. The elimination of extracellular calcium or addition of 50 mM KCl has no major effect on secretory rate of either fibroblasts or macrophages. Electron microscopic examination of all cell types shows that monensin causes a rapid and impressive dilation of Golgi elements. Combined cell fractionation and autoradiographic studies of the pancreas show that the effect of monensin is exerted at the point of the exit of secretory protein from the Golgi apparatus. Other steps in intracellular transport proceed at normal rates. These observations suggest a common effect of the cytoplasmic Na/K balance at the Golgi level and lead to a model of intracellular transport in which secretory product obligatorily passes through Golgi elements (cisternae?) that are sensitive to monensin. Thus, intracellular transport follows a similar course in both regulated and nonregulated secretory cells up to the level of distal Golgi elements. PMID:103883

  12. Supramolecular nanoreactors for intracellular singlet-oxygen sensitization

    Science.gov (United States)

    Swaminathan, Subramani; Fowley, Colin; Thapaliya, Ek Raj; McCaughan, Bridgeen; Tang, Sicheng; Fraix, Aurore; Burjor, Captain; Sortino, Salvatore; Callan, John F.; Raymo, Françisco M.

    2015-08-01

    An amphiphilic polymer with multiple decyl and oligo(ethylene glycol) chains attached to a common poly(methacrylate) backbone assembles into nanoscaled particles in aqueous environments. Hydrophobic anthracene and borondipyrromethene (BODIPY) chromophores can be co-encapsulated within the self-assembling nanoparticles and transported across hydrophilic media. The reversible character of the noncovalent bonds, holding the supramolecular containers together, permits the exchange of their components with fast kinetics in aqueous solution. Incubation of cervical cancer (HeLA) cells with a mixture of two sets of nanoparticles, pre-loaded independently with anthracene or BODIPY chromophores, results in guest scrambling first and then transport of co-entrapped species to the intracellular space. Alternatively, incubation of cells with the two sets of nanocarriers in consecutive steps permits the sequential transport of the anthracene and BODIPY chromophores across the plasma membrane and only then allows their co-encapsulation within the same supramolecular containers. Both mechanisms position the two sets of chromophores with complementary spectral overlap in close proximity to enable the efficient transfer of energy intracellularly from the anthracene donors to the BODIPY acceptors. In the presence of iodine substituents on the BODIPY platform, intersystem crossing follows energy transfer. The resulting triplet state can transfer energy further to molecular oxygen with the concomitant production of singlet oxygen to induce cell mortality. Furthermore, the donor can be excited with two near-infrared photons simultaneously to permit the photoinduced generation of singlet oxygen intracellularly under illumination conditions compatible with applications in vivo. Thus, these supramolecular strategies to control the excitation dynamics of multichromophoric assemblies in the intracellular environment can evolve into valuable protocols for photodynamic therapy.An amphiphilic

  13. How cholesterol interacts with proteins and lipids during its intracellular transport.

    Science.gov (United States)

    Wüstner, Daniel; Solanko, Katarzyna

    2015-09-01

    Sterols, as cholesterol in mammalian cells and ergosterol in fungi, are indispensable molecules for proper functioning and nanoscale organization of the plasma membrane. Synthesis, uptake and efflux of cholesterol are regulated by a variety of protein-lipid and protein-protein interactions. Similarly, membrane lipids and their physico-chemical properties directly affect cholesterol partitioning and thereby contribute to the highly heterogeneous intracellular cholesterol distribution. Movement of cholesterol in cells is mediated by vesicle trafficking along the endocytic and secretory pathways as well as by non-vesicular sterol exchange between organelles. In this article, we will review recent progress in elucidating sterol-lipid and sterol-protein interactions contributing to proper sterol transport in living cells. We outline recent biophysical models of cholesterol distribution and dynamics in membranes and explain how such models are related to sterol flux between organelles. An overview of various sterol-transfer proteins is given, and the physico-chemical principles of their function in non-vesicular sterol transport are explained. We also discuss selected experimental approaches for characterization of sterol-protein interactions and for monitoring intracellular sterol transport. Finally, we review recent work on the molecular mechanisms underlying lipoprotein-mediated cholesterol import into mammalian cells and describe the process of cellular cholesterol efflux. Overall, we emphasize how specific protein-lipid and protein-protein interactions help overcoming the extremely low water solubility of cholesterol, thereby controlling intracellular cholesterol movement. This article is part of a Special Issue entitled: Lipid-protein interactions. PMID:26004840

  14. Analysing intracellular deformation of polymer capsules using structured illumination microscopy

    Science.gov (United States)

    Chen, Xi; Cui, Jiwei; Sun, Huanli; Müllner, Markus; Yan, Yan; Noi, Ka Fung; Ping, Yuan; Caruso, Frank

    2016-06-01

    Understanding the behaviour of therapeutic carriers is important in elucidating their mechanism of action and how they are processed inside cells. Herein we examine the intracellular deformation of layer-by-layer assembled polymer capsules using super-resolution structured illumination microscopy (SIM). Spherical- and cylindrical-shaped capsules were studied in three different cell lines, namely HeLa (human epithelial cell line), RAW264.7 (mouse macrophage cell line) and differentiated THP-1 (human monocyte-derived macrophage cell line). We observed that the deformation of capsules was dependent on cell line, but independent of capsule shape. This suggests that the mechanical forces, which induce capsule deformation during cell uptake, vary between cell lines, indicating that the capsules are exposed to higher mechanical forces in HeLa cells, followed by RAW264.7 and then differentiated THP-1 cells. Our study demonstrates the use of super-resolution SIM in analysing intracellular capsule deformation, offering important insights into the cellular processing of drug carriers in cells and providing fundamental knowledge of intracellular mechanobiology. Furthermore, this study may aid in the design of novel drug carriers that are sensitive to deformation for enhanced drug release properties.Understanding the behaviour of therapeutic carriers is important in elucidating their mechanism of action and how they are processed inside cells. Herein we examine the intracellular deformation of layer-by-layer assembled polymer capsules using super-resolution structured illumination microscopy (SIM). Spherical- and cylindrical-shaped capsules were studied in three different cell lines, namely HeLa (human epithelial cell line), RAW264.7 (mouse macrophage cell line) and differentiated THP-1 (human monocyte-derived macrophage cell line). We observed that the deformation of capsules was dependent on cell line, but independent of capsule shape. This suggests that the mechanical forces

  15. Intracellular pH Modulates Autophagy and Mitophagy.

    Science.gov (United States)

    Berezhnov, Alexey V; Soutar, Marc P M; Fedotova, Evgeniya I; Frolova, Maria S; Plun-Favreau, Helene; Zinchenko, Valery P; Abramov, Andrey Y

    2016-04-15

    The specific autophagic elimination of mitochondria (mitophagy) plays the role of quality control for this organelle. Deregulation of mitophagy leads to an increased number of damaged mitochondria and triggers cell death. The deterioration of mitophagy has been hypothesized to underlie the pathogenesis of several neurodegenerative diseases, most notably Parkinson disease. Although some of the biochemical and molecular mechanisms of mitochondrial quality control are described in detail, physiological or pathological triggers of mitophagy are still not fully characterized. Here we show that the induction of mitophagy by the mitochondrial uncoupler FCCP is independent of the effect of mitochondrial membrane potential but dependent on acidification of the cytosol by FCCP. The ionophore nigericin also reduces cytosolic pH and induces PINK1/PARKIN-dependent and -independent mitophagy. The increase of intracellular pH with monensin suppresses the effects of FCCP and nigericin on mitochondrial degradation. Thus, a change in intracellular pH is a regulator of mitochondrial quality control. PMID:26893374

  16. Zinc Chelation Mediates the Lysosomal Disruption without Intracellular ROS Generation

    Science.gov (United States)

    Matias, Andreza Cândido; Manieri, Tânia Maria; Cerchiaro, Giselle

    2016-01-01

    We report the molecular mechanism for zinc depletion caused by TPEN (N,N,N′,N′-Tetrakis(2-pyridylmethyl)ethylenediamine) in neuroblastoma cells. The activation of p38 MAP kinase and subsequently caspase 3 is not due to or followed by redox imbalance or ROS generation, though these are commonly observed in literature. We found that TPEN is not responsible for ROS generation and the mechanism involves essentially lysosomal disruption caused by intracellular zinc depletion. We also observed a modest activation of Bax and no changes in the Bcl-2 proteins. As a result, we suggest that TPEN causes intracellular zinc depletion which can influence the breakdown of lysosomes and cell death without ROS generation. PMID:27123155

  17. Intracellular transport proteins: classification, structure and function of kinesins

    Directory of Open Access Journals (Sweden)

    Agnieszka Chudy

    2011-09-01

    Full Text Available Correct cell functioning, division and morphogenesis rely on efficient intracellular transport. Apart from dyneins and myosins, kinesins are the main proteins responsible for intracellular movement. Kinesins are a large, diverse group of motor proteins, which based on phylogenetic similarity were classified into fourteen families. Among these families, due to the location of their motor domains, three groups have been characterized: N-, C- and M-kinesin. As molecular motors, kinesins transport various molecules and vesicles mainly towards the microtubule plus end (from the cell body participating in anterograde transport, although there are also kinesins involved in retrograde transport (C-kinesins. Kinesins are also involved in spindle formation, chromosome segregation, and spermatogenesis. Because of their great importance for the correct functioning of cells, mutations in kinesin coding genes may lead to such neurodegenerative diseases as dominant hereditary spastic paraplegia or Charcot-Marie-Tooth disease.

  18. Tangier disease: a disorder of intracellular membrane traffic

    International Nuclear Information System (INIS)

    The interaction of human high density lipoproteins (HDL) with isolated human monocytes from control and Tangier patients was studied in tissue culture experiments. It was observed that normal monocytes, similar to mouse peritoneal macrophages, bind HDL to a cell surface receptor, internalize the bound HDL particles, transport the internalized HDL intracellularly through the cytoplasmic compartment without significant degradation, and ultimately resecrete intact HDL. The cellular interaction of Tangier monocytes with normal HDL was markedly different from control monocytes. HDL binding to Tangier monocytes was moderately increased and cell associated 125I-HDL was 6- to 10-fold enhanced in Tangier monocytes. The bulk of the internalized HDL, however, was detected in secondary lysosomes. These data suggest that the cellular metabolism of HDL is abnormal in Tangier monocytes. It is postulated that Tangier disease may be a disorder of intracellular membrane traffic in which HDL is diverted into the lysosomal compartment and degraded instead of being secreted through its regular transcellular route

  19. Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

    CERN Document Server

    Appert-Rolland, Cecile; Santen, Ludger

    2015-01-01

    Cells are strongly out-of-equilibrium systems driven by continuous energy supply. They carry out many vital functions requiring active transport of various ingredients and organelles, some being small, others being large. The cytoskeleton, composed of three types of filaments, determines the shape of the cell and plays a role in cell motion. It also serves as a road network for the so-called cytoskeletal motors. These molecules can attach to a cytoskeletal filament, perform directed motion, possibly carrying along some cargo, and then detach. It is a central issue to understand how intracellular transport driven by molecular motors is regulated, in particular because its breakdown is one of the signatures of some neuronal diseases like the Alzheimer. We give a survey of the current knowledge on microtubule based intracellular transport. We first review some biological facts obtained from experiments, and present some modeling attempts based on cellular automata. We start with background knowledge on the origi...

  20. Regulation of dopamine transporter trafficking by intracellular amphetamine

    DEFF Research Database (Denmark)

    Kahlig, Kristopher M; Lute, Brandon J; Wei, Yuqiang;

    2006-01-01

    -induced cell surface DAT redistribution may result in long-lasting changes in DA homeostasis. The molecular mechanism by which AMPH induces trafficking is not clear. Because AMPH is a substrate, we do not know whether extracellular AMPH stimulates trafficking through its interaction with DAT and subsequent...... alteration in DAT function, thereby triggering intracellular signaling or whether AMPH must be transported and then act intracellularly. In agreement with our previous studies, extracellular AMPH caused cytosolic redistribution of the wild-type human DAT (WT-hDAT). However, AMPH did not induce cytosolic...... redistribution in an uptake-impaired hDAT (Y335A-hDAT) that still binds AMPH. The divalent cation zinc (Zn(2+)) inhibits WT-hDAT activity, but it restores Y335A-hDAT uptake. Coadministration of Zn(2+) and AMPH consistently reduced WT-hDAT trafficking but stimulated cytosolic redistribution of Y335A...

  1. Siderocalin inhibits the intracellular replication of Mycobacterium tuberculosis in macrophages

    DEFF Research Database (Denmark)

    Johnson, Erin E; Srikanth, Chittur V; Sandgren, Andreas;

    2010-01-01

    variant form of siderocalin, which is expressed only in the macrophage cytosol, inhibited intracellular M.tb growth as effectively as the normal, secreted form, an observation that provides mechanistic insight into how siderocalin might influence iron acquisition by the bacteria in the phagosome. Our...... siderocalin expression is upregulated following M.tb infection of mouse macrophage cell lines and primary murine alveolar macrophages. Furthermore, siderocalin added exogenously as a recombinant protein or overexpressed in the RAW264.7 macrophage cell line inhibited the intracellular growth of the pathogen. A......Siderocalin is a secreted protein that binds to siderophores to prevent bacterial iron acquisition. While it has been shown to inhibit the growth of Mycobacterium tuberculosis (M.tb) in extracellular cultures, its effect on this pathogen within macrophages is not clear. Here, we show that...

  2. Monitoring the intracellular calcium response to a dynamic hypertonic environment

    Science.gov (United States)

    Huang, Xiaowen; Yue, Wanqing; Liu, Dandan; Yue, Jianbo; Li, Jiaqian; Sun, Dong; Yang, Mengsu; Wang, Zuankai

    2016-03-01

    The profiling of physiological response of cells to external stimuli at the single cell level is of importance. Traditional approaches to study cell responses are often limited by ensemble measurement, which is challenging to reveal the complex single cell behaviors under a dynamic environment. Here we report the development of a simple microfluidic device to investigate intracellular calcium response to dynamic hypertonic conditions at the single cell level in real-time. Interestingly, a dramatic elevation in the intracellular calcium signaling is found in both suspension cells (human leukemic cell line, HL-60) and adherent cells (lung cancer cell line, A549), which is ascribed to the exposure of cells to the hydrodynamic stress. We also demonstrate that the calcium response exhibits distinct single cell heterogeneity as well as cell-type-dependent responses to the same stimuli. Our study opens up a new tool for tracking cellular activity at the single cell level in real time for high throughput drug screening.

  3. Design of biomaterials for intracellular delivery of carbon monoxide.

    Science.gov (United States)

    Inaba, Hiroshi; Fujita, Kenta; Ueno, Takafumi

    2015-11-01

    Carbon monoxide (CO) is recognized as one of the most important gas signaling molecules involved in governing various therapeutic responses. Intracellular generation of CO is spatiotemporally controlled by catalytic reactions of heme oxygenases (HOs). Thus, the ability to control intracellular CO delivery with modulation of the CO-release rate in specific amounts and locations is expected to improve our fundamental understanding of the functions of CO and the development of clinical applications. For this purpose, CO-releasing molecules (CORMs) have been developed and investigated in vitro and in vivo. Most CORMs are based on transition metal carbonyl complexes. Recently, various biomaterials consisting of metal carbonyls with biomacromolecular scaffolds have been reported to improve the properties of bare metal carbonyls. In this mini-review, current progress in CO delivery, recent strategies for the development of CORMs, and future directions in this field are discussed. PMID:26252321

  4. An Intracellular Calcium Oscillations Model Including Mitochondrial Calcium Cycling

    Institute of Scientific and Technical Information of China (English)

    SHI Xiao-Min; LIU Zeng-Rong

    2005-01-01

    @@ Calcium is a ubiquitous second messenger. Mitochondria contributes significantly to intracellular Ca2+ dynamics.The experiment of Kaftan et al. [J. Biol. Chem. 275(2000) 25465] demonstrated that inhibiting mitochondrial Ca2+ uptake can reduce the frequency of cytosolic Ca2+ concentration oscillations of gonadotropes. By considering the mitochondrial Ca2+ cycling we develop a three-variable model of intracellular Ca2+ oscillations based on the models of Atri et al. [Biophys. J. 65 (1993) 1727] and Falcke et al. [Biophys. J. 77 (1999) 37]. The model reproduces the fact that mitochondrial Ca2+ cycling increases the frequency of cytosolic Ca2+ oscillations, which accords with Kaftan's results. Moreover the model predicts that when the mitochondria overload with Ca2+, the cytosolic Ca2+ oscillations vanish, which may trigger apoptosis.

  5. Characterization of a Mycobacterium intracellulare Variant Strain by Molecular Techniques

    Science.gov (United States)

    Menendez, M. C.; Palenque, E.; Navarro, M. C.; Nuñez, M. C.; Rebollo, M. J.; Garcia, M. J.

    2001-01-01

    This paper describes a Mycobacterium intracellulare variant strain causing an unusual infection. Several isolates obtained from an immunocompromised patient were identified as members of the Mycobacterium avium complex (MAC) by the commercial AccuProbe system and biochemical standard identification. Further molecular approaches were undertaken for a more accurate characterization of the bacteria. Up to seven different genomic sequences were analyzed, ranging from conserved mycobacterial genes such as 16S ribosomal DNA to MAC-specific genes such as mig (macrophage-induced gene). The results obtained identify the isolates as a variant of M. intracellulare, an example of the internal variability described for members of the MAC, particularly within that species. The application of other molecular approaches is recommended for more accurate identification of bacteria described as MAC members. PMID:11724827

  6. Isolation of peptide aptamers that inhibit intracellular processes

    OpenAIRE

    Blum, Jonathan H.; Dove, Simon L.; Hochschild, Ann; Mekalanos, John J.

    2000-01-01

    We have developed a method for isolation of random peptides that inhibit intracellular processes in bacteria. A library of random peptides expressed as fusions to Escherichia coli thioredoxin (aptamers) were expressed under the tight control of the arabinose-inducible PBAD promoter. A selection was applied to the library to isolate aptamers that interfered with the activity of thymidylate synthase (ThyA) in vivo. Expression of an aptamer isolated by this method resulted in a ThyA− phenotype t...

  7. Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans.

    OpenAIRE

    Emily R Troemel; Marie-Anne Félix; Whiteman, Noah K.; Antoine Barrière; Ausubel, Frederick M.

    2008-01-01

    For decades the soil nematode Caenorhabditis elegans has been an important model system for biology, but little is known about its natural ecology. Recently, C. elegans has become the focus of studies of innate immunity and several pathogens have been shown to cause lethal intestinal infections in C. elegans. However none of these pathogens has been shown to invade nematode intestinal cells, and no pathogen has been isolated from wild-caught C. elegans. Here we describe an intracellular patho...

  8. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

    OpenAIRE

    Cuomo, Christina A.; Desjardins, Christopher A.; Malina A Bakowski; Goldberg, Jonathan; Ma, Amy T.; Becnel, James J.; Didier, Elizabeth S.; Fan, Lin; Heiman, David I.; Levin, Joshua Z.; Young, Sarah; Zeng, Qiandong; Emily R Troemel

    2012-01-01

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time ...

  9. Estrogen receptor of primary breast cancers: evidence for intracellular proteolysis

    OpenAIRE

    Maaroufi, Younes; Lacroix, Marc; Lespagnard, Laurence; Journé, Fabrice; Larsimont, Denis; Leclercq, Guy

    2000-01-01

    Introduction: We previously reported that about two-thirds of [125I]oestradiol-labelled cytosolic ERs from breast cancer samples eluted as low-molecular-weight isoforms (≤ 37 kDa, size-exclusion fast pressure liquid chromatography [FPLC]). These isoforms failed to adsorb strongly to hydroxylapatite at high ionic strength, a property that was ascribed to receptors devoid of amino-terminal ABC domains. In view of recent data concerning intracellular proteolysis of several transcriptional regula...

  10. Intracellular and circulating neuronal antinuclear antibodies in human epilepsy

    OpenAIRE

    Iffland, Philip H.; Carvalho-Tavares, Juliana; Trigunaite, Abhishek; Man, Shumei; Rasmussen, Peter; Alexopoulos, Andreas; Ghosh, Chaitali; Jørgensen, Trine N.; Janigro, Damir

    2013-01-01

    There are overwhelming data supporting the inflammatory origin of some epilepsies (e.g., Rasmussen's encephalitis and limbic encephalitis). Inflammatory epilepsies with an autoimmune component are characterized by autoantibodies against membrane-bound, intracellular or secreted proteins (e.g., voltage gated potassium channels). Comparably, little is known regarding autoantibodies targeting nuclear antigen. We tested the hypothesis that in addition to known epilepsy-related autoantigens, human...

  11. Control of intracellular heme levels: Heme transporters and Heme oxygenases

    OpenAIRE

    Khan, Anwar A.; Quigley, John G.

    2011-01-01

    Heme serves as a co-factor in proteins involved in fundamental biological processes including oxidative metabolism, oxygen storage and transport, signal transduction and drug metabolism. In addition, heme is important for systemic iron homeostasis in mammals. Heme has important regulatory roles in cell biology, yet excessive levels of intracellular heme are toxic; thus, mechanisms have evolved to control the acquisition, synthesis, catabolism and expulsion of cellular heme. Recently, a number...

  12. Effects of Francisella tularensis infection on macrophage intracellular signaling

    OpenAIRE

    Telepnev, Maxim

    2005-01-01

    Microbes contain a number of structural components, also known as pathogen associated molecular patterns (PAMP), which can be recognized by the host defense system. The PAMP serve as ligands for Toll-like receptors (TLR) expressed on phagocytic cells. Binding of PAMP to TLR leads to activation of a number of intracellular transduction pathways including NF-�B and mitogen-activated protein kinase pathways (MAPK). Activation of those pathways in turn leads to activation of proinflammatory immun...

  13. Intracellular insulin in human tumors: examples and implications

    OpenAIRE

    Radulescu Razvan T

    2011-01-01

    Abstract Insulin is one of the major metabolic hormones regulating glucose homeostasis in the organism and a key growth factor for normal and neoplastic cells. Work conducted primarily over the past 3 decades has unravelled the presence of insulin in human breast cancer tissues and, more recently, in human non-small cell lung carcinomas (NSCLC). These findings have suggested that intracellular insulin is involved in the development of these highly prevalent human tumors. A potential mechanism...

  14. Chelation of intracellular calcium blocks insulin action in the adipocyte

    Energy Technology Data Exchange (ETDEWEB)

    Pershadsingh, H.A.; Shade, D.L.; Delfert, D.M.; McDonald, J.M.

    1987-02-01

    The hypothesis that intracellular Ca/sup 2 +/ is an essential component of the intracellular mechanism of insulin action in the adipocyte was evaluated. Cells were loaded with the Ca/sup 2 +/ chelator quin-2, by preincubating them with quin-2 AM, the tetrakis(acetoxymethyl) ester of quin-2. Quin-2 loading inhibited insulin-stimulated glucose transport without affecting basal activity. The ability of insulin to stimulate glucose uptake in quin-2-loaded cells could be partially restored by preincubating cells with buffer supplemented with 1.2 mM CaCl/sub 2/ and the Ca/sup 2 +/ ionophore A23187. These conditions had no effect on basal activity and omission of CaCl/sub 2/ from the buffer prevented the restoration of insulin-stimulated glucose uptake by A23187. Quin-2 loading also inhibited insulin-stimulated glucose oxidation and the ability of insulin to inhibit cAMP-stimulated lipolysis without affecting their basal activities. Incubation of cells with 100 ..mu..M quin-2 or quin-2 AM had no effect on intracellular ATP concentration or the specific binding of /sup 125/I=labeled insulin to adipocytes. These findings suggest that intracellular Ca/sup 2 +/ is an essential component in the coupling of the insulin-activated receptor complex to cellular physiological/metabolic machinery. Furthermore, differing quin-2 AM dose-response profiles suggest the presence of dual Ca/sup 2 +/-dependent pathways in the adipocyte. One involves insulin stimulation of glucose transport and oxidation, whereas the other involves the antilipolytic action of insulin.

  15. Chelation of intracellular calcium blocks insulin action in the adipocyte

    International Nuclear Information System (INIS)

    The hypothesis that intracellular Ca2+ is an essential component of the intracellular mechanism of insulin action in the adipocyte was evaluated. Cells were loaded with the Ca2+ chelator quin-2, by preincubating them with quin-2 AM, the tetrakis(acetoxymethyl) ester of quin-2. Quin-2 loading inhibited insulin-stimulated glucose transport without affecting basal activity. The ability of insulin to stimulate glucose uptake in quin-2-loaded cells could be partially restored by preincubating cells with buffer supplemented with 1.2 mM CaCl2 and the Ca2+ ionophore A23187. These conditions had no effect on basal activity and omission of CaCl2 from the buffer prevented the restoration of insulin-stimulated glucose uptake by A23187. Quin-2 loading also inhibited insulin-stimulated glucose oxidation and the ability of insulin to inhibit cAMP-stimulated lipolysis without affecting their basal activities. Incubation of cells with 100 μM quin-2 or quin-2 AM had no effect on intracellular ATP concentration or the specific binding of 125I=labeled insulin to adipocytes. These findings suggest that intracellular Ca2+ is an essential component in the coupling of the insulin-activated receptor complex to cellular physiological/metabolic machinery. Furthermore, differing quin-2 AM dose-response profiles suggest the presence of dual Ca2+-dependent pathways in the adipocyte. One involves insulin stimulation of glucose transport and oxidation, whereas the other involves the antilipolytic action of insulin

  16. Autophagic clearance of bacterial pathogens: molecular recognition of intracellular microorganisms

    OpenAIRE

    Mansilla Pareja, Maria Eugenia; Colombo, Maria I

    2013-01-01

    Autophagy is involved in several physiological and pathological processes. One of the key roles of the autophagic pathway is to participate in the first line of defense against the invasion of pathogens, as part of the innate immune response. Targeting of intracellular bacteria by the autophagic machinery, either in the cytoplasm or within vacuolar compartments, helps to control bacterial proliferation in the host cell, controlling also the spreading of the infection. In this review we will d...

  17. Intracellular chloride concentration of the mouse vomeronasal neuron

    OpenAIRE

    Kim, Sangseong; Ma, Limei; Unruh, Jay; McKinney, Sean; Yu, C. Ron

    2015-01-01

    Background The vomeronasal organ (VNO) is specialized in detecting pheromone and heterospecific cues in the environment. Recent studies demonstrate the involvement of multiple ion channels in VNO signal transduction, including the calcium-activated chloride channels (CACCs). Opening of CACCs appears to result in activation of VNO neuron through outflow of Cl− ions. However, the intracellular Cl− concentration remains undetermined. Results We used the chloride ion quenching dye, MQAE, to measu...

  18. Evaluation of two novel methods for assessing intracellular oxygen

    International Nuclear Information System (INIS)

    The ability to resolve the spatio-temporal complexity of intracellular O2 distribution is the ‘Holy Grail’ of cellular physiology. In an effort to obtain a non-invasive approach of mapping intracellular O2 tensions, two methods of phosphorescent lifetime imaging microscopy were examined in the current study. These were picosecond time-resolved epiphosphorescence microscopy (single 0.5 µm focused spot) and two-photon confocal laser scanning microscopy with pinhole shifting. Both methods utilized nanoparticle-embedded Ru complex (45 nm diameter) as the phosphorescent probe, excited using pulsed outputs of Ti–sapphire Tsunami lasers (710–1050 nm). The former method used a 1 ps pulse width excitation beam with vertical polarization via a dichroic mirror (610 nm, XF43) and a 20× objective (NA 0.55, Nikon). Transmitted luminescence (1–2 × 104 counts s−1) was collected and time-correlated single photon counted decay times measured. Alternatively, an unmodified Zeiss LSM510 Confocal NLO microscope with 40× objective (NA 1.3) used successively shifted pinhole positions to collect image data from the lagging trail of the raster scan. Images obtained from two-photon excitation of a yeast (Schizosaccharomyces pombe) and a flagellate fish parasite (Spironucleus vortens), electroporated with Ru complex, indicated the intracellular location and magnitude of O2 gradients, thus confirming the feasibility of optical mapping under different external O2 concentrations. Both methods gave similar lifetimes for Ru complex phosphorescence under aerobic and anaerobic gas phases. Estimation of O2 tensions within individual fibroblasts (human dermal fibroblast (HDF)) and mammary adenocarcinoma (MCF-7) cells was possible using epiphosphorescence microscopy. MCF-7 cells showed lower intracellular O2 concentrations than HDF cells, possibly due to higher metabolic rates in the former. Future work should involve construction of higher resolution 3D maps of Ru coordinate complex

  19. Intracellular zinc distribution in mitochondria, ER and the Golgi apparatus

    OpenAIRE

    Lu, Qiping; Haragopal, Hariprakash; Slepchenko, Kira G.; Stork, Christian; Li, Yang V

    2016-01-01

    Zinc (Zn2+) is required for numerous cellular functions. As such, the homeostasis and distribution of intracellular zinc can influence cellular metabolism and signaling. However, the exact distribution of free zinc within live cells remains elusive. Previously we showed the release of zinc from thapsigargin/IP3-sensitive endoplasmic reticulum (ER) storage in cortical neurons. In the present study, we investigated if other cellular organelles also contain free chelatable zinc and function as o...

  20. Scaling of immune responses against intracellular bacterial infection

    OpenAIRE

    Abdullah, Zeinab; Knolle, Percy A.

    2014-01-01

    Macrophages detect bacterial infection through pattern recognition receptors (PRRs) localized at the cell surface, in intracellular vesicles or in the cytosol. Discrimination of viable and virulent bacteria from non-virulent bacteria (dead or viable) is necessary to appropriately scale the anti-bacterial immune response. Such scaling of anti-bacterial immunity is necessary to control the infection, but also to avoid immunopathology or bacterial persistence. PRR-mediated detection of bacterial...

  1. NAD+-Glycohydrolase Promotes Intracellular Survival of Group A Streptococcus.

    Directory of Open Access Journals (Sweden)

    Onkar Sharma

    2016-03-01

    Full Text Available A global increase in invasive infections due to group A Streptococcus (S. pyogenes or GAS has been observed since the 1980s, associated with emergence of a clonal group of strains of the M1T1 serotype. Among other virulence attributes, the M1T1 clone secretes NAD+-glycohydrolase (NADase. When GAS binds to epithelial cells in vitro, NADase is translocated into the cytosol in a process mediated by streptolysin O (SLO, and expression of these two toxins is associated with enhanced GAS intracellular survival. Because SLO is required for NADase translocation, it has been difficult to distinguish pathogenic effects of NADase from those of SLO. To resolve the effects of the two proteins, we made use of anthrax toxin as an alternative means to deliver NADase to host cells, independently of SLO. We developed a novel method for purification of enzymatically active NADase fused to an amino-terminal fragment of anthrax toxin lethal factor (LFn-NADase that exploits the avid, reversible binding of NADase to its endogenous inhibitor. LFn-NADase was translocated across a synthetic lipid bilayer in vitro in the presence of anthrax toxin protective antigen in a pH-dependent manner. Exposure of human oropharyngeal keratinocytes to LFn-NADase in the presence of protective antigen resulted in cytosolic delivery of NADase activity, inhibition of protein synthesis, and cell death, whereas a similar construct of an enzymatically inactive point mutant had no effect. Anthrax toxin-mediated delivery of NADase in an amount comparable to that observed during in vitro infection with live GAS rescued the defective intracellular survival of NADase-deficient GAS and increased the survival of SLO-deficient GAS. Confocal microscopy demonstrated that delivery of LFn-NADase prevented intracellular trafficking of NADase-deficient GAS to lysosomes. We conclude that NADase mediates cytotoxicity and promotes intracellular survival of GAS in host cells.

  2. Hijacking of eukaryotic functions by intracellular bacterial pathogens

    OpenAIRE

    Alonso, Ana; García del Portillo, Francisco

    2004-01-01

    Intracellular bacterial pathogens have evolved as a group of microorganisms endowed with weapons to hijack many biological processes of eukaryotic cells. This review discusses how these pathogens perturb diverse host cell functions, such as cytoskeleton dynamics and organelle vesicular trafficking. Alteration of the cytoskeleton is discussed in the context of the bacterial entry process (invasion), which occurs either by activation of membrane-located host receptors ("zipper" mechani...

  3. Legionella Pneumophila Transcriptome during Intracellular Multiplication in Human Macrophages

    OpenAIRE

    Faucher, Sébastien P.; Mueller, Catherine A.; Shuman, Howard A.

    2011-01-01

    Legionella pneumophila is the causative agent of Legionnaires’ disease, an acute pulmonary infection. L. pneumophila is able to infect and multiply in both phagocytic protozoa, such as Acanthamoeba castellanii, and mammalian professional phagocytes. The best-known L. pneumophila virulence determinant is the Icm/Dot type IVB secretion system, which is used to translocate more than 150 effector proteins into host cells. While the transcriptional response of Legionella to the intracellular envir...

  4. Nutrient Salvaging and Metabolism by the Intracellular Pathogen Legionella pneumophila

    OpenAIRE

    Fonseca, Maris V.; Michele S Swanson

    2014-01-01

    The Gram-negative bacterium Legionella pneumophila is ubiquitous in freshwater environments as a free-swimming organism, resident of biofilms, or parasite of protozoa. If the bacterium is aerosolized and inhaled by a susceptible human host, it can infect alveolar macrophages and cause a severe pneumonia known as Legionnaires’ disease. A sophisticated cell differentiation program equips L. pneumophila to persist in both extracellular and intracellular niches. During its life cycle, L. pneum...

  5. Handcuffs for bacteria - NDP52 orchestrates xenophagy of intracellular Salmonella

    OpenAIRE

    Pauline Verlhac; Christophe Viret; Mathias Faure

    2015-01-01

    Eukaryotic cells can selectively target and degrade intracellular pathogens using autophagy, a process referred to as xenophagy. This selectivity is controlled by proteins called autophagy receptors, which can recognise pathogens and address them to the autophagy machinery. Among them, NDP52 can recognise Salmonella Typhimurium on the one hand and the ATG8 family member LC3C on the other hand, thus allowing the docking of the bacteria to a growing autophagosome. Additionally, we...

  6. Role of envelope glycoproteins in intracellular virus maturation

    International Nuclear Information System (INIS)

    The possible role viral glycoproteins in intracellular maturation was studied by using two different viruses, avian infectious bronchitis virus (IBV), a coronavirus, and Punta Toro virus (PTV), a bunyavirus. Using the antibiotic tunicamycin, which inhibits glycosylation of N-linked glycoproteins, it was shown that coronavirus particles are formed in the absence of glycosylation. Analysis of the protein composition of these particles indicated that they contain an unglycosylated form of the membrane-associated E1 glycoprotein but lack the E2 spike glycoprotein. A cDNA clone derived from the PTV M RNA genome segment, which encodes the G1 and G2 glycoproteins, was cloned into vaccinia virus. Studies by indirect immunofluorescence microscopy revealed that the glycoproteins synthesized from this recombinant were found to accumulate intracellularly at the Golgi complex, where virus budding usually takes place. Surface immunoprecipitation and 125I-protein A binding assays also demonstrated that a majority of the glycoproteins are retained intracellularly and are not transported to the cellular surface. The sequences which encode the G1 and G2 glycoproteins were independently cloned into vaccinia virus as well

  7. Probing cytoskeleton dynamics by intracellular particle transport analysis

    Science.gov (United States)

    Götz, M.; Hodeck, K. F.; Witzel, P.; Nandi, A.; Lindner, B.; Heinrich, D.

    2015-07-01

    All cellular functions arise from the transport of molecules through a heterogeneous, highly dynamic cell interior for intracellular signaling. Here, the impact of intracellular architecture and cytoskeleton dynamics on transport processes is revealed by high-resolution single particle tracking within living cells, in combination with time-resolved local mean squared displacement (I-MSD) analysis. We apply the I-MSD analysis to trajectories of 200 nm silica particles within living cells of Dictyostelium discoideum obtained by high resolution spinning disc confocal microscopy with a frame rate of 100 fps and imaging in one fixed focal plane. We investigate phases of motor-driven active transport and subdiffusion, normal diffusion, as well as superdiffusion with high spatial and temporal resolution. Active directed intracellular motion is attributed to microtubule associated molecular motor driven transport with average absolute velocities of 2.8 μm s-1 for 200 nm diameter particles. Diffusion processes of these particles within wild-type cells are found to exhibit diffusion constants ranging across two orders of magnitude from subdiffusive to superdiffusive behavior. This type of analysis might prove of ample importance for medical applications, like targeted drug treatment of cells by nano-sized carriers or innovative diagnostic assays.

  8. Evaluation of Intracellular Signaling Downstream Chimeric Antigen Receptors.

    Directory of Open Access Journals (Sweden)

    Hannah Karlsson

    Full Text Available CD19-targeting CAR T cells have shown potency in clinical trials targeting B cell leukemia. Although mainly second generation (2G CARs carrying CD28 or 4-1BB have been investigated in patients, preclinical studies suggest that third generation (3G CARs with both CD28 and 4-1BB have enhanced capacity. However, little is known about the intracellular signaling pathways downstream of CARs. In the present work, we have analyzed the signaling capacity post antigen stimulation in both 2G and 3G CARs. 3G CAR T cells expanded better than 2G CAR T cells upon repeated stimulation with IL-2 and autologous B cells. An antigen-driven accumulation of CAR+ cells was evident post antigen stimulation. The cytotoxicity of both 2G and 3G CAR T cells was maintained by repeated stimulation. The phosphorylation status of intracellular signaling proteins post antigen stimulation showed that 3G CAR T cells had a higher activation status than 2G. Several proteins involved in signaling downstream the TCR were activated, as were proteins involved in the cell cycle, cell adhesion and exocytosis. In conclusion, 3G CAR T cells had a higher degree of intracellular signaling activity than 2G CARs which may explain the increased proliferative capacity seen in 3G CAR T cells. The study also indicates that there may be other signaling pathways to consider when designing or evaluating new generations of CARs.

  9. Evaluation of Intracellular Signaling Downstream Chimeric Antigen Receptors.

    Science.gov (United States)

    Karlsson, Hannah; Svensson, Emma; Gigg, Camilla; Jarvius, Malin; Olsson-Strömberg, Ulla; Savoldo, Barbara; Dotti, Gianpietro; Loskog, Angelica

    2015-01-01

    CD19-targeting CAR T cells have shown potency in clinical trials targeting B cell leukemia. Although mainly second generation (2G) CARs carrying CD28 or 4-1BB have been investigated in patients, preclinical studies suggest that third generation (3G) CARs with both CD28 and 4-1BB have enhanced capacity. However, little is known about the intracellular signaling pathways downstream of CARs. In the present work, we have analyzed the signaling capacity post antigen stimulation in both 2G and 3G CARs. 3G CAR T cells expanded better than 2G CAR T cells upon repeated stimulation with IL-2 and autologous B cells. An antigen-driven accumulation of CAR+ cells was evident post antigen stimulation. The cytotoxicity of both 2G and 3G CAR T cells was maintained by repeated stimulation. The phosphorylation status of intracellular signaling proteins post antigen stimulation showed that 3G CAR T cells had a higher activation status than 2G. Several proteins involved in signaling downstream the TCR were activated, as were proteins involved in the cell cycle, cell adhesion and exocytosis. In conclusion, 3G CAR T cells had a higher degree of intracellular signaling activity than 2G CARs which may explain the increased proliferative capacity seen in 3G CAR T cells. The study also indicates that there may be other signaling pathways to consider when designing or evaluating new generations of CARs. PMID:26700307

  10. Fatty Acid Signaling: The New Function of Intracellular Lipases

    Directory of Open Access Journals (Sweden)

    Zuzana Papackova

    2015-02-01

    Full Text Available Until recently, intracellular triacylglycerols (TAG stored in the form of cytoplasmic lipid droplets have been considered to be only passive “energy conserves”. Nevertheless, degradation of TAG gives rise to a pleiotropic spectrum of bioactive intermediates, which may function as potent co-factors of transcription factors or enzymes and contribute to the regulation of numerous cellular processes. From this point of view, the process of lipolysis not only provides energy-rich equivalents but also acquires a new regulatory function. In this review, we will concentrate on the role that fatty acids liberated from intracellular TAG stores play as signaling molecules. The first part provides an overview of the transcription factors, which are regulated by fatty acids derived from intracellular stores. The second part is devoted to the role of fatty acid signaling in different organs/tissues. The specific contribution of free fatty acids released by particular lipases, hormone-sensitive lipase, adipose triacylglycerol lipase and lysosomal lipase will also be discussed.

  11. Correlation between intracellular accumulation of peptidoglycan precursors and streptomycin formation

    International Nuclear Information System (INIS)

    When the mycelium of Streptomyces HUT 6037 was suspended in 0.5% NaCl solution containing 14C-glucosamine, peptidoglycan precursors accumulated in the cells. While UDP-N-acetylglucosamine accumulated in the largest amount among the precursors, extracellularly added and intracellularly accumulated UDP-N-acetylglucosamine were not used to synthesize streptomycin and were probably used for peptidoglycan formation. On the other hand, correlation was recognized between accumulation of glucosamine-6-phosphate (GlcN-6P) and streptomycin formation. Addition of an inhibitor of peptidoglycan synthesis such as enduracidin, vancomycin or cycloserine to a mycelium-suspended culture changed the ratio of accumulated peptidoglycan precursors. When streptomycin formation was stimulated by addition of enduracidin or vancomycin, intracellular GlcN-6P remarkably increased and then decreased rapidly. On the contrary, when cycloserine was added to the culture, no increase of GlcN-6P was observed and streptomycin formation was not stimulated. These results suggest that an increase in the intracellular concentration of GlcN-6P is required for activation or induction of the system for utilizing GlcN-6P for streptomycin formation. (author)

  12. Effect of ticlopidine ex vivo on platelet intracellular calcium mobilization

    Energy Technology Data Exchange (ETDEWEB)

    Derian, C.K.; Friedman, P.A.

    1988-04-01

    The antiplatelet compound ticlopidine exerts its potent inhibitory activity through an as yet undetermined mechanism(s). The goal of this study was to determine the effect, if any, of ticlopidine ex vivo on platelet calcium mobilization. Ticlopidine inhibited ADP-induced platelet aggregation by 50-80%. In the presence of 1 mM EGTA, ticlopidine inhibited ADP- and thrombin-stimulated increases in (Ca2+)i in fura-2 loaded platelets. We evaluated further the effect of ticlopidine on calcium mobilization by examining both agonist-stimulated formation of inositol trisphosphate in intact platelets and the ability of inositol trisphosphate to release /sup 45/Ca from intracellular sites in permeabilized cells. We show here that while ticlopidine significantly affected agonist-induced intracellular calcium mobilization in intact platelets, the drug was without effect on agonist-stimulated formation of inositol trisphosphate in intact platelets and on inositol trisphosphate-induced /sup 45/Ca release in saponin-permeabilized platelets. Our study demonstrates that ticlopidine exerts at least part of its effect via inhibition of intracellular calcium mobilization but that its site of action remains to be determined.

  13. Are extracellular osmolality and sodium concentration determined by Donnan effects of intracellular protein charges and of pumped sodium?

    Science.gov (United States)

    Kurbel, Sven

    2008-06-21

    Although we are used to attribute almost identical extracellular fluid (ECF) sodium concentrations in birds, amphibians, reptiles, and mammals to the composition of the primordial oceans in which, presumably, all life originated, this interpretation is not supported by geological data suggesting that the ocean salinity was never much lower than the present-day values, still four times higher than our plasma sodium. Here presented interpretation is that the similar ECF salt concentrations are dictated by the opposed Donnan effects on the cell membrane. The only way for the cell to reach the osmotic equilibrium is to alter cell volume, until concentration of nondiffusible intracellular ions (mainly charges on intracellular proteins) is equal to the ECF restricted ions (mainly Na+ ions, restricted by pumping out of cells). The achievement of electroneutrality requires that the sum of all anions equals concentration of positive ions in the cell (mainly K+). Negative charges on cytoplasmic proteins are the most stable component among ionized particles and other ions have to adapt to their concentration. Positive and negative soluble intracellular ions are all osmotically active and to achieve balance of osmotic forces on the cell membrane, the sum of their intracellular concentrations must equal the concentration of osmotically active extracellular particles. Since almost half the osmotically active ECF particles are sodium ions, the ECF sodium concentration seems related to concentration of charges on cytoplasmic proteins and concentration of intracellular phosphates. Our ancestors could not leave the salty ocean and move to brackish, or even fresh waters, without adequate regulation of their ECF sodium concentration and osmolality. Concentration of charges on cytoplasmic proteins or of intracellular phosphate buffers could not be altered, since this would compromise cell functioning. The remaining solution was to maintain the lowest ECF Na+ concentration effective in

  14. Intracellular diffusion restrictions in isolated cardiomyocytes from rainbow trout

    Directory of Open Access Journals (Sweden)

    Birkedal Rikke

    2009-12-01

    Full Text Available Abstract Background Restriction of intracellular diffusion of adenine nucleotides has been studied intensively on adult rat cardiomyocytes. However, their cause and role in vivo is still uncertain. Intracellular membrane structures have been suggested to play a role. We therefore chose to study cardiomyocytes from rainbow trout (Oncorhynchus mykiss, which are thinner and have fewer intracellular membrane structures than adult rat cardiomyocytes. Previous studies suggest that trout permeabilized cardiac fibers also have diffusion restrictions. However, results from fibers may be affected by incomplete separation of the cells. This is avoided when studying permeabilized, isolated cardiomyocytes. The aim of this study was to verify the existence of diffusion restrictions in trout cardiomyocytes by comparing ADP-kinetics of mitochondrial respiration in permeabilized fibers, permeabilized cardiomyocytes and isolated mitochondria from rainbow trout heart. Experiments were performed at 10, 15 and 20°C in the absence and presence of creatine. Results Trout cardiomyocytes hypercontracted in the solutions used for mammalian cardiomyocytes. We developed a new solution in which they retained their shape and showed stable steady state respiration rates throughout an experiment. The apparent ADP-affinity of permeabilized cardiomyocytes was different from that of fibers. It was higher, independent of temperature and not increased by creatine. However, it was still about ten times lower than in isolated mitochondria. Conclusions The differences between fibers and cardiomyocytes suggest that results from trout heart fibers were affected by incomplete separation of the cells. However, the lower ADP-affinity of cardiomyocytes compared to isolated mitochondria indicate that intracellular diffusion restrictions are still present in trout cardiomyocytes despite their lower density of intracellular membrane structures. The lack of a creatine effect indicates that

  15. DMPD: Intracellular DNA sensors in immunity. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18573338 Intracellular DNA sensors in immunity. Takeshita F, Ishii KJ. Curr Opin Im...munol. 2008 Aug;20(4):383-8. Epub 2008 Jun 23. (.png) (.svg) (.html) (.csml) Show Intracellular DNA sensors ...in immunity. PubmedID 18573338 Title Intracellular DNA sensors in immunity. Authors Takeshita F, Ishii KJ. P

  16. DMPD: NOD-like receptors (NLRs): bona fide intracellular microbial sensors. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18585455 NOD-like receptors (NLRs): bona fide intracellular microbial sensors. Shaw...tml) (.csml) Show NOD-like receptors (NLRs): bona fide intracellular microbial sensors. PubmedID 18585455 Ti...tle NOD-like receptors (NLRs): bona fide intracellular microbial sensors. Authors

  17. Quantifying intracellular metabolites in yeast using a matrix with minimal interference from naturally occurring analytes

    DEFF Research Database (Denmark)

    Magdenoska, Olivera; Knudsen, Peter Boldsen; Svenssen, Daniel Killerup; Nielsen, Kristian Fog

    2015-01-01

    For quantification of intracellular metabolites, mass spectrometry combined with liquid chromatography, capillary electrophoresis, or gas chromatography is currently the method of choice, especially when combined with stable isotope-labeled internal standards (SIL-ISs). Due to the difficulties in...... [13C6]glucose/nonlabeled glucose (50:50, w/w) growth medium. The areas of both 12C6 and 13C6 fractions of ATP in the matrix were measured to be 2% of the sum of the areas of all ATP isotopes detected. The matrix allowed for spiking of both the nonlabeled and SIL-ISs and more straightforward validation...... analysis of the redox compounds was challenging due to the oxidation of NADH and NADPH, when dissolved in water or tributylamine. The oxidation was reduced by dissolving them in ammonium acetate solution (pH 8.0)....

  18. Intracellular calcium affects prestin's voltage operating point indirectly via turgor-induced membrane tension

    Science.gov (United States)

    Song, Lei; Santos-Sacchi, Joseph

    2015-12-01

    Recent identification of a calmodulin binding site within prestin's C-terminus indicates that calcium can significantly alter prestin's operating voltage range as gauged by the Boltzmann parameter Vh (Keller et al., J. Neuroscience, 2014). We reasoned that those experiments may have identified the molecular substrate for the protein's tension sensitivity. In an effort to understand how this may happen, we evaluated the effects of turgor pressure on such shifts produced by calcium. We find that the shifts are induced by calcium's ability to reduce turgor pressure during whole cell voltage clamp recording. Clamping turgor pressure to 1kPa, the cell's normal intracellular pressure, completely counters the calcium effect. Furthermore, following unrestrained shifts, collapsing the cells abolishes induced shifts. We conclude that calcium does not work by direct action on prestin's conformational state. The possibility remains that calcium interaction with prestin alters water movements within the cell, possibly via its anion transport function.

  19. Surface functionalized mesoporous silica nanoparticles for intracellular drug delivery

    Science.gov (United States)

    Vivero-Escoto, Juan Luis

    Mesoporous silica nanoparticles (MSNs) are a highly promising platform for intracellular controlled release of drugs and biomolecules. Despite that the application of MSNs in the field of intracellular drug delivery is still at its infancy very exciting breakthroughs have been achieved in the last years. A general review of the most recent progress in this area of research is presented, including a description of the latest findings on the pathways of entry into live mammalian cells together with the intracellular trafficking, a summary on the contribution of MSNs to the development of site-specific drug delivery systems, a report on the biocompatibility of this material in vitro andin vivo, and a discussion on the most recent breakthroughs in the synthesis and application of stimuli-responsive mesoporous silica-based delivery vehicles. A gold nanoparticles (AuNPs)-capped MSNs-based intracellular photoinduced drug delivery system (PR-AuNPs-MSNs) for the controlled release of anticancer drug inside of human fibroblast and liver cells was synthesized and characterized. We found that the mesoporous channels of MSNs could be efficiently capped by the photoresponsive AuNPs without leaking the toxic drug, paclitaxel, inside of human cells. Furthermore, we demonstrated that the cargo-release property of this PR-AuNPs-MSNs system could be easily photo-controlled under mild and biocompatible conditions in vitro. In collaboration with Renato Mortera (a visiting student from Italy), a MSNs based intracellular delivery system for controlled release of cell membrane impermeable cysteine was developed. A large amount of cysteine molecules were covalently attached to the silica surface of MSNs through cleavable disulfide linkers. These cysteine-containing nanoparticles were efficiently endocytosed by human cervical cancer cells HeLa. These materials exhibit 450 times higher cell growth inhibition capability than that of the conventional N-acetylcysteine prodrug. The ability to

  20. Fluorescence detection of intracellular cadmium with Leadmium Green.

    Science.gov (United States)

    Malaiyandi, Latha M; Sharthiya, Harsh; Dineley, Kirk E

    2016-08-01

    Leadmium Green is a commercially available, small molecule, fluorescent probe advertised as a detector of free intracellular cadmium (Cd(2+)) and lead (Pb(2+)). Leadmium Green has been used in various paradigms, such as tracking Cd(2+) sequestration in plant cells, heavy metal export in protozoa, and Pb(2+) absorption by vascular endothelial cells. However very little information is available regarding its affinity and selectivity for Cd(2+), Pb(2+), and other metals. We evaluated the in vitro selectivity of Leadmium Green using spectrofluorimetry. Consistent with manufacturer's claims, Leadmium Green was sensitive to Cd(2+) (KD ~600 nM) and also Pb(2+) (KD ~9.0 nM) in a concentration-dependent manner, and furthermore proved insensitive to Ca(2+), Co(2+), Mn(2+) and Ni(2+). Leadmium Green also responded to Zn(2+) with a KD of ~82 nM. Using fluorescence microscopy, we evaluated Leadmium Green in live mouse hippocampal HT22 cells. We demonstrated that Leadmium Green detected ionophore-mediated acute elevations of Cd(2+) or Zn(2+) in a concentration-dependent manner. However, the maximum fluorescence produced by ionophore-delivered Zn(2+) was much less than that produced by Cd(2+). When tested in a model of oxidant-induced liberation of endogenous Zn(2+), Leadmium Green responded weakly. We conclude that Leadmium Green is an effective probe for monitoring intracellular Cd(2+), particularly in models where Cd(2+) accumulates rapidly, and when concomitant fluctuations of intracellular Zn(2+) are minimal. PMID:27260023

  1. Fluorescence Lifetime Imaging Microscopy of Intracellular Glucose Dynamics

    Science.gov (United States)

    Veetil, Jithesh V.; Jin, Sha; Ye, Kaiming

    2012-01-01

    Background One of the major hurdles in studying diabetes pathophysiology is the lack of adequate methodology that allows for direct and real-time determination of glucose transport and metabolism in cells and tissues. In this article, we present a new methodology that adopts frequency-domain fluorescence lifetime imaging microscopy (FD-FLIM) to visualize and quantify the dynamics of intracellular glucose within living cells using a biosensor protein based on fluorescence resonance energy transfer (FRET). Method The biosensor protein was developed by fusing a FRET pair, an AcGFP1 donor and a mCherry acceptor to N- and C- termini of a mutant glucose-binding protein (GBP), respectively. The probe was expressed and biosynthesized inside the cells, offering continuous monitoring of glucose dynamics in real time through fluorescence lifetime imaging microscopy (FLIM) measurement. Results We transfected the deoxyribonucleic acid of the AcGFP1-GBP-mCherry sensor into murine myoblast cells, C2C12, and continuously monitored the changes in intracellular glucose concentrations in response to the variation in extracellular glucose, from which we determined glucose uptake and clearance rates. The distribution of intracellular glucose concentration was also characterized. We detected a high glucose concentration in a region close to the cell membrane and a low glucose concentration in a region close to the nucleus. The monoexponential decay of AcGFP1 was distinguished using FD-FLIM. Conclusions This work enables continuous glucose monitoring (CGM) within living cells using FD-FLIM and a biosensor protein. The sensor protein developed offers a new means for quantitatively analyzing glucose homeostasis at the cellular level. Data accumulated from these studies will help increase our understanding of the pathology of diabetes. PMID:23294772

  2. Polymeric gel nanoparticle pH sensors for intracellular measurements

    OpenAIRE

    Almdal, Kristoffer; Andresen, Thomas Lars; Benjaminsen, Rikke Vicki; Christensen, Nynne Meyn; Henriksen, Jonas Rosager; Sun, Honghao

    2011-01-01

    Precise measurements of pH in cells and intracellular compartments are of importance to both the fundamental understanding of metabolism and to the development of drugs that are released from the endosomes-lysome pathway. We have developed polymer gel nanoparticles as carriers of covalently bound fluorophores for ratiometric measurements of pH. One pH insensitive fluorophore serves as a reference while one or more pH sensitive fluorophores serve to give the desired pH dependence of the output...

  3. Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming.

    Directory of Open Access Journals (Sweden)

    Xiaoyun Liu

    Full Text Available Campylobacter jejuni is the major cause of bacterial food-borne illness in the USA and Europe. An important virulence attribute of this bacterial pathogen is its ability to enter and survive within host cells. Here we show through a quantitative proteomic analysis that upon entry into host cells, C. jejuni undergoes a significant metabolic downshift. Furthermore, our results indicate that intracellular C. jejuni reprograms its respiration, favoring the respiration of fumarate. These results explain the poor ability of C. jejuni obtained from infected cells to grow under standard laboratory conditions and provide the bases for the development of novel anti microbial strategies that would target relevant metabolic pathways.

  4. Evaluation of Intracellular Signaling Downstream Chimeric Antigen Receptors

    OpenAIRE

    Karlsson, Hannah; Svensson, Emma; Gigg, Camilla; Jarvius, Malin; Olsson-Strömberg, Ulla; Savoldo, Barbara; Dotti, Gianpietro; Loskog, Angelica

    2015-01-01

    CD19-targeting CAR T cells have shown potency in clinical trials targeting B cell leukemia. Although mainly second generation (2G) CARs carrying CD28 or 4-1BB have been investigated in patients, preclinical studies suggest that third generation (3G) CARs with both CD28 and 4-1BB have enhanced capacity. However, little is known about the intracellular signaling pathways downstream of CARs. In the present work, we have analyzed the signaling capacity post antigen stimulation in both 2G and 3G C...

  5. Intracellular pH gradients in migrating cells

    DEFF Research Database (Denmark)

    Martin, Christine; Pedersen, Stine Helene Falsig; Schwab, Albrecht;

    2011-01-01

    might function as such unevenly distributed regulators as they modulate the interaction of focal adhesion proteins and components of the cytoskeleton in vitro. However, an intracellular pH (pH(i)) gradient reflecting a spatial asymmetry of protons has not been shown so far. One major regulator of p......Cell polarization along the axis of movement is required for migration. The localization of proteins and regulators of the migratory machinery to either the cell front or its rear results in a spatial asymmetry enabling cells to simultaneously coordinate cell protrusion and retraction. Protons...

  6. Bifurcation in a generic model of intracellular viral kinetics

    International Nuclear Information System (INIS)

    The key steps of intracellular virion reproduction include viral genome replication, mRNA synthesis and degradation, protein synthesis and degradation, capsid assembly and virion release from a cell. Our analysis, incorporating these steps (with no deterioration of the cell machinery), indicates that asymptotically depending on the values of the model parameters the viral kinetics either reach a steady state or are out of control due to an exponential growth of the virion population. In the latter case, the cell is expected to rapidly die or the virion growth should be limited by other steps. (letter to the editor)

  7. Intracellular Ca(2+) release as irreversible Markov process.

    OpenAIRE

    Rengifo, Juliana; Rosales, Rafael; González, Adom; Cheng, Heping; Stern, Michael D.; Ríos, Eduardo

    2002-01-01

    In striated muscles, intracellular Ca(2+) release is tightly controlled by the membrane voltage sensor. Ca(2+) ions are necessary mediators of this control in cardiac but not in skeletal muscle, where their role is ill-understood. An intrinsic gating oscillation of Ca(2+) release-not involving the voltage sensor-is demonstrated in frog skeletal muscle fibers under voltage clamp. A Markov model of the Ca(2+) release units is shown to reproduce the oscillations, and it is demonstrated that for ...

  8. Evidence of RNA in D loops of intracellular lambda DNA.

    OpenAIRE

    Chattoraj, D K; Stahl, F. W.

    1980-01-01

    If lambda DNA replication is blocked by mutation in any one of several genes essential for replication, intracellular lambda DNA often shows short three-stranded regions called D loops. In this report we show that one arm of a D loop is an RNA . DNA hybrid, whereas the remaining arm is made up of single-stranded DNA. The RNA can be partially removed by RNase A and totally removed by RNase H. Also, D loops do not appear if infections are made in cells treated with rifampin, a potent inhibitor ...

  9. Intracellular iron minerals in a dissimilatory iron-reducing bacterium.

    Science.gov (United States)

    Glasauer, Susan; Langley, Sean; Beveridge, Terry J

    2002-01-01

    Among prokaryotes, there are few examples of controlled mineral formation; the formation of crystalline iron oxides and sulfides [magnetite (Fe3O4) or greigite (Fe3S4)] by magnetotactic bacteria is an exception. Shewanella putrefaciens CN32, a Gram-negative, facultative anaerobic bacterium that is capable of dissimilatory iron reduction, produced microscopic intracellular grains of iron oxide minerals during growth on two-line ferrihydrite in a hydrogen-argon atmosphere. The minerals, formed at iron concentrations found in the soil and sedimentary environments where these bacteria are active, could represent an unexplored pathway for the cycling of iron by bacteria. PMID:11778045

  10. An Intracellular Calcium Oscillation Model and its Property

    Institute of Scientific and Technical Information of China (English)

    应阳君; 李卫华

    2003-01-01

    Intracellular Ca2+ concentration oscillation is one of the typical nonlinear dynamical phenomena in biophysics.According to the experimental facts that when stimulated by different agonists, the cytosolic Ca2+ oscillations of hepatocytes show nearly constant amplitude for two different oscillation-form, simple spikes and complex bursts,we build a new 4-variables model based on the two models proposed by Hoefer [Biophys J. 77 (1999) 1244] and Kummer et al. [Biophys. J. 79 (2000) 1188] Our model can simulate both simple-spike and multi-spike-burst oscillations with amplitude of 0.5-0. 7μmol/L in a rather wide range of parameters.

  11. Direct Determination of the Intracellular Oxidation State of Plutonium

    OpenAIRE

    Gorman-Lewis, Drew; Aryal, Baikuntha P.; Paunesku, Tatjana; Vogt, Stefan; Lai, Barry; Woloschak, Gayle E; Jensen, Mark P.

    2011-01-01

    Microprobe X-ray absorption near edge structure (μ-XANES) measurements were used to determine directly, for the first time, the oxidation state of intracellular plutonium in individual 0.1 μm2 areas within single rat pheochromocytoma cells (PC12). The living cells were incubated in vitro for 3 hours in the presence of Pu added to the media in different oxidation states (Pu(III), Pu(IV), and Pu(VI)) and in different chemical forms. Regardless of the initial oxidation state or chemical form of ...

  12. An intracellular transcriptomic atlas of the giant coenocyte Caulerpa taxifolia.

    Directory of Open Access Journals (Sweden)

    Aashish Ranjan

    2015-01-01

    Full Text Available Convergent morphologies have arisen in plants multiple times. In non-vascular and vascular land plants, convergent morphology in the form of roots, stems, and leaves arose. The morphology of some green algae includes an anchoring holdfast, stipe, and leaf-like fronds. Such morphology occurs in the absence of multicellularity in the siphonous algae, which are single cells. Morphogenesis is separate from cellular division in the land plants, which although are multicellular, have been argued to exhibit properties similar to single celled organisms. Within the single, macroscopic cell of a siphonous alga, how are transcripts partitioned, and what can this tell us about the development of similar convergent structures in land plants? Here, we present a de novo assembled, intracellular transcriptomic atlas for the giant coenocyte Caulerpa taxifolia. Transcripts show a global, basal-apical pattern of distribution from the holdfast to the frond apex in which transcript identities roughly follow the flow of genetic information in the cell, transcription-to-translation. The analysis of the intersection of transcriptomic atlases of a land plant and Caulerpa suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances. Our results not only provide an intracellular atlas of transcript localization, but also demonstrate the contribution of transcript partitioning to morphology, independent from multicellularity, in plants.

  13. Intracellular iron concentration of neurons with and without perineuronal nets

    Energy Technology Data Exchange (ETDEWEB)

    Fiedler, Anja [Paul Flechsig Institute for Brain Research, University of Leipzig, Jahnallee 59, D-04109 Leipzig (Germany) and Institute for Experimental Physics II, University of Leipzig, Linnestrasse 5, D-04103 Leipzig (Germany)]. E-mail: afiedler@uni-leipzig.de; Reinert, Tilo [Institute for Experimental Physics II, University of Leipzig, Linnestrasse 5, D-04103 Leipzig (Germany); Morawski, Markus [Paul Flechsig Institute for Brain Research, University of Leipzig, Jahnallee 59, D-04109 Leipzig (Germany); Brueckner, Gert [Paul Flechsig Institute for Brain Research, University of Leipzig, Jahnallee 59, D-04109 Leipzig (Germany); Arendt, Thomas [Paul Flechsig Institute for Brain Research, University of Leipzig, Jahnallee 59, D-04109 Leipzig (Germany); Butz, Tilman [Institute for Experimental Physics II, University of Leipzig, Linnestrasse 5, D-04103 Leipzig (Germany)

    2007-07-15

    Neurodegenerative diseases like Parkinson's disease, Alzheimer's disease and Huntington's disease are characterized by abnormally high concentrations of iron in the affected brain areas. Iron is believed to contribute to oxidative stress by catalysing radical generation and subsequently causing neuronal death. Interestingly, subpopulations of neurons are less vulnerable against degeneration. One of these subpopulations possesses a specialized extracellular matrix arranged as a perineuronal net (PN), a structure with poorly understood functions. In order to differentiate between neurons with and without PN according to their iron concentrations we have performed a {mu}PIXE study at the Leipzig LIPSION laboratory. PN-ensheathed neurons in selected brain areas were detected by lectin-histochemical staining with Wisteria floribunda agglutinin (WFA). The staining was intensified by DAB-nickel by an established method enabling the visualisation of the PNs by nuclear microscopy. The cellular concentration of iron in the rat brain was about 1 mmol/l (ca. 30 {mu}g/g dw). First results of subcellular analysis showed that the intracellular iron concentration of PN-ensheathed neurons tends to be slightly increased in comparison to neurons without PNs. The difference in intracellular iron concentrations could be an effect of the PNs.

  14. Intracellular iron concentration of neurons with and without perineuronal nets

    International Nuclear Information System (INIS)

    Neurodegenerative diseases like Parkinson's disease, Alzheimer's disease and Huntington's disease are characterized by abnormally high concentrations of iron in the affected brain areas. Iron is believed to contribute to oxidative stress by catalysing radical generation and subsequently causing neuronal death. Interestingly, subpopulations of neurons are less vulnerable against degeneration. One of these subpopulations possesses a specialized extracellular matrix arranged as a perineuronal net (PN), a structure with poorly understood functions. In order to differentiate between neurons with and without PN according to their iron concentrations we have performed a μPIXE study at the Leipzig LIPSION laboratory. PN-ensheathed neurons in selected brain areas were detected by lectin-histochemical staining with Wisteria floribunda agglutinin (WFA). The staining was intensified by DAB-nickel by an established method enabling the visualisation of the PNs by nuclear microscopy. The cellular concentration of iron in the rat brain was about 1 mmol/l (ca. 30 μg/g dw). First results of subcellular analysis showed that the intracellular iron concentration of PN-ensheathed neurons tends to be slightly increased in comparison to neurons without PNs. The difference in intracellular iron concentrations could be an effect of the PNs

  15. Detection of ubiquitinated huntingtin species in intracellular aggregates

    Directory of Open Access Journals (Sweden)

    Katrin eJuenemann

    2015-01-01

    Full Text Available Protein conformation diseases, including polyglutamine diseases, result from the accumulation and aggregation of misfolded proteins. Huntington’s disease is one of nine diseases caused by an expanded polyglutamine repeat within the affected protein and is hallmarked by intracellular inclusion bodies composed of aggregated N-terminal huntingtin fragments and other sequestered proteins. Fluorescence microscopy and filter trap assay are conventional methods to study protein aggregates, but cannot be used to analyze the presence and levels of post-translational modifications of aggregated huntingtin such as ubiquitination. Ubiquitination of proteins can be a signal for degradation and intracellular localization, but also affects protein activity and protein-protein interactions. The function of ubiquitination relies on its mono- and polymeric isoforms attached to protein substrates. Studying the ubiquitination pattern of aggregated huntingtin fragments offers an important possibility to understand huntingtin degradation and aggregation processes within the cell. For the identification of aggregated huntingtin and its ubiquitinated species, solubilization of the cellular aggregates is mandatory. Here we describe methods to identify post-translational modifications such as ubiquitination of aggregated mutant huntingtin. This approach is specifically described for use with mammalian cell culture and is suitable to study other disease-related proteins prone to aggregate.

  16. Intracellular iron concentration of neurons with and without perineuronal nets

    Science.gov (United States)

    Fiedler, Anja; Reinert, Tilo; Morawski, Markus; Brückner, Gert; Arendt, Thomas; Butz, Tilman

    2007-07-01

    Neurodegenerative diseases like Parkinson's disease, Alzheimer's disease and Huntington's disease are characterized by abnormally high concentrations of iron in the affected brain areas. Iron is believed to contribute to oxidative stress by catalysing radical generation and subsequently causing neuronal death. Interestingly, subpopulations of neurons are less vulnerable against degeneration. One of these subpopulations possesses a specialized extracellular matrix arranged as a perineuronal net (PN), a structure with poorly understood functions. In order to differentiate between neurons with and without PN according to their iron concentrations we have performed a μPIXE study at the Leipzig LIPSION laboratory. PN-ensheathed neurons in selected brain areas were detected by lectin-histochemical staining with Wisteria floribunda agglutinin (WFA). The staining was intensified by DAB- nickel by an established method enabling the visualisation of the PNs by nuclear microscopy. The cellular concentration of iron in the rat brain was about 1 mmol/l (ca. 30 μg/g dw). First results of subcellular analysis showed that the intracellular iron concentration of PN-ensheathed neurons tends to be slightly increased in comparison to neurons without PNs. The difference in intracellular iron concentrations could be an effect of the PNs.

  17. Transient light-induced intracellular oxidation revealed by redox biosensor

    International Nuclear Information System (INIS)

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition

  18. Silica nanoparticles for cell imaging and intracellular sensing

    Science.gov (United States)

    Korzeniowska, B.; Nooney, R.; Wencel, D.; McDonagh, C.

    2013-11-01

    There is increasing interest in the use of nanoparticles (NPs) for biomedical applications. In particular, nanobiophotonic approaches using fluorescence offers the potential of high sensitivity and selectivity in applications such as cell imaging and intracellular sensing. In this review, we focus primarily on the use of fluorescent silica NPs for these applications and, in so doing, aim to enhance and complement the key recent review articles on these topics. We summarize the main synthetic approaches, namely the Stöber and microemulsion processes, and, in this context, we deal with issues in relation to both covalent and physical incorporation of different types of dyes in the particles. The important issue of NP functionalization for conjugation to biomolecules is discussed and strategies published in the recent literature are highlighted and evaluated. We cite recent examples of the use of fluorescent silica NPs for cell imaging in the areas of cancer, stem cell and infectious disease research, and we review the current literature on the use of silica NPs for intracellular sensing of oxygen, pH and ionic species. We include a short final section which seeks to identify the main challenges and obstacles in relation to the potential widespread use of these particles for in vivo diagnostics and therapeutics.

  19. Cell fate reprogramming by control of intracellular network dynamics

    Science.gov (United States)

    Zanudo, Jorge G. T.; Albert, Reka

    Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Although the topic of controlling the dynamics of a system has a long history in control theory, most of this work is not directly applicable to intracellular networks. Here we present a network control method that integrates the structural and functional information available for intracellular networks to predict control targets. Formulated in a logical dynamic scheme, our control method takes advantage of certain function-dependent network components and their relation to steady states in order to identify control targets, which are guaranteed to drive any initial state to the target state with 100% effectiveness and need to be applied only transiently for the system to reach and stay in the desired state. We illustrate our method's potential to find intervention targets for cancer treatment and cell differentiation by applying it to a leukemia signaling network and to the network controlling the differentiation of T cells. We find that the predicted control targets are effective in a broad dynamic framework. Moreover, several of the predicted interventions are supported by experiments. This work was supported by NSF Grant PHY 1205840.

  20. CIRRHOSIS INDUCES APOPTOSIS IN RENAL TISSUE THROUGH INTRACELLULAR OXIDATIVE STRESS

    Directory of Open Access Journals (Sweden)

    Keli Cristina Simões da SILVEIRA

    2015-03-01

    Full Text Available Background Renal failure is a frequent and serious complication in patients with decompensated cirrhosis. Objectives We aimed to evaluate the renal oxidative stress, cell damage and impaired cell function in animal model of cirrhosis. Methods Secondary biliary cirrhosis was induced in rats by ligation of the common bile duct. We measured TBARS, ROS and mitochondrial membrane potential in kidney as markers of oxidative stress, and activities of the antioxidant enzymes. Relative cell viability was determined by trypan blue dye-exclusion assay. Annexin V-PE was used with a vital dye, 7-AAD, to distinguish apoptotic from necrotic cells and comet assay was used for determined DNA integrity in single cells. Results In bile duct ligation animals there was significant increase in the kidney lipoperoxidation and an increase of the level of intracellular ROS. There was too an increase in the activity of all antioxidant enzymes evaluated in the kidney. The percentage viability was above 90% in the control group and in bile duct ligation was 64.66% and the dominant cell death type was apoptosis. DNA damage was observed in the bile duct ligation. There was a decreased in the mitochondrial membrane potential from 71.40% ± 6.35% to 34.48% ± 11.40% in bile duct ligation. Conclusions These results indicate that intracellular increase of ROS cause damage in the DNA and apoptosis getting worse the renal function in cirrhosis.

  1. Utilizing Natural and Engineered Peroxiredoxins As Intracellular Peroxide Reporters.

    Science.gov (United States)

    Van Laer, Koen; Dick, Tobias P

    2016-01-31

    It is increasingly apparent that nature evolved peroxiredoxins not only as H2O2 scavengers but also as highly sensitive H2O2 sensors and signal transducers. Here we ask whether the H2O2 sensing role of Prx can be exploited to develop probes that allow to monitor intracellular H2O2 levels with unprecedented sensitivity. Indeed, simple gel shift assays visualizing the oxidation of endogenous 2-Cys peroxiredoxins have already been used to detect subtle changes in intracellular H2O2 concentration. The challenge however is to create a genetically encoded probe that offers real-time measurements of H2O2 levels in intact cells via the Prx oxidation state. We discuss potential design strategies for Prx-based probes based on either the redox-sensitive fluorophore roGFP or the conformation-sensitive fluorophore cpYFP. Furthermore, we outline the structural and chemical complexities which need to be addressed when using Prx as a sensing moiety for H2O2 probes. We suggest experimental strategies to investigate the influence of these complexities on probe behavior. In doing so, we hope to stimulate the development of Prx-based probes which may spearhead the further study of cellular H2O2 homeostasis and Prx signaling. PMID:26810074

  2. Crystallographic study of FABP5 as an intracellular endocannabinoid transporter

    Energy Technology Data Exchange (ETDEWEB)

    Sanson, Benoît; Wang, Tao [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Sun, Jing; Wang, Liqun; Kaczocha, Martin [Stony Brook University, Stony Brook, NY 11794-5213 (United States); Ojima, Iwao [Stony Brook University, Stony Brook, NY 1794-3400 (United States); Stony Brook University, Stony Brook, NY 11794-3400 (United States); Deutsch, Dale, E-mail: dale.deutsch@stonybrook.edu [Stony Brook University, Stony Brook, NY 11794-5213 (United States); Stony Brook University, Stony Brook, NY 11794-3400 (United States); Li, Huilin, E-mail: dale.deutsch@stonybrook.edu [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Stony Brook University, Stony Brook, NY 11794-5213 (United States); Stony Brook University, Stony Brook, NY 11794-3400 (United States)

    2014-02-01

    FABP5 was recently found to intracellularly transport endocannabinoid signaling lipids. The structures of FABP5 complexed with two endocannabinoids and an inhibitor were solved. Human FABP5 was found to dimerize via a domain-swapping mechanism. This work will help in the development of inhibitors to raise endocannabinoid levels. In addition to binding intracellular fatty acids, fatty-acid-binding proteins (FABPs) have recently been reported to also transport the endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), arachidonic acid derivatives that function as neurotransmitters and mediate a diverse set of physiological and psychological processes. To understand how the endocannabinoids bind to FABPs, the crystal structures of FABP5 in complex with AEA, 2-AG and the inhibitor BMS-309403 were determined. These ligands are shown to interact primarily with the substrate-binding pocket via hydrophobic interactions as well as a common hydrogen bond to the Tyr131 residue. This work advances our understanding of FABP5–endocannabinoid interactions and may be useful for future efforts in the development of small-molecule inhibitors to raise endocannabinoid levels.

  3. Downregulation of transferrin receptor surface expression by intracellular antibody

    International Nuclear Information System (INIS)

    To deplete cellular iron uptake, and consequently inhibit the proliferation of tumor cells, we attempt to block surface expression of transferrin receptor (TfR) by intracellular antibody technology. We constructed two expression plasmids (scFv-HAK and scFv-HA) coding for intracellular single-chain antibody against TfR with or without endoplasmic reticulum (ER) retention signal, respectively. Then they were transfected tumor cells MCF-7 by liposome. Applying RT-PCR, Western blotting, immunofluorescence microscopy and immunoelectron microscope experiments, we insure that scFv-HAK intrabody was successfully expressed and retained in ER contrasted to the secreted expression of scFv-HA. Flow cytometric analysis confirmed that the TfR surface expression was markedly decreased approximately 83.4 ± 2.5% in scFv-HAK transfected cells, while there was not significantly decrease in scFv-HA transfected cells. Further cell growth and apoptosis characteristics were evaluated by cell cycle analysis, nuclei staining and MTT assay. Results indicated that expression of scFv-HAK can dramatically induce cell cycle G1 phase arrest and apoptosis of tumor cells, and consequently significantly suppress proliferation of tumor cells compared with other control groups. For First time this study demonstrates the potential usage of anti-TfR scFv-intrabody as a growth inhibitor of TfR overexpressing tumors

  4. Multistability and dynamic transitions of intracellular Min protein patterns.

    Science.gov (United States)

    Wu, Fabai; Halatek, Jacob; Reiter, Matthias; Kingma, Enzo; Frey, Erwin; Dekker, Cees

    2016-01-01

    Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during growth up to defined large dimensions. De novo formation of patterns from homogenous starting conditions is observed and studied both experimentally and in simulations. A new theoretical approach is developed for probing pattern stability under perturbations. Quantitative experiments and simulations show that, once established, Min oscillations tolerate a large degree of intracellular heterogeneity, allowing distinctly different patterns to persist in different cells with the same geometry. Min patterns maintain their axes for hours in experiments, despite imperfections, expansion, and changes in cell shape during continuous cell growth. Transitions between multistable Min patterns are found to be rare events induced by strong intracellular perturbations. The instances of multistability studied here are the combined outcome of boundary growth and strongly nonlinear kinetics, which are characteristic of the reaction-diffusion patterns that pervade biology at many scales. PMID:27279643

  5. Uptake and intracellular trafficking of superantigens in dendritic cells.

    Directory of Open Access Journals (Sweden)

    María B Ganem

    Full Text Available Bacterial superantigens (SAgs are exotoxins produced mainly by Staphylococcus aureus and Streptococcus pyogenes that can cause toxic shock syndrome (TSS. According to current paradigm, SAgs interact directly and simultaneously with T cell receptor (TCR on the T cell and MHC class II (MHC-II on the antigen-presenting cell (APC, thereby circumventing intracellular processing to trigger T cell activation. Dendritic cells (DCs are professional APCs that coat nearly all body surfaces and are the most probable candidate to interact with SAgs. We demonstrate that SAgs are taken up by mouse DCs without triggering DC maturation. SAgs were found in intracellular acidic compartment of DCs as biologically active molecules. Moreover, SAgs co-localized with EEA1, RAB-7 and LAMP-2, at different times, and were then recycled to the cell membrane. DCs loaded with SAgs are capable of triggering in vitro lymphocyte proliferation and, injected into mice, stimulate T cells bearing the proper TCR in draining lymph nodes. Transportation and trafficking of SAgs in DCs might increase the local concentration of these exotoxins where they will produce the highest effect by promoting their encounter with both MHC-II and TCR in lymph nodes, and may explain how just a few SAg molecules can induce the severe pathology associated with TSS.

  6. Roles of Rho GTPases in Intracellular Transport and Cellular Transformation

    Directory of Open Access Journals (Sweden)

    Ji-Long Chen

    2013-03-01

    Full Text Available Rho family GTPases belong to the Ras GTPase superfamily and transduce intracellular signals known to regulate a variety of cellular processes, including cell polarity, morphogenesis, migration, apoptosis, vesicle trafficking, viral transport and cellular transformation. The three best-characterized Rho family members are Cdc42, RhoA and Rac1. Cdc42 regulates endocytosis, the transport between the endoplasmic reticulum and Golgi apparatus, post-Golgi transport and exocytosis. Cdc42 influences trafficking through interaction with Wiskott-Aldrich syndrome protein (N-WASP and the Arp2/3 complex, leading to changes in actin dynamics. Rac1 mediates endocytic and exocytic vesicle trafficking by interaction with its effectors, PI3kinase, synaptojanin 2, IQGAP1 and phospholipase D1. RhoA participates in the regulation of endocytosis through controlling its downstream target, Rho kinase. Interestingly, these GTPases play important roles at different stages of viral protein and genome transport in infected host cells. Importantly, dysregulation of Cdc42, Rac1 and RhoA leads to numerous disorders, including malignant transformation. In some cases, hyperactivation of Rho GTPases is required for cellular transformation. In this article, we review a number of findings related to Rho GTPase function in intracellular transport and cellular transformation.

  7. Estradiol induces functional inactivation of p53 by intracellular redistribution.

    Science.gov (United States)

    Molinari, A M; Bontempo, P; Schiavone, E M; Tortora, V; Verdicchio, M A; Napolitano, M; Nola, E; Moncharmont, B; Medici, N; Nigro, V; Armetta, I; Abbondanza, C; Puca, G A

    2000-05-15

    Estrogen treatment of MCF-7 cells grown in serum-free medium induced a modification of the intracellular distribution of p53 protein. Western blot analysis and immunofluorescence staining showed that p53 was localized in the nucleus of untreated cell and that after 48 h of hormone treatment, it was mostly localized in the cytoplasm. This effect was blocked by the antiestrogen ICI182,780. Intracellular redistribution of p53 was correlated to a reduced expression of the WAF1/CIP1 gene product and to the presence of degradation fragments of p53 in the cytosol. Estradiol treatment prevented the growth inhibition induced by oligonucleotide transfection, simulating DNA damage. This observation indicated that the wild-type p53 gene product present in the MCF-7 cell could be inactivated by estradiol through nuclear exclusion to permit the cyclin-dependent phosphorylation events leading to the G1-S transition. In addition, the estradiol-induced inactivation of p53 could be involved in the tumorigenesis of estrogen-dependent neoplasm. PMID:10825127

  8. Intracellular cytokine production and cognition in healthy older adults.

    Science.gov (United States)

    Simpson, Ellen E A; Hodkinson, Claire F; Maylor, Elizabeth A; McCormack, Jacqueline M; Rae, Gordon; Strain, Sean; Alexander, H Denis; Wallace, Julie M W

    2013-10-01

    Elevated concentrations of the pro-inflammatory cytokines IL-1β and IL-6 have been associated with impaired cognitive performance. There are, however, few studies that have examined the relationship between cytokine production and specific aspects of cognition in healthy older individuals. Two-colour flow cytometry was used to determine intracellular cytokine production by activated monocytes, and neuropsychological tests were performed using the Cambridge Neuropsychological Test Automated Battery (CANTAB) in 93 apparently healthy men and women aged 55-70 years. A series of hierarchical regression analyses was carried out to examine the contribution of IL-1β and IL-6 (% expression and production (antibody binding capacity (ABC))) to recognition, attention and working memory, after controlling for socio-demographic variables (age, sex and social class). IL-1β% expression and IL-6 production predicted aspects of working memory. Recognition memory was found to be sensitive to the affects of age and social class. The current study suggests that higher intracellular cytokine production by activated monocytes may be predictive of lower cognitive performance in working memory in healthy older individuals. These findings indicate that utilization of models for in vivo cytokine production upon immune challenge may be useful in studying specific aspects of memory affected during inflammatory responses, for example in individuals at risk for cognitive decline owing to age-related inflammatory disorders. PMID:23664267

  9. Hybrid micro-/nanogels for optical sensing and intracellular imaging

    Directory of Open Access Journals (Sweden)

    Shuiqin Zhou

    2010-12-01

    Full Text Available Hybrid micro-/nanogels are playing an increasing important part in a diverse range of applications, due to their tunable dimensions, large surface area, stable interior network structure, and a very short response time. We review recent advances and challenges in the developments of hybrid micro-/nanogels toward applications for optical sensing of pH, temperature, glucose, ions, and other species as well as for intracellular imaging. Due to their unique advantages, hybrid micro-/nanogels as optical probes are attracting substantial interests for continuous monitoring of chemical parameters in complex samples such as blood and bioreactor fluids, in chemical research and industry, and in food quality control. In particular, their intracellular probing ability enables the monitoring of the biochemistry and biophysics of live cells over time and space, thus contributing to the explanation of intricate biological processes and the development of novel diagnoses. Unlike most other probes, hybrid micro-/nanogels could also combine other multiple functions into a single probe. The rational design of hybrid micro-/nanogels will not only improve the probing applications as desirable, but also implement their applications in new arenas. With ongoing rapid advances in bionanotechnology, the well-designed hybrid micro-/nanogel probes will be able to provide simultaneous sensing, imaging diagnosis, and therapy toward clinical applications.

  10. Transient light-induced intracellular oxidation revealed by redox biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Kolossov, Vladimir L., E-mail: viadimer@illinois.edu [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Beaudoin, Jessica N. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Hanafin, William P. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); DiLiberto, Stephen J. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Kenis, Paul J.A. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Avenue, Urbana, IL 61801 (United States); Rex Gaskins, H. [Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1207 W. Gregory Drive, Urbana, IL 61801 (United States); Department of Pathobiology, University of Illinois at Urbana-Champaign, 2001 S. Lincoln Avenue, Urbana, IL 61801 (United States); Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 S. Goodwin Avenue, Urbana, IL 61801 (United States)

    2013-10-04

    Highlights: •Time-resolved live cell imaging revealed light-induced oxidation. •Only the roGFP probe fused with glutaredoxin reveals photooxidation. •The transient oxidation is rapidly reduced by the cytosolic antioxidant system. •Intracellular photooxidation is media-dependent. •Oxidation is triggered exclusively by exposure to short wavelength excitation. -- Abstract: We have implemented a ratiometric, genetically encoded redox-sensitive green fluorescent protein fused to human glutaredoxin (Grx1-roGFP2) to monitor real time intracellular glutathione redox potentials of mammalian cells. This probe enabled detection of media-dependent oxidation of the cytosol triggered by short wavelength excitation. The transient nature of light-induced oxidation was revealed by time-lapse live cell imaging when time intervals of less than 30 s were implemented. In contrast, transient ROS generation was not observed with the parental roGFP2 probe without Grx1, which exhibits slower thiol-disulfide exchange. These data demonstrate that the enhanced sensitivity of the Grx1-roGFP2 fusion protein enables the detection of short-lived ROS in living cells. The superior sensitivity of Grx1-roGFP2, however, also enhances responsiveness to environmental cues introducing a greater likelihood of false positive results during image acquisition.

  11. Intracellular inclusions of a n-alkane-grown Arthrobacter

    International Nuclear Information System (INIS)

    The ultrastructural changes associated with the growth of a marine Arthrobacter sp. on n-hexadecane were demonstrated by transmission electron microscopy. Multiple electron translucent areas (ETI), similar to inclusions described by other investigators, were found in hydrocarbon-grown cells but not in peptone-grown cells. Stereological planimetry demonstrated that the ETI occupy as much as 40% of the hydrocarbon-grown cell's volume. Electron dense structures (EDI) were observed in hexadecane and in peptone-grown cells. Gas chromatographic analysis indicated traces of n-hexadecane associated with the hydrocarbon-grown cells: however, the hydrocarbon levels were not high enough to suggest the presence of hydrocarbon inclusions in the cells. Solvent partition studies with disrupted 14C-n-hexadecane-grown cells suggested that the intracellular radioactivity was associated with polar compounds. Acrylate-inhibited, hydrocarbon-grown Arthrobacter sp. did not form ETI, suggesting that the formation of ETI involves the participation of Coenzyme A. Thin-layer and gas chromatography indicated that the major intracellular components were glycerides, with one or more R groups composed of palmitic acid and free palmitic acid. 27 references, 5 figures, 2 tables

  12. Intracellular imaging of Qdots-labeled DNA in cyanobacteria.

    Science.gov (United States)

    Loukanov, Alexandre; Zhelyazkov, Veselin; Hihara, Yukako; Nakabayashi, Seiichiro

    2016-05-01

    In this contribution, they have attempted to develop a labeling technique for in vivo imaging of functionally active plasmid DNA in cyanobacterial cells through its decoration with semiconductor quantum dots (Qdots) as fluorescent nanoprobes. For that purpose biotinylated plasmid slr2060 DNA was conjugated with Qdots-streptavidine. The intact DNA was visualized in a single green color by light microscopy. These Qdots-DNA conjugates were capable of expressing the acyltransferase enzyme. Qdots-DNA conjugates and confocal microscope imaging technique were adopted to visualize the gene transport across the membrane of the live cyanobacteria cell in real time. Long-term kinetic study enabled to reveal the steps of extracellular and intracellular microenvironment for plasmid transportation into the live cell. To confirm these processes a confocal microscope and indicator plate assay test were applied in tandem. In this contribution, Qdots-labeled plasmid DNA was utilized for the first time for long-term intracellular imaging studies in cyanobacteria species PCC6803. The results showed that the Qdots-labeled plasmid DNA detection could be used as a powerful labeling technique for visualization of exogenous DNA entry and tracking into living cells by confocal microscopy. Microsc. Res. Tech. 79:447-452, 2016. © 2016 Wiley Periodicals, Inc. PMID:26957226

  13. Radiotoxicity of intracellular 67Ga, 125I and 3H

    International Nuclear Information System (INIS)

    L1210 leukaemia cells were labelled with various doses of 67Ga-citrate, 3H-thymidine, or 125I-iododeoxyuridine to evaluate the cytocidal effects of the intracellular decay of the three radionuclides. Based on radioisotope incorporation data, cellular dimensions, and intracellular radioisotope distributions (3H and 125I intranuclear, 67Ga cytoplasmic) the rates of deposition of cellular, nuclear, and cytoplasmic energy were calculated. In terms of energy absorption/cell, 67Ga (LD50: 2250 keV/hr; 69 rad/hr) was much less toxic than either 3H (LD50: 325 keV/hr; 10 rad/hr) or 125I (LD50: 50 keV/hr; 1.5 rad/hr). In terms of energy absorption/nucleus, 67Ga and 3H produced almost identical effects (LD50: 230 versus 255 keV/hr; 22.2 versus 24.6 rad/hr), but 125I remained much more toxic (LD50: 40 keV/hr; 3.9 rad/hr). (author)

  14. High prevalence, genetic diversity and intracellular growth ability of Legionella in hot spring environments.

    Directory of Open Access Journals (Sweden)

    Tian Qin

    Full Text Available BACKGROUND: Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. METHODS: Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE and sequence-based typing (SBT were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. RESULTS: Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (p<0.01. The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01. Legionella pneumophila was the most frequently isolated species (98.9%, and the isolated serogroups included serogroups 3 (25.3%, 6 (23.4%, 5 (19.2%, 1 (18.5%, 2 (10.2%, 8 (0.4%, 10 (0.8%, 9 (1.9% and 12 (0.4%. Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. CONCLUSIONS: Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control

  15. Autophagy Induced by Intracellular Infection of Propionibacterium acnes

    Science.gov (United States)

    Nakamura, Teruko; Furukawa, Asuka; Uchida, Keisuke; Ogawa, Tomohisa; Tamura, Tomoki; Sakonishi, Daisuke; Wada, Yuriko; Suzuki, Yoshimi; Ishige, Yuki; Minami, Junko; Akashi, Takumi

    2016-01-01

    Background Sarcoidosis is caused by Th1-type immune responses to unknown agents, and is linked to the infectious agent Propionibacterium acnes. Many strains of P. acnes isolated from sarcoid lesions cause intracellular infection and autophagy may contribute to the pathogenesis of sarcoidosis. We examined whether P. acnes induces autophagy. Methods Three cell lines from macrophages (Raw264.7), mesenchymal cells (MEF), and epithelial cells (HeLa) were infected by viable or heat-killed P. acnes (clinical isolate from sarcoid lymph node) at a multiplicity of infection (MOI) of 100 or 1000 for 1 h. Extracellular bacteria were killed by washing and culturing infected cells with antibiotics. Samples were examined by colony assay, electron-microscopy, and fluorescence-microscopy with anti-LC3 and anti-LAMP1 antibodies. Autophagy-deficient (Atg5-/-) MEF cells were also used. Results Small and large (≥5 μm in diameter) LC3-positive vacuoles containing few or many P. acnes cells (LC3-positive P. acnes) were frequently found in the three cell lines when infected by viable P. acnes at MOI 1000. LC3-positive large vacuoles were mostly LAMP1-positive. A few small LC3-positive/LAMP1-negative vacuoles were consistently observed in some infected cells for 24 h postinfection. The number of LC3-positive P. acnes was decreased at MOI 100 and completely abolished when heat-killed P. acnes was used. LC3-positive P. acnes was not found in autophagy-deficient Atg5-/- cells where the rate of infection was 25.3 and 17.6 times greater than that in wild-type Atg5+/+ cells at 48 h postinfection at MOI 100 and 1000, respectively. Electron-microscopic examination revealed bacterial cells surrounded mostly by a single-membrane including the large vacuoles and sometimes a double or multi-layered membrane, with occasional undigested bacterial cells in ruptured late endosomes or in the cytoplasm. Conclusion Autophagy was induced by intracellular P. acnes infection and contributed to intracellular

  16. Detection of intracellular bacterial communities in human urinary tract infection.

    Directory of Open Access Journals (Sweden)

    David A Rosen

    2007-12-01

    Full Text Available BACKGROUND: Urinary tract infections (UTIs are one of the most common bacterial infections and are predominantly caused by uropathogenic Escherichia coli (UPEC. While UTIs are typically considered extracellular infections, it has been recently demonstrated that UPEC bind to, invade, and replicate within the murine bladder urothelium to form intracellular bacterial communities (IBCs. These IBCs dissociate and bacteria flux out of bladder facet cells, some with filamentous morphology, and ultimately establish quiescent intracellular reservoirs that can seed recurrent infection. This IBC pathogenic cycle has not yet been investigated in humans. In this study we sought to determine whether evidence of an IBC pathway could be found in urine specimens from women with acute UTI. METHODS AND FINDINGS: We collected midstream, clean-catch urine specimens from 80 young healthy women with acute uncomplicated cystitis and 20 asymptomatic women with a history of UTI. Investigators were blinded to culture results and clinical history. Samples were analyzed by light microscopy, immunofluorescence, and electron microscopy for evidence of exfoliated IBCs and filamentous bacteria. Evidence of IBCs was found in 14 of 80 (18% urines from women with UTI. Filamentous bacteria were found in 33 of 80 (41% urines from women with UTI. None of the 20 urines from the asymptomatic comparative group showed evidence of IBCs or filaments. Filamentous bacteria were present in all 14 of the urines with IBCs compared to 19 (29% of 66 samples with no evidence of IBCs (p < 0.001. Of 65 urines from patients with E. coli infections, 14 (22% had evidence of IBCs and 29 (45% had filamentous bacteria, while none of the gram-positive infections had IBCs or filamentous bacteria. CONCLUSIONS: The presence of exfoliated IBCs and filamentous bacteria in the urines of women with acute cystitis suggests that the IBC pathogenic pathway characterized in the murine model may occur in humans. The

  17. Cotransporters as molecular water pumps

    DEFF Research Database (Denmark)

    Zeuthen, Thomas; MacAulay, Nanna

    2002-01-01

    for such cotransport can be ruled out for both experimental and theoretical reasons. Indeed, substrate fluxes mediated by channels or ionophores generate much smaller water fluxes than those observed with cotransporters. Theoretical models, using reasonable values for the intracellular diffusion coefficient, indicate...

  18. Effects of microgravity environment on intracellular signal transduction pathways

    Directory of Open Access Journals (Sweden)

    De CHANG

    2012-09-01

    Full Text Available Microgravity environment is a stress and extracellular signal that affects cellular morphology and function through signal transduction system, thus leading to certain biological effect. At present, many signaling pathways have been reported to be involved in the regulation of cell function under microgravity environment, such as NF-κB signaling pathway, Notch signaling pathway, MAPK signaling pathway, HSP signaling pathway and so on, and these reports have laid a foundation for the molecular studies of cytolergy under outer space environment. The recent progress in the researches on intracellular signaling pathways affected by microgravity is herewith reviewed in present paper in the hope of providing references for understanding the cell activity in space environment, and to find the ways to alleviate the harmful effects caused by the microgravity environment.

  19. Intracellular probes for imaging oxygen concentration: how good are they?

    Science.gov (United States)

    Dmitriev, Ruslan I.; Papkovsky, Dmitri B.

    2015-09-01

    In the last decade a number of cell-permeable phosphorescence based probes for imaging of (intra)cellular oxygen (icO2) have been described. These small molecule, supramolecular and nanoparticle structures, although allowing analysis of hypoxia, local gradients and fluctuations in O2, responses to stimulation and drug treatment at sub-cellular level with high spatial and temporal resolution, differ significantly in their operational performance and applicability to different cell and tissue models. Here we discuss and compare these probes with respect to their staining efficiency, brightness, photostability, toxicity, cell specificity, compatibility with different cell and tissue models, and analytical performance. Merits and limitations of particular probes are highlighted and strategies for development of new high-performance O2 imaging probes defined. Key application areas in hypoxia research, stem cells, cancer biology and tissue physiology are also discussed.

  20. Subcellular site and nature of intracellular cadmium in plants

    International Nuclear Information System (INIS)

    The mechanisms underlying heavy metal accumulation, toxicity and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent of, subcellular site of and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied 109CdCl2 or 112CdSO4 accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissue followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. Particulate materials containing other cell components were also labeled. Of the 109Cd supplied to plants, 2 to 10% was recovered in both cytosol preparations and in particulate materials. Cytosol contained proteinaceous--Cd complexes, free metal and low molecular weight Cd complexes. Labeling of protoplasts gave similar results. No evidence was obtained for the production of volatile Cd complexes in tobacco

  1. Intracellular Signaling Mediators in the Circulatory and Ventilatory Systems

    CERN Document Server

    Thiriet, Marc

    2013-01-01

    The volumes in this authoritative series present a multidisciplinary approach to modeling and simulation of flows in the cardiovascular and ventilatory systems, especially multiscale modeling and coupled simulations. The cardiovascular and respiratory systems are tightly coupled, as their primary function is to supply oxygen to and remove carbon dioxide from the body's cells. Because physiological conduits have deformable and reactive walls, macroscopic flow behavior and prediction must be coupled to phenomenological models of nano- and microscopic events in a corrector scheme of regulated mechanisms when the vessel lumen caliber varies markedly. Therefore, investigation of flows of blood and air in physiological conduits requires an understanding of the biology, chemistry, and physics of these systems together with the mathematical tools to describe their functioning. Volume 4 is devoted to major sets of intracellular mediators that transmit signals upon stimulation of cell-surface receptors.  Activation of...

  2. Intracellular pH in rat pancreatic ducts

    DEFF Research Database (Denmark)

    Novak, I; Hug, M; Greger, R

    1997-01-01

    buffers (20 mmol/l) led to pHi changes in accordance with entry of lipid-soluble forms of the buffers, followed by back-regulation of pHi by duct cells. In another type of experiment, changes in extracellular pH of solutions containing HEPES or HCO3-/CO2 buffers led to significant changes in pHi that did......- exchanger. Under some conditions, these exchangers can be invoked to regulate cell pH.......In order to study the mechanism of H+ and HCO3- transport in a HCO3- secreting epithelium, pancreatic ducts, we have measured the intracellular pH (pHi) in this tissue using the pH sensitive probe BCECF. We found that exposures of ducts to solutions containing acetate/acetic acid or NH4+/NH3...

  3. Measuring intracellular redox conditions using GFP-based sensors

    DEFF Research Database (Denmark)

    Björnberg, Olof; Ostergaard, Henrik; Winther, Jakob R

    2006-01-01

    Recent years have seen the development of methods for analyzing the redox conditions in specific compartments in living cells. These methods are based on genetically encoded sensors comprising variants of Green Fluorescent Protein in which vicinal cysteine residues have been introduced at solvent......-exposed positions. Several mutant forms have been identified in which formation of a disulfide bond between these cysteine residues results in changes of their fluorescence properties. The redox sensors have been characterized biochemically and found to behave differently, both spectroscopically and in terms...... of redox properties. As genetically encoded sensors they can be expressed in living cells and used for analysis of intracellular redox conditions; however, which parameters are measured depends on how the sensors interact with various cellular redox components. Results of both biochemical and cell...

  4. [Isolation of Mycobacterium avium-intracellulare from a hepatic biopsy].

    Science.gov (United States)

    Ruiz, Aroldo; Mederos, Lilian; Capó, Virginia

    2002-01-01

    A 64 years-old patient, who was a farmer suffering from chronic fever for two years, loss of weight and acute asthenia, was studied. He was admitted to "Pedro Kourí" Tropical Medicine Institute where the studies were conducted and revealed a globular sedimentation rate of 116 mm in 2 hours, and anemia of 9,8g% hemoglobin. The laparoscopic study indicated hepatic granulomatosis that was confirmed by hepatic biopsy in which a sample was taken from the liver to be microbiologically and cytologically examined. By microbiological methods, a non-pigmented slowly-growing strain was isolated, which was classified by conventional diagnostic techniques for the non-tuberculous mycobacteria classification and the alternative diagnosing technique known as bidimensional thin layer chromatography to confirm the previous classification and set the mycolic acid patterns. The isolated strain belonged to group III of Rynyon and was identified as Mycobacterium avium-intracellulare. PMID:15849945

  5. Intracellular behaviour of samarium and europium in lactating mammary gland

    Institute of Scientific and Technical Information of China (English)

    Ayadi Ahlem; Maghraoui Samira; El Hili Ali; Galle Pierre; Tekaya Leila

    2012-01-01

    The subcellular localization of samarium and europium,two rare-earths,increasingly used in both medical and industrial fields,has been studied in several organs such as liver and kidney but never in the mammary gland despite of its importance in the biology of lactation and nutrition domains.The intracellular behaviour of samarium and europium after their intra-peritoneal administration in the lactating mammary gland cells was investigated.The results showed the presence of very electron dense deposits in the glandular epithelial cell lysosomes.These particular lysosomes were never observed in the marnrnary cell lysosomes of control rats.These intralysosomal deposits were probably composed of insoluble samarium or europium phosphates by analogy with previous studies,the transmission electron microscopy,the ion mass microscopy and the electron probe microanalysis,and other techniques allowing the identification of the chemical structure of the intralysosomal deposits.

  6. Handcuffs for bacteria - NDP52 orchestrates xenophagy of intracellular Salmonella

    Directory of Open Access Journals (Sweden)

    Pauline Verlhac

    2015-05-01

    Full Text Available Eukaryotic cells can selectively target and degrade intracellular pathogens using autophagy, a process referred to as xenophagy. This selectivity is controlled by proteins called autophagy receptors, which can recognise pathogens and address them to the autophagy machinery. Among them, NDP52 can recognise Salmonella Typhimurium on the one hand and the ATG8 family member LC3C on the other hand, thus allowing the docking of the bacteria to a growing autophagosome. Additionally, we recently reported that NDP52 is involved in the maturation of the bacteria-containing autophagosome and hence necessary for the ultimate degradation of the bacteria. These two functions of NDP52 are independent as they rely on distinct binding domains and protein partners. Therefore, NDP52 plays a dual role during xenophagy, first by targeting the bacteria to the autophagy machinery and then by regulating its degradation.

  7. Superdiffusion dominates intracellular particle motion in the supercrowded space of pathogenic Acanthamoeba castellanii

    CERN Document Server

    Reverey, J F; Bao, H; Leippe, M; Metzler, R; Selhuber-Unkel, C

    2015-01-01

    Acanthamoebae are free-living protists and human pathogens, whose cellular functions and pathogenicity strongly depend on the transport of intracellular vesicles and granules through the cytosol. Using high-speed live cell imaging in combination with single-particle tracking analysis, we show here that the motion of endogenous intracellular particles in the size range from a few hundred nanometers to several micrometers in Acanthamoeba castellanii is strongly superdiffusive and influenced by cell locomotion, cytoskeletal elements, and myosin II. We demonstrate that cell locomotion significantly contributes to intracellular particle motion, but is clearly not the only origin of superdiffusivity. By analyzing the contribution of microtubules, actin, and myosin II motors we show that myosin II is a major driving force of intracellular motion in A. castellanii. The cytoplasm of A. castellanii is supercrowded with intracellular vesicles and granules, such that significant intracellular motion can only be achieved ...

  8. EFFECTS OF PDGF-BB ON INTRACELLULAR CALCIUM CONCENTRATION AND PROLIFERATION IN CULTURED GLOMERULAR MESANGIAL CELLS

    Institute of Scientific and Technical Information of China (English)

    WEN Li-ping; ZHANG Chong; BIAN Fan; ZOU Jun; JIANG Geng-ru; ZHU Han-wei

    2006-01-01

    Objective To investigate the relationship between the alteration of intracellular calcium concentration and proliferation in cultured glomerular mesangial cells. Methods Rat mesangial cells were cultured.Intracellular calcium concentrations were measured by confocal Laser Scanning Microscopy and Fura-3 fluorescence dyeing techniques. Cell growth was measured by MTT assay. Results PDGF-BB increased intracellular calcium concentrations in a dose-dependent manner, and at the same time promote the proliferation of mesangial cells. After preincubation with calcium channel blocker nifedipine or angiotensin converting enzyme inhibitor captopril, both the increase of intracellular calcium concentrations and cell proliferations induced by PDGF-BB were inhibited. Tripterigium Wilfordii Glycosides (TMG) significantly inhibited the mesangial cell proliferations, but it had no significant effect on intracellular calcium concentrations. Conclusion There was a positive relationship between the elevation of intracellular calcium concentration and cell proliferation in glomerular mesangial cells, but the increase of in- tracellular calcium concentrations wasn't the only way for proliferation.

  9. Endothelial tubes assemble from intracellular vacuoles in vivo.

    Science.gov (United States)

    Kamei, Makoto; Saunders, W Brian; Bayless, Kayla J; Dye, Louis; Davis, George E; Weinstein, Brant M

    2006-07-27

    The formation of epithelial tubes is crucial for the proper development of many different tissues and organs, and occurs by means of a variety of different mechanisms. Morphogenesis of seamless, properly patterned endothelial tubes is essential for the development of a functional vertebrate circulatory system, but the mechanism of vascular lumenization in vivo remains unclear. Evidence dating back more than 100 years has hinted at an important function for endothelial vacuoles in lumen formation. More than 25 years ago, in some of the first endothelial cell culture experiments in vitro, Folkman and Haudenschild described "longitudinal vacuoles" that "appeared to be extruded and connected from one cell to the next", observations confirmed and extended by later studies in vitro showing that intracellular vacuoles arise from integrin-dependent and cdc42/Rac1-dependent pinocytic events downstream of integrin-extracellular-matrix signalling interactions. Despite compelling data supporting a model for the assembly of endothelial tubes in vitro through the formation and fusion of vacuoles, conclusive evidence in vivo has been lacking, primarily because of difficulties associated with imaging the dynamics of subcellular endothelial vacuoles deep within living animals. Here we use high-resolution time-lapse two-photon imaging of transgenic zebrafish to examine how endothelial tubes assemble in vivo, comparing our results with time-lapse imaging of human endothelial-cell tube formation in three-dimensional collagen matrices in vitro. Our results provide strong support for a model in which the formation and intracellular and intercellular fusion of endothelial vacuoles drives vascular lumen formation. PMID:16799567

  10. Intracellular Ascorbate Prevents Endothelial Barrier Permeabilization by Thrombin.

    Science.gov (United States)

    Parker, William H; Qu, Zhi-chao; May, James M

    2015-08-28

    Intracellular ascorbate (vitamin C) has previously been shown to tighten the endothelial barrier and maintain barrier integrity during acute inflammation in vitro. However, the downstream effectors of ascorbate in the regulation of endothelial permeability remain unclear. In this study, we evaluated ascorbate as a mediator of thrombin-induced barrier permeabilization in human umbilical vein endothelial cells and their immortalized hybridoma line, EA.hy926. We found that the vitamin fully prevented increased permeability to the polysaccharide inulin by thrombin in a dose-dependent manner, and it took effect both before and after subjection to thrombin. Thrombin exposure consumed intracellular ascorbate but not the endogenous antioxidant GSH. Likewise, the antioxidants dithiothreitol and tempol did not reverse permeabilization. We identified a novel role for ascorbate in preserving cAMP during thrombin stimulation, resulting in two downstream effects. First, ascorbate maintained the cortical actin cytoskeleton in a Rap1- and Rac1-dependent manner, thus preserving stable adherens junctions between adjacent cells. Second, ascorbate prevented actin polymerization and formation of stress fibers by reducing the activation of RhoA and phosphorylation of myosin light chain. Although ascorbate and thrombin both required calcium for their respective effects, ascorbate did not prevent thrombin permeabilization by obstructing calcium influx. However, preservation of cAMP by ascorbate was found to depend on both the production of nitric oxide by endothelial nitric-oxide synthase, which ascorbate is known to activate, and the subsequent generation cGMP by guanylate cyclase. Together, these data implicate ascorbate in the prevention of inflammatory endothelial barrier permeabilization and explain the underlying signaling mechanism. PMID:26152729

  11. Bioreducible Lipid-like Nanoparticles for Intracellular Protein Delivery

    Science.gov (United States)

    Arellano, Carlos Luis

    Protein-based therapy is one of the most direct ways to manipulate cell function and treat human disease. Although protein therapeutics has made its way to clinical practice, with five of the top fifteen global pharmaceuticals being peptide or protein-based drugs, one common limitation is that the effects of protein therapy are only achieved through the targeting of cell surface receptors and intracellular domains. Due to the impermeability of the cell membrane to most foreign materials, entire classes of potentially therapeutic proteins cannot thoroughly be studied without a safe and efficient method of transporting proteins into the cytosol. We report the use of a combinatorially-designed bioreducible lipid-like material (termed "lipidoid") - based protein delivery platform for the transfection of human cancer cell lines. Lipidoid nanoparticles are synthesized through a thin film dispersion method. The degradation of the bioreducible nanoparticles was observed when exposed to glutathione, a highly reductive compound present in the cytosol. We demonstrate that the nanoparticles are capable of transfecting a dose-dependent concentration of our model protein, beta-galactosidase into HeLa cells. Furthermore, formulations of the lipidoid containing the cytotoxic proteins saporin and RNase-A are both capable of inhibiting tumor cell proliferation as observed in in vitro treatment of different human cancer cell lines. There was no observed loss in protein activity after lyophilization and long--term storage, indicating the potential of pre-clinical applications. Overall, we demonstrate an effective approach to protein formulation and intracellular delivery. We believe that our formulations will lead to the study of a whole class of previously untapped therapeutics that may generate new solutions for previously untreatable diseases.

  12. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.

    Science.gov (United States)

    Cuomo, Christina A; Desjardins, Christopher A; Bakowski, Malina A; Goldberg, Jonathan; Ma, Amy T; Becnel, James J; Didier, Elizabeth S; Fan, Lin; Heiman, David I; Levin, Joshua Z; Young, Sarah; Zeng, Qiandong; Troemel, Emily R

    2012-12-01

    Microsporidia comprise a large phylum of obligate intracellular eukaryotes that are fungal-related parasites responsible for widespread disease, and here we address questions about microsporidia biology and evolution. We sequenced three microsporidian genomes from two species, Nematocida parisii and Nematocida sp1, which are natural pathogens of Caenorhabditis nematodes and provide model systems for studying microsporidian pathogenesis. We performed deep sequencing of transcripts from a time course of N. parisii infection. Examination of pathogen gene expression revealed compact transcripts and a dramatic takeover of host cells by Nematocida. We also performed phylogenomic analyses of Nematocida and other microsporidian genomes to refine microsporidian phylogeny and identify evolutionary events of gene loss, acquisition, and modification. In particular, we found that all microsporidia lost the tumor-suppressor gene retinoblastoma, which we speculate could accelerate the parasite cell cycle and increase the mutation rate. We also found that microsporidia acquired transporters that could import nucleosides to fuel rapid growth. In addition, microsporidian hexokinases gained secretion signal sequences, and in a functional assay these were sufficient to export proteins out of the cell; thus hexokinase may be targeted into the host cell to reprogram it toward biosynthesis. Similar molecular changes appear during formation of cancer cells and may be evolutionary strategies adopted independently by microsporidia to proliferate rapidly within host cells. Finally, analysis of genome polymorphisms revealed evidence for a sexual cycle that may provide genetic diversity to alleviate problems caused by clonal growth. Together these events may explain the emergence and success of these diverse intracellular parasites. PMID:22813931

  13. Squalestatin alters the intracellular trafficking of a neurotoxic prion peptide

    Directory of Open Access Journals (Sweden)

    Williams Alun

    2007-11-01

    Full Text Available Abstract Background Neurotoxic peptides derived from the protease-resistant core of the prion protein are used to model the pathogenesis of prion diseases. The current study characterised the ingestion, internalization and intracellular trafficking of a neurotoxic peptide containing amino acids 105–132 of the murine prion protein (MoPrP105-132 in neuroblastoma cells and primary cortical neurons. Results Fluorescence microscopy and cell fractionation techniques showed that MoPrP105-132 co-localised with lipid raft markers (cholera toxin and caveolin-1 and trafficked intracellularly within lipid rafts. This trafficking followed a non-classical endosomal pathway delivering peptide to the Golgi and ER, avoiding classical endosomal trafficking via early endosomes to lysosomes. Fluorescence resonance energy transfer analysis demonstrated close interactions of MoPrP105-132 with cytoplasmic phospholipase A2 (cPLA2 and cyclo-oxygenase-1 (COX-1, enzymes implicated in the neurotoxicity of prions. Treatment with squalestatin reduced neuronal cholesterol levels and caused the redistribution of MoPrP105-132 out of lipid rafts. In squalestatin-treated cells, MoPrP105-132 was rerouted away from the Golgi/ER into degradative lysosomes. Squalestatin treatment also reduced the association between MoPrP105-132 and cPLA2/COX-1. Conclusion As the observed shift in peptide trafficking was accompanied by increased cell survival these studies suggest that the neurotoxicity of this PrP peptide is dependent on trafficking to specific organelles where it activates specific signal transduction pathways.

  14. Modulation of intracellular Ca2+ levels by Scorpaenidae venoms.

    Science.gov (United States)

    Church, Jarrod E; Moldrich, Randal X; Beart, Philip M; Hodgson, Wayne C

    2003-05-01

    The crude venoms of the soldierfish (Gymnapistes marmoratus), the lionfish (Pterois volitans) and the stonefish (Synanceia trachynis) display pronounced neuromuscular activity. Since [Ca(2+)](i) is a key regulator in many aspects of neuromuscular function we sought to determine its involvement in the neuromuscular actions of the venoms. In the chick biventer cervicis muscle, all three venoms produced a sustained contraction (approx 20-30% of 1mM acetylcholine). Blockade of nicotinic receptors with tubocurarine (10 micro M) failed to attenuate the contractile response to either G. marmoratus venom or P. volitans venom, but produced slight inhibition of the response to S. trachynis venom. All three venoms produced a rise in intracellular Ca(2+) (approx. 200-300% of basal) in cultured murine cortical neurons. The Ca(2+)-channel blockers omega-conotoxin MVIIC, omega-conotoxin GVIA, omega-agatoxin IVa and nifedipine (each at 1 micro M) potentiated the increase in [Ca(2+)](i) in response to G. marmoratus venom and P. volitans venom, while attenuating the response to S. trachynis venom. Removal of extracellular Ca(2+), replacement of Ca(2+) with La(3+) (0.5mM), or addition of stonefish antivenom (3units/ml) inhibited both the venom-induced increase in [Ca(2+)](i) in cultured neurones and contraction in chick biventer cervicis muscle. Venom-induced increases in [Ca(2+)](i) correlated with an increased cell death of cultured neurones as measured using propidium iodide (1 micro g/ml). Morphological analysis revealed cellular swelling and neurite loss consistent with necrosis. These data indicate that the effects of all three venoms are due in part to an increase in intracellular Ca(2+), possibly via the formation of pores in the cellular membrane which, under certain conditions, can lead to necrosis. PMID:12727272

  15. Intracellular MMP-2 Activity in Skeletal Muscle is Associated with Type II Fibers

    OpenAIRE

    Hadler-Olsen, Elin Synnøve; Solli, Ann Iren; Hafstad, Anne Dragøy; Winberg, Jan-Olof; Uhlin-Hansen, Lars

    2014-01-01

    Matrix metalloproteinase 2 (MMP-2) is a proteolytic enzyme implicated in motility, differentiation, and regeneration of skeletal muscle fibers through processing of extracellular substrates. Although MMP-2 has been found to be localized intracellularly in cardiomyocytes where the enzyme is thought to contribute to post-ischemic loss of contractility, little is known about intracellular MMP-2 activity in skeletal muscle fibers. In the present study we demonstrate intracellular MMP-2 in normal ...

  16. Intracellular Ca2+ thresholds that determine survival or death of energy-deprived cells.

    OpenAIRE

    Dong, Z.; Saikumar, P; Griess, G A; Weinberg, J. M.; Venkatachalam, M. A.

    1998-01-01

    Increase of intracellular ionized or free Ca2+ is thought to play a central role in cell death due to ATP depletion. However, concurrently operative mechanisms of injury that do not require intracellular Ca2+ increases have made it difficult to test this hypothesis or to determine the concentrations at which intracellular Ca2+ becomes lethal. The predominant Ca2+-independent mechanism of injury during ATP depletion involves the loss of cellular glycine. This type of damage can be fully inhibi...

  17. Intracellular Trypsin Induces Pancreatic Acinar Cell Death but Not NF-κB Activation*

    OpenAIRE

    JI, BAOAN; Gaiser, Sebastian; Chen, Xueqing; Ernst, Stephen A.; Logsdon, Craig D.

    2009-01-01

    Premature intracellular activation of the digestive enzyme trypsinogen is considered to be the initiating event in pancreatitis. However, the direct consequences of intracellular trypsin activity have not previously been examined. In the current study, a mutant trypsinogen (paired basic amino acid cleaving enzyme (PACE)-trypsinogen), which is activated intracellularly by the endogenous protease PACE, was developed. This new construct allowed for the first time direct examination of the effect...

  18. Intracellular Activity of Antibiotics against Staphylococcus aureus in a Mouse Peritonitis Model ▿

    OpenAIRE

    Sandberg, Anne; Hessler, Jonas H. R.; Skov, Robert L.; Blom, Jens; Frimodt-Møller, Niels

    2009-01-01

    Antibiotic treatment of Staphylococcus aureus infections is often problematic due to the slow response to therapy and the high frequency of infection recurrence. The intracellular persistence of staphylococci has been recognized and could offer a good explanation for these treatment difficulties. Knowledge of the interplay between intracellular antibiotic activity and the overall outcome of infection is therefore important. Several intracellular in vitro models have been developed, but few ex...

  19. Rapid Method To Determine Intracellular Drug Concentrations in Cellular Uptake Assays: Application to Metformin in Organic Cation Transporter 1-Transfected Human Embryonic Kidney 293 Cells.

    Science.gov (United States)

    Chien, Huan-Chieh; Zur, Arik A; Maurer, Tristan S; Yee, Sook Wah; Tolsma, John; Jasper, Paul; Scott, Dennis O; Giacomini, Kathleen M

    2016-03-01

    Because of the importance of intracellular unbound drug concentrations in the prediction of in vivo concentrations that are determinants of drug efficacy and toxicity, a number of assays have been developed to assess in vitro unbound concentrations of drugs. Here we present a rapid method to determine the intracellular unbound drug concentrations in cultured cells, and we apply the method along with a mechanistic model to predict concentrations of metformin in subcellular compartments of stably transfected human embryonic kidney 293 (HEK293) cells. Intracellular space (ICS) was calculated by subtracting the [(3)H]-inulin distribution volume (extracellular space, ECS) from the [(14)C]-urea distribution volume (total water space, TWS). Values obtained for intracellular space (mean ± S.E.M.; μl/10(6) cells) of monolayers of HEK cells (HEK-empty vector [EV]) and cells overexpressing human organic cation transporter 1 (HEK-OCT1), 1.21± 0.07 and 1.25±0.06, respectively, were used to determine the intracellular metformin concentrations. After incubation of the cells with 5 µM metformin, the intracellular concentrations were 26.4 ± 7.8 μM and 268 ± 11.0 μM, respectively, in HEK-EV and HEK-OCT1. In addition, intracellular metformin concentrations were lower in high K(+) buffer (140 mM KCl) compared with normal K(+) buffer (5.4 mM KCl) in HEK-OCT1 cells (54.8 ± 3.8 μM and 198.1 ± 11.2 μM, respectively; P < 0.05). Our mechanistic model suggests that, depending on the credible range of assumed physiologic values, the positively charged metformin accumulates to particularly high levels in endoplasmic reticulum and/or mitochondria. This method together with the computational model can be used to determine intracellular unbound concentrations and to predict subcellular accumulation of drugs in other complex systems such as primary cells. PMID:26700958

  20. The small GTPase RAB-11 directs polarized exocytosis of the intracellular pathogen N. parisii for fecal-oral transmission from C. elegans

    OpenAIRE

    Szumowski, Suzannah C.; Botts, Michael R.; Popovich, John J.; Smelkinson, Margery G.; Troemel, Emily R.

    2014-01-01

    Microbial pathogens cause food and water-borne disease through infection of the intestine. Many of these pathogens invade intestinal cells to replicate, but they ultimately need to exit out of these cells to spread to new hosts. We use the transparent nematode Caenorhabditis elegans to show that a natural intracellular pathogen called Nematocida parisii escapes from intestinal cells by using host trafficking pathways and a host small GTPase protein called RAB-11 for directional exocytosis int...

  1. Quantitative measurement of absolute cell volume and intracellular integral refractive index (RI) with dual-wavelength digital holographic microscopy (DHM)

    Science.gov (United States)

    Boss, Daniel; Kühn, Jonas; Depeursinge, Christian; Magistretti, Pierre J.; Marquet, Pierre

    2012-06-01

    Quantitative Phase Imaging techniques including DHM have been applied recently in the field of cell imaging to monitor and quantify non-invasively dynamic cellular processes modifying cell morphology and/or content . Concretely, the DHM phase signal is highly sensitive to cell thickness and intracellular integral RI variations associated with transmembrane water movements. As net water flow across the cell membrane leads at the same time to changes in cell thickness and intracellular RI, the interpretation of phase signal variations remains difficult. To overcome this drawback, we have developed a Dual-wavelength Digital Holographic Microscopy (DHM) setup allowing to separately measure, with a single CCD camera acquisition, thickness and integral RI of living cells. The method is based on the use of an absorbing dye that enhances the refractive index dispersion of the extracellular medium. Practically, two significantly different phase signals can be obtained when measuring at two appropriate wavelengths. From the two phase measurements, both cell RI and thickness can be univocally determined.

  2. Comparative Salt Stress Study on Intracellular Ion Concentration in Marine and Salt-adapted Freshwater Strains of Microalgae

    Directory of Open Access Journals (Sweden)

    Ahmad Farhad TALEBI

    2013-08-01

    Full Text Available Salinity imposes significant stresses in various living organisms including microalgae. High extracellular concentration of Na+ directly influences ionic balance inside the cell and subsequently the cellular activities. In the present study, the effect of such stress on growth and intracellular ions concentration (IIC of Dunaliella salina and Chlorella Spp. was investigated. IIC was analyzed using Ion chromatography technique. D. salina showed the highest degree of resistance to increase in salinity as little changes occurred both in IIC and in growth parameters. D. salina could maintain the balance of K+ inside the cell and eject the excess Na+ even at NaCl concentrations above 1M. Moreover, D. salina accumulated β-carotene in order to protect its photosynthetic apparatus. Among Chlorella species, C. vulgaris showed signs of adaptation to high content of salinity, though it is a fresh water species by nature. Moreover, the response shown by C. vulgaris to rise in salinity was even stronger than that of C. salina, which is presumably a salt-water resistant species. In fact, C. vulgaris could maintain intracellular K+ better than C. salina in response to increasing salinity, and as a result, it could survive at NaCl concentrations as high as 0.75 M. Marine strains such as D. salina well cope with the fluctuations in salinity through the existing adaptation mechanisms i.e. maintaining the K+/N+ balance inside the cell, K+ accumulation and Na+ ejection, accumulation of photosynthetic pigments like β-carotene.

  3. Intracellular trafficking of silicon particles and logic-embedded vectors

    Science.gov (United States)

    Ferrati, Silvia; Mack, Aaron; Chiappini, Ciro; Liu, Xuewu; Bean, Andrew J.; Ferrari, Mauro; Serda, Rita E.

    2010-08-01

    Mesoporous silicon particles show great promise for use in drug delivery and imaging applications as carriers for second-stage nanoparticles and higher order particles or therapeutics. Modulation of particle geometry, surface chemistry, and porosity allows silicon particles to be optimized for specific applications such as vascular targeting and avoidance of biological barriers commonly found between the site of drug injection and the final destination. In this study, the intracellular trafficking of unloaded carrier silicon particles and carrier particles loaded with secondary iron oxide nanoparticles was investigated. Following cellular uptake, membrane-encapsulated silicon particles migrated to the perinuclear region of the cell by a microtubule-driven mechanism. Surface charge, shape (spherical and hemispherical) and size (1.6 and 3.2 μm) of the particle did not alter the rate of migration. Maturation of the phagosome was associated with an increase in acidity and acquisition of markers of late endosomes and lysosomes. Cellular uptake of iron oxide nanoparticle-loaded silicon particles resulted in sorting of the particles and trafficking to unique destinations. The silicon carriers remained localized in phagosomes, while the second stage iron oxide nanoparticles were sorted into multi-vesicular bodies that dissociated from the phagosome into novel membrane-bound compartments. Release of iron from the cells may represent exocytosis of iron oxide nanoparticle-loaded vesicles. These results reinforce the concept of multi-functional nanocarriers, in which different particles are able to perform specific tasks, in order to deliver single- or multi-component payloads to specific sub-cellular compartments.Mesoporous silicon particles show great promise for use in drug delivery and imaging applications as carriers for second-stage nanoparticles and higher order particles or therapeutics. Modulation of particle geometry, surface chemistry, and porosity allows silicon

  4. Intracellular activity of antibiotics against Staphylococcus aureus in a mouse peritonitis model.

    Science.gov (United States)

    Sandberg, Anne; Hessler, Jonas H R; Skov, Robert L; Blom, Jens; Frimodt-Møller, Niels

    2009-05-01

    Antibiotic treatment of Staphylococcus aureus infections is often problematic due to the slow response to therapy and the high frequency of infection recurrence. The intracellular persistence of staphylococci has been recognized and could offer a good explanation for these treatment difficulties. Knowledge of the interplay between intracellular antibiotic activity and the overall outcome of infection is therefore important. Several intracellular in vitro models have been developed, but few experimental animal models have been published. The mouse peritonitis/sepsis model was used as the basic in vivo model exploring a quantitative ex vivo extra- and intracellular differentiation assay. The intracellular presence of S. aureus was documented by electron microscopy. Five antibiotics, dicloxacillin, cefuroxime, gentamicin, azithromycin, and rifampin (rifampicin), were tested in the new in vivo model; and the model was able to distinguish between their extra- and intracellular effects. The intracellular effects of the five antibiotics could be ranked as follows as the mean change in the log(10) number of CFU/ml (Delta log(10) CFU/ml) between treated and untreated mice after 4 h of treatment: dicloxacillin (3.70 Delta log(10) CFU/ml) > cefuroxime (3.56 Delta log(10) CFU/ml) > rifampin (1.86 Delta log(10) CFU/ml) > gentamicin (0.61 Delta log(10) CFU/ml) > azithromycin (0.21 Delta log(10) CFU/ml). We could also show that the important factors during testing of intracellular activity in vivo are the size, number, and frequency of doses; the time of exposure; and the timing between the start of infection and treatment. A poor correlation between the intracellular accumulation of the antibiotics and the actual intracellular effect was found. This stresses the importance of performing experimental studies, like those with the new in vivo model described here, to measure actual intracellular activity instead of making predictions based on cellular pharmacokinetic and MICs. PMID

  5. Use of designed experiments for the improvement of pre-analytical workflow for the quantification of intracellular nucleotides in cultured cell lines.

    Science.gov (United States)

    Machon, Christelle; Bordes, Claire; Cros-Perrial, Emeline; Clement, Yohann; Jordheim, Lars Petter; Lanteri, Pierre; Guitton, Jérôme

    2015-07-31

    The present study is focused on the development of a pre-analytical strategy for the quantification of intracellular nucleotides from cultured cell lines. Different protocols, including cell recovery, nucleotide extraction and purification, were compared on a panel of nucleoside mono-, di- and triphosphates from four cell lines (adherent and suspension cells). The quantification of nucleotides was performed using a validated technique with on-line solid-phase extraction coupled with liquid chromatography-triple quadrupole tandem mass spectrometry (LC-MS/MS). Designed experiments were implemented to investigate, in a rigorous and limited-testing experimental approach, the influence of several operating parameters. Results showed that the technique used to harvest adherent cells drastically affected the amounts of intracellular nucleotides. Scraping cells was deleterious because of a major leakage (more than 70%) of intracellular nucleotides during scraping. Moreover, some other tested conditions should be avoided, such as using pure methanol as extraction solvent (decrease over 50% of intracellular nucleotides extracted from NCI-H292 cells) or adding a purification step with chloroform. Designed experiments allowed identifying an interaction between the percentage of methanol and the presence of chloroform. The mixture methanol/water (70/30, v/v) was considered as the best compromise according to the nucleoside mono-, di-, or triphosphates and the four cell lines studied. This work highlights the importance of pre-analytical step combined with the cell lines studied associated to sensitive and validated assay for the quantification of nucleotides in biological matrices. PMID:26094139

  6. Study on intracellular trafficking of Mac-1 by direct visualization

    Institute of Scientific and Technical Information of China (English)

    YAN Ming; MAO Jifang; WEI Yi; ZHONG Jigen; YANG Shengsheng; XU Renbao

    2004-01-01

    Previously, we constructed DNA vectors containing cDNA of Mac-1 subunits (CD11b or CD18b) fused with fluorescence protein (FP). cDNA fragments and the DNA constructs were then transfected into CHO cells (as CHO-Mac-1-FP). The structure and function of Mac-1-FP obtained from the CHO-Mac-1-FP cells are nearly identical to that expressed in wild type leukocytes. In the present study, the intracellular trafficking of Mac-1 was visualized directly by monitoring the fluorescent intensities of YFP-CD18 and PE-conjugated monoclonal antibody against CD11b under a confocal microscope in CHO-Mac-1-FP cells. The results indicate that: (ⅰ) although Mac-1 was not detected in the cell membrane at resting state, it had been translocated and clustered into the cell membrane by 1 h and internalized 2 h after PMA stimulation, at which point the fluorescence intensity began to diminish gradually, probably due to partial degradation of Mac-1. The fluorescence of CD18 and CD11b reappeared on the cell membrane 1 h after re-treatment with PMA, suggesting the recycling of non-degraded Mac-1. (ⅱ) The adhesion rate of CHO-Mac-1-FP to magnetic beads coupled ICAM-1 increased within 4 h after their initial interaction, accompanied by the clustering of Mac-1-FP. After 8 h,the adhesion rate declined and fluorescence also decreased simultaneously. The pattern of change in fluorescence in CHO-Mac-1-FP cells elicited by ICAM-1 beads was similar to that elicited by PMA, suggesting that endocytosis and degradation of Mac-1 occurred after the interaction with ICAM-1. Thus, we conclude that the intracellular trafficking of Mac-1 after activation is associated with membrane translocation, endocytosis, degradation and recycling. These changes are in parallel with the adhesion of CHO-Mac-1-FP cells with ICAM-1, and may be involved in the adhesion and detachment of leukocytes. The detachment of leukocytes may be caused by endocytosis of Mac-1.

  7. [Role of defective intracellular proteolysis in human degenerative diseases].

    Science.gov (United States)

    Nezelof, Christian

    2012-11-01

    Although intracellular protein synthesis has been studied extensively, protein degradation and disposal, know as proteolysis, has been relatively neglected. Modern studies which led two Nobel prizes (de Duve in 1950 and Herschko, Rose and Ciechanover in 1980) established that proteolysis is ensured by two separate but complementary mechanisms: lysosomes responsible for auto and heterophagy and the Ubiquitin-Proteasome System (UPS). The UPS involves ubiquitin, a small molecule consisting of 76 amino acids found in all eukaryotic cells that ensures the identification of the protein to be degraded and its transport to the proteasome, an intracellular complex with enzymes which degrade unneeded or damaged proteins. The proteasome, acting as a composting agent, ensures the enzymatic dissociation of the protein. In this degradation process, as infinite screw, ubiquitin, peptides and amino acids are released and made available for a new cycle. Knowledge of the UPS and its related disorders is continually expanding. Concurrent with lysosomes which work in acidic environment, it is currently known that the UPS provides 80% to 90% of the proteolysis of the short-life proteins and ensures, as chaperon-molecules, the right conformation and hence the correct function of the proteins. The proteolytic activity generates abnormal residues (tau protein, amyloid and related proteins) and various soluble and insoluble wastes. Some are precipitated as inclusion-bodies or aggregosomes, identified years ago by pathologists. These aggregosomes affect almost exclusively long-lived cells (nervous and muscular, macophages). Pigment deposits, such as lipofuscines made by the peroxydation of cell membranes, are the most abundant. Due to their diverse chemical composition, they cannot be empoyed for a scientific classification. Failures of these systems are numerous. They vary not according to the chemical nature of the abnormal protein and wastes but the life span of the targeted cells and

  8. Cell-specific intracellular anticancer drug delivery from mesoporous silica nanoparticles with pH sensitivity.

    Science.gov (United States)

    Luo, Zhong; Cai, Kaiyong; Hu, Yan; Zhang, Beilu; Xu, Dawei

    2012-05-01

    A nanoreservoir for efficient intracellular anticancer drug delivery based on mesoporous silica nanoparticles end-capped with lactobionic acid-grafted bovine serum albumin is fabricated. It demonstrates great potential for both cell-specific endocytosis and intracellular pH-responsive controlled release of drugs. A possible endocytosis pathway/mechanism of the smart controlled drug release system is proposed. PMID:23184747

  9. Photoactivatable Drug-Caged Fluorophore Conjugate Allows Direct Quantification of Intracellular Drug Transport

    OpenAIRE

    Agasti, Sarit S.; Laughney, Ashley M.; Kohler, Rainer H.; Weissleder, Ralph

    2013-01-01

    We report here a method that utilizes photoactivatable drug-caged fluorophore conjugate to quantify intracellular drug trafficking processes at single cell resolution. Photoactivation is performed in labeled cellular compartments to visualize intracellular drug exchange at physiologic conditions, without the need for washing, facilitating its translation to in vivo cancer models.

  10. Regulation of the Glutamate-Glutamine Transport System by Intracellular pH in Streptococcus lactis

    NARCIS (Netherlands)

    POOLMAN, B; HELLINGWERF, KJ; KONINGS, WN

    1987-01-01

    Various methods of manipulation of the intracellular pH in Streptococcus lactis result in a unique relationship between the rate of glutamate and glutamine transport and the cytoplasmic pH. The initial rate of glutamate uptake by S. lactis cells increases more than 30-fold when the intracellular pH

  11. DMPD: Intracellular TLR signaling: a structural perspective on human disease. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16785490 Intracellular TLR signaling: a structural perspective on human disease. La...gnaling: a structural perspective on human disease. PubmedID 16785490 Title Intracellular TLR signaling: a s...tructural perspective on human disease. Authors Lasker MV, Nair SK. Publication J

  12. Microscopy tools for the investigation of intracellular lipid storage and dynamics

    Directory of Open Access Journals (Sweden)

    Sabine Daemen

    2016-03-01

    Major conclusions: The continuous development of lipid probes in combination with the rapid development of microscopic techniques can provide new insights in the role and dynamics of intracellular lipids. Moreover, in situ identification of intracellular lipids is now possible and promises to add a new dimensionality to analysis of lipid biochemistry, and its relation to (pathophysiology.

  13. Thioredoxin 80-Activated-Monocytes (TAMs) Inhibit the Replication of Intracellular Pathogens

    DEFF Research Database (Denmark)

    Cortes-Bratti, Ximena; Brasseres, Eugenie; Herrera-Rodriquez, Fabiola; Botero-Kleiven, Silvia; Coppotelli, Giuseppe; Andersen, Jens Bo; G. Masucci, Maria; Holmgren, Arne; Chaves-Olarte, Esteban; Frisan, Teresa; Avila-Carino, Javier

    2011-01-01

    a role of TAMs in the control of intracellular bacterial infections. As model pathogens we have chosen Listeria monocytogenes and Brucella abortus which replicate in the cytosol and the endoplasmic reticulum respectively. Our data indicate that TAMs efficiently inhibit intracellular growth of both L...

  14. Nanoscale-Tipped High-Aspect-Ratio Vertical Microneedle Electrodes for Intracellular Recordings.

    Science.gov (United States)

    Kubota, Yoshihiro; Oi, Hideo; Sawahata, Hirohito; Goryu, Akihiro; Ando, Yoriko; Numano, Rika; Ishida, Makoto; Kawano, Takeshi

    2016-06-01

    Intracellular recording nanoscale electrode devices provide the advantages of a high spatial resolution and high sensitivity. However, the length of nanowire/nanotube-based nanoelectrodes is currently limited to 100 μm long nanoscale-tipped electrodes, which show intracellular recording capability. PMID:27062044

  15. Transepithelial Na+ transport and the intracellular fluids: a computer study.

    Science.gov (United States)

    Civan, M M; Bookman, R J

    1982-01-01

    Computer simulations of tight epithelia under three experimental conditions have been carried out, using the rheogenic nonlinear model of Lew, Ferreira and Moura (Proc. Roy. Soc. London. B 206:53-83, 1979) based largely on the formulation of Koefoed-Johnsen and Ussing (Acta Physiol. Scand. 42: 298-308. 1958). First, analysis of the transition between the short-circuited and open-circuited states has indicated that (i) apical Cl- permeability is a critical parameter requiring experimental definition in order to analyze cell volume regulation, and (ii) contrary to certain experimental reports, intracellular Na+ concentration (ccNa) is expected to be a strong function of transepithelial clamping voltage. Second, analysis of the effects of lowering serosal K+ concentration (csK) indicates that the basic model cannot simulate several well-documented observations; these defects can be overcome, at least qualitatively, by modifying the model to take account of the negative feedback interaction likely to exist between the apical Na+ permeability and ccNa. Third, analysis of the strongly supports the concept that osmotically induced permeability changes in the apical intercellular junctions play a physiological role in conserving the body's stores of NaCl. The analyses also demonstrate that the importance of Na+ entry across the basolateral membrane is strongly dependent upon transepithelial potential, cmNa and csK; under certain conditions, net Na+ entry could be appreciably greater across the basolateral than across the apical membrane. PMID:7057462

  16. Cell-targeting aptamers act as intracellular delivery vehicles.

    Science.gov (United States)

    Gopinath, Subash C B; Lakshmipriya, Thangavel; Chen, Yeng; Arshad, M K Md; Kerishnan, Jesinda P; Ruslinda, A R; Al-Douri, Yarub; Voon, C H; Hashim, Uda

    2016-08-01

    Aptamers are single-stranded nucleic acids or peptides identified from a randomized combinatorial library through specific interaction with the target of interest. Targets can be of any size, from small molecules to whole cells, attesting to the versatility of aptamers for binding a wide range of targets. Aptamers show drug properties that are analogous to antibodies, with high specificity and affinity to their target molecules. Aptamers can penetrate disease-causing microbial and mammalian cells. Generated aptamers that target surface biomarkers act as cell-targeting agents and intracellular delivery vehicles. Within this context, the "cell-internalizing aptamers" are widely investigated via the process of cell uptake with selective binding during in vivo systematic evolution of ligands by exponential enrichment (SELEX) or by cell-internalization SELEX, which targets cell surface antigens to be receptors. These internalizing aptamers are highly preferable for the localization and functional analyses of multiple targets. In this overview, we discuss the ways by which internalizing aptamers are generated and their successful applications. Furthermore, theranostic approaches featuring cell-internalized aptamers are discussed with the purpose of analyzing and diagnosing disease-causing pathogens. PMID:27350620

  17. Manipulation of costimulatory molecules by intracellular pathogens: veni, vidi, vici!!

    Directory of Open Access Journals (Sweden)

    Nargis Khan

    Full Text Available Some of the most successful pathogens of human, such as Mycobacterium tuberculosis (Mtb, HIV, and Leishmania donovani not only establish chronic infections but also remain a grave global threat. These pathogens have developed innovative strategies to evade immune responses such as antigenic shift and drift, interference with antigen processing/presentation, subversion of phagocytosis, induction of immune regulatory pathways, and manipulation of the costimulatory molecules. Costimulatory molecules expressed on the surface of various cells play a decisive role in the initiation and sustenance of immunity. Exploitation of the "code of conduct" of costimulation pathways provides evolutionary incentive to the pathogens and thereby abates the functioning of the immune system. Here we review how Mtb, HIV, Leishmania sp., and other pathogens manipulate costimulatory molecules to establish chronic infection. Impairment by pathogens in the signaling events delivered by costimulatory molecules may be responsible for defective T-cell responses; consequently organisms grow unhindered in the host cells. This review summarizes the convergent devices that pathogens employ to tune and tame the immune system using costimulatory molecules. Studying host-pathogen interaction in context with costimulatory signals may unveil the molecular mechanism that will help in understanding the survival/death of the pathogens. We emphasize that the very same pathways can potentially be exploited to develop immunotherapeutic strategies to eliminate intracellular pathogens.

  18. pH sensing by intracellular Salmonella induces effector translocation.

    Science.gov (United States)

    Yu, Xiu-Jun; McGourty, Kieran; Liu, Mei; Unsworth, Kate E; Holden, David W

    2010-05-21

    Salmonella enterica is an important intracellular bacterial pathogen of humans and animals. It replicates within host-cell vacuoles by delivering virulence (effector) proteins through a vacuolar membrane pore made by the Salmonella pathogenicity island 2 (SPI-2) type III secretion system (T3SS). T3SS assembly follows vacuole acidification, but when bacteria are grown at low pH, effector secretion is negligible. We found that effector secretion was activated at low pH from mutant strains lacking a complex of SPI-2-encoded proteins SsaM, SpiC, and SsaL. Exposure of wild-type bacteria to pH 7.2 after growth at pH 5.0 caused dissociation and degradation of SsaM/SpiC/SsaL complexes and effector secretion. In infected cells, loss of the pH 7.2 signal through acidification of host-cell cytosol prevented complex degradation and effector translocation. Thus, intravacuolar Salmonella senses host cytosolic pH, resulting in the degradation of regulatory complex proteins and effector translocation. PMID:20395475

  19. Involvement of myosin in intracellular motility and cytomorphogenesis in Micrasterias.

    Science.gov (United States)

    Oertel, Anke; Holzinger, Andreas; Lütz-Meindl, Ursula

    2003-01-01

    Myosin was detected on Western blots of Micrasterias denticulata extracts by use of antibodies from different sources. Inhibitors with different targets of the actomyosin system, such as the myosin ATPase-blockers N-ethylmaleimide (NEM) and 2,3-butanedione monoxime (BDM), or the myosin light chain kinase inhibitor 1-(5-iodonaphthalene-1-sulfonyl)-1H-hexhydro-1,4-diazapine (ML7), had similar effects on intracellular motility during cell development in the green alga Micrasterias, thus pointing towards a participation of myosin in these processes. The drugs markedly altered the mode of postmitotic nuclear migration, slowed down cytoplasmic streaming, changed cell pattern development and prevented normal chloroplast distribution and spreading into the growing semicell. In addition, an increase and dilatations in ER cisternae and marked morphological changes of the Golgi system were observed by transmission electron microscopy after exposure of growing cells to BDM. Neither BDM nor ML7 exhibited any effect on the distribution or arrangement of the cortical F-actin network nor on the F-actin basket around the nucleus, characteristic of untreated growing Micrasterias cells (J Cell Sci 107 (1994) 1929). This is particularly interesting since BDM caused disintegration of the microtubule system co-localized to the F-actin cage during normal nuclear migration. Together with the fact that other microtubules not connected to the F-actin system remained uninfluenced by BDM, this observation is evidence of an integrative function of myosin between the cytoskeleton elements. PMID:14642529

  20. Initial intracellular proteome profile of Aspergillus niger biofilms

    Directory of Open Access Journals (Sweden)

    Gretty K. Villena

    2011-07-01

    Full Text Available An initial profiling of the intracellular proteome of Aspergillus niger ATCC 10864 biofilm cultures developed on polyester cloth was carried out by using 2D-PAGE and MS-TOF analysis and it was compared to the proteome of conventionally grown free-living submerged cultures. A number of 2D-PAGE protein spots from both types of cultures were subjected to MS-TOF analysis and data interrogation of the NCBI nr database available for this species. Proteomic maps showed different expression patterns in both culture systems with differentially expressed proteins in each case. In biofilm cultures, 19% and 32% of the selected protein spots were over- expressed and differentially expressed, respectively. On the contrary, in free-living cultures, 44% and 7% of the selected protein spots were over-expressed and differentially expressed, respectively. Although preliminary, results presented in this paper show that there are significant differences between the proteomes of A. niger biofilm and free-living mycelia. It seems that cell adhesion is the most important stimulus responsible for biofilm development which is the basis of Surface Adhesion Fermentation.

  1. Subcellular site and nature of intracellular cadmium in plants

    Energy Technology Data Exchange (ETDEWEB)

    Wagner, George J.

    1979-01-01

    The mechanisms underlying heavy metal accumulation, toxicity and tolerance in higher plants are poorly understood. Since subcellular processes are undoubtedly involved in all these phenomena, it is of interest to study the extent of, subcellular site of and nature of intracellularly accumulated cadmium in higher plants. Whole plants supplied /sup 109/CdCl/sub 2/ or /sup 112/CdSO/sub 4/ accumulated Cd into roots and aerial tissues. Preparation of protoplasts from aerial tissue followed by subcellular fractionation of the protoplasts to obtain intact vacuoles, chloroplasts and cytosol revealed the presence of Cd in the cytosol but not in vacuoles or chloroplasts. Particulate materials containing other cell components were also labeled. Of the /sup 109/Cd supplied to plants, 2 to 10% was recovered in both cytosol preparations and in particulate materials. Cytosol contained proteinaceous--Cd complexes, free metal and low molecular weight Cd complexes. Labeling of protoplasts gave similar results. No evidence was obtained for the production of volatile Cd complexes in tobacco.

  2. Intracellular Oceanospirillales bacteria inhabit gills of Acesta bivalves.

    Science.gov (United States)

    Jensen, Sigmund; Duperron, Sébastien; Birkeland, Nils-Kåre; Hovland, Martin

    2010-12-01

    A novel bacterium was discovered in the gills of the large bivalve Acesta excavata (Limidae) from coral reefs on the northeast Atlantic margin near the shelf break of the fishing ground Haltenbanken of Norway, and confirmed present in A. excavata from a rock-wall in the Trondheimsfjord. Purified gill DNA contained one dominant bacterial rRNA operon as indicated from analysis of broad range bacterial PCR amplicons in denaturant gradient gels, in clone libraries and by direct sequencing. The sequences originated from an unknown member of the order Oceanospirillales and its 16S rRNA gene fell within a clade of strictly marine invertebrate-associated Gammaproteobacteria. Visual inspection by fluorescent in situ hybridization and transmission electron microscopy indicated a pleomorphic bacterium with no visible cell wall, located in aggregates inside vacuoles scattered within the gill cells cytoplasm. Intracellular Oceanospirillales exist in bathymodiolin mussels (parasites), Osedax worms and whiteflies (symbionts). This bacterium apparently lives in a specific association with the Acesta. PMID:21044098

  3. Intracellular distribution of Tankyrases as detected by multicolor immunofluorescence techniques

    Directory of Open Access Journals (Sweden)

    M.G. Bottone

    2012-01-01

    Full Text Available Poly(ADP-ribose polymerases are a family of enzymes that catalyze the conversion of NAD+ into ADP-ribose. Among them, Tankyrases have been found to bind to centrosome, mitotic spindle and microsome proteins, in the cytoplasm, and to telomeres in the nucleus, where they play a relevant role in telomere metabolism. However, their precise intracellular localization during interphase has not been so far fully elucidated. We investigated this aspect in situ by double immunofluorescence experiments using antibodies recognizing Tankyrases 1-2 or other proteins residing in specific organelles (Golgi apparatus, mitochondria, lysosomes, endoplasmic reticulum. We used HeLa cells as a model system in vitro, before and after treatment with either actinomycin D or etoposide, to also investigate the possible relocation of Tankyrases during apoptosis. We observed that Tankyrases are distributed both in the nucleus and in the cytoplasm; in this latter compartment, they were found to colocate with the Golgi apparatus but never with the mitochondria; a pool of Tankyrases also colocates with the endoplasmic reticulum and lysosomes. Interestingly, in cells with clear signs of apoptosis, Tankyrases were detectable in the cytoplasmic blebs: this suggests that they are not massively cleaved during apoptosis and persist in the largely heterogeneous apoptotic remnants which are known to contain components of cytoplasmic and nuclear origin.

  4. Hydrodynamic regulation of monocyte inflammatory response to an intracellular pathogen.

    Directory of Open Access Journals (Sweden)

    Shankar J Evani

    Full Text Available Systemic bacterial infections elicit inflammatory response that promotes acute or chronic complications such as sepsis, arthritis or atherosclerosis. Of interest, cells in circulation experience hydrodynamic shear forces, which have been shown to be a potent regulator of cellular function in the vasculature and play an important role in maintaining tissue homeostasis. In this study, we have examined the effect of shear forces due to blood flow in modulating the inflammatory response of cells to infection. Using an in vitro model, we analyzed the effects of physiological levels of shear stress on the inflammatory response of monocytes infected with chlamydia, an intracellular pathogen which causes bronchitis and is implicated in the development of atherosclerosis. We found that chlamydial infection alters the morphology of monocytes and trigger the release of pro-inflammatory cytokines TNF-α, IL-8, IL-1β and IL-6. We also found that the exposure of chlamydia-infected monocytes to short durations of arterial shear stress significantly enhances the secretion of cytokines in a time-dependent manner and the expression of surface adhesion molecule ICAM-1. As a functional consequence, infection and shear stress increased monocyte adhesion to endothelial cells under flow and in the activation and aggregation of platelets. Overall, our study demonstrates that shear stress enhances the inflammatory response of monocytes to infection, suggesting that mechanical forces may contribute to disease pathophysiology. These results provide a novel perspective on our understanding of systemic infection and inflammation.

  5. Somatostatin regulates intracellular signaling in human carotid endothelial cells

    International Nuclear Information System (INIS)

    Somatostatin (somatotropin release inhibitory factor; SRIF) is an endogenous peptide produced at sites of inflammation, making the SRIF a candidate in regulating vascular inflammation. We have used primary human coronary artery endothelial cells (hCAEC) as a model to study SRIF's vascular actions. RT-PCR analysis of hCAEC total mRNA demonstrated the presence of the sst4 receptor subtype, providing a target for SRIF intracellular signaling. Western blotting with phospho-specific ERK1/2 antibodies showed that SRIF-14 acutely inhibited basal phosphorylation of the extracellular regulated kinases (ERK1/2) by 80%. In addition, SRIF-14 treated hCAEC cell lysates showed a 2.6-fold increase in phosphatase activity, which was inhibited by sodium vanadate. Furthermore, SRIF-14 appeared to be anti-inflammatory in hCAEC as IL-1β-induced adhesion molecule expression was reduced by 50%. Together, these results show that the coronary artery endothelium is a direct target of SRIF action

  6. Intracellular transport and egress of hepatitis B virus.

    Science.gov (United States)

    Blondot, Marie-Lise; Bruss, Volker; Kann, Michael

    2016-04-01

    Hepatitis B virus (HBV) replicates its genomic information in the nucleus via transcription and therefore has to deliver its partially double stranded DNA genome into the nucleus. Like other viruses with a nuclear replication phase, HBV genomes are transported inside the viral capsids first through the cytoplasm towards the nuclear envelope. Following the arrival at the nuclear pore, the capsids are transported through, using classical cellular nuclear import pathways. The arrest of nuclear import at the nucleoplasmic side of the nuclear pore is unique, however, and is where the capsids efficiently disassemble leading to genome release. In the latter phase of the infection, newly formed nucleocapsids in the cytosol have to move to budding sites at intracellular membranes carrying the three viral envelope proteins. Capsids containing single stranded nucleic acid are not enveloped, in contrast to empty and double stranded DNA containing capsids. A small linear domain in the large envelope protein and two areas on the capsid surface have been mapped, where point mutations strongly block nucleocapsid envelopment. It is possible that these domains are involved in the envelope - with capsid interactions driving the budding process. Like other enveloped viruses, HBV also uses the cellular endosomal sorting complexes required for transport (ESCRT) machinery for catalyzing budding through the membrane and away from the cytosol. PMID:27084037

  7. Intracellular Action of a Secreted Peptide Required for Fungal Virulence.

    Science.gov (United States)

    Homer, Christina M; Summers, Diana K; Goranov, Alexi I; Clarke, Starlynn C; Wiesner, Darin L; Diedrich, Jolene K; Moresco, James J; Toffaletti, Dena; Upadhya, Rajendra; Caradonna, Ippolito; Petnic, Sarah; Pessino, Veronica; Cuomo, Christina A; Lodge, Jennifer K; Perfect, John; Yates, John R; Nielsen, Kirsten; Craik, Charles S; Madhani, Hiten D

    2016-06-01

    Quorum sensing (QS) is a bacterial communication mechanism in which secreted signaling molecules impact population function and gene expression. QS-like phenomena have been reported in eukaryotes with largely unknown contributing molecules, functions, and mechanisms. We identify Qsp1, a secreted peptide, as a central signaling molecule that regulates virulence in the fungal pathogen Cryptococcus neoformans. QSP1 is a direct target of three transcription factors required for virulence, and qsp1Δ mutants exhibit attenuated infection, slowed tissue accumulation, and greater control by primary macrophages. Qsp1 mediates autoregulatory signaling that modulates secreted protease activity and promotes cell wall function at high cell densities. Peptide production requires release from a secreted precursor, proQsp1, by a cell-associated protease, Pqp1. Qsp1 sensing requires an oligopeptide transporter, Opt1, and remarkably, cytoplasmic expression of mature Qsp1 complements multiple phenotypes of qsp1Δ. Thus, C. neoformans produces an autoregulatory peptide that matures extracellularly but functions intracellularly to regulate virulence. PMID:27212659

  8. Polyarginine nanocapsules: a new platform for intracellular drug delivery

    International Nuclear Information System (INIS)

    This report describes the development of a new nanocarrier, named as polyarginine (PArg) nanocapsules, specifically designed for overcoming cellular barriers. These nanocapsules are composed of an oily core and a PArg corona. The attachment of the PArg corona was mediated by its interaction with the oily core, which was conveniently stabilized with phosphatidylcholine. Hybrid PArg/PEG nanocapsules could also be obtained by introducing PEG-stearate in the nanocapsules formation process. The nanocapsules had an average size in the range of 120–160 nm, and a positive surface charge, which varied between +56 and +28 mV for PArg and PArg/PEG nanocapsules, respectively. They could accommodate significant amounts of lipophilic drugs, i.e., docetaxel, in their core, and also polar negatively charged molecules, i.e., plasmid DNA, on their coating. As a preliminary proof-of-principle, we explored the ability of these nanocarriers to enter cancer cells and to inhibit proliferation in the non-small cell lung cancer NCI-H460 cell line, using flow cytometry and confocal microscopy analysis. The results indicated that PArg nanocapsules are rapidly and massively accumulated into the NCI-H460 cells and that the PArg shell plays a critical role in the internalization process. Moreover, the incubation with docetaxel-loaded nanocapsules with NCI-H460 cells led to an enhanced inhibition of their proliferation, as compared to the free drug. Overall, this is the first report of the potential of PArg nanocapsules as intracellular drug delivery vehicles.

  9. Intracellular transport of insulin granules is a subordinated random walk.

    Science.gov (United States)

    Tabei, S M Ali; Burov, Stanislav; Kim, Hee Y; Kuznetsov, Andrey; Huynh, Toan; Jureller, Justin; Philipson, Louis H; Dinner, Aaron R; Scherer, Norbert F

    2013-03-26

    We quantitatively analyzed particle tracking data on insulin granules expressing fluorescent fusion proteins in MIN6 cells to better understand the motions contributing to intracellular transport and, more generally, the means for characterizing systems far from equilibrium. Care was taken to ensure that the statistics reflected intrinsic features of the individual granules rather than details of the measurement and overall cell state. We find anomalous diffusion. Interpreting such data conventionally requires assuming that a process is either ergodic with particles working against fluctuating obstacles (fractional brownian motion) or nonergodic with a broad distribution of dwell times for traps (continuous-time random walk). However, we find that statistical tests based on these two models give conflicting results. We resolve this issue by introducing a subordinated scheme in which particles in cages with random dwell times undergo correlated motions owing to interactions with a fluctuating environment. We relate this picture to the underlying microtubule structure by imaging in the presence of vinblastine. Our results provide a simple physical picture for how diverse pools of insulin granules and, in turn, biphasic secretion could arise. PMID:23479621

  10. Ornithine decarboxylase antizyme inhibitor 2 regulates intracellular vesicle trafficking

    Energy Technology Data Exchange (ETDEWEB)

    Kanerva, Kristiina; Maekitie, Laura T. [Department of Pathology, Haartman Institute, University of Helsinki, Helsinki (Finland); Baeck, Nils [Department of Anatomy, Institute of Biomedicine, University of Helsinki, Helsinki (Finland); Andersson, Leif C., E-mail: leif.andersson@helsinki.fi [Department of Pathology, Haartman Institute, University of Helsinki, Helsinki (Finland); HUSLAB, Helsinki (Finland); Department of Oncology and Pathology, Karolinska Institutet, Stockholm (Sweden)

    2010-07-01

    Antizyme inhibitor 1 (AZIN1) and 2 (AZIN2) are proteins that activate ornithine decarboxylase (ODC), the key enzyme of polyamine biosynthesis. Both AZINs release ODC from its inactive complex with antizyme (AZ), leading to formation of the catalytically active ODC. The ubiquitously expressed AZIN1 is involved in cell proliferation and transformation whereas the role of the recently found AZIN2 in cellular functions is unknown. Here we report the intracellular localization of AZIN2 and present novel evidence indicating that it acts as a regulator of vesicle trafficking. We used immunostaining to demonstrate that both endogenous and FLAG-tagged AZIN2 localize to post-Golgi vesicles of the secretory pathway. Immuno-electron microscopy revealed that the vesicles associate mainly with the trans-Golgi network (TGN). RNAi-mediated knockdown of AZIN2 or depletion of cellular polyamines caused selective fragmentation of the TGN and retarded the exocytotic release of vesicular stomatitis virus glycoprotein. Exogenous addition of polyamines normalized the morphological changes and reversed the inhibition of protein secretion. Our findings demonstrate that AZIN2 regulates the transport of secretory vesicles by locally activating ODC and polyamine biosynthesis.

  11. DNA uptake, intracellular trafficking and gene transfection after ultrasound exposure.

    Science.gov (United States)

    Liu, Ying; Yan, Jing; Santangelo, Philip J; Prausnitz, Mark R

    2016-07-28

    Ultrasound has been studied as a promising tool for intracellular gene delivery. In this work, we studied gene transfection of a human prostate cancer cell line exposed to megahertz pulsed ultrasound in the presence of contrast agent and assessed the efficiency of fluorescently labelled DNA delivery into cell nuclei, which is necessary for gene transfection. At the sonication conditions studied, ~30% of cells showed DNA uptake 30min after sonication, but that fraction decreased over time to ~10% of cells after 24h. Most cells containing DNA had DNA in their nuclei, but the amount varied significantly. Transfection efficiency peaked at ~10% at 8h post sonication. Among those cells containing DNA, ~30% of DNA was localized in the cell nuclei, ~30% was in autophagosomes/autophagolysosomes and the remainder was "free" in the cytoplasm 30min after sonication. At later times up to 24h, ~30% of DNA continued to be found in the nuclei and most or all of the rest of the DNA was in autophagosomes/autophagolysosomes. These results demonstrate that ultrasound can deliver DNA into cell nuclei shortly after sonication and that the rest of the DNA can be cleared by autophagosomes/autophagolysosomes. PMID:27165808

  12. Viral evasion of intracellular DNA and RNA sensing.

    Science.gov (United States)

    Chan, Ying Kai; Gack, Michaela U

    2016-06-01

    The co-evolution of viruses with their hosts has led to the emergence of viral pathogens that are adept at evading or actively suppressing host immunity. Pattern recognition receptors (PRRs) are key components of antiviral immunity that detect conserved molecular features of viral pathogens and initiate signalling that results in the expression of antiviral genes. In this Review, we discuss the strategies that viruses use to escape immune surveillance by key intracellular sensors of viral RNA or DNA, with a focus on RIG-I-like receptors (RLRs), cyclic GMP-AMP synthase (cGAS) and interferon-γ (IFNγ)-inducible protein 16 (IFI16). Such viral strategies include the sequestration or modification of viral nucleic acids, interference with specific post-translational modifications of PRRs or their adaptor proteins, the degradation or cleavage of PRRs or their adaptors, and the sequestration or relocalization of PRRs. An understanding of viral immune-evasion mechanisms at the molecular level may guide the development of vaccines and antivirals. PMID:27174148

  13. Comparison of the intracellular trafficking itinerary of ctla-4 orthologues.

    Directory of Open Access Journals (Sweden)

    Satdip Kaur

    Full Text Available CTLA-4 is an essential inhibitor of T cell immune responses. At steady state, most CTLA-4 resides in intracellular compartments due to constitutive internalisation mediated via a tyrosine based endocytic motif (YVKM within the cytoplasmic domain. This domain is highly conserved in mammals suggesting strong selective pressure. In contrast, the C-terminal domain varies considerably in non-mammals such as fish, xenopus and birds. We compared the ability of the C-terminus of these species to direct the trafficking of CTLA-4 with human CTLA-4. Using a chimeric approach, endocytosis was found to be conserved between human, xenopus and chicken CTLA-4 but was reduced substantially in trout CTLA-4, which lacks the conserved YXXM motif. Nevertheless, we identified an alternative YXXF motif in trout CTLA-4 that permitted limited endocytosis. Post-internalisation, CTLA-4 was either recycled or targeted for degradation. Human and chicken CTLA-4, which contain a YVKM motif, showed efficient recycling compared to xenopus CTLA-4 which contains a less efficient YEKM motif. Specific mutation of this motif in human CTLA-4 reduced receptor recycling. These findings suggest evolutionary development in the endocytic and recycling potential of CTLA-4, which may facilitate more refined functions of CTLA-4 within the mammalian immune system.

  14. Intracellular transport of pancreatic zymogens during caerulein supramaximal stimulation

    International Nuclear Information System (INIS)

    Rats infused with a dose of the secretagogue caerulein that is in excess of that which stimulates a maximal rate of pancreatic digestive enzyme secretion develop acute edematous pancreatitis. The authors have previously noted that infusion of this dose of caerulein induces the appearance of large heterogeneous vacuoles in acinar cell, blockage of exocytosis, and intracellular accumulation of digestive zymogens. The current studies were performed to further elucidate these phenomena at the electron microscopic level of resolution and employed the techniques of pulse labeling, radioautography, and immunolocalization. Rats were infused with caerulein for 1 h, given a pulse of [3H]phenylalanine, and killed at selected times during the subsequent 5- to 180-min postpulse period during which caerulein infusion was continued. Transport from the endoplasmic reticulum to the Golgi cisternae was not altered by supramaximal stimulation, but transport through post-Golgi elements was altered. In particular, the maturation of condensing vacuoles into zymogen granules was found to be impaired. Thus these studies indicate that the large heterogeneous vacuoles that appear during supramaximal secretagogue stimulation and that contain admixed digestive zymogens and lysosomal hydrolases arise by at least two mechanisms, impaired condensing vacuole maturation and crinophagy

  15. Intracellular imaging of targeted proteins labeled with quantum dots

    International Nuclear Information System (INIS)

    We developed a new method for imaging the movement of targeted proteins in living cancer cells with photostable and bright quantum dots (QDs). QDs were conjugated with various molecules and proteins, such as phalloidin, anti-tubulin antibody and kinesin. These bioconjugated QDs were mixed with a transfection reagent and successfully internalized into living cells. The movements of individual QDs were tracked for long periods of time. Phalloidin conjugated QDs bound to actin filaments and showed almost no movement. In contrast, anti-tubulin antibody conjugated QDs bound to microtubules and revealed dynamic movement of microtubules. Kinesin showed an interesting behavior whereby kinesin came to be almost paused briefly for a few seconds and then moved once again. This is in direct contrast to the smoothly continuous movement of kinesin in an in vitro assay. The maximum velocity of kinesin in cells was faster than that in the in vitro assay. These results suggest that intracellular movement of kinesin is different from that in the in vitro assay. This newly described method will be a powerful tool for investigating the functions of proteins in living cells

  16. Iron in intracellular infection: to provide or to deprive?

    Directory of Open Access Journals (Sweden)

    Sandro eSilva-Gomes

    2013-12-01

    Full Text Available Due to their chemical versatility, transition metals were incorporated as cofactors for several basic metabolic pathways in living organisms. This same characteristic makes them potentially harmful, since they can be engaged in deleterious reactions like Fenton chemistry. As such, organisms have evolved highly specialized mechanisms to supply their own metal needs while keeping their toxic potential in check.This dual character comes into play in host-pathogen interactions, given that the host can either deprive the pathogen of these key nutrients or exploit them to induce toxicity towards the invading agent. Iron stands as the prototypic example of how a metal can be used to limit the growth of pathogens by nutrient deprivation, a mechanism widely studied in Mycobacterium infections. However, the host can also take advantage of iron-induced toxicity to control pathogen proliferation, as observed in infections caused by Leishmania. Whether we may harness either of the two pathways for therapeutical purposes is still ill-defined.In this review, we discuss how modulation of the host iron availability impacts the course of infections, focusing on those caused by two relevant intracellular pathogens, Mycobacterium and Leishmania.

  17. Polyarginine nanocapsules: a new platform for intracellular drug delivery

    Energy Technology Data Exchange (ETDEWEB)

    Lozano, M. V.; Lollo, G. [University of Santiago de Compostela, Department of Pharmaceutical Technology, Faculty of Pharmacy (Spain); Alonso-Nocelo, M. [Complexo Hospitalario, Universitario de Santiago de Compostela/SERGAS, Translational Laboratory, Medical Oncology Department (Spain); Brea, J. [University of Santiago de Compostela, Department of Pharmacology, Faculty of Pharmacy (Spain); Vidal, A. [University of Santiago de Compostela, Department of Physiology (Spain); Torres, D.; Alonso, M. J., E-mail: mariaj.alonso@usc.es [University of Santiago de Compostela, Department of Pharmaceutical Technology, Faculty of Pharmacy (Spain)

    2013-03-15

    This report describes the development of a new nanocarrier, named as polyarginine (PArg) nanocapsules, specifically designed for overcoming cellular barriers. These nanocapsules are composed of an oily core and a PArg corona. The attachment of the PArg corona was mediated by its interaction with the oily core, which was conveniently stabilized with phosphatidylcholine. Hybrid PArg/PEG nanocapsules could also be obtained by introducing PEG-stearate in the nanocapsules formation process. The nanocapsules had an average size in the range of 120-160 nm, and a positive surface charge, which varied between +56 and +28 mV for PArg and PArg/PEG nanocapsules, respectively. They could accommodate significant amounts of lipophilic drugs, i.e., docetaxel, in their core, and also polar negatively charged molecules, i.e., plasmid DNA, on their coating. As a preliminary proof-of-principle, we explored the ability of these nanocarriers to enter cancer cells and to inhibit proliferation in the non-small cell lung cancer NCI-H460 cell line, using flow cytometry and confocal microscopy analysis. The results indicated that PArg nanocapsules are rapidly and massively accumulated into the NCI-H460 cells and that the PArg shell plays a critical role in the internalization process. Moreover, the incubation with docetaxel-loaded nanocapsules with NCI-H460 cells led to an enhanced inhibition of their proliferation, as compared to the free drug. Overall, this is the first report of the potential of PArg nanocapsules as intracellular drug delivery vehicles.

  18. Enlightening intracellular complexity of living cells with quantitative phase microscopy

    Science.gov (United States)

    Martinez Torres, C.; Laperrousaz, B.; Berguiga, L.; Boyer Provera, E.; Elezgaray, J.; Nicolini, F. E.; Maguer-Satta, V.; Arneodo, A.; Argoul, F.

    2016-03-01

    The internal distribution of refractive indices (RIs) of a living cell is much more complex than usually admitted in multi-shell models. The reconstruction of RI maps from single phase images has rarely been achieved for several reasons: (i) we still have very little knowledge of the impact of internal macromolecular complexes on the local RI and (ii) phase changes produced by light propagation through the sample are mixed with diffraction effects by internal cell bodies. We propose the implementation a 2D wavelet-based contour chain detection method to distinguish internal boundaries thanks to their greatest optical path difference gradients. These contour chains correspond to the highest image phase contrast and follow the local RI inhomogeneities linked to the intracellular structural intricacy. Their statistics and spatial distribution are morphological indicators for distinguishing cells of different origins and to follow their transformation in pathologic situations. We use this method to compare non adherent blood cells from primary and laboratory culture origins, in healthy and pathological situations (chronic myelogenous leukaemia). In a second part of this presentation, we concentrate on the temporal dynamics of the phase contour chains and we discuss the spectral decomposition of their dynamics in both health and disease.

  19. The mechanical environment modulates intracellular calcium oscillation activities of myofibroblasts.

    Directory of Open Access Journals (Sweden)

    Charles Godbout

    Full Text Available Myofibroblast contraction is fundamental in the excessive tissue remodeling that is characteristic of fibrotic tissue contractures. Tissue remodeling during development of fibrosis leads to gradually increasing stiffness of the extracellular matrix. We propose that this increased stiffness positively feeds back on the contractile activities of myofibroblasts. We have previously shown that cycles of contraction directly correlate with periodic intracellular calcium oscillations in cultured myofibroblasts. We analyze cytosolic calcium dynamics using fluorescent calcium indicators to evaluate the possible impact of mechanical stress on myofibroblast contractile activity. To modulate extracellular mechanics, we seeded primary rat subcutaneous myofibroblasts on silicone substrates and into collagen gels of different elastic modulus. We modulated cell stress by cell growth on differently adhesive culture substrates, by restricting cell spreading area on micro-printed adhesive islands, and depolymerizing actin with Cytochalasin D. In general, calcium oscillation frequencies in myofibroblasts increased with increasing mechanical challenge. These results provide new insight on how changing mechanical conditions for myofibroblasts are encoded in calcium oscillations and possibly explain how reparative cells adapt their contractile behavior to the stresses occurring in normal and pathological tissue repair.

  20. Rare earth nanoparticles prevent retinal degeneration induced by intracellular peroxides:

    Science.gov (United States)

    Chen, Junping; Patil, Swanand; Seal, Sudipta; McGinnis, James F.

    2006-11-01

    Photoreceptor cells are incessantly bombarded with photons of light, which, along with the cells' high rate of oxygen metabolism, continuously exposes them to elevated levels of toxic reactive oxygen intermediates (ROIs). Vacancy-engineered mixed-valence-state cerium oxide nanoparticles (nanoceria particles) scavenge ROIs. Our data show that nanoceria particles prevent increases in the intracellular concentrations of ROIs in primary cell cultures of rat retina and, in vivo, prevent loss of vision due to light-induced degeneration of photoreceptor cells. These data indicate that the nanoceria particles may be effective in inhibiting the progression of ROI-induced cell death, which is thought to be involved in macular degeneration, retinitis pigmentosa and other blinding diseases, as well as the ROI-induced death of other cell types in diabetes, Alzheimer's disease, atherosclerosis, stroke and so on. The use of nanoceria particles as a direct therapy for multiple diseases represents a novel strategy and suggests that they may represent a unique platform technology.

  1. Physiological water model development

    Science.gov (United States)

    Doty, Susan

    1993-01-01

    The water of the human body can be categorized as existing in two main compartments: intracellular water and extracellular water. The intracellular water consists of all the water within the cells and constitutes over half of the total body water. Since red blood cells are surrounded by plasma, and all other cells are surrounded by interstitial fluid, the intracellular compartment has been subdivided to represent these two cell types. The extracellular water, which includes all of the fluid outside of the cells, can be further subdivided into compartments which represent the interstitial fluid, circulating blood plasma, lymph, and transcellular water. The interstitial fluid surrounds cells outside of the vascular system whereas plasma is contained within the blood vessels. Avascular tissues such as dense connective tissue and cartilage contain interstitial water which slowly equilibrates with tracers used to determine extracellular fluid volume. For this reason, additional compartments are sometimes used to represent these avascular tissues. The average size of each compartment, in terms of percent body weight, has been determined for adult males and females. These compartments and the forces which cause flow between them are presented. The kidneys, a main compartment, receive about 25 percent of the cardiac output and filters out a fluid similar to plasma. The composition of this filtered fluid changes as it flows through the kidney tubules since compounds are continually being secreted and reabsorbed. Through this mechanism, the kidneys eliminate wastes while conserving body water, electrolytes, and metabolites. Since sodium accounts for over 90 percent of the cations in the extracellular fluid, and the number of cations is balanced by the number of anions, considering the renal handling sodium and water only should sufficiently describe the relationship between the plasma compartment and kidneys. A kidney function model is presented which has been adapted from a

  2. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  3. Nuclear spin pair coherence in diamond for atomic scale magnetometry

    OpenAIRE

    Zhao, Nan; Hu, Jian-Liang; Ho, Sai-Wah; Wen, Tsz-Kai; Liu, R. B.

    2010-01-01

    The nitrogen-vacancy (NV) centre, as a promising candidate solid state system of quantum information processing, its electron spin coherence is influenced by the magnetic field fluctuations due to the local environment. In pure diamonds, the environment consists of hundreds of C-13 nuclear spins randomly spreading in several nanometers range forming a spin bath. Controlling and prolonging the electron spin coherence under the influence of spin bath are challenging tasks for the quantum inform...

  4. Atomic-scale nanowires: physical and electronic structure

    International Nuclear Information System (INIS)

    The technology to build and study nanowires with sizes ranging from individual atoms to tens of nanometres has been developing rapidly over the last few years. We survey the motivation behind these developments, and summarize the basics behind quantized conduction. Several of the different experimental techniques and materials systems used in the creation of nanowires are examined, and the range of theoretical methods developed both for examining open systems (especially their conduction properties) and for modelling large systems are considered. We present various noteworthy example results from the field, before concluding with a look at future directions. (topical review)

  5. Atomic-Scale Control of Electron Transport through Single Molecules

    DEFF Research Database (Denmark)

    Wang, Y. F.; Kroger, J.; Berndt, R.;

    2010-01-01

    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of...

  6. Atomic-scale disproportionation in amorphous silicon monoxide

    OpenAIRE

    Hirata, Akihiko; Kohara, Shinji; Asada, Toshihiro; Arao, Masazumi; Yogi, Chihiro; Imai, Hideto; Tan, Yongwen; Fujita, Takeshi; Chen, Mingwei

    2016-01-01

    Solid silicon monoxide is an amorphous material which has been commercialized for many functional applications. However, the amorphous structure of silicon monoxide is a long-standing question because of the uncommon valence state of silicon in the oxide. It has been deduced that amorphous silicon monoxide undergoes an unusual disproportionation by forming silicon- and silicon-dioxide-like regions. Nevertheless, the direct experimental observation is still missing. Here we report the amorphou...

  7. Modeling DNA bubble formation at the atomic scale

    International Nuclear Information System (INIS)

    We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequence dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.

  8. Lateral vibration effects in atomic-scale friction

    Energy Technology Data Exchange (ETDEWEB)

    Roth, R. [Climate and Environment Physics, Physics Institute, University of Bern, Bern (Switzerland); Oeschger Centre for Climate Change Research, University of Bern, Bern (Switzerland); Fajardo, O. Y.; Mazo, J. J. [Departamento de Física de la Materia Condensada and Instituto de Ciencia de Materiales de Aragón, CSIC-Universidad de Zaragoza, 50009 Zaragoza (Spain); Meyer, E. [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Gnecco, E. [Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, 28049 Madrid (Spain)

    2014-02-24

    The influence of lateral vibrations on the stick-slip motion of a nanotip elastically pulled on a flat crystal surface is studied by atomic force microscopy measurements on a NaCl(001) surface in ultra-high vacuum. The slippage of the nanotip across the crystal lattice is anticipated at increasing driving amplitude, similarly to what is observed in presence of normal vibrations. This lowers the average friction force, as explained by the Prandtl-Tomlinson model with lateral vibrations superimposed at finite temperature. Nevertheless, the peak values of the lateral force, and the total energy losses, are expected to increase with the excitation amplitude, which may limit the practical relevance of this effect.

  9. Electronic and Atomic-Scale Properties of Ultraflat CVD Graphene

    Science.gov (United States)

    Gutierrez, Christopher; Rosenthal, Ethan; Dadgar, Ali; Brown, Lola; Lochocki, Edward; Shen, Kyle; Park, Jiwoong; Pasupathy, Abhay

    2014-03-01

    Chemical vapor deposition (CVD) growth on copper foils has proven to be a reliable and cost-effective method for the production of graphene. However, most films grown by this method suffer from misoriented graphene grains as well as topographic roughness due to the polycrystallinity of the underlying copper foil substrate. Recent methods of copper foil treatment have allowed for the growth of graphene predominantly on large single crystal Cu(111) facets. In this talk we discuss scanning tunneling microscope (STM) measurements on such samples that reveal large terraces and atomically-resolved images that allow us to analyze the graphene-copper interaction during the growth. Scanning tunneling spectroscopy (STS) measurements and mapping are further employed to probe the electronic interaction between the graphene and copper substrate.

  10. The study of materials at the atomic scale

    International Nuclear Information System (INIS)

    The atom probe is a projection microscope whose principle is based on the pin effect: the sample is shaped under the form of a very sharp pin and is submitted to a high electrical potential. Under the influence of the electrical field, the atoms are ejected and the sample surface can be peeled away atom by atom. The ejected atom carries 2 pieces of information: its trajectory and its speed. The knowledge of the trajectory allows the determination of the initial position site of the atom on the surface and the measurement of the time taken by the ion to reach the detector allows the identification of the atom through the use of a time-of-flight spectroscopy method. The development of new position detectors that can detect and record simultaneous impacts has led to the possibility of 3-dimensional imaging of the sample. The last generation of 3-dimensional atom probes has been used to study the position of the different species of atoms in an alloy and to study the formation of atom clusters around impurities in neutron irradiated ferritic steels. (A.C.)

  11. Electronic transport properties of copper and gold at atomic scale

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadzadeh, Saeideh

    2010-11-23

    The factors governing electronic transport properties of copper and gold atomic-size contacts are theoretically examined in the present work. A two-terminal conductor using crystalline electrodes is adopted. The non-equilibrium Green's function combined with the density functional tight-binding method is employed via gDFTB simulation tool to calculate the transport at both equilibrium and non-equilibrium conditions. The crystalline orientation, length, and arrangement of electrodes have very weak influence on the electronic characteristics of the considered atomic wires. The wire width is found to be the most effective geometric aspect determining the number of conduction channels. The obtained conductance oscillation and linear current-voltage curves are interpreted. To analyze the conduction mechanism in detail, the transmission channels and their decomposition to the atomic orbitals are calculated in copper and gold single point contacts. The presented results offer a possible explanation for the relation between conduction and geometric structure. Furthermore, the results are in good agreement with available experimental and theoretical studies. (orig.)

  12. Tuning magnetotransport in a compensated semimetal at the atomic scale

    OpenAIRE

    Wang, Lin; Gutierrez Lezama, Ignacio; Barreteau, Céline; Ubrig, Nicolas; Giannini, Enrico; Morpurgo, Alberto

    2015-01-01

    Either in bulk form, or when exfoliated into atomically thin crystals, layered transition metal dichalcogenides are continuously leading to the discovery of new phenomena. The latest example is provided by 1T'-WTe$_2$, a semimetal recently found to exhibit the largest known magnetoresistance in bulk crystals, and predicted to become a two-dimensional topological insulator in strained monolayers. Here, we show that reducing the thickness through facile exfoliation provides an effective experim...

  13. Evidence for contact delocalization in atomic scale friction

    OpenAIRE

    Abel, D; Krylov, S. Yu.; Frenken, J. W. M.

    2007-01-01

    We analyze an advanced two-spring model with an ultra-low effective tip mass to predict nontrivial and physically rich 'fine structure' in the atomic stick-slip motion in Friction Force Microscopy (FFM) experiments. We demonstrate that this fine structure is present in recent, puzzling experiments. This shows that the tip apex can be completely or partially delocalized, thus shedding new light on what is measured in FFM and, possibly, what can happen with the asperities that establish the con...

  14. Evidence for Contact Delocalization in Atomic Scale Friction

    Science.gov (United States)

    Abel, D. G.; Krylov, S. Yu.; Frenken, J. W. M.

    2007-10-01

    We analyze an advanced two-spring model with an ultralow effective tip mass to predict nontrivial and physically rich “fine structure” in the atomic stick-slip motion in friction force microscopy (FFM) experiments. We demonstrate that this fine structure is present in recent, puzzling experiments. This shows that the tip apex can be completely or partially delocalized, thus shedding new light on what is measured in FFM and, possibly, what can happen with the asperities that establish the contact between macroscopic sliding bodies.

  15. Mycobacterium avium-intracellulare cellulitis occurring with septic arthritis after joint injection: a case report

    Directory of Open Access Journals (Sweden)

    Murdoch David M

    2007-02-01

    Full Text Available Abstract Background Cellulitis caused by Mycobacterium avium-intracellulare has rarely been described. Mycobacterium avium-intracellulare is a rare cause of septic arthritis after intra-articular injection, though the causative role of injection is difficult to ascertain in such cases. Case presentation A 57-year-old with rheumatoid arthritis treated with prednisone and azathioprine developed bilateral painful degenerative shoulder arthritis. After corticosteroid injections into both acromioclavicular joints, he developed bilateral cellulitis centered over the injection sites. Skin biopsy showed non-caseating granulomas, and culture grew Mycobacterium avium-intracellulare. Joint aspiration also revealed Mycobacterium avium-intracellulare infection. Conclusion Although rare, skin and joint infections caused by Mycobacterium avium-intracellulare should be considered in any immunocompromised host, particularly after intra-articular injection. Stains for acid-fast bacilli may be negative in pathologic samples even in the presence of infection; cultures of tissue specimens should always be obtained.

  16. A model system using confocal fluorescence microscopy for examining real-time intracellular sodium ion regulation.

    Science.gov (United States)

    Lee, Jacqueline A; Collings, David A; Glover, Chris N

    2016-08-15

    The gills of euryhaline fish are the ultimate ionoregulatory tissue, achieving ion homeostasis despite rapid and significant changes in external salinity. Cellular handling of sodium is not only critical for salt and water balance but is also directly linked to other essential functions such as acid-base homeostasis and nitrogen excretion. However, although measurement of intracellular sodium ([Na(+)]i) is important for an understanding of gill transport function, it is challenging and subject to methodological artifacts. Using gill filaments from a model euryhaline fish, inanga (Galaxias maculatus), the suitability of the fluorescent dye CoroNa Green as a probe for measuring [Na(+)]i in intact ionocytes was confirmed via confocal microscopy. Cell viability was verified, optimal dye loading parameters were determined, and the dye-ion dissociation constant was measured. Application of the technique to freshwater- and 100% seawater-acclimated inanga showed salinity-dependent changes in branchial [Na(+)]i, whereas no significant differences in branchial [Na(+)]i were determined in 50% seawater-acclimated fish. This technique facilitates the examination of real-time changes in gill [Na(+)]i in response to environmental factors and may offer significant insight into key homeostatic functions associated with the fish gill and the principles of sodium ion transport in other tissues and organisms. PMID:27235170

  17. Gas transfer system in Alvinella pompejana (Annelida polychaeta, Terebellida): functional properties of intracellular and extracellular hemoglobins.

    Science.gov (United States)

    Hourdez, S; Lallier, F H; De Cian, M C; Green, B N; Weber, R E; Toulmond, A

    2000-01-01

    Alvinella pompejana is a tubicolous polychaete that dwells in the hottest part of the hydrothermal vent ecosystem in a highly variable mixture of vent (350 degrees C, anoxic, CO(2)- and sulfide-rich) and deep-sea (2 degrees C, mildly hypoxic) waters. This species has developed distinct-and specifically respiratory-adaptations to this challenging environment. An internal gas exchange system has recently been described, along with the report of an intracellular coelomic hemoglobin, in addition to the previously known extracellular vascular hemoglobin. This article reports the structure of coelomic hemoglobin and the functional properties of both hemoglobins in order to assess possible oxygen transfer. Coelomocytes contain a unique monomeric hemoglobin with a molecular weight of 14,810+/-1.5 Da, as determined by mass spectrometry. The functional properties of both hemoglobins are unexpectedly very similar under the same conditions of pH (6.1-8.2) and temperature (10 degrees -40 degrees C). The oxygen affinity of both proteins is relatively high (P50=0.66 Torr at 20 degrees C and pH 7), which facilitates oxygen uptake from the hypoxic environment. A strong Bohr effect (Phi ranging from -0.8 to -1.0) allows the release of oxygen to acidic tissues. Such similar properties imply a possible bidirectional transfer of oxygen between the two hemoglobins in the perioesophagal pouch, a mechanism that could moderate environmental variations of oxygen concentration and maintain brain oxygenation. PMID:10893176

  18. A new technique for reversible permeabilization of live cells for intracellular delivery of quantum dots

    International Nuclear Information System (INIS)

    A major challenge with the use of quantum dots (QDs) for cellular imaging and biomolecular delivery is the attainment of QDs freely dispersed inside the cells. Conventional methods such as endocytosis, lipids based delivery and electroporation are associated with delivery of QDs in vesicles and/or as aggregates that are not monodispersed. In this study, we demonstrate a new technique for reversible permeabilization of cells to enable the introduction of freely dispersed QDs within the cytoplasm. Our approach combines osmosis driven fluid transport into cells achieved by creating a hypotonic environment and reversible permeabilization using low concentrations of cell permeabilization agents like Saponin. Our results confirm that highly efficient endocytosis-free intracellular delivery of QDs can be accomplished using this method. The best results were obtained when the cells were treated with 50 μg ml−1 Saponin in a hypotonic buffer at a 3:2 physiological buffer:DI water ratio for 5 min at 4 ° C. (paper)

  19. Dual-Cross-Linked Methacrylated Alginate Sub-Microspheres for Intracellular Chemotherapeutic Delivery.

    Science.gov (United States)

    Fenn, Spencer L; Miao, Tianxin; Scherrer, Ryan M; Oldinski, Rachael A

    2016-07-20

    Intracellular delivery vehicles comprised of methacrylated alginate (Alg-MA) were developed for the internalization and release of doxorubicin hydrochloride (DOX). Alg-MA was synthesized via an anhydrous reaction, and a mixture of Alg-MA and DOX was formed into sub-microspheres using a water/oil emulsion. Covalently cross-linked sub-microspheres were formed via exposure to green light, in order to investigate effects of cross-linking on drug release and cell internalization, compared to traditional techniques, such as ultraviolet (UV) light irradiation. Cross-linking was performed using light exposure alone or in combination with ionic cross-linking using calcium chloride (CaCl2). Alg-MA sub-microsphere diameters were between 88 and 617 nm, and ζ-potentials were between -20 and -37 mV. Using human lung epithelial carcinoma cells (A549) as a model, cellular internalization was confirmed using flow cytometry; different sub-microsphere formulations varied the efficiency of internalization, with UV-cross-linked sub-microspheres achieving the highest internalization percentages. While blank (nonloaded) Alg-MA submicrospheres were noncytotoxic to A549 cells, DOX-loaded sub-microspheres significantly reduced mitochondrial activity after 5 days of culture. Photo-cross-linked Alg-MA sub-microspheres may be a potential chemotherapeutic delivery system for cancer treatment. PMID:27378419

  20. A new technique for reversible permeabilization of live cells for intracellular delivery of quantum dots

    Science.gov (United States)

    Medepalli, Krishnakiran; Alphenaar, Bruce W.; Keynton, Robert S.; Sethu, Palaniappan

    2013-05-01

    A major challenge with the use of quantum dots (QDs) for cellular imaging and biomolecular delivery is the attainment of QDs freely dispersed inside the cells. Conventional methods such as endocytosis, lipids based delivery and electroporation are associated with delivery of QDs in vesicles and/or as aggregates that are not monodispersed. In this study, we demonstrate a new technique for reversible permeabilization of cells to enable the introduction of freely dispersed QDs within the cytoplasm. Our approach combines osmosis driven fluid transport into cells achieved by creating a hypotonic environment and reversible permeabilization using low concentrations of cell permeabilization agents like Saponin. Our results confirm that highly efficient endocytosis-free intracellular delivery of QDs can be accomplished using this method. The best results were obtained when the cells were treated with 50 μg ml-1 Saponin in a hypotonic buffer at a 3:2 physiological buffer:DI water ratio for 5 min at 4 ° C.

  1. Target-specific intracellular delivery of siRNA using degradable hyaluronic acid nanogels.

    Science.gov (United States)

    Lee, Hyukjin; Mok, Hyejung; Lee, Soohyeon; Oh, Yu-Kyoung; Park, Tae Gwan

    2007-06-01

    Novel hyaluronic acid (HA) nanogels physically encapsulating small interfering RNA (siRNA) were fabricated by an inverse water-in-oil emulsion method. Thiol-conjugated HA dissolved in aqueous emulsion droplets was ultrasonically crosslinked via the formation of disulfide linkages to produce HA nanogels with a size distribution from 200 to 500 nm. Green fluorescence protein (GFP) siRNA was physically entrapped within the HA nanogels during the emulsion/crosslinking process. The HA/siRNA nanogels were readily taken up by HA receptor positive cells (HCT-116 cells) having HA-specific CD44 receptors on the surface. Release rates of siRNA from the HA nanogels could be modulated by changing the concentration of glutathione (GSH) in the buffer solution, indicating that the degradation/erosion of disulfide crosslinked HA nanogels, triggered by an intracellular reductive agent, controlled the release pattern of siRNA. When HA nanogels containing GFP siRNA were co-transfected with GFP plasmid/Lipofectamine to HCT-116 cells, a significant extent of GFP gene silencing was observed in both serum and non-serum conditions. The gene silencing effect was reduced in the presence of free HA in the transfection medium, revealing that HA nanogels were selectively taken up by HCT-116 cells via receptor mediated endocytosis. PMID:17408798

  2. Two-dimensional polyacrylamide gel electrophoresis of intracellular proteins

    International Nuclear Information System (INIS)

    Since two-dimensional electrophoresis was established by O'Farrell for analysis of intracellular proteins of Escherichia coli, it has been applied to separation of proteins of animal cells and tissues, and especially to identification of stress proteins. Using this technique, proteins are separated by isoelectric focusing containing 8 m urea in the first dimension and by SDS-PAGE in the second dimension. The gels are stained with Coomassie Blue R-250 dye, followed by silver staining. In the case of radio-labeled proteins, the gels are dried and then autoradiographed. In order to identify a specific protein separated by two-dimensional electrophoresis, a technique determining the N-terminal amino acid sequence of the protein has been developed recently. After the proteins in the gel were electrotransferred to a polyvinylidene difluoride membrane, the membrane was stained for protein with Commassie Blue and a stained membrane fragment was applied to a protein sequencer. Our recent studies demonstrated that fish cells newly synthesized various proteins in response to heat shock, cold nd osmotic stresses. For example, when cellular proteins extracted from cold-treated rainbow trout cells were subjected to two-dimensional gel electrophoresis, the 70 kDa protein was found to be synthesized during the cold-treatment. N-Terminal sequence analysis showed that the cold-inducible protein was a homolog of mammalian valosin-containing protein and yeast cell division cycle gene product CDC48p. Furthermore, the sequence data were useful for preparing PCR primers and a rabbit antibody against a synthetic peptide to analyze a role for the protein in the function of trout cells and mechanisms for regulation

  3. Monitoring of intracellular free calcium in perfused rat liver.

    Science.gov (United States)

    Ruttner, Z; Ligeti, L; Reinlib, L; Hines, K; McLaughlin, A C

    1993-06-01

    Fluorescent calcium indicators have been widely used to assess cytoplasmic calcium concentration in cells. To examine the role of calcium ions on different physiological functions (e.g. in case of liver; bile secretion, glucose metabolism, etc.) there is a need for whole organ studies. We have developed a technique to estimate intracellular free calcium changes in perfused rat liver. Krebs-Henseleit perfused livers were loaded with 7 microM or 35 microM Indo-1/AM. An area 3 mm in diameter and approximately 300 microns in depth was illuminated at 340 nm. Fluorescence was monitored with photomultiplier tubes at 3 wavelengths (400 nm for Ca-bound dye, 504 nm for free dye and 464 nm for NADH). The viability of liver preparations was assessed by measurement of the concentrations of lactate dehydrogenase and alanine aminotransferase in the effluent. Loading of the livers with 7 microM Indo-1/AM via the portal vein resulted in a 5-fold increase of fluorescence at 400 nm. However the dye 'leaked' out of the liver with a half-time of 18 min. Probenecid (a specific anion carrier blocker) inhibited loss of dye in a dose dependent fashion (2.5-10 mM). Transient calcium elevations were observed in response to vasopressin (5-50 nM) at physiological levels, ethanol (0.3-0.8 M) and the calcium ionophore, ionomycin. Certain limitations were apparent with this approach: (1) it was necessary to use an anion carrier blocker to maintain a relatively steady dye concentration; (2) endogenous NADH fluorescence interfered with the calcium signal; and (3) absolute values of calcium concentration could not be determined. PMID:8358770

  4. Intracellular mechanisms of hydroquinone toxicity on endotoxin-activated neutrophils.

    Science.gov (United States)

    Hebeda, Cristina Bichels; Pinedo, Fernanda Júdice; Bolonheis, Simone Marques; Ferreira, Zulma F; Muscará, Marcelo Nicolas; Teixeira, Simone Aparecida; Farsky, Sandra Helena Poliselli

    2012-11-01

    Circulating neutrophils promptly react to different substances in the blood and orchestrate the beginning of the innate inflammatory response. We have shown that in vivo exposure to hydroquinone (HQ), the most oxidative compound of cigarette smoke and a toxic benzene metabolite, affects circulating neutrophils, making them unresponsive to a subsequent bacterial infection. In order to understand the action of toxic molecular mechanisms on neutrophil functions, in vitro HQ actions on pro-inflammatory mediator secretions evoked by Escherichia coli lipopolysaccharide (LPS) were investigated. Neutrophils from male Wistar rats were cultured with vehicle or HQ (5 or 10 μM; 2 h) and subsequently incubated with LPS (5 μg/ml; 18 h). Hydroquinone treatment impaired LPS-induced nitric oxide (NO), tumour necrosis factor α (TNF-α), interleukin (IL)-1β and IL-6 secretions by neutrophils. The toxic effect was not dependent on cell death, reduced expression of the LPS receptor or toll-like receptor-4 (TLR-4) or cell priming, as HQ did not induce reactive oxygen species generation or β(2)integrin membrane expression. The action of toxic mechanisms on cytokine secretion was dependent on reduced gene synthesis, which may be due to decreased nuclear factor κB (NF-κB) nuclear translocation. Conversely, this intracellular pathway was not involved in impaired NO production because HQ treatments only affected inducible nitric oxide synthase protein expression and activity, suggesting posttranscriptional and/or posttranslational mechanisms of action. Altogether, our data show that HQ alters the action of different LPS-activated pathways on neutrophils, which may contribute to the impaired triggering of the host innate immune reaction detected during in vivo HQ exposure. PMID:22717997

  5. Intracellular fate of spherical nucleic acid nanoparticle conjugates.

    Science.gov (United States)

    Wu, Xiaochen A; Choi, Chung Hang J; Zhang, Chuan; Hao, Liangliang; Mirkin, Chad A

    2014-05-28

    Spherical nucleic acid (SNA) nanoparticle conjugates are a class of bionanomaterials that are extremely potent in many biomedical applications. Their unique ability to enter multiple mammalian cell types as single-entity agents arises from their novel three-dimensional architecture, which consists of a dense shell of highly oriented oligonucleotides chemically attached typically to a gold nanoparticle core. This architecture allows SNAs to engage certain cell surface receptors to facilitate entry. Here, we report studies aimed at determining the intracellular fate of SNAs and the trafficking events that occur inside C166 mouse endothelial cells after cellular entry. We show that SNAs traffic through the endocytic pathway into late endosomes and reside there for up to 24 h after incubation. Disassembly of oligonucleotides from the nanoparticle core is observed 16 h after cellular entry, most likely due to degradation by enzymes such as DNase II localized in late endosomes. Our observations point to these events being likely independent of core composition and treatment conditions, and they do not seem to be particularly dependent upon oligonucleotide sequence. Significantly and surprisingly, the SNAs do not enter the lysosomes under the conditions studied. To independently track the fate of the particle core and the fluorophore-labeled oligonucleotides that comprise its shell, we synthesized a novel class of quantum dot SNAs to determine that as the SNA structures are broken down over the 24 h time course of the experiment, the oligonucleotide fragments are recycled out of the cell while the nanoparticle core is not. This mechanistic insight points to the importance of designing and synthesizing next-generation SNAs that can bypass the degradation bottleneck imposed by their residency in late endosomes, and it also suggests that such structures might be extremely useful for endosomal signaling pathways by engaging receptors that are localized within the endosome

  6. Changes in intracellular calcium in brain cells of aged rats

    Institute of Scientific and Technical Information of China (English)

    Yu Li; Yunpeng Cao

    2008-01-01

    BACKGROUND: Studies have shown that voltage-dependent calcium influx, and enhancement of certain calcium-dependent processes in neurons, is related to aging. OBJECTIVE: To observe changes in intracellular calcium ([Ca2+]i) in neurons of aged rats, and to compare with young rats. DESIGN, TIME AND SETTING: A randomized control experiment of neurophysiology was performed at the Central Laboratory of School of Pharmaceutical Science, China Medical University from June to August 2004. MATERIALS: Ten male, healthy, Wistar rats, 19 months old, were selected for the aged group. Ten male, 3-month-old, Wistar rats were selected for the young control group. Fura-2/AM was provided by the Institute of Pharmaceutical Research of Chinese Academy of Medical Sciences, and the F-2000 fluorospectrophotometer was a product of Hitachi, Japan. METHODS: Fluorescence Fura-2 spectrophotometer was used to measure [Ca2+]i in acutely dissociated brain cells of aged and young rats. The concentration of extracellular potassium was controlled by adding different volumes of chloridated potassium solution of high concentration. MAIN OUTCOME MEASURES: [Ca2+]i in neurons of young and aged rats in the presence of 1 mmol/L extracellular calcium concentration and 0 mmol/L (resting state), 5, 10, 20, and 40 mmol/L extracellular potassium. Absolute increase of [Ca2+]i in neurons of young and aged rats when extraceUular potassium was 5,10,20, 40 mmol/L. RESULTS: In the presence of 1 mmol/L extracellular Ca2+ and 0 mmol/L (resting state), 5, 10, 20, and 40 mmol/L extracellular potassium, [Ca2+]i in the neurons of aged rats was significantly less than that in young rats (P 0.05). CONCLUSION: The overload of [Ca2+]i in neurons of aged rats is greater than that of young rats under the same circumstances.

  7. Molecular targeting of intracellular compartments specifically in cancer cells.

    Science.gov (United States)

    Pandya, Hetal; Gibo, Denise M; Debinski, Waldemar

    2010-05-01

    We have implemented a strategy in which a genetically engineered, single-chain protein specifically recognizes cancer cells and is trafficked to a targeted subcellular compartment, such as the nucleus. The recombinant protein termed IL-13.E13K-D2-NLS has a triple functional property: (1) it binds a cancer-associated receptor, interleukin 13 receptor alpha 2 (IL-13Rα2), using modified IL-13 ligand, IL-13.E13K; (2) it exports its C-terminal portion out of the endosomal compartment using Pseudomonas aeruginosa exotoxin A (PE) translocation domain (D2); and (3) it travels to and accumulates in the nucleus guided by the nuclear localization signal (NLS). Here, we have demonstrated that this protein is transported into the brain tumor cells' nucleus, using 3 different methods of protein conjugation to dyes for the purpose of direct visualization of the protein's intracellular trafficking. IL-13.E13K-D2-NLS, and not the controls such as IL-13.E13K-D2, IL-13.E13K-NLS, or IL-13.E13K, accumulated in nuclei very efficiently, which increased with the time the cells were exposed to the protein. Also, IL-13.E13K-D2-NLS did not exhibit nuclear transport in cells with low expression levels of IL-13Rα2. Thus, it is possible to recognize cancer cells through their specific receptors and deliver a conjugated protein that travels specifically to the nucleus. Hence, our molecular targeting strategy succeeded in generating a single-chain proteinaceous agent capable of delivering drugs/labels needed to be localized to the cells' nuclei or potentially any other subcellular compartment, for their optimal efficacy or ability to exert their specific action. PMID:20740056

  8. Intracellular performance of tailored nanoparticle tracers in magnetic particle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Arami, Hamed; Krishnan, Kannan M., E-mail: kannanmk@uw.edu [Department of Materials Science and Engineering, University of Washington, P.O. Box 352120, Seattle, Washington 98195-2120 (United States)

    2014-05-07

    Magnetic Particle Imaging (MPI) is a quantitative mass-sensitive, tracer-based imaging technique, with potential applications in various cellular imaging applications. The spatial resolution of MPI, in the first approximation, improves by decreasing the full width at half maximum (FWHM) of the field-derivative of the magnetization, dm/dH of the nanoparticle (NP) tracers. The FWHM of dm/dH depends critically on NPs’ size, size distribution, and their environment. However, there is limited information on the MPI performance of the NPs after their internalization into cells. In this work, 30 to 150 μg of the iron oxide NPs were incubated in a lysosome-like acidic buffer (0.2 ml, 20 mM citric acid, pH 4.7) and investigated by vibrating sample magnetometry, magnetic particle spectroscopy, transmission electron microscopy, and dynamic light scattering (DLS). The FWHM of the dm/dH curves of the NPs increased with incubation time and buffer to NPs ratio, consistent with a decrease in the median core size of the NPs from ∼20.1 ± 0.98 to ∼18.5 ± 3.15 nm. Further, these smaller degraded NPs formed aggregates that responded to the applied field by hysteretic reversal at higher field values and increased the FWHM. The rate of core size decrease and aggregation were inversely proportional to the concentration of the incubated NPs, due to their slower biodegradation kinetics. The results of this model experiment show that the MPI performance of the NPs in the acidic environments of the intracellular organelles (i.e., lysosomes and endosomes) can be highly dependent on their rate of internalization, residence time, and degradation.

  9. Intracellular performance of tailored nanoparticle tracers in magnetic particle imaging

    Science.gov (United States)

    Arami, Hamed; Krishnan, Kannan M.

    2014-05-01

    Magnetic Particle Imaging (MPI) is a quantitative mass-sensitive, tracer-based imaging technique, with potential applications in various cellular imaging applications. The spatial resolution of MPI, in the first approximation, improves by decreasing the full width at half maximum (FWHM) of the field-derivative of the magnetization, dm/dH of the nanoparticle (NP) tracers. The FWHM of dm/dH depends critically on NPs' size, size distribution, and their environment. However, there is limited information on the MPI performance of the NPs after their internalization into cells. In this work, 30 to 150 μg of the iron oxide NPs were incubated in a lysosome-like acidic buffer (0.2 ml, 20 mM citric acid, pH 4.7) and investigated by vibrating sample magnetometry, magnetic particle spectroscopy, transmission electron microscopy, and dynamic light scattering (DLS). The FWHM of the dm/dH curves of the NPs increased with incubation time and buffer to NPs ratio, consistent with a decrease in the median core size of the NPs from ˜20.1 ± 0.98 to ˜18.5 ± 3.15 nm. Further, these smaller degraded NPs formed aggregates that responded to the applied field by hysteretic reversal at higher field values and increased the FWHM. The rate of core size decrease and aggregation were inversely proportional to the concentration of the incubated NPs, due to their slower biodegradation kinetics. The results of this model experiment show that the MPI performance of the NPs in the acidic environments of the intracellular organelles (i.e., lysosomes and endosomes) can be highly dependent on their rate of internalization, residence time, and degradation.

  10. Estrogen receptor of primary breast cancers: evidence for intracellular proteolysis

    International Nuclear Information System (INIS)

    Iodinated oestradiol-labeled oestrogen receptor (ER) isoforms devoid of amino-terminal ABC domains represent about two-thirds of the whole receptor population detected in cytosol samples from human breast cancers. This high frequency could not be ascribed to the expression of truncated mRNAs, or to the proteolysis of the native ER peptide at the time of homogenization or assay, suggesting an intracellular proteolysis. Free amino-terminal and ligand-binding domains maintained together within oligomeric structure(s); increase of ionic strength separated them. The amino-terminal region was consistently detected in the cell nucleus by specific immunohistochemistry leading to the concept of a potential intranuclear association between ER cleavage products and/or other regulatory proteins. We previously reported that about two-thirds of [125I]oestradiol-labelled cytosolic ERs from breast cancer samples eluted as low-molecular-weight isoforms (≤ 37 kDa, size-exclusion fast pressure liquid chromatography [FPLC]). These isoforms failed to adsorb strongly to hydroxylapatite at high ionic strength, a property that was ascribed to receptors devoid of amino-terminal ABC domains. In view of recent data concerning intracellular proteolysis of several transcriptional regulators, the possibility of such behaviour for ER was assessed. The clinical significance of ER measurement in breast cancer cytosols is well established; approximately 50% of ER-positive cases respond to endocrine therapy. Whether such a poor correlation is related to a high proportion of cleaved ER is a question of prime importance. Failure of routine ER assays to discriminate between full-length and cleaved receptors led us to develop an oestradiol-binding assay based on hydroxylapatite adsorption. The aims of the present study were to demonstrate that hydroxylapatite adsorption assay easily identifies cleaved cytosolic ER forms and to assess the origin of such ER forms. Breast cancer cytosols classified as ER

  11. Antithrombotic activities of ferulic acid via intracellular cyclic nucleotide signaling.

    Science.gov (United States)

    Hong, Qian; Ma, Zeng-Chun; Huang, Hao; Wang, Yu-Guang; Tan, Hong-Ling; Xiao, Cheng-Rong; Liang, Qian-De; Zhang, Han-Ting; Gao, Yue

    2016-04-15

    Ferulic acid (FA) produces protective effects against cardiovascular dysfunctions. However, the mechanisms of FA is still not known. Here we examined the antithrombotic effects of FA and its potential mechanisms. Anticoagulation assays and platelet aggregation was evaluated in vitro and in vivo. Thromboxane B2 (TXB2), cyclic adenosine monophosphate(cAMP), and cyclic guanosine monophosphate (cGMP) was determined using enzyme immunoassay kits. Nitric oxide (NO) production was measured using the Griess reaction. Protein expression was detected by Western blotting analysis. Oral administration of FA prevented death caused by pulmonary thrombosis and prolonged the tail bleeding and clotting time in mice,while, it did not alter the coagulation parameters, including the activated partial thromboplastin time (APTT), prothrombin time (PT), and thrombin time (TT). In addition, FA (50-200µM) dose-dependently inhibited platelet aggregation induced by various platelet agonists, including adenosine diphosphate (ADP), thrombin, collagen, arachidonic acid (AA), and U46619. Further, FA attenuated intracellular Ca(2)(+) mobilization and TXB2 production induced by the platelet agonists. FA increased the levels of cAMP and cGMP and phosphorylated vasodilator-stimulated phosphoprotein (VASP) while decreased phospho-MAPK (mitogen-activated protein kinase) and phosphodiesterase (PDE) in washed rat platelets, VASP is a substrate of cyclic nucleotide and PDE is an enzyme family responsible for hydrolysis of cAMP/cGMP. These results suggest that antithrombotic activities of FA may be regulated by inhibition of platelet aggregation, rather than through inhibiting the release of thromboplastin or formation of thrombin. The mechanism of this action may involve activation of cAMP and cGMP signaling. PMID:26948317

  12. Production of intracellular selenium-enriched polysaccharides from thin stillage by Cordyceps sinensis and its bioactivities

    Directory of Open Access Journals (Sweden)

    Shengli Yang

    2016-02-01

    Full Text Available Background: Thin stillage was used as the substrate to produce intracellular selenium-enriched polysaccharides (ISPS from Cordyceps sinensis to increase the value of agricultural coproducts. Methods: Fermentation parameters were optimized using response surface methodology (RSM to improve the production of ISPS. Then, the effects of ISPS on the antioxidant activities in vitro, as well as the glycosylated serum protein concentration, malondialdehyde level, and total antioxidant capacity of streptozotocin-induced diabetic rats were studied. Results: The optimized conditions were as follows: sodium selenite concentration, 33.78 µg/L; incubation time, 8.24 days; and incubation temperature, 26.69°C. A maximum yield of 197.35 mg/g ISPS was obtained from the validation experiments, which was quite close to the predicted maximum yield of 198.6839 mg/g. FT-IR spectra indicated that ISPS has been successfully selenylation modified with similar structure to polysaccharide of intracellular polysaccharides. The in vitro scavenging effects of 1.0 mg/mL ISPS on hydroxyl, superoxide, and 1,1-diphenyl-2-picrylhydrazyl radicals were 74.62±4.05, 71.45±3.63, and 79.48±4.75%, respectively. The reducing power of ISPS was 0.45±0.01 (absorbance at 700 nm. Fasting blood glucose and glycosylated serum protein of group C (rats with diabetes that received drinking water with ISPS were significantly lower than those of group B (rats with diabetes (P<0.01 after treatment was administered for 2 and 4 weeks. Serum malonaldehyde content of group C was significantly lower than that of group B at 4 weeks (P<0.01. At 4 weeks, malonaldehyde contents in heart, liver, and kidney tissues of group C were significantly lower than those of group B; however, malonaldehyde content in pancreas tissue of group C was not significantly different. Total antioxidant capacities in liver, pancreas and kidney tissues of group C were significantly higher than those of group B, but total

  13. Aluminum-dependent regulation of intracellular silicon in the aquatic invertebrate Lymnaea stagnalis

    Science.gov (United States)

    Desouky, Mahmoud; Jugdaohsingh, Ravin; McCrohan, Catherine R.; White, Keith N.; Powell, Jonathan J.

    2002-01-01

    Silicon is essential for some plants, diatoms, and sponges but, in higher animals, its endogenous regulation has not been demonstrated. Silicate ions may be natural ligands for aluminum and here we show that, in the freshwater snail (Lymnaea stagnalis), intracellular silicon seems specifically up-regulated in response to sublethal aluminum exposure. X-ray microanalysis showed that exposure of snails to low levels of aluminum led to its accumulation in lysosomal granules, accompanied by marked up-regulation of silicon. Increased lysosomal levels of silicon were a specific response to aluminum because cadmium and zinc had no such effect. Furthermore, intra-lysosomal sulfur from metallothionein and other sulfur-containing ligands was increased after exposure to cadmium and zinc but not aluminum. To ensure that these findings indicated a specific in vivo response, and not ex vivo formation of hydroxy-aluminosilicates (HAS) from added aluminum (555 μg/liter) and water-borne silicon (43 μg/liter), two further studies were undertaken. In a ligand competition assay the lability of aluminum (527 μg/liter) was completely unaffected by the presence of silicon (46 μg/liter), suggesting the absence of HAS. In addition, exogenous silicon (6.5 mg/liter), added to the water column to promote formation of HAS, caused a decrease in lysosomal aluminum accumulation, showing that uptake of HAS would not explain the loading of aluminum into lysosomal granules. These findings, and arguments on the stability, lability, and kinetics of aluminum–silicate interactions, suggest that a silicon-specific mechanism exists for the in vivo detoxification of aluminum, which provides regulatory evidence of silicon in a multicellular organism. PMID:11891333

  14. Nucleation temperature-controlled synthesis and in vitro toxicity evaluation of L-cysteine-capped Mn:ZnS quantum dots for intracellular imaging.

    Science.gov (United States)

    Pandey, Vivek; Pandey, Gajanan; Tripathi, Vinay Kumar; Yadav, Sapna; Mudiam, Mohana Krishna Reddy

    2016-03-01

    Quantum dots (QDs), one of the fastest developing and most exciting fluorescent materials, have attracted increasing interest in bioimaging and biomedical applications. The long-term stability and emission in the visible region of QDs have proved their applicability as a significant fluorophore in cell labelling. In this study, an attempt has been made to explore the efficacy of L-cysteine as a capping agent for Mn-doped ZnS QD for intracellular imaging. A room temperature nucleation strategy was adopted to prepare non-toxic, water-dispersible and biocompatible Mn:ZnS QDs. Aqueous and room temperature QDs with L-cysteine as a capping agent were found to be non-toxic even at a concentration of 1500 µg/mL and have wide applications in intracellular imaging. PMID:26179189

  15. Fluorescent probes and nanoparticles for intracellular sensing of pH values

    International Nuclear Information System (INIS)

    Intracellular pH regulates a number of cell metabolism processes and its sensing is thus of great importance for cell studies. Among various methods, fluorescent probes have been widely used for sensing intracellular pH values because of their high sensitivity and spatiotemporal resolution capability. In this article, the development of fluorescent probes with good practicability in sensing intracellular pH values and pH variation during 2009 − 2014 is reviewed. These fluorescence probes are divided into two kinds: small molecules and nanoparticles. Photophysical properties, advantages/disadvantages and applications of the two kinds of probes are discussed in detail. (topical review)

  16. Dynamic modulation of intracellular glucose imaged in single cells using a FRET-based glucose nanosensor

    OpenAIRE

    John, Scott A.; Ottolia, Michela; James N Weiss; Ribalet, Bernard

    2007-01-01

    To study intracellular glucose homeostasis, the glucose nanosensor FLIPglu-600µM, which undergoes changes in fluorescence resonance energy transfer (FRET) upon interaction with glucose, was expressed in four mammalian cell lines: COS-7, CHO, HEK293, and C2C12. Upon addition of extracellular glucose, the intracellular FRET ratio decreased rapidly as intracellular glucose increased. The kinetics were fast (τ =5 to 15 s) in COS and C2C12 cells and slow (τ =20 to 40 s) in HEK and CHO cells. Upon ...

  17. Intracellular imaging of nanoparticles: Is it an elemental mistake to believe what you see?

    Directory of Open Access Journals (Sweden)

    Mühlfeld Christian

    2010-06-01

    Full Text Available Abstract In order to understand how nanoparticles (NPs J774.A1 murine macrophage-like cells were exposed to NH2 polyethylene (PEG QDs and elemental co-localization analysis of two elements present in the QDs (sulfur and cadmium was performed on putative intracellular QDs with electron spectroscopic imaging (ESI. Both elements were shown on a single particle level and QDs were confirmed to be located inside intracellular vesicles. Nevertheless, ESI analysis showed that not all nano-sized structures, initially identified as QDs, were confirmed. This observation emphasizes the necessity to perform elemental analysis when investigating intracellular NP localization using TEM.

  18. pH-sensitive intracellular photoluminescence of carbon nanotube-fluorescein conjugates in human ovarian cancer cells

    Science.gov (United States)

    Chen, M. T.; Gomez, L. M.; Ishikawa, F. N.; Vernier, P. T.; Zhou, C.; Gundersen, M. A.

    2009-07-01

    To add to the understanding of the properties of functionalized carbon nanotubes in biological applications, we report a monotonic pH sensitivity of the intracellular fluorescence emission of single-walled carbon nanotube-fluorescein carbazide (SWCNT-FC) conjugates in human ovarian cancer cells. Light-stimulated intracellular hydrolysis of the amide linkage and localized intracellular pH changes are proposed as mechanisms. SWCNT-FC conjugates may serve as intracellular pH sensors.

  19. Plectasin shows intracellular activity against Staphylococcus aureus in human THP-1 monocytes and in a mouse peritonitis model

    DEFF Research Database (Denmark)

    Brinch, Karoline Sidelmann; Sandberg, Anne; Baudoux, Pierre; Van Bambeke, Françoise; Tulkens, Paul M; Frimodt-Møller, Niels; Hoiby, Niels; Kristensen, Hans-Henrik

    2009-01-01

    Antimicrobial therapy of infections with Staphylococcus aureus can pose a challenge due to slow response to therapy and recurrence of infection. These treatment difficulties can partly be explained by intracellular survival of staphylococci, which is why the intracellular activity of...... antistaphylococcal compounds has received increased attention within recent years. The intracellular activity of plectasin, an antimicrobial peptide, against S. aureus was determined both in vitro and in vivo. In vitro studies using THP-1 monocytes showed that some intracellular antibacterial activity of plectasin...

  20. Function of chloride intracellular channel 1 in gastric cancer cells

    Directory of Open Access Journals (Sweden)

    Bo-Pei Li

    2012-01-01

    Full Text Available AIM: To investigate the effect of chloride intracellular channel 1 (CLIC1 on the cell proliferation, apoptosis, migration and invasion of gastric cancer cells. METHODS: CLIC1 expression was evaluated in human gastric cancer cell lines SGC-7901 and MGC-803 by real time polymerase chain reaction (RT-PCR. Four segments of small interference RNA (siRNA targeting CLIC1 mRNA and a no-sense control segment were designed by bioinformatics technology. CLIC1 siRNA was selected using Lipofectamine 2000 and transfected transiently into human gastric cancer SGC-7901 and MGC-803 cells. The transfected efficiency was observed under fluorescence microscope. After transfection, mRNA expression of CLIC1 was detected with RT-PCR and Western blotting was used to detect the protein expression. Proliferation was examined by methyl thiazolyl tetrazolium and apoptosis was detected with flow cytometry. Polycarbonate membrane transwell chamber and Matrigel were used for the detection of the changes of invasion and migration of the two cell lines. RESULTS: In gastric cancer cell lines SGC-7901 and MGC-803, CLIC1 was obviously expressed and CLIC1 siRNA could effectively suppress the expression of CLIC1 protein and mRNA. Proliferation of cells transfected with CLIC1 siRNA3 was enhanced notably, and the highest proliferation rate was 23.3% (P = 0.002 in SGC-7901 and 35.55% (P = 0.001 in MGC-803 cells at 48 h. The G2/M phase proportion increased, while G0/G1 and S phase proportions decreased. The apoptotic rate of the CLIC1 siRNA3 group obviously decreased in both SGC-7901 cells (62.24%, P = 0.000 and MGC-803 cells (52.67%, P = 0.004. Down-regulation of CLIC1 led to the inhibition of invasion and migration by 54.31% (P = 0.000 and 33.62% (P = 0.001 in SGC-7901 and 40.74% (P = 0.000 and 29.26% (P = 0.002 in MGC-803. However, there was no significant difference between the mock group cells and the negative control group cells. CONCLUSION: High CLIC1 expression can efficiently