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Sample records for cellular structure formation

  1. Predictive modeling of multicellular structure formation by using Cellular Particle Dynamics simulations

    NASA Astrophysics Data System (ADS)

    McCune, Matthew; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2014-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method for describing and predicting the time evolution of biomechanical relaxation processes of multicellular systems. A typical example is the fusion of spheroidal bioink particles during post bioprinting structure formation. In CPD cells are modeled as an ensemble of cellular particles (CPs) that interact via short-range contact interactions, characterized by an attractive (adhesive interaction) and a repulsive (excluded volume interaction) component. The time evolution of the spatial conformation of the multicellular system is determined by following the trajectories of all CPs through integration of their equations of motion. CPD was successfully applied to describe and predict the fusion of 3D tissue construct involving identical spherical aggregates. Here, we demonstrate that CPD can also predict tissue formation involving uneven spherical aggregates whose volumes decrease during the fusion process. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  2. Formation of ordered cellular structures in suspension via label-free negative magnetophoresis

    PubMed Central

    Krebs, Melissa D.; Erb, Randall M.; Yellen, Benjamin B.; Samanta, Bappaditya; Bajaj, Avinash; Rotello, Vincent M.; Alsberg, Eben

    2009-01-01

    The creation of ordered cellular structures is important for tissue engineering research. Here we present a novel strategy for the assembly of cells into linear arrangements by negative magnetophoresis using inert, cytocompatible magnetic nanoparticles. In this approach, magnetic nanoparticles dictate the cellular assembly without relying on cell binding or uptake. The linear cell structures are stable and can be further cultured without the magnetic field or nanoparticles, making this an attractive tool for tissue engineering. PMID:19326920

  3. Wrinkling in Cellular Structured Composites

    NASA Astrophysics Data System (ADS)

    Kaynia, Narges; Li, Yaning; Boyce, Mary C.

    2013-03-01

    Many structured composites found in nature possess undulating and wrinkled interfacial layers that regulate mechanical, chemical, acoustic, adhesive, thermal, electrical and optical functions of the material. This research focused on the formation of wrinkling patterns in cellular structured composites and the effect of the wrinkling pattern on the overall structural response. The cellular composites consisted of stiffer interfacial layers constructing a network submerged in a soft matrix. Analytical and finite element models were developed to capture various aspects of the wrinkling mechanism. The characteristics of the undulation patterns and the instability modes were investigated as functions of model geometry and material composition. Mechanical experiments were designed to further explore the modeling results. The cellular composite samples were fabricated by using different types of elastomers and by varying the geometry and the material properties. The experimental and numerical results were consistent with the analytical predictions. The results in this research improve understanding of the mechanisms governing the undulation pattern formation in cellular composites and can be used to enable on-demand tunability of different functions to provide, among others, active control of wave propagation, mechanical stiffness and deformation, and material swelling and growth.

  4. Formin’ cellular structures

    PubMed Central

    Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg

    2014-01-01

    Members of the Diaphanous (Dia) protein family are key regulators of fundamental actin driven cellular processes, which are conserved from yeast to humans. Researchers have uncovered diverse physiological roles in cell morphology, cell motility, cell polarity, and cell division, which are involved in shaping cells into tissues and organs. The identification of numerous binding partners led to substantial progress in our understanding of the differential functions of Dia proteins. Genetic approaches and new microscopy techniques allow important new insights into their localization, activity, and molecular principles of regulation. PMID:24719676

  5. Phase separation and the formation of cellular bodies

    NASA Astrophysics Data System (ADS)

    Xu, Bin; Broedersz, Chase P.; Meir, Yigal; Wingreen, Ned S.

    Cellular bodies in eukaryotic cells spontaneously assemble to form cellular compartments. Among other functions, these bodies carry out essential biochemical reactions. Cellular bodies form micron-sized structures, which, unlike canonical cell organelles, are not surrounded by membranes. A recent in vitro experiment has shown that phase separation of polymers in solution can explain the formation of cellular bodies. We constructed a lattice-polymer model to capture the essential mechanism leading to this phase separation. We used both analytical and numerical tools to predict the phase diagram of a system of two interacting polymers, including the concentration of each polymer type in the condensed and dilute phase.

  6. Pressure-actuated cellular structures.

    PubMed

    Pagitz, M; Lamacchia, E; Hol, J M A M

    2012-03-01

    Shape changing structures will play an important role in future engineering designs since rigid structures are usually only optimal for a small range of service conditions. Hence, a concept for reliable and energy-efficient morphing structures that possess a large strength to self-weight ratio would be widely applicable. We propose a novel concept for morphing structures that is inspired by the nastic movement of plants. The idea is to connect prismatic cells with tailored pentagonal and/or hexagonal cross sections such that the resulting cellular structure morphs into given target shapes for certain cell pressures. An efficient algorithm for computing equilibrium shapes as well as cross-sectional geometries is presented. The potential of this novel concept is demonstrated by several examples that range from a flagellum like propulsion device to a morphing aircraft wing. PMID:22278936

  7. Open cellular structure in marine stratocumulus sheets

    SciTech Connect

    Wood, Robert; Comstock, K. K.; Bretherton, Christopher S.; Cornish, C.; Tomlinson, Jason M.; Collins, Donald R.; Fairall, C.

    2008-06-25

    Geostationary and sunsynchronous satellite data and in-situ observations from ship cruises are used to investigate the formation of open cellular structure in marine stratocumulus clouds over the Southeast Pacific (SEP). Open cellular convection either forms spontaneously as pockets of open cells (POCs) within overcast stratocumulus, or is advected into the region from midlatitude regions. POC formation occurs most frequently during the latter part of the night demonstrating that this transition is not caused by solar absorption-driven decoupling. The transition preferentially occurs in clouds with low 11-3.7 microns nighttime brightness temperature difference (BTD) which is found to be well correlated with both in-situ measured accumulation mode aerosol concentration and cloud droplet concentration estimates derived from MODIS. Besides indicating that night time BTD is an excellent proxy for stratocumulus cloud droplet concentration Nd, this also suggests that low aerosol concentrations favor POC formation. Indeed, extremely low accumulation mode aerosol concentrations are found during the passage of open cell events over the ship. Free-tropospheric moisture is not found to be an important factor in POC formation. Significant subseasonal variability occurs in the fractional coverage of open cellular convection over the broader SEP. This coverage is well correlated with a MODIS-derived drizzle proxy (MDP) proportional to the ratio of liquid water path (LWP) to Nd for predominantly overcast regions. Both LWP and Nd variability influences the MDP. Periods of low MDP have significant positive large scale Nd anomalies and are preceded byoffshore winds at 850 hPa, which suggests a potential continental influence upon open cell formation over the SEP. Together, the results suggest important two-way interactions between aerosols and drizzle in marine stratocumulus and a role for drizzle in modulating the large scale albedo of these cloud systems.

  8. Cellular and molecular mechanisms underlying presynapse formation

    PubMed Central

    Chia, Poh Hui; Li, Pengpeng

    2013-01-01

    Synapse formation is a highly regulated process that requires the coordination of many cell biological events. Decades of research have identified a long list of molecular components involved in assembling a functioning synapse. Yet how the various steps, from transporting synaptic components to adhering synaptic partners and assembling the synaptic structure, are regulated and precisely executed during development and maintenance is still unclear. With the improvement of imaging and molecular tools, recent work in vertebrate and invertebrate systems has provided important insight into various aspects of presynaptic development, maintenance, and trans-synaptic signals, thereby increasing our understanding of how extrinsic organizers and intracellular mechanisms contribute to presynapse formation. PMID:24127213

  9. Integrated segmentation of cellular structures

    NASA Astrophysics Data System (ADS)

    Ajemba, Peter; Al-Kofahi, Yousef; Scott, Richard; Donovan, Michael; Fernandez, Gerardo

    2011-03-01

    Automatic segmentation of cellular structures is an essential step in image cytology and histology. Despite substantial progress, better automation and improvements in accuracy and adaptability to novel applications are needed. In applications utilizing multi-channel immuno-fluorescence images, challenges include misclassification of epithelial and stromal nuclei, irregular nuclei and cytoplasm boundaries, and over and under-segmentation of clustered nuclei. Variations in image acquisition conditions and artifacts from nuclei and cytoplasm images often confound existing algorithms in practice. In this paper, we present a robust and accurate algorithm for jointly segmenting cell nuclei and cytoplasm using a combination of ideas to reduce the aforementioned problems. First, an adaptive process that includes top-hat filtering, Eigenvalues-of-Hessian blob detection and distance transforms is used to estimate the inverse illumination field and correct for intensity non-uniformity in the nuclei channel. Next, a minimum-error-thresholding based binarization process and seed-detection combining Laplacian-of-Gaussian filtering constrained by a distance-map-based scale selection is used to identify candidate seeds for nuclei segmentation. The initial segmentation using a local maximum clustering algorithm is refined using a minimum-error-thresholding technique. Final refinements include an artifact removal process specifically targeted at lumens and other problematic structures and a systemic decision process to reclassify nuclei objects near the cytoplasm boundary as epithelial or stromal. Segmentation results were evaluated using 48 realistic phantom images with known ground-truth. The overall segmentation accuracy exceeds 94%. The algorithm was further tested on 981 images of actual prostate cancer tissue. The artifact removal process worked in 90% of cases. The algorithm has now been deployed in a high-volume histology analysis application.

  10. Actions of ultraviolet light on cellular structures.

    PubMed

    Pattison, David I; Davies, Michael J

    2006-01-01

    Solar radiation is the primary source of human exposure to ultraviolet (UV) radiation. Overexposure without suitable protection (i.e., sunscreen and clothing) has been implicated in mutagenesis and the onset of skin cancer. These effects are believed to be initiated by UV-mediated cellular damage, with proteins and DNA as primary targets due to a combination of their UV absorption characteristics and their abundance in cells. UV radiation can mediate damage via two different mechanisms: (a) direct absorption of the incident light by the cellular components, resulting in excited state formation and subsequent chemical reaction, and (b) photosensitization mechanisms, where the light is absorbed by endogenous (or exogenous) sensitizers that are excited to their triplet states. The excited photosensitizers can induce cellular damage by two mechanisms: (a) electron transfer and hydrogen abstraction processes to yield free radicals (Type I); or (b) energy transfer with O2 to yield the reactive excited state, singlet oxygen (Type II). Direct UV absorption by DNA leads to dimers of nucleic acid bases including cyclobutane pyrimidine species and pyrimidine (6-4) pyrimidone compounds, together with their Dewar isomers. These three classes of dimers are implicated in the mutagenicity of UV radiation, which is typified by a high level of CC-->TT and C-->T transversions. Single base modifications can also occur via sensitized reactions including Type 1 and Type II processes. The main DNA product generated by (1)O2 is 8-oxo-Gua; this is a common lesion in DNA and is formed by a range of other oxidants in addition to UV. The majority of UV-induced protein damage appears to be mediated by (1)O2, which reacts preferentially with Trp, His, Tyr, Met, Cys and cystine side chains. Direct photo-oxidation reactions (particularly with short-wavelength UV) and radicals can also be formed via triplet excited states of some of these side chains. The initial products of (1)O2-mediated

  11. Chemically Specific Cellular Imaging of Biofilm Formation

    SciTech Connect

    Herberg, J L; Schaldach, C; Horn, J; Gjersing, E; Maxwell, R

    2006-02-09

    organism, we needed to first turn our attention to a well understood organism. Pseudomonas aeruginosa (PA) is a well-studied organism and will be used to compare our results with others. Then, we will turn our attention to TD. It is expected that the research performed will provide key data to validate biochemical studies of TD and result in high profile publications in leading journals. For this project, our ultimate goal was to combine both Magnetic Resonance Imaging (MRI) and Nuclear Magnetic Resonance (NMR) experimental analysis with computer simulations to provide unique 3D molecular structural, dynamics, and functional information on the order of microns for this DOE mission relevant microorganism, T. denitrificans. For FY05, our goals were to: (1) Determine proper media for optimal growth of PA; growth rate measurements in that media and characterization of metabolite signatures during growth via {sup 1}H and {sup 13}C NMR, (2) Determine and build mineral, metal, and implant material surfaces to support growth of PA, (3) Implementing new MRI sequences to image biofilms more efficiently and increase resolution with new hardware design, (4) Develop further diffusion and flow MRI measurements of biofilms and biofilm formation with different MRI pulse sequences and different hardware design, and (5) Develop a zero dimension model of the rate of growth and the metabolite profiles of PA. Our major accomplishments are discussed in the following text. However, the bulk of this work is described in the attached manuscript entitled, ''NMR Metabolomics of Planktonic and Biofilm Modes of Growth in Pseudomonas aeruginosa''. This paper will be submitted to the Journal of Bacteriology in coming weeks. In addition, this one-year effort has lead to our incorporation into the Enhanced Surveillance Campaign during FY05 for some proof-of-principle MRI measurements on polymers. We are currently using similar methods to evaluate these polymers. In addition, this work on MRI measurements

  12. Formation of Tethers from Spreading Cellular Aggregates.

    PubMed

    Beaune, Grégory; Winnik, Françoise M; Brochard-Wyart, Françoise

    2015-12-01

    Membrane tubes are commonly extruded from cells and vesicles when a point-like force is applied on the membrane. We report here the unexpected formation of membrane tubes from lymph node cancer prostate (LNCaP) cell aggregates in the absence of external applied forces. The spreading of LNCaP aggregates deposited on adhesive glass substrates coated with fibronectin is very limited because cell-cell adhesion is stronger than cell-substrate adhesion. Some cells on the aggregate periphery are very motile and try to escape from the aggregate, leading to the formation of membrane tubes. Tethered networks and exchange of cargos between cells were observed as well. Growth of the tubes is followed by either tube retraction or tube rupture. Hence, even very cohesive cells are successful in escaping aggregates, which may lead to epithelial mesenchymal transition and tumor metastasis. We interpret the dynamics of formation and retraction of tubes in the framework of membrane mechanics. PMID:26509898

  13. Parametric study of double cellular detonation structure

    NASA Astrophysics Data System (ADS)

    Khasainov, B.; Virot, F.; Presles, H.-N.; Desbordes, D.

    2013-05-01

    A parametric numerical study is performed of a detonation cellular structure in a model gaseous explosive mixture whose decomposition occurs in two successive exothermic reaction steps with markedly different characteristic times. Kinetic and energetic parameters of both reactions are varied in a wide range in the case of one-dimensional steady and two-dimensional (2D) quasi-steady self-supported detonations. The range of governing parameters of both exothermic steps is defined where a "marked" double cellular structure exists. It is shown that the two-level cellular structure is completely governed by the kinetic parameters and the local overdrive ratio of the detonation front propagating inside large cells. Furthermore, since it is quite cumbersome to use detailed chemical kinetics in unsteady 2D case, the proposed work should help to identify the mixtures and the domain of their equivalence ratio where double detonation structure could be observed.

  14. Cellular pattern formation in circular domains.

    PubMed

    Palacios, Antonio; Gunaratne, Gemunu H.; Gorman, Michael; Robbins, Kay A.

    1997-09-01

    An analysis of stationary and nonstationary cellular patterns observed in premixed flames on a circular, porous plug burner is presented. A phenomenological model is introduced, that exhibits patterns similar to the experimental states. The primary modes of the model are combinations of Fourier-Bessel functions, whose radial parts have neighboring zeros. This observation explains several features of patterns, such as the existence of concentric rings of cells and the weak coupling between rings. Properties of rotating rings of cells, including the existence of modulated rotations and heteroclinic cycles can be deduced using mode coupling. For nonstationary patterns, the modal decomposition of experimental data can be carried out using the Karhunen-Loeve (KL) analysis. Experimental states are used to demonstrate the possibility of using KL analysis to differentiate between uniform and nonuniform rotations. The methodology can be extended to study more complicated nonstationary patterns. In particular, it is shown how the complexity of "hopping states" can be unraveled through the analysis. (c) 1997 American Institute of Physics. PMID:12779674

  15. Cellular pattern formation during Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Höfer, Thomas; Sherratt, Jonathan A.; Maini, Philip K.

    The development of multicellularity in the life cycle of Dictyostelium discoideum provides a paradigm model system for biological pattern formation. Previously, mathematical models have shown how a collective pattern of cell communication by waves of the messenger molecule cyclic adenosine 3‧5‧-monophosphate (cAMP) arises from excitable local cAMP kinetics and cAMP diffusion. Here we derive a model of the actual cell aggregation process by considering the chemotactic cell response to cAMP and its interplay with the cAMP dynamics. Cell density, which previously has been treated as a spatially homogeneous parameter, is a crucial variable of the aggregation model. We find that the coupled dynamics of cell chemotaxis and cAMP reaction-diffusion lead to the break-up of the initially uniform cell layer and to the formation of the striking cell stream morphology which characterizes the aggregation process in situ. By a combination of stability analysis and two-dimensional simulations of the model equations, we show cell streaming to be the consequence of the growth of a small-amplitude pattern in cell density forced by the large-amplitude cAMP waves, thus representing a novel scenario of spatial patterning in a cell chemotaxis system. The instability mechanism is further analysed by means of an analytic caricature of the model, and the condition for chemotaxis-driven instability is found to be very similar to the one obtained for the standard (non-oscillatory) Keller-Segel system. The growing cell stream pattern feeds back into the cAMP dynamics, which can explain in some detail experimental observations on the time evolution of the cAMP wave pattern, and suggests the characterization of the Dictyostelium aggregation field as a self-organized excitable medium.

  16. Structure Formation in Astrophysics

    NASA Astrophysics Data System (ADS)

    Chabrier, Gilles

    2009-01-01

    Part I. Physical Processes and Numerical Methods Common to Structure Formations in Astrophysics: 1. The physics of turbulence E. Levêque; 2. The numerical simulation of turbulence W. Schmidt; 3. Numerical methods for radiation magnetohydrodynamics in astrophysics R. Klein and J. Stone; 4. The role of jets in the formation of planets, stars, and galaxies R. Banerjee, R. Pudritz and R. Ouyed; 5. Advanced numerical methods in astrophysical fluid dynamics A. Hujeirat and F. Heitsch; Part II. Structure and Star Formation in the Primordial Universe: 6. New frontiers in cosmology and galaxy formation challenges for the future R. Ellis and J. Silk; 7. Galaxy formation physics T. Abel, G. Bryan and R. Teyssier; 8. First stars formation, evolution, feedback effects V. Bromm, A. Ferrara and A. Heger; Part III. Contemporary Star and Brown Dwarf Formation: a) Cloud Formation and Fragmentation: 9. Diffuse interstellar medium and the formation of molecular clouds P. Hennebelle, M. Mac Low and E. Vazquez-Semadeni; 10. The formation of distributed and clustered stars in molecular clouds T. Megeath, Z. -Y. Li and A. Nordlund; b) Core Fragmentation and Star Formation: 11. The formation and evolution of prestellar cores P. André, S. Basu and S. Inutsuka; 12. Models for the formation of massive stars; Part IV. Protoplanetary Disks and Planet Formation M. Krumholz and I. Bonnell: 13. Observational properties of disks and young stellar objects G. Duchêne, F. Ménard, J. Muzzerolle and S. Mohanty; 14. Structure and dynamics of protoplanetary disks C. Dullemond, R. Durisen and J. Papaloizou; 15. Planet formation and evolution theory and observation Y. Alibert, I. Baraffe, W. Benz, G. Laughlin and S. Udry; 16. Planet formation assembling the puzzle G. Wurm and T. Guillot; Part V. Summary: 17. Open issues in small- and large-scale structure formation R. Klessen and M. Mac Low; 18. Final word E. Salpeter.

  17. Structure Formation in Astrophysics

    NASA Astrophysics Data System (ADS)

    Chabrier, Gilles

    2011-02-01

    Part I. Physical Processes and Numerical Methods Common to Structure Formations in Astrophysics: 1. The physics of turbulence E. Levêque; 2. The numerical simulation of turbulence W. Schmidt; 3. Numerical methods for radiation magnetohydrodynamics in astrophysics R. Klein and J. Stone; 4. The role of jets in the formation of planets, stars, and galaxies R. Banerjee, R. Pudritz and R. Ouyed; 5. Advanced numerical methods in astrophysical fluid dynamics A. Hujeirat and F. Heitsch; Part II. Structure and Star Formation in the Primordial Universe: 6. New frontiers in cosmology and galaxy formation challenges for the future R. Ellis and J. Silk; 7. Galaxy formation physics T. Abel, G. Bryan and R. Teyssier; 8. First stars formation, evolution, feedback effects V. Bromm, A. Ferrara and A. Heger; Part III. Contemporary Star and Brown Dwarf Formation: a) Cloud Formation and Fragmentation: 9. Diffuse interstellar medium and the formation of molecular clouds P. Hennebelle, M. Mac Low and E. Vazquez-Semadeni; 10. The formation of distributed and clustered stars in molecular clouds T. Megeath, Z. -Y. Li and A. Nordlund; b) Core Fragmentation and Star Formation: 11. The formation and evolution of prestellar cores P. André, S. Basu and S. Inutsuka; 12. Models for the formation of massive stars; Part IV. Protoplanetary Disks and Planet Formation M. Krumholz and I. Bonnell: 13. Observational properties of disks and young stellar objects G. Duchêne, F. Ménard, J. Muzzerolle and S. Mohanty; 14. Structure and dynamics of protoplanetary disks C. Dullemond, R. Durisen and J. Papaloizou; 15. Planet formation and evolution theory and observation Y. Alibert, I. Baraffe, W. Benz, G. Laughlin and S. Udry; 16. Planet formation assembling the puzzle G. Wurm and T. Guillot; Part V. Summary: 17. Open issues in small- and large-scale structure formation R. Klessen and M. Mac Low; 18. Final word E. Salpeter.

  18. Crack Propagation in Bamboo's Hierarchical Cellular Structure

    PubMed Central

    Habibi, Meisam K.; Lu, Yang

    2014-01-01

    Bamboo, as a natural hierarchical cellular material, exhibits remarkable mechanical properties including excellent flexibility and fracture toughness. As far as bamboo as a functionally graded bio-composite is concerned, the interactions of different constituents (bamboo fibers; parenchyma cells; and vessels.) alongside their corresponding interfacial areas with a developed crack should be of high significance. Here, by using multi-scale mechanical characterizations coupled with advanced environmental electron microscopy (ESEM), we unambiguously show that fibers' interfacial areas along with parenchyma cells' boundaries were preferred routes for crack growth in both radial and longitudinal directions. Irrespective of the honeycomb structure of fibers along with cellular configuration of parenchyma ground, the hollow vessels within bamboo culm affected the crack propagation too, by crack deflection or crack-tip energy dissipation. It is expected that the tortuous crack propagation mode exhibited in the present study could be applicable to other cellular natural materials as well. PMID:24998298

  19. Cellular Structure Pattern in Dielectric Barrier Discharge

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Dong, Lifang; Liu, Weibo; Gao, Xing; Wei, Lingyan

    2015-12-01

    We report the observation of a cellular structure pattern in a dielectric barrier discharge system. The evolution sequence and phase diagram of the pattern are given. It is firstly observed that the "cell nucleus" fire three or even more times at a fixed location at the rising edge of the applied voltage, and that the "cell walls" which have the same discharge times with the "cell nucleus" are ignited slightly after the "cell nucleus". By observing a series of frames recorded by a high speed video camera, it is found that the cellular structure pattern consists of volume discharges (VDs) and surface discharges (SDs) corresponding to the "cell nucleus" and "cell walls" respectively. That VDs and SDs are ignited in turn for several times in each half cycle of the applied voltage confirms the fact that VDs induce the SDs and SDs also affect the following VDs.

  20. Light weight cellular structures based on aluminium

    SciTech Connect

    Prakash, O.; Embury, J.D.; Sinclair, C.; Sang, H.; Silvetti, P.

    1997-02-01

    An interesting form of lightweight material which has emerged in the past 2 decades is metallic foam. This paper deals with the basic concepts of making metallic foams and a detailed study of foams produced from Al-SiC. In addition, some aspects of cellular solids based on honeycomb structures are outlined including the concept of producing both two-phase foams and foams with composite walls.

  1. Gravitational Effects on Cellular Flame Structure

    NASA Technical Reports Server (NTRS)

    Dunsky, C. M.; Fernandez-Pello, A. C.

    1991-01-01

    An experimental investigation has been conducted of the effect of gravity on the structure of downwardly propagating, cellular premixed propane-oxygen-nitrogen flames anchored on a water-cooled porous-plug burner. The flame is subjected to microgravity conditions in the NASA Lewis 2.2-second drop tower, and flame characteristics are recorded on high-speed film. These are compared to flames at normal gravity conditions with the same equivalence ratio, dilution index, mixture flow rate, and ambient pressure. The results show that the cellular instability band, which is located in the rich mixture region, changes little under the absence of gravity. Lifted normal-gravity flames near the cellular/lifted limits, however, are observed to become cellular when gravity is reduced. Observations of a transient cell growth period following ignition point to heat loss as being an important mechanism in the overall flame stability, dominating the stabilizing effect of buoyancy for these downwardly-propagating burner-anchored flames. The pulsations that are observed in the plume and diffusion flame generated downstream of the premixed flame in the fuel rich cases disappear in microgravity, verifying that these fluctuations are gravity related.

  2. Elements of the cellular metabolic structure

    PubMed Central

    De la Fuente, Ildefonso M.

    2015-01-01

    A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell. PMID:25988183

  3. Cosmological structure formation

    NASA Technical Reports Server (NTRS)

    Schramm, David N.

    1991-01-01

    A summary of the current forefront problem of physical cosmology, the formation of structures (galaxies, clusters, great walls, etc.) in the universe is presented. Solutions require two key ingredients: (1) matter; and (2) seeds. Regarding the matter, it now seems clear that both baryonic and non-baryonic matter are required. Whether the non-baryonic matter is hot or cold depends on the choice of seeds. Regarding the seeds, both density fluctuations and topological defects are discussed. The combination of isotropy of the microwave background and the recent observations indicating more power on large scales have severly constrained, if not eliminated, Gaussian fluctuations with equal power on all scales, regardless of the eventual resolution of both the matter and seed questions. It is important to note that all current structure formation ideas require new physics beyond SU(3) x SU(2) x U(1).

  4. Cellularization in locust embryos occurs before blastoderm formation.

    PubMed

    Ho, K; Dunin-Borkowski, O M; Akam, M

    1997-07-01

    In Drosophila intracellular gradients establish the pattern of segmentation by controlling gene expression during a critical syncytial stage, prior to cellularization. To investigate whether a similar mechanism may be exploited by other insects, we examined the timing of cellularization with respect to blastoderm formation in an insect with extreme short-germ development, the African desert locust, Schistocerca gregaria. Using light and electron microscopic techniques, we show that the islands of cytoplasm surrounding cleavage nuclei are largely isolated from their neighbours, allowing cleavage to proceed asynchronously. Within a short time of their arrival at the surface and prior to blastoderm formation, nuclei become surrounded by complete cell membranes that block the free uptake of dye (10,000 kDa) from the yolk. Our results imply that the formation of the blastoderm disc involves the aggregation of cells at the posterior pole of the egg and not the migration of nuclei within a syncytial cytoplasm. These findings suggest that the primary cleavage syncytium does not play the same role in patterning the locust embryo as it does in Drosophila. However, we do identify a syncytial nuclear layer that underlies the forming blastoderm and remains in continuity with the yolk. PMID:9226447

  5. Neural and cellular mechanisms of fear and extinction memory formation.

    PubMed

    Orsini, Caitlin A; Maren, Stephen

    2012-08-01

    Over the course of natural history, countless animal species have evolved adaptive behavioral systems to cope with dangerous situations and promote survival. Emotional memories are central to these defense systems because they are rapidly acquired and prepare organisms for future threat. Unfortunately, the persistence and intrusion of memories of fearful experiences are quite common and can lead to pathogenic conditions, such as anxiety and phobias. Over the course of the last 30 years, neuroscientists and psychologists alike have attempted to understand the mechanisms by which the brain encodes and maintains these aversive memories. Of equal interest, though, is the neurobiology of extinction memory formation as this may shape current therapeutic techniques. Here we review the extant literature on the neurobiology of fear and extinction memory formation, with a strong focus on the cellular and molecular mechanisms underlying these processes. PMID:22230704

  6. Neural and Cellular Mechanisms of Fear and Extinction Memory Formation

    PubMed Central

    Orsini, Caitlin A.; Maren, Stephen

    2012-01-01

    Over the course of natural history, countless animal species have evolved adaptive behavioral systems to cope with dangerous situations and promote survival. Emotional memories are central to these defense systems because they are rapidly acquired and prepare organisms for future threat. Unfortunately, the persistence and intrusion of memories of fearful experiences are quite common and can lead to pathogenic conditions, such as anxiety and phobias. Over the course of the last thirty years, neuroscientists and psychologists alike have attempted to understand the mechanisms by which the brain encodes and maintains these aversive memories. Of equal interest, though, is the neurobiology of extinction memory formation as this may shape current therapeutic techniques. Here we review the extant literature on the neurobiology of fear and extinction memory formation, with a strong focus on the cellular and molecular mechanisms underlying these processes. PMID:22230704

  7. A structural basis for cellular senescence

    PubMed Central

    Aranda-Anzaldo, Armando

    2009-01-01

    Replicative senescence (RS) that limits the proliferating potential of normal eukaryotic cells occurs either by a cell-division counting mechanism linked to telomere erosion or prematurely through induction by cell stressors such as oncogene hyper-activation. However, there is evidence that RS also occurs by a stochastic process that is independent of number of cell divisions or cellular stress and yet it leads to a highly-stable, non-reversible post-mitotic state that may be long-lasting and that such a process is widely represented among higher eukaryotes. Here I present and discuss evidence that the interactions between DNA and the nuclear substructure, commonly known as the nuclear matrix, define a higher-order structure within the cell nucleus that following thermodynamic constraints, stochastically evolves towards maximum stability, thus becoming limiting for mitosis to occur. It is suggested that this process is responsible for ultimate replicative senescence and yet it is compatible with long-term cell survival. PMID:20157542

  8. Cellular automata modeling of weld solidification structure

    SciTech Connect

    Dress, W.B.; Zacharia, T.; Radhakrishnan, B.

    1993-12-31

    The authors explore the use of cellular automata in modeling arc-welding processes. A brief discussion of cellular automata and their previous use in micro-scale solidification simulations is presented. Macro-scale thermal calculations for arc-welding at a thin plate are shown to give good quantitative and qualitative results. Combining the two calculations in a single cellular array provides a realistic simulation of grain growth in a welding process. Results of simulating solidification in a moving melt pool in a poly-crystalline alloy sheet are presented.

  9. Elastomeric Cellular Structure Enhanced by Compressible Liquid Filler

    PubMed Central

    Sun, Yueting; Xu, Xiaoqing; Xu, Chengliang; Qiao, Yu; Li, Yibing

    2016-01-01

    Elastomeric cellular structures provide a promising solution for energy absorption. Their flexible and resilient nature is particularly relevant to protection of human bodies. Herein we develop an elastomeric cellular structure filled with nanoporous material functionalized (NMF) liquid. Due to the nanoscale infiltration in NMF liquid and its interaction with cell walls, the cellular structure has a much enhanced mechanical performance, in terms of loading capacity and energy absorption density. Moreover, it is validated that the structure is highly compressible and self-restoring. Its hyper-viscoelastic characteristics are elucidated. PMID:27221079

  10. Elastomeric Cellular Structure Enhanced by Compressible Liquid Filler

    NASA Astrophysics Data System (ADS)

    Sun, Yueting; Xu, Xiaoqing; Xu, Chengliang; Qiao, Yu; Li, Yibing

    2016-05-01

    Elastomeric cellular structures provide a promising solution for energy absorption. Their flexible and resilient nature is particularly relevant to protection of human bodies. Herein we develop an elastomeric cellular structure filled with nanoporous material functionalized (NMF) liquid. Due to the nanoscale infiltration in NMF liquid and its interaction with cell walls, the cellular structure has a much enhanced mechanical performance, in terms of loading capacity and energy absorption density. Moreover, it is validated that the structure is highly compressible and self-restoring. Its hyper-viscoelastic characteristics are elucidated.

  11. Elastomeric Cellular Structure Enhanced by Compressible Liquid Filler.

    PubMed

    Sun, Yueting; Xu, Xiaoqing; Xu, Chengliang; Qiao, Yu; Li, Yibing

    2016-01-01

    Elastomeric cellular structures provide a promising solution for energy absorption. Their flexible and resilient nature is particularly relevant to protection of human bodies. Herein we develop an elastomeric cellular structure filled with nanoporous material functionalized (NMF) liquid. Due to the nanoscale infiltration in NMF liquid and its interaction with cell walls, the cellular structure has a much enhanced mechanical performance, in terms of loading capacity and energy absorption density. Moreover, it is validated that the structure is highly compressible and self-restoring. Its hyper-viscoelastic characteristics are elucidated. PMID:27221079

  12. Cellular bases of experimental amebic liver abscess formation.

    PubMed Central

    Tsutsumi, V.; Mena-Lopez, R.; Anaya-Velazquez, F.; Martinez-Palomo, A.

    1984-01-01

    The complete sequence of morphologic events during amebic liver abscess formation in the hamster has been studied, from the lodgement of amebas in the hepatic sinusoids to the development of extensive liver necrosis. Following intraportal inoculation of live amebas, the early stages of the lesion (from 1 to 12 hours) were characterized by acute cellular infiltration composed of an increasingly large number of polymorphonuclear leukocytes, which surrounded centrally located trophozoites. Histiocytes and lysed leukocytes were situated on the periphery of the lesions. Hepatocytes close to the early lesions showed degenerative changes which led to necrosis; however, direct contact of liver cells with amebas was very rarely observed. At later stages, the extent of necrosis increased, macrophages and epithelioid cells replaced most leukocytes, and well-organized granulomas developed. Extensive necrosis associated with fused granulomas was present by Day 7. The results suggest that Entamoeba histolytica trophozoites do not produce amebic liver abscesses in hamsters through direct lysis of hepatocytes. Rather, tissue destruction is the result of the accumulation and subsequent lysis of leukocytes and macrophages surrounding the amebas. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:6385728

  13. Subfailure damage in ligament: a structural and cellular evaluation.

    PubMed

    Provenzano, Paolo P; Heisey, Dennis; Hayashi, Kei; Lakes, Roderic; Vanderby, Ray

    2002-01-01

    Subfailure damage in ligaments was evaluated macroscopically from a structural perspective (referring to the entire ligament as a structure) and microscopically from a cellular perspective. Freshly harvested rat medial collateral ligaments (MCLs) were used as a model in ex vivo experiments. Ligaments were preloaded with 0.1 N to establish a consistent point of reference for length (and strain) measurements. Ligament structural damage was characterized by nonrecoverable difference in tissue length after a subfailure stretch. The tissue's mechanical properties (via stress vs. strain curves measured from a preloaded state) after a single subfailure stretch were also evaluated (n = 6 pairs with a different stretch magnitude applied to each stretched ligament). Regions containing necrotic cells were used to characterize cellular damage after a single stretch. It should be noted that the number of damaged cells was not quantified and the difference between cellular area and area of fluorescence is not known. Structural and cellular damage were represented and compared as functions of subfailure MCL strains. Statistical analysis indicated that the onset of structural damage occurs at 5.14% strain (referenced from a preloaded length). Subfailure strains above the damage threshold changed the shape of the MCL stress-strain curve by elongating the toe region (i.e., increasing laxity) as well as decreasing the tangential modulus and ultimate stress. Cellular damage was induced at ligament strains significantly below the structural damage threshold. This cellular damage is likely to be part of the natural healing process in mildly sprained ligaments. PMID:11744679

  14. Evolutionary Relationships Based on Cellular Structure.

    ERIC Educational Resources Information Center

    Van Winkle, Lon J.

    1979-01-01

    This laboratory exercise integrates the topics of cell structure, classification of living organisms, and evolution. It is suitable for secondary or college biology courses and was used in an interdisciplinary science course for nonscience majors. (BB)

  15. Cellular network formation of hydrophobic alkanethiol capped gold nanoparticles on mica surface mediated by water islands.

    PubMed

    John, Neena S; Raina, Gargi; Sharma, Ashutosh; Kulkarni, Giridhar U

    2010-09-01

    Dendritic and cellular networks of nanoparticles are known to form commonly either by random diffusion-limited aggregation or by solvent evaporation dynamics. Using alkanethiol capped gold nanoparticles deposited on mica imaged under ambient and controlled water vapor conditions by atomic force microscope and in situ scanning electron microscope, respectively, we show a third mechanism in action. The cellular network consisting of open and closed polygons is formed by the nucleation and lateral growth of adsorbed water islands, the contact lines of which push the randomly distributed hydrophobic nanoparticles along the growth directions, eventually leading to the polygonal structure formation as the boundaries of the growing islands meet. Such nanoparticle displacement has been possible due to the weakly adhering nature of the hydrophilic substrate, mica. These results demonstrate an important but hitherto neglected effect of adsorbed water in the structure formation on hydrophilic substrates and provide a facile tool for the fabrication of nanoparticle networks without specific particle or substrate modifications and without a tight control on particle deposition conditions during the solvent evaporation. PMID:20831330

  16. Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Stampfl, J.; Pettermann, H. E.; Liska, R.

    Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

  17. Chiral hexagonal cellular sandwich structure: a vibro-acoustic assessment

    NASA Astrophysics Data System (ADS)

    Lew, Tze L.; Spadoni, Alessandro; Scarpa, Fabrizio; Ruzzene, Massimo

    2005-05-01

    In this work we describe the vibroacoustic behavior of a novel concept of core for sandwich structures featuring auxetic characteristics, enhanced shear stiffness and compressive strength compared to classical cellular cores in sandwich components for sandwich applications. The out-plane properties and density values are described in terms of geometric parameters of the honeycomb unit cells. Opposite to classical honeycomb cellular applications, the hexagonal chiral structure presents a noncentresymemetric configuration, i.e., a "mirror" symmetrical topology. The derived mechanical properties are used to assess the modal behaviour and modal densities of sandwich plate elements with chiral and standard cellular cores. The analytical findings are backed up by structural tests on chiral honeycomb plates and sandwich beams.

  18. Cellular interactions during tracheary elements formation and function.

    PubMed

    Ménard, Delphine; Pesquet, Edouard

    2015-02-01

    The survival of higher plant species on land depends on the development and function of an efficient vascular system distributing water and minerals absorbed by roots to all aerial organs. This conduction and distribution of plant sap relies on specialized cells named tracheary elements (TEs). In contrast to many other cell types in plants, TEs are functionalized by cell death that hollows the cell protoplast to make way for the sap. To maintain a stable conducting function during plant development, recovery from vascular damages as well as to adapt to environmental changes, TEs are completely dependent on direct cellular interactions with neighboring xylem parenchyma cells (XPs). PMID:25545993

  19. FORMATION BY IRRADIATION OF AN EXPANDED, CELLULAR, POLYMERIC BODY

    DOEpatents

    Charlesby, A.; Ross, M.

    1958-12-01

    The treatment of polymeric esters of methacrylic acid having a softening polnt above 40 icient laborato C to form an expanded cellular mass with a smooth skin is discussed. The disclosed method comprises the steps of subjecting the body at a temperature below the softenpoint to a dose of at least 5 x lO/sup 6/ roentgen of gamma radiation from cobalt-60 source until its average molecular weight is reduced to a value within the range of 3 x lO/sup 5/ to 10/sup 4/, and heating at a temperature within the range of 0 to lO icient laborato C above its softening point to effect expansion.

  20. Coupled pulsating and cellular structure in the propagation of globally planar detonations in free space

    SciTech Connect

    Han, Wenhu; Gao, Yang; Wang, Cheng; Law, Chung K.

    2015-10-15

    The globally planar detonation in free space is numerically simulated, with particular interest to understand and quantify the emergence and evolution of the one-dimensional pulsating instability and the two-dimensional cellular structure which is inherently also affected by pulsating instability. It is found that the pulsation includes three stages: rapid decay of the overdrive, approach to the Chapman-Jouguet state and emergence of weak pulsations, and the formation of strong pulsations; while evolution of the cellular structure also exhibits distinct behavior at these three stages: no cell formation, formation of small-scale, irregular cells, and formation of regular cells of a larger scale. Furthermore, the average shock pressure in the detonation front consists of fine-scale oscillations reflecting the collision dynamics of the triple-shock structure and large-scale oscillations affected by the global pulsation. The common stages of evolution between the cellular structure and the pulsating behavior, as well as the existence of shock-front pressure oscillation, suggest highly correlated mechanisms between them. Detonations with period doubling, period quadrupling, and chaotic amplitudes were also observed and studied for progressively increasing activation energies.

  1. Coupled pulsating and cellular structure in the propagation of globally planar detonations in free space

    NASA Astrophysics Data System (ADS)

    Han, Wenhu; Gao, Yang; Wang, Cheng; Law, Chung K.

    2015-10-01

    The globally planar detonation in free space is numerically simulated, with particular interest to understand and quantify the emergence and evolution of the one-dimensional pulsating instability and the two-dimensional cellular structure which is inherently also affected by pulsating instability. It is found that the pulsation includes three stages: rapid decay of the overdrive, approach to the Chapman-Jouguet state and emergence of weak pulsations, and the formation of strong pulsations; while evolution of the cellular structure also exhibits distinct behavior at these three stages: no cell formation, formation of small-scale, irregular cells, and formation of regular cells of a larger scale. Furthermore, the average shock pressure in the detonation front consists of fine-scale oscillations reflecting the collision dynamics of the triple-shock structure and large-scale oscillations affected by the global pulsation. The common stages of evolution between the cellular structure and the pulsating behavior, as well as the existence of shock-front pressure oscillation, suggest highly correlated mechanisms between them. Detonations with period doubling, period quadrupling, and chaotic amplitudes were also observed and studied for progressively increasing activation energies.

  2. HMG Nuclear Proteins: Linking Chromatin Structure to Cellular Phenotype

    PubMed Central

    Reeves, Raymond

    2009-01-01

    I. Summary Although the three families of mammalian HMG proteins (HMGA, HMGB and HMGN) participate in many of the same nuclear processes, each family plays its own unique role in modulating chromatin structure and regulating genomic function. This review focuses on the similarities and differences in the mechanisms by which the different HMG families impact chromatin structure and influence cellular phenotype. The biological implications of having three architectural transcription factor families with complementary, but partially overlapping, nuclear functions are discussed. PMID:19748605

  3. Multi-scale Imaging of Cellular and Sub-cellular Structures using Scanning Probe Recognition Microscopy.

    NASA Astrophysics Data System (ADS)

    Chen, Q.; Rice, A. F.

    2005-03-01

    Scanning Probe Recognition Microscopy is a new scanning probe capability under development within our group to reliably return to and directly interact with a specific nanobiological feature of interest. In previous work, we have successfully recognized and classified tubular versus globular biological objects from experimental atomic force microscope images using a method based on normalized central moments [ref. 1]. In this paper we extend this work to include recognition schemes appropriate for cellular and sub-cellular structures. Globular cells containing tubular actin filaments are under investigation. Thus there are differences in external/internal shapes and scales. Continuous Wavelet Transform with a differential Gaussian mother wavelet is employed for multi- scale analysis. [ref. 1] Q. Chen, V. Ayres and L. Udpa, ``Biological Investigation Using Scanning Probe Recognition Microscopy,'' Proceedings 3rd IEEE Conference on Nanotechnology, vol. 2, p 863-865 (2003).

  4. Computer Modeling of the Earliest Cellular Structures and Functions

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl

    2000-01-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

  5. Global Self-Organization of the Cellular Metabolic Structure

    PubMed Central

    De La Fuente, Ildefonso M.; Martínez, Luis; Pérez-Samartín, Alberto L.; Ormaetxea, Leire; Amezaga, Cristian; Vera-López, Antonio

    2008-01-01

    Background Over many years, it has been assumed that enzymes work either in an isolated way, or organized in small catalytic groups. Several studies performed using “metabolic networks models” are helping to understand the degree of functional complexity that characterizes enzymatic dynamic systems. In a previous work, we used “dissipative metabolic networks” (DMNs) to show that enzymes can present a self-organized global functional structure, in which several sets of enzymes are always in an active state, whereas the rest of molecular catalytic sets exhibit dynamics of on-off changing states. We suggested that this kind of global metabolic dynamics might be a genuine and universal functional configuration of the cellular metabolic structure, common to all living cells. Later, a different group has shown experimentally that this kind of functional structure does, indeed, exist in several microorganisms. Methodology/Principal Findings Here we have analyzed around 2.500.000 different DMNs in order to investigate the underlying mechanism of this dynamic global configuration. The numerical analyses that we have performed show that this global configuration is an emergent property inherent to the cellular metabolic dynamics. Concretely, we have found that the existence of a high number of enzymatic subsystems belonging to the DMNs is the fundamental element for the spontaneous emergence of a functional reactive structure characterized by a metabolic core formed by several sets of enzymes always in an active state. Conclusions/Significance This self-organized dynamic structure seems to be an intrinsic characteristic of metabolism, common to all living cellular organisms. To better understand cellular functionality, it will be crucial to structurally characterize these enzymatic self-organized global structures. PMID:18769681

  6. Cellular structure of detonation utilized in propulsion system

    NASA Astrophysics Data System (ADS)

    Zhang, XuDong; Fan, BaoChun; Gui, MingYue; Pan, ZhenHua

    2012-10-01

    How to confine a detonation in a combustor is a key issue of detonation applications in propulsion systems. Based on achieving schemes, detonations applied in the combustor, including pulse detonation wave (PDW), oblique detonation wave (ODW) and rotating detonation wave (RDW), are different from that described by the classic CJ theory in fine structures and its self-sustaining mechanisms. In this work, the cellular structures and flow fields of ODW and RDW were obtained numerically, and the fundamental characteristics and self-sustaining mechanisms of the detonations were analyzed and discussed. ODW front consists of three parts: the ZND-like front, the single-headed triple point front and the dual-headed triple point front. Cellular structures of RDW are heterogeneous, and the cell size near the outer wall is smaller than that near the inner wall.

  7. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

    PubMed Central

    de la Fuente, Ildefonso Martínez

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

  8. Charged group surface accessibility determines micelleplexes formation and cellular interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Liu, Yang; Sen, Soumyo; Král, Petr; Gemeinhart, Richard A.

    2015-04-01

    Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The model micelle system was formed from methoxy-poly(ethylene glycol)-b-poly(lactide) (mPEG-PLA) mixed with methoxy-poly(ethylene glycol)-b-poly(lactide)-b-oligoarginine (mPEG-PLA-Rx, x = 8 or 15). Surface properties of the micelles were varied by controlling the oligoarginine block length and conjugation density. Micelles were observed to have a core-shell conformation in the aqueous environment where the PLA block constituted the hydrophobic core, mPEG and oligoarginine formed a hydrophilic corona. Significantly different thermodynamic behaviors were observed during the interaction of single stranded miRNA with micelles of different surface properties, and the resulting micelleplexes mediated substantial cellular association. Depending upon the oligoarginine length and density, micelles exhibited miRNA loading capacity directly related to the presentation of charged groups on the surface. The effect of charged group accessibility of cationic micelle on micelleplex properties provides guidance on future miRNA delivery system design.Micelleplexes are a class of nucleic acid carriers that have gained acceptance due to their size, stability, and ability to synergistically carry small molecules. MicroRNAs (miRNAs) are small non-coding RNA gene regulator that is consists of 19-22 nucleotides. Altered expression of miRNAs plays an important role in many human diseases. Using a model 22-nucleotide miRNA sequence, we investigated the interaction between charged groups on the micelle surface and miRNA. The

  9. Additive Manufacturing of Metal Cellular Structures: Design and Fabrication

    NASA Astrophysics Data System (ADS)

    Yang, Li; Harrysson, Ola; Cormier, Denis; West, Harvey; Gong, Haijun; Stucker, Brent

    2015-03-01

    With the rapid development of additive manufacturing (AM), high-quality fabrication of lightweight design-efficient structures no longer poses an insurmountable challenge. On the other hand, much of the current research and development with AM technologies still focuses on material and process development. With the design for additive manufacturing in mind, this article explores the design issue for lightweight cellular structures that could be efficiently realized via AM processes. A unit-cell-based modeling approach that combines experimentation and limited-scale simulation was demonstrated, and it was suggested that this approach could potentially lead to computationally efficient design optimizations with the lightweight structures in future applications.

  10. Freeform inkjet printing of cellular structures with bifurcations.

    PubMed

    Christensen, Kyle; Xu, Changxue; Chai, Wenxuan; Zhang, Zhengyi; Fu, Jianzhong; Huang, Yong

    2015-05-01

    Organ printing offers a great potential for the freeform layer-by-layer fabrication of three-dimensional (3D) living organs using cellular spheroids or bioinks as building blocks. Vascularization is often identified as a main technological barrier for building 3D organs. As such, the fabrication of 3D biological vascular trees is of great importance for the overall feasibility of the envisioned organ printing approach. In this study, vascular-like cellular structures are fabricated using a liquid support-based inkjet printing approach, which utilizes a calcium chloride solution as both a cross-linking agent and support material. This solution enables the freeform printing of spanning and overhang features by providing a buoyant force. A heuristic approach is implemented to compensate for the axially-varying deformation of horizontal tubular structures to achieve a uniform diameter along their axial directions. Vascular-like structures with both horizontal and vertical bifurcations have been successfully printed from sodium alginate only as well as mouse fibroblast-based alginate bioinks. The post-printing fibroblast cell viability of printed cellular tubes was found to be above 90% even after a 24 h incubation, considering the control effect. PMID:25421556

  11. Kinetically guided colloidal structure formation

    PubMed Central

    Hecht, Fabian M.; Bausch, Andreas R.

    2016-01-01

    The self-organization of colloidal particles is a promising approach to create novel structures and materials, with applications spanning from smart materials to optoelectronics to quantum computation. However, designing and producing mesoscale-sized structures remains a major challenge because at length scales of 10–100 μm equilibration times already become prohibitively long. Here, we extend the principle of rapid diffusion-limited cluster aggregation (DLCA) to a multicomponent system of spherical colloidal particles to enable the rational design and production of finite-sized anisotropic structures on the mesoscale. In stark contrast to equilibrium self-assembly techniques, kinetic traps are not avoided but exploited to control and guide mesoscopic structure formation. To this end the affinities, size, and stoichiometry of up to five different types of DNA-coated microspheres are adjusted to kinetically control a higher-order hierarchical aggregation process in time. We show that the aggregation process can be fully rationalized by considering an extended analytical DLCA model, allowing us to produce mesoscopic structures of up to 26 µm in diameter. This scale-free approach can easily be extended to any multicomponent system that allows for multiple orthogonal interactions, thus yielding a high potential of facilitating novel materials with tailored plasmonic excitation bands, scattering, biochemical, or mechanical behavior. PMID:27444018

  12. Periodic Cellular Structure Technology for Shape Memory Alloys

    NASA Technical Reports Server (NTRS)

    Chen, Edward Y.

    2015-01-01

    Shape memory alloys are being considered for a wide variety of adaptive components for engine and airframe applications because they can undergo large amounts of strain and then revert to their original shape upon heating or unloading. Transition45 Technologies, Inc., has developed an innovative periodic cellular structure (PCS) technology for shape memory alloys that enables fabrication of complex bulk configurations, such as lattice block structures. These innovative structures are manufactured using an advanced reactive metal casting technology that offers a relatively low cost and established approach for constructing near-net shape aerospace components. Transition45 is continuing to characterize these structures to determine how best to design a PCS to better exploit the use of shape memory alloys in aerospace applications.

  13. From structure to cellular mechanism with infrared microspectroscopy

    PubMed Central

    Miller, Lisa M; Dumas, Paul

    2014-01-01

    Current efforts in structural biology aim to integrate structural information within the context of cellular organization and function. X-rays and infrared radiation stand at opposite ends of the electromagnetic spectrum and act as complementary probes for achieving this goal. Intense and bright beams are produced by synchrotron radiation, and are efficiently used in the wavelength domain extending from hard X-rays to the far-infrared (or THz) regime. While X-ray crystallography provides exquisite details on atomic structure, Fourier transform infrared microspectroscopy (FTIRM) is emerging as a spectroscopic probe and imaging tool for correlating molecular structure to biochemical dynamics and function. In this manuscript, the role of synchrotron FTIRM in bridging the gap towards ‘functional biology’ is discussed based upon recent achievements, with a critical assessment of the contributions to biological and biomedical research. PMID:20739176

  14. The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

    PubMed Central

    Tyrrell, Jillian; McGinnis, Jennifer L.; Weeks, Kevin M.; Pielak, Gary J.

    2016-01-01

    There are large differences between the intracellular environment and the conditions widely used to study RNA structure and function in vitro. To assess the effects of the crowded cellular environment on RNA, we examined the structure and ligand-binding function of the adenine riboswitch aptamer domain in healthy, growing Escherichia coli cells at single-nucleotide resolution on the minute timescale using SHAPE. The ligand-bound aptamer structure is essentially the same in cells and in buffer at 1 mM Mg2+, the approximate Mg2+ concentration we measured in cells. In contrast, the in-cell conformation of the ligand-free aptamer is much more similar to the fully folded ligand-bound state. Even adding high Mg2+ concentrations to the buffer used for in vitro analyses did not yield the conformation observed for the free aptamer in cells. The cellular environment thus stabilizes the aptamer significantly more than does Mg2+ alone. Our results show that the intracellular environment has a large effect on RNA structure that ultimately favors highly organized conformations. PMID:24215455

  15. Computer Modeling of the Earliest Cellular Structures and Functions

    NASA Astrophysics Data System (ADS)

    Pohorille, Andrew

    2000-03-01

    In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells), the most direct way to test ourunderstanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform protocellular functions. Many of these functions, such as import of nutrients, capture and storage of energy, and response to changes in the environment are carried out by proteins bound to membranes. We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides)organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (e.g. channels), and (c) by what mechanisms such aggregates perform essential protocellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each atom in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10^6-10^8 time steps.

  16. Label-Free Analysis of Cellular Lipid Droplet Formation by Non-Linear Microscopy

    NASA Astrophysics Data System (ADS)

    Schie, Iwan W.

    Cellular lipid droplets (LD) are cellular organelles that can be found in every cell type. Recent research indicates that cellular LD are involved in a large number of cellular metabolic functions, such as lipid metabolism, protection from lipotoxicity, protein storage and degradation, and many more. LD formation is frequently associated with adverse health effects, i.e. alcoholic and non-alcoholic fatty liver disease, diabetes type-2, as well as many cardiovascular disorders. Despite their wide presence, LDs are the least studied and most poorly understood cellular organelles. Typically, LDs are investigated using fluorescence-based techniques that require staining with exogenous fluorophores. Other techniques, e.g. biochemical assays, require the destruction of cells that prohibit the analysis of living cells. Therefore, in my thesis research I developed a novel compound fast-scanning nonlinear optical microscope equipped with the ability to also acquire Raman spectra at specific image locations. This system allows us to image label-free cellular LD formation in living cells and analyze the composition of single cellular LDs. Images can be acquired at near video-rate (˜16 frames/s). Furthermore, the system has the ability to acquire very large images of tissue of up to 7.5x15 cm2 total area by stitching together scans with dimensions of 1x1 mm2 in less than 1 minute. The system also enables the user to acquire Raman spectra from points of interest in the multiphoton images and provides chemically-specific data from sample volumes as small as 1 femtoliter. In my thesis I used this setup to determine the effects of VLDL lipolysis products on primary rat hepatocytes. By analyzing the Raman spectra and comparing the peak ratios for saturated and unsaturated fatty acid it was determined that the small cellular LD are highly saturated, while large cellular LDs contain mostly unsaturated lipids. Furthermore, I established a method to determine the specific contribution

  17. Kontur: Observations of cloud streets and open cellular structures

    NASA Astrophysics Data System (ADS)

    Brümmer, B.; Bakan, S.; Hinzpeter, H.

    1985-08-01

    In September and October 1981 the experiment KonTur (Convection and turbulence) was conducted over the North Sea. Its objectives were to investigate organized convective patterns, like cloud streets (boundary layer rolls) and cellular cloud structures. Two aircraft (British Hercules C-130 and German Falcon 20) performed detailed measurements within these patterns. Several cases of cloud streets and open cells were observed. Boundary layer rolls appear to be connected with an inflection point in the cross-roll wind component. The aspect ratio of the rolls (wavelength versus depth) is between three and four in accordance with other observations and linear stability analysis. Four scales of motion are involved: the mean flow, the roll circulation, individual clouds and turbulence. The vertical transport are dominated at lower levels by turbulence and at higher levels by roll-scale motions. Open cellular cloud structures are connected with large air-sea temperature differences due to cold air outbreaks from the northwest. The aspect ratio of the cells is of the order of 10. The bulk contribution to the total transport of heat and momentum originates from the cloudy walls of the cells. A vertical cross section through a composite open cell is presented.

  18. Modelling of detonation cellular structure in aluminium suspensions

    NASA Astrophysics Data System (ADS)

    Briand, A.; Veyssiere, B.; Khasainov, B. A.

    2010-12-01

    Heterogeneous detonations involving aluminium suspensions have been studied for many years for industrial safety policies, and for military and propulsion applications. Owing to their weak detonability and to the lack of available experimental results on the detonation cellular structure, numerical simulations provide a convenient way to improve the knowledge of such detonations. One major difficulty arising in numerical study of heterogeneous detonations involving suspensions of aluminium particles in oxidizing atmospheres is the modelling of aluminium combustion. Our previous two-step model provided results on the effect on the detonation cellular structure of particle diameter and characteristic chemical lengths. In this study, a hybrid model is incorporated in the numerical code EFAE, combining both kinetic and diffusion regimes in parallel. This more realistic model provides good agreement with the previous two-step model and confirms the correlations found between the detonation cell width, and particle diameter and characteristic lengths. Moreover, the linear dependence found between the detonation cell width and the induction length remains valid with the hybrid model.

  19. Shape-variable seals for pressure actuated cellular structures

    NASA Astrophysics Data System (ADS)

    Gramüller, B.; Tempel, A.; Hühne, C.

    2015-09-01

    Sealing concepts that allow a large change of cross-sectional area are investigated. Shape variable seals are indispensable for biologically inspired pressure actuated cellular structures (PACS), which can be utilized to develop energy efficient, lightweight and adaptive structures for diverse applications. The extensibility, stiffness and load capacity requirements exceed the characteristics of state of the art solutions. This work focuses on the design of seals suitable for extensional deformations of more than 25%. In a first step, a number of concepts are generated. Then the most suitable concept is chosen, based on numerical characterization and experimental examination. The deformation supportive end cap (DSEC) yields satisfying results as it displays a stress optimized shape under maximum load, an energetically inexpensive bending-based deformation mechanism and utilizes the applied forces to support distortion. In the first real-life implementation of a double row PACS demonstrator, which contains the DSEC, the proof of concept is demonstrated.

  20. Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation

    SciTech Connect

    Hazawa, Masaharu; Tomiyama, Kenichi; Saotome-Nakamura, Ai; Obara, Chizuka; Yasuda, Takeshi; Gotoh, Takaya; Tanaka, Izumi; Yakumaru, Haruko; Ishihara, Hiroshi; Tajima, Katsushi

    2014-04-18

    Highlights: • Radiation increases cellular uptake of exosomes. • Radiation induces colocalization of CD29 and CD81. • Exosomes selectively bind the CD29/CD81 complex. • Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation. - Abstract: Exosomes mediate intercellular communication, and mesenchymal stem cells (MSC) or their secreted exosomes affect a number of pathophysiologic states. Clinical applications of MSC and exosomes are increasingly anticipated. Radiation therapy is the main therapeutic tool for a number of various conditions. The cellular uptake mechanisms of exosomes and the effects of radiation on exosome–cell interactions are crucial, but they are not well understood. Here we examined the basic mechanisms and effects of radiation on exosome uptake processes in MSC. Radiation increased the cellular uptake of exosomes. Radiation markedly enhanced the initial cellular attachment to exosomes and induced the colocalization of integrin CD29 and tetraspanin CD81 on the cell surface without affecting their expression levels. Exosomes dominantly bound to the CD29/CD81 complex. Knockdown of CD29 completely inhibited the radiation-induced uptake, and additional or single knockdown of CD81 inhibited basal uptake as well as the increase in radiation-induced uptake. We also examined possible exosome uptake processes affected by radiation. Radiation-induced changes did not involve dynamin2, reactive oxygen species, or their evoked p38 mitogen-activated protein kinase-dependent endocytic or pinocytic pathways. Radiation increased the cellular uptake of exosomes through CD29/CD81 complex formation. These findings provide essential basic insights for potential therapeutic applications of exosomes or MSC in combination with radiation.

  1. Topology regulates pattern formation capacity of binary cellular automata on graphs

    NASA Astrophysics Data System (ADS)

    Marr, Carsten; Hütt, Marc-Thorsten

    2005-08-01

    We study the effect of topology variation on the dynamic behavior of a system with local update rules. We implement one-dimensional binary cellular automata on graphs with various topologies by formulating two sets of degree-dependent rules, each containing a single parameter. We observe that changes in graph topology induce transitions between different dynamic domains (Wolfram classes) without a formal change in the update rule. Along with topological variations, we study the pattern formation capacities of regular, random, small-world and scale-free graphs. Pattern formation capacity is quantified in terms of two entropy measures, which for standard cellular automata allow a qualitative distinction between the four Wolfram classes. A mean-field model explains the dynamic behavior of random graphs. Implications for our understanding of information transport through complex, network-based systems are discussed.

  2. Quantification of asymmetric microtubule nucleation at sub-cellular structures

    PubMed Central

    Zhu, Xiaodong; Kaverina, Irina

    2012-01-01

    Cell polarization is important for multiple physiological processes. In polarized cells, microtubules (MTs) are organized into a spatially polarized array. Generally, in non-differentiated cells, it is assumed that MTs are symmetrically nucleated exclusively from centrosome (microtubule organizing center, MTOC) and then reorganized into the asymmetric array. We have recently identified the Golgi complex as an additional MTOC that asymmetrically nucleates MTs toward one side of the cell. Methods used for alternative MTOC identification include microtubule re-growth after complete drug-induced depolymerization and tracking of growing microtubules using fluorescence labeled MT +TIP binding proteins in living cells. These approaches can be used for quantification of MT nucleation sites at diverse sub-cellular structures. PMID:21773933

  3. Teneurin-4 promotes cellular protrusion formation and neurite outgrowth through focal adhesion kinase signaling

    PubMed Central

    Suzuki, Nobuharu; Numakawa, Tadahiro; Chou, Joshua; de Vega, Susana; Mizuniwa, Chihiro; Sekimoto, Kaori; Adachi, Naoki; Kunugi, Hiroshi; Arikawa-Hirasawa, Eri; Yamada, Yoshihiko; Akazawa, Chihiro

    2014-01-01

    Teneurin-4 (Ten-4), a transmembrane protein, is highly expressed in the central nervous system; however, its cellular and molecular function in neuronal differentiation remains unknown. In this study, we aimed to elucidate the function of Ten-4 in neurite outgrowth. Ten-4 expression was induced during neurite outgrowth of the neuroblastoma cell line Neuro-2a. Ten-4 protein was localized at the neurite growth cones. Knockdown of Ten-4 expression in Neuro-2a cells decreased the formation of the filopodia-like protrusions and the length of individual neurites. Conversely, overexpression of Ten-4 promoted filopodia-like protrusion formation. In addition, knockdown and overexpression of Ten-4 reduced and elevated the activation of focal adhesion kinase (FAK) and Rho-family small GTPases, Cdc42 and Rac1, key molecules for the membranous protrusion formation downstream of FAK, respectively. Inhibition of the activation of FAK and neural Wiskott-Aldrich syndrome protein (N-WASP), which is a downstream regulator of FAK and Cdc42, blocked protrusion formation by Ten-4 overexpression. Further, Ten-4 colocalized with phosphorylated FAK in the filopodia-like protrusion regions. Together, our findings show that Ten-4 is a novel positive regulator of cellular protrusion formation and neurite outgrowth through the FAK signaling pathway.—Suzuki, N., Numakawa, T., Chou, J., de Vega, S., Mizuniwa, C., Sekimoto, K., Adachi, N., Kunugi, H., Arikawa-Hirasawa, E., Yamada, Y., Akazawa, C. Teneurin-4 promotes cellular protrusion formation and neurite outgrowth through focal adhesion kinase signaling. PMID:24344332

  4. New structural and functional defects in polyphosphate deficient bacteria: A cellular and proteomic study

    PubMed Central

    2010-01-01

    Background Inorganic polyphosphate (polyP), a polymer of tens or hundreds of phosphate residues linked by ATP-like bonds, is found in all organisms and performs a wide variety of functions. PolyP is synthesized in bacterial cells by the actions of polyphosphate kinases (PPK1 and PPK2) and degraded by exopolyphosphatase (PPX). Bacterial cells with polyP deficiencies due to knocking out the ppk1 gene are affected in many structural and important cellular functions such as motility, quorum sensing, biofilm formation and virulence among others. The cause of this pleiotropy is not entirely understood. Results The overexpression of exopolyphosphatase in bacteria mimicked some pleitropic defects found in ppk1 mutants. By using this approach we found new structural and functional defects in the polyP-accumulating bacteria Pseudomonas sp. B4, which are most likely due to differences in the polyP-removal strategy. Colony morphology phenotype, lipopolysaccharide (LPS) structure changes and cellular division malfunction were observed. Finally, we used comparative proteomics in order to elucidate the cellular adjustments that occurred during polyP deficiency in this bacterium and found some clues that helped to understand the structural and functional defects observed. Conclusions The results obtained suggest that during polyP deficiency energy metabolism and particularly nucleoside triphosphate (NTP) formation were affected and that bacterial cells overcame this problem by increasing the flux of energy-generating metabolic pathways such as tricarboxilic acid (TCA) cycle, β-oxidation and oxidative phosphorylation and by reducing energy-consuming ones such as active transporters and amino acid biosynthesis. Furthermore, our results suggest that a general stress response also took place in the cell during polyP deficiency. PMID:20067623

  5. Holistic design and implementation of pressure actuated cellular structures

    NASA Astrophysics Data System (ADS)

    Gramüller, B.; Köke, H.; Hühne, C.

    2015-12-01

    Providing the possibility to develop energy-efficient, lightweight adaptive components, pressure-actuated cellular structures (PACS) are primarily conceived for aeronautics applications. The realization of shape-variable flaps and even airfoils provides the potential to safe weight, increase aerodynamic efficiency and enhance agility. The herein presented holistic design process points out and describes the necessary steps for designing a real-life PACS structure, from the computation of truss geometry to the manufacturing and assembly. The already published methods for the form finding of PACS are adjusted and extended for the exemplary application of a variable-camber wing. The transfer of the form-finding truss model to a cross-sectional design is discussed. The end cap and sealing concept is described together with the implementation of the integral fluid flow. Conceptual limitations due to the manufacturing and assembly processes are discussed. The method’s efficiency is evaluated by finite element method. In order to verify the underlying methods and summarize the presented work a modular real-life demonstrator is experimentally characterized and validates the numerical investigations.

  6. NFI-C2 temporal-spatial expression and cellular localization pattern during tooth formation.

    PubMed

    Lamani, Ejvis; Gluhak-Heinrich, Jelica; MacDougall, Mary

    2015-12-01

    Currently, little is known regarding critical signaling pathways during later stages of tooth development, especially those associated with root formation. Nfi-c null mice, lacking molar roots, have implicated the transcription factor NFI-C as having an essential role in root development. Previously, we identified three NFI-C isoforms expressed in dental tissues with NFI-C2 being the major transcript. However, the expression pattern of the NFI-C2 protein is not characterized. In this study we performed in situ hybridization and immunohistochemistry using isoform specific probes. We show the production of a NFI-C2 peptide antibody, its characterization, the temporal-spatial expression pattern of the NFI-C2 protein during odontogenesis and sub-cellular localization in dental cells. Moderate NFI-C2 staining, as early as bud stage, was detected mostly in the condensing dental ectomesenchyme. This staining intensified within the dental pulp at later stages culminating in high expression in the dentin producing odontoblasts. The dental epithelium showed slight staining until cytodifferentiation of enamel organ into ameloblasts and stratum intermedium. During root formation NFI-C2 expression was high in the Hertwig's epithelial root sheath and later was found in the fully developed root and its supporting tissues. NFI-C2 cellular staining was cytosolic, associated with the Golgi, and nuclear. These data suggest a broader role for NFI-C during tooth formation than limited to root and periodontal ligament development. PMID:26687982

  7. Cellular Structure and Oscillating Behavior of PBX Detonations

    NASA Astrophysics Data System (ADS)

    Plaksin, Igor; Mendes, Ricardo

    2013-03-01

    Efforts are aimed on bridging experimental and theoretical studies of localizations/instabilities manifested in detonation reaction zone (DRZ) at micro-, meso-, and macro-scale. In molecular level, the theoretical/computational studies of detonation (RDX, HMX) show: reaction localizations onset/growth is caused by kinetic nonequilibrium stimulated by different levels of activation barriers/reaction energies at bonds dissociation processes (C-NH2, C-NO2, C =C). At micro- and meso-scale levels, leading role of kinetic nonequilibrium in reaction localizations onset was established in experiments with single beta-HMX crystals-in-binder subjected to 20 GPa-shock and PBX detonation. Reaction localizations and further ejecta formation were spatially resolved by 96-channel optical analyzer at simultaneous recording reaction light and stress field around crystal. Spatially-resolved measurements reveal fundamental role of shear-strain in triggering initiation chemistry. At macro-scale level, formation of the cell-structures and oscillating detonation regimes revealed in HMX- and RDX-based PBXs at wide variation of grain-sizes, wt. % filler/binder, residual micro-voids and binder nature. Emphasizes placed on effect of DRZ-induced radiation upon oscillating regimes of detonation front motion. This work was supported by the Office of Naval Research under the ONR and ONR Global Grants N00014-12-1-0477 and N62909-12-1-7131 with Drs. Clifford Bedford and Shawn Thorne Program Managers.

  8. Cellular Structure and Oscillating Behavior of PBX Detonations

    NASA Astrophysics Data System (ADS)

    Plaksin, Igor; Rodrigues, Luis; Mendes, Ricardo; Plaksin, Svyatoslav; Ferreira, Claudia; Fernandes, Eduardo

    2015-06-01

    Efforts are aimed on experimental study of reaction localization/instabilities manifested in detonation reaction zone (DRZ) of PBXs at micro-, meso- and macro-scale. At micro- and meso-scale levels, leading role of kinetic nonequilibrium in reaction localizations onset was established in experiments with single beta-HMX crystals-in-binder subjected to 20 GPa-shock and PBX detonation. Reaction localizations and further ejecta formation were spatially resolved by 96-channel optical analyzer at simultaneous recording reaction light and stress field around crystal. Spatially resolved measurements reveal fundamental role of shear-strain in triggering initiation chemistry. At macro-scale level, formation of the cell-structures and oscillating detonation regimes revealed in HMX- and RDX-based PBXs at wide variation of grain-sizes, wt. % filler/binder, residual micro-voids and binder nature. Emphasizes placed on effect of DRZ-induced radiation upon oscillating regimes of detonation front motion. Work was supported by the ONR and ONR Global Grants N00014-12-1-0477 and N62909-12-1-7131 with Drs. Clifford Bedford and John Zimmerman Program Managers.

  9. Experimental Salmonellosis XI. Induction of Cellular Immunity and Formation of Antibody by Transfer Agent of Mouse Mononuclear Phagocytes

    PubMed Central

    Mitsuhashi, Susumu; Saito, Kazuko; Osawa, Nobutaka; Kurashige, Satonori

    1967-01-01

    When mice were injected intraperitoneally with a ribonucleic acid (RNA) preparation extracted from the peritoneal mononuclear phagocytes (termed monocytes) of immunized mice, these macrophages developed cellular immunity and cellular antibodies. The peritoneal monocytes were obtained from normal mice and maintained in tissue culture bottles in a homogeneous cell population. When they were treated in vitro with an immune RNA preparation, they acquired cellular immunity, and cellular antibodies were detectable in such monocytes. These results suggest that the mononuclear phagocytic cell line constitutes a cell line responsible for antibody formation. PMID:6051363

  10. Unravelling lignin formation and structure

    SciTech Connect

    Lewis, N.G. . Inst. of Biological Chemistry)

    1991-01-01

    During this study, we established that the Fagaceae exclusively accumulate Z-monolignois/glucosides, and not the E-isomers. Evidence for the presence of a novel E{yields}Z isomerse has been obtained. Our pioneering work in lignin biosynthesis and structure in situ has also progressed smoothly. We established the bonding environments of a woody angiosperm, Leucanea leucocephala, as well as wheat (T. aestivum) and tobacco (N. tabacum). A cell culture system from Pinus taeda was developed which seems ideal for investigating the early stages of lignification. These cultures excrete peroxidase isozymes, considered to be specifically involved in lignin deposition. We also studied the effect of the putative lignin-degrading enzyme, lignin peroxidase, on monolignols and dehydropolymerisates therefrom. In all cases, polymerization was observed, and not degradation; these polymers are identical to that obtained with horseradish peroxidases/H{sub 2}O{sub 2}. It seems inconceivable that these enzymes can be considered as being primarily responsible for lignin biodegradation.

  11. Instabilities and structure formation in laser processing

    SciTech Connect

    Baeuerle, D.; Arenholz, E.; Arnold, N.; Heitz, J.; Kargl, P.B.

    1996-12-31

    This paper gives an overview on different types of instabilities and structure formation in various fields of laser processing. Among the examples discussed in detail are non-coherent structures observed in laser-induced chemical vapor deposition (LCVD), in laser-induced surface modifications, and in laser ablation of polymers.

  12. Role of Spatial Distribution of Rain in Formation of Open Cellular Circulation

    NASA Astrophysics Data System (ADS)

    Yamaguchi, T.; Feingold, G.

    2014-12-01

    Precipitation alone is not sufficient to transform closed cellular circulation capped by stratocumulus cloud to open cellular circulation with cumulus clouds; observations often show high rainrates existing within the closed cell state. It has been suggested that the spatial distribution of precipitation plays an important role in the transition from closed-to-open convection but this hypothesis has to date not been rigorously tested. In this study, a series of idealized 3-dimensional simulations are conducted to evaluate the dependency of areal coverage of rain on the transformation, and to explore the role of interactions between multiple rainy areas in the formation of the open cell state. This is done by inserting a low aerosol concentration patch (or multiple patches separated by specified distance) into a non-precipitating closed cell state. We show that when rain is restricted to a small area, even significant rain does not result in a transition. The rain event is quickly filled in by adjacent non-precipitating closed cells and the rain ceases without significant trace. With increasing areal coverage of the rain, the transition becomes possible provided the rainrate is sufficiently large. When multiple rain regions interact with each other, the transition to the open cell state is reinforced over a wider area, provided the distance between the rain regions is small enough. When the distance between the rain areas is large, rainy areas are initially filled in by neighboring closed cells, but the transition eventually occurs, albeit slowly. These results suggest a connection to the remote control of open cell formation hypothesized in the recent past.

  13. Interface Pattern Selection Criterion for Cellular Structures in Directional Solidification

    NASA Technical Reports Server (NTRS)

    Trivedi, R.; Tewari, S. N.; Kurtze, D.

    1999-01-01

    The aim of this investigation is to establish key scientific concepts that govern the selection of cellular and dendritic patterns during the directional solidification of alloys. We shall first address scientific concepts that are crucial in the selection of interface patterns. Next, the results of ground-based experimental studies in the Al-4.0 wt % Cu system will be described. Both experimental studies and theoretical calculations will be presented to establish the need for microgravity experiments.

  14. Impact of nano titanium dioxide exposure on cellular structure of Anabaena variabilis and evidence of internalization.

    PubMed

    Cherchi, Carla; Chernenko, Tatyana; Diem, Max; Gu, April Z

    2011-04-01

    The present study investigated the impact of nano titanium dioxide (nTiO(2) ) exposure on the cellular structures of the nitrogen-fixing cyanobacteria Anabaena variabilis. Results of the present study showed that nTiO(2) exposure led to observable alteration in various intracellular structures and induced a series of recognized stress responses, including production of reactive oxygen species (ROS), appearance and increase in the abundance of membrane crystalline inclusions, membrane mucilage layer formation, opening of intrathylakoidal spaces, and internal plasma membrane disruption. The production of total ROS in A. variabilis cells increased with increasing nTiO(2) doses and exposure time, and the intracellular ROS contributed to only a small fraction (<10%) of the total ROS measured. The percentage of cells with loss of thylakoids and growth of membrane crystalline inclusions increased as the nTiO(2) dose and exposure time increased compared with controls, suggesting their possible roles in stress response to nTiO(2) , as previously shown for metals. Algal cell surface morphology and mechanical properties were modified by nTiO(2) exposure, as indicated by the increase in cell surface roughness and shifts in cell spring constant determined by atomic force microscopy analysis. The change in cell surface structure and increase in the cellular turgor pressure likely resulted from the structural membrane damage mediated by the ROS production. Transmission electron microscopy (TEM) analysis of nTiO(2) aggregates size distribution seems to suggest possible disaggregation of nTiO(2) aggregates when in close contact with microbial cells, potentially as a result of biomolecules such as DNA excreted by organisms that may serve as a biodispersant. The present study also showed, for the first time, with both TEM and Raman imaging that internalization of nTiO(2) particles through multilayered membranes in algal cells is possible. Environ. Toxicol. Chem. 2011; 30:861-869.

  15. Nanoscale Cellular Structures at Phase Boundaries of Ni-Cr-Al-Ti and Ni-Cr-Mo-Al-Ti Superalloys

    NASA Astrophysics Data System (ADS)

    Wang, Cong; Dunand, David C.

    2015-06-01

    The microstructural evolution of Ni-20 pct Cr wires was studied during pack cementation where Al and Ti, with and without prior cementation with Mo, are deposited to the surface of the Ni-Cr wires and subsequently homogenized in their volumes. Mo deposition promotes the formation of Kirkendall pores and subsequent co-deposition of Al and Ti creates a triple-layered diffusional coating on the wire surface. Subsequent homogenization drives the alloying element to distribute evenly in the wires which upon further heat treatment exhibit the γ + γ' superalloy structure. Unexpectedly, formation of cellular structures is observed at some of the boundaries between primary γ' grains and γ matrix grains. Based on additional features ( i.e., ordered but not perfectly periodic structure, confinement at γ + γ' phase boundaries as a cellular film with ~100 nm width, as well as lack of topologically close-packed phases), and considering that similar, but much larger, microstructures were reported in commercial superalloys, it is concluded that the present cellular structure solidified as a thin film, composed of eutectic γ + γ' and from which the γ' phase was subsequently etched, which was created by incipient melting of a region near the phase boundary with high solute segregation.

  16. Intragranular cellular segregation network structure strengthening 316L stainless steel prepared by selective laser melting

    NASA Astrophysics Data System (ADS)

    Zhong, Yuan; Liu, Leifeng; Wikman, Stefan; Cui, Daqing; Shen, Zhijian

    2016-03-01

    A feasibility study was performed to fabricate ITER In-Vessel components by Selective Laser Melting (SLM) supported by Fusion for Energy (F4E). Almost fully dense 316L stainless steel (SS316L) components were prepared from gas-atomized powder and with optimized SLM processing parameters. Tensile tests and Charpy-V tests were carried out at 22 °C and 250 °C and the results showed that SLM SS316L fulfill the RCC-MR code. Microstructure characterization reveals the presence of hierarchical macro-, micro- and nano-structures in as-built samples that were very different from SS316L microstructures prepared by other established methods. The formation of a characteristic intragranular cellular segregation network microstructure appears to contribute to the increase of yield strength without losing ductility. Silicon oxide nano-inclusions were formed during the SLM process that generated a micro-hardness fluctuation in the building direction. The combined influence of a cellular microstructure and the nano-inclusions constraints the size of ductile dimples to nano-scale. The crack propagation is hindered by a pinning effect that improves the defect-tolerance of the SLM SS316L. This work proves that it was possible to manufacture SS316L with properties suitable for ITER First Wall panels. Further studies on irradiation properties of SLM SS316L and manufacturing of larger real-size components are needed.

  17. Cryo-Microscopic Analysis of the Effects of Extra Cellular Proteins on Polycrystalline Ice Structure

    NASA Astrophysics Data System (ADS)

    Brox, T.; Skidmore, M. L.; Christner, B. C.; Achberger, A.

    2010-12-01

    Recent work has demonstrated that microorganisms can occupy the liquid filled inter-crystalline veins in ice and maintain their metabolic activity under these conditions. While these discoveries have increased the extent of the biosphere to include the large continental ice sheets of Antarctica and Greenland as biomes, the habitat of the microorganisms within the inter-crystalline liquid veins is poorly understood. Certain cold tolerant organisms produce extra cellular proteins (i.e., ice-binding proteins) that have the ability to bind to the prism face of an ice crystal and inhibit recrystallization of ice. This phenotype affects the physical ice structure and the liquid vein network, potentially providing ice-inhabiting species a protective mechanism with which to control their habitat. One such microorganism is Chryseobacterium sp. V3519-10, a bacterium isolated from a depth of 3519 m in the Vostok Ice Core. Our investigation is examining the impact of extra cellular proteins from this ice-adapted bacterium on the formation of ice crystals and characterizing the inter-crystalline liquid filled vein network using cryo-microscopy.

  18. Iterative approach to joint segmentation of cellular structures

    NASA Astrophysics Data System (ADS)

    Ajemba, Peter; Scott, Richard; Ramachandran, Janakiramanan; Liu, Qiuhua; Khan, Faisal; Zeineh, Jack; Donovan, Michael; Fernandez, Gerardo

    2012-02-01

    Accurate segmentation of overlapping nuclei is essential in determining nuclei count and evaluating the sub-cellular localization of protein biomarkers in image Cytometry and Histology. Current cellular segmentation algorithms generally lack fast and reliable methods for disambiguating clumped nuclei. In immuno-fluorescence segmentation, solutions to challenges including nuclei misclassification, irregular boundaries, and under-segmentation require reliable separation of clumped nuclei. This paper presents a fast and accurate algorithm for joint segmentation of cellular cytoplasm and nuclei incorporating procedures for reliably separating overlapping nuclei. The algorithm utilizes a combination of ideas and is a significant improvement on state-of-the-art algorithms for this application. First, an adaptive process that includes top-hat filtering, blob detection and distance transforms estimates the inverse illumination field and corrects for intensity non-uniformity. Minimum-error-thresholding based binarization augmented by statistical stability estimation is applied prior to seed-detection constrained by a distance-map-based scale-selection to identify candidate seeds for nuclei segmentation. The nuclei clustering step also incorporates error estimation based on statistical stability. This enables the algorithm to perform localized error correction. Final steps include artifact removal and reclassification of nuclei objects near the cytoplasm boundary as epithelial or stroma. Evaluation using 48 realistic phantom images with known ground-truth shows overall segmentation accuracy exceeding 96%. It significantly outperformed two state-of-the-art algorithms in clumped nuclei separation. Tests on 926 prostate biopsy images (326 patients) show that the segmentation improvement improves the predictive power of nuclei architecture features based on the minimum spanning tree algorithm. The algorithm has been deployed in a large scale pathology application.

  19. Monoacylated Cellular Prion Protein Modifies Cell Membranes, Inhibits Cell Signaling, and Reduces Prion Formation*

    PubMed Central

    Bate, Clive; Williams, Alun

    2011-01-01

    Prion diseases occur following the conversion of the cellular prion protein (PrPC) into a disease related, protease-resistant isoform (PrPSc). In these studies, a cell painting technique was used to introduce PrPC to prion-infected neuronal cell lines (ScGT1, ScN2a, or SMB cells). The addition of PrPC resulted in increased PrPSc formation that was preceded by an increase in the cholesterol content of cell membranes and increased activation of cytoplasmic phospholipase A2 (cPLA2). In contrast, although PrPC lacking one of the two acyl chains from its glycosylphosphatidylinositol (GPI) anchor (PrPC-G-lyso-PI) bound readily to cells, it did not alter the amount of cholesterol in cell membranes, was not found within detergent-resistant membranes (lipid rafts), and did not activate cPLA2. It remained within cells for longer than PrPC with a conventional GPI anchor and was not converted to PrPSc. Moreover, the addition of high amounts of PrPC-G-lyso-PI displaced cPLA2 from PrPSc-containing lipid rafts, reduced the activation of cPLA2, and reduced PrPSc formation in all three cell lines. In addition, ScGT1 cells treated with PrPC-G-lyso-PI did not transmit infection following intracerebral injection to mice. We propose that that the chemical composition of the GPI anchor attached to PrPC modified the local membrane microenvironments that control cell signaling, the fate of PrPC, and hence PrPSc formation. In addition, our observations raise the possibility that pharmacological modification of GPI anchors might constitute a novel therapeutic approach to prion diseases. PMID:21212283

  20. Network, cellular, and molecular mechanisms underlying long-term memory formation.

    PubMed

    Carasatorre, Mariana; Ramírez-Amaya, Víctor

    2013-01-01

    The neural network stores information through activity-dependent synaptic plasticity that occurs in populations of neurons. Persistent forms of synaptic plasticity may account for long-term memory storage, and the most salient forms are the changes in the structure of synapses. The theory proposes that encoding should use a sparse code and evidence suggests that this can be achieved through offline reactivation or by sparse initial recruitment of the network units. This idea implies that in some cases the neurons that underwent structural synaptic plasticity might be a subpopulation of those originally recruited; However, it is not yet clear whether all the neurons recruited during acquisition are the ones that underwent persistent forms of synaptic plasticity and responsible for memory retrieval. To determine which neural units underlie long-term memory storage, we need to characterize which are the persistent forms of synaptic plasticity occurring in these neural ensembles and the best hints so far are the molecular signals underlying structural modifications of the synapses. Structural synaptic plasticity can be achieved by the activity of various signal transduction pathways, including the NMDA-CaMKII and ACh-MAPK. These pathways converge with the Rho family of GTPases and the consequent ERK 1/2 activation, which regulates multiple cellular functions such as protein translation, protein trafficking, and gene transcription. The most detailed explanation may come from models that allow us to determine the contribution of each piece of this fascinating puzzle that is the neuron and the neural network. PMID:22976275

  1. Structure formation in the quasispherical Szekeres model

    SciTech Connect

    Bolejko, Krzysztof

    2006-06-15

    Structure formation in the Szekeres model is investigated. Since the Szekeres model is an inhomogeneous model with no symmetries, it is possible to examine the interaction of neighboring structures and its impact on the growth of a density contrast. It has been found that the mass flow from voids to clusters enhances the growth of the density contrast. In the model presented here, the growth of the density contrast is almost 8 times faster than in the linear approach.

  2. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement

  3. Structure formation, backreaction and weak gravitational fields

    NASA Astrophysics Data System (ADS)

    Paranjape, Aseem; Singh, T. P.

    2008-03-01

    There is an ongoing debate in the literature as to whether the effects of averaging out inhomogeneities ('backreaction') in cosmology can be large enough to account for the acceleration of the scale factor in the Friedmann-Lemaître-Robertson-Walker (FLRW) models. In particular, some simple models of structure formation studied in the literature seem to indicate that this is indeed possible, and it has also been suggested that the perturbed FLRW framework is no longer a good approximation during structure formation, when the density contrast becomes non-linear. In this work we attempt to clarify the situation to some extent, using a fully relativistic model of pressureless spherical collapse. We find that whereas averaging during structure formation can lead to acceleration via a selective choice of averaging domains, the acceleration is not present when more generic domains are used for averaging. Further, we show that for most of the duration of the collapse, matter velocities remain small, and the perturbed FLRW form of the metric can be explicitly recovered, in the structure formation phase. We also discuss the fact that the magnitude of the average effects of inhomogeneities depends on the scale of averaging, and while it may not be completely negligible on intermediate scales, it is expected to remain small when averaging on suitably large scales.

  4. Evolution of atomic structure during nanoparticle formation

    PubMed Central

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; Christensen, Mogens; Bøjesen, Espen D.; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J. L.; Iversen, Bo B.

    2014-01-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  5. Evolution of atomic structure during nanoparticle formation.

    PubMed

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M Ø; Christensen, Mogens; Bøjesen, Espen D; Emerich, Hermann; Vaughan, Gavin; Billinge, Simon J L; Iversen, Bo B

    2014-05-01

    Understanding the mechanism of nanoparticle formation during synthesis is a key prerequisite for the rational design and engineering of desirable materials properties, yet remains elusive due to the difficulty of studying structures at the nanoscale under real conditions. Here, the first comprehensive structural description of the formation of a nanoparticle, yttria-stabilized zirconia (YSZ), all the way from its ionic constituents in solution to the final crystal, is presented. The transformation is a complicated multi-step sequence of atomic reorganizations as the material follows the reaction pathway towards the equilibrium product. Prior to nanoparticle nucleation, reagents reorganize into polymeric species whose structure is incompatible with the final product. Instead of direct nucleation of clusters into the final product lattice, a highly disordered intermediate precipitate forms with a local bonding environment similar to the product yet lacking the correct topology. During maturation, bond reforming occurs by nucleation and growth of distinct domains within the amorphous intermediary. The present study moves beyond kinetic modeling by providing detailed real-time structural insight, and it is demonstrated that YSZ nanoparticle formation and growth is a more complex chemical process than accounted for in conventional models. This level of mechanistic understanding of the nanoparticle formation is the first step towards more rational control over nanoparticle synthesis through control of both solution precursors and reaction intermediaries. PMID:25075335

  6. Early structure formation from cosmic string loops

    SciTech Connect

    Shlaer, Benjamin; Vilenkin, Alexander; Loeb, Abraham E-mail: vilenkin@cosmos.phy.tufts.edu

    2012-05-01

    We examine the effects of cosmic strings on structure formation and on the ionization history of the universe. While Gaussian perturbations from inflation are known to provide the dominant contribution to the large scale structure of the universe, density perturbations due to strings are highly non-Gaussian and can produce nonlinear structures at very early times. This could lead to early star formation and reionization of the universe. We improve on earlier studies of these effects by accounting for high loop velocities and for the filamentary shape of the resulting halos. We find that for string energy scales Gμ∼>10{sup −7}, the effect of strings on the CMB temperature and polarization power spectra can be significant and is likely to be detectable by the Planck satellite. We mention shortcomings of the standard cosmological model of galaxy formation which may be remedied with the addition of cosmic strings, and comment on other possible observational implications of early structure formation by strings.

  7. Cellular porous anodic alumina grown in neutral organic electrolyte. 1. Structure, composition, and properties of the films

    SciTech Connect

    Liu, Y.; Alwitt, R.S.; Shimizu, K.

    2000-04-01

    Anodic alumina films with cellular porous structure grow in neutral organic electrolytes with low water content and containing ethylene glycol and a large dicarboxylic acid. An Al carboxylate precipitates in the pore and is extruded from the coating. The porous structure develops even though the current efficiency for film formation is near 95%. The coating matrix contains substantial organic material, 15 wt % by thermal analysis. It is an oxide/organic composite with higher field strength and lower dielectric constant than pure anodic alumina.

  8. The Temporal Structure of Scientific Consensus Formation

    PubMed Central

    Shwed, Uri; Bearman, Peter S.

    2011-01-01

    This article engages with problems that are usually opaque: What trajectories do scientific debates assume, when does a scientific community consider a proposition to be a fact, and how can we know that? We develop a strategy for evaluating the state of scientific contestation on issues. The analysis builds from Latour’s black box imagery, which we observe in scientific citation networks. We show that as consensus forms, the importance of internal divisions to the overall network structure declines. We consider substantive cases that are now considered facts, such as the carcinogenicity of smoking and the non-carcinogenicity of coffee. We then employ the same analysis to currently contested cases: the suspected carcinogenicity of cellular phones, and the relationship between vaccines and autism. Extracting meaning from the internal structure of scientific knowledge carves a niche for renewed sociological commentary on science, revealing a typology of trajectories that scientific propositions may experience en route to consensus. PMID:21886269

  9. Functional and Structural Mimicry of Cellular Protein Kinase A Anchoring Proteins by a Viral Oncoprotein

    PubMed Central

    King, Cason R.; Cohen, Michael J.; Fonseca, Gregory J.; Dirk, Brennan S.; Dikeakos, Jimmy D.; Mymryk, Joe S.

    2016-01-01

    The oncoproteins of the small DNA tumor viruses interact with a plethora of cellular regulators to commandeer control of the infected cell. During infection, adenovirus E1A deregulates cAMP signalling and repurposes it for activation of viral gene expression. We show that E1A structurally and functionally mimics a cellular A-kinase anchoring protein (AKAP). E1A interacts with and relocalizes protein kinase A (PKA) to the nucleus, likely to virus replication centres, via an interaction with the regulatory subunits of PKA. Binding to PKA requires the N-terminus of E1A, which bears striking similarity to the amphipathic α-helical domain present in cellular AKAPs. E1A also targets the same docking-dimerization domain of PKA normally bound by cellular AKAPs. In addition, the AKAP like motif within E1A could restore PKA interaction to a cellular AKAP in which its normal interaction motif was deleted. During infection, E1A successfully competes with endogenous cellular AKAPs for PKA interaction. E1A’s role as a viral AKAP contributes to viral transcription, protein expression and progeny production. These data establish HAdV E1A as the first known viral AKAP. This represents a unique example of viral subversion of a crucial cellular regulatory pathway via structural mimicry of the PKA interaction domain of cellular AKAPs. PMID:27137912

  10. Three-Dimensional Cellular Structures Enhanced By Shape Memory Alloys

    NASA Technical Reports Server (NTRS)

    Nathal, Michael V.; Krause, David L.; Wilmoth, Nathan G.; Bednarcyk, Brett A.; Baker, Eric H.

    2014-01-01

    This research effort explored lightweight structural concepts married with advanced smart materials to achieve a wide variety of benefits in airframe and engine components. Lattice block structures were cast from an aerospace structural titanium alloy Ti-6Al-4V and a NiTi shape memory alloy (SMA), and preliminary properties have been measured. A finite element-based modeling approach that can rapidly and accurately capture the deformation response of lattice architectures was developed. The Ti-6-4 and SMA material behavior was calibrated via experimental tests of ligaments machined from the lattice. Benchmark testing of complete lattice structures verified the main aspects of the model as well as demonstrated the advantages of the lattice structure. Shape memory behavior of a sample machined from a lattice block was also demonstrated.

  11. Biomimetic cellular metals-using hierarchical structuring for energy absorption.

    PubMed

    Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

    2016-01-01

    Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form-structure

  12. Surfactant tuning of hydrophilicity of porous degradable copolymer scaffolds promotes cellular proliferation and enhances bone formation.

    PubMed

    Yassin, Mohammed A; Leknes, Knut N; Sun, Yang; Lie, Stein A; Finne-Wistrand, Anna; Mustafa, Kamal

    2016-08-01

    Poly(l-lactide-co-ɛ-caprolactone) (poly(LLA-co-CL)) has been blended with Tween 80 to tune the material properties and optimize cell-material interactions. Accordingly, the aims of this study were fourfold: to evaluate the effect of low concentrations of Tween 80 on the surface microstructure of 3D poly(LLA-co-CL) porous scaffolds: to determine the effect of different concentrations of Tween 80 on proliferation of bone marrow stromal cells (BMSCs) in vitro under dynamic cell culture at 7 and 21 days; to assess the influence of Tween 80 on the degradation rate of poly(LLA-co-CL) at 7 and 21 days; and in a subcutaneous rat model, to evaluate the effect on bone formation of porous scaffolds modified with 3% Tween 80 at 2 and 8 weeks. Blending 3% (w/w) Tween 80 with poly(LLA-co-CL) improves the surface wettability (p < 0.001). Poly(LLA-co-CL)/3% Tween 80 shows significantly increased cellular proliferation at days 7 and 21 (p < 0.001). Moreover, the presence of Tween 80 facilitates the degradation of poly(LLA-co-CL). Two weeks post-implantation, the poly(LLA-co-CL)/3% Tween 80 scaffolds exhibit significant mRNA expression of Runx2 (p = 0.004). After 8 weeks, poly(LLA-co-CL)/3% Tween 80 scaffolds show significantly increased de novo bone formation, demonstrated by μ-CT (p = 0.0133) and confirmed histologically. It can be concluded that blending 3% (w/w) Tween 80 with poly (LLA-co-CL) improves the hydrophilicity and osteogenic potential of the scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 2049-2059, 2016. PMID:27086867

  13. Analysis of autophagosome formation using lentiviral biosensors for live fluorescent cellular imaging.

    PubMed

    Long, Kevin; Mohan, Chandra; Anderl, Janet; Huryn-Selvar, Karyn; Liu, Haizhen; Su, Kevin; Santos, Mark; Hsu, Matthew; Armstrong, Lucas; Ma, Jun

    2015-01-01

    Autophagy, a highly regulated homeostatic degradative process, allows cells to reallocate nutrients from less important to more essential processes under extreme conditions of starvation. Autophagy also prevents the buildup of damaged proteins and organelles that cause chronic tissue damage and disease. Although a topic of great interest with involvement of multiple signaling pathways, there are limitations in real-time detection of the autophagic process. EMD Millipore has developed technologies where prepackaged, ready-to-use, high-titer lentiviral particles, "lentiviral biosensors," encoding GFP- or RFP-tagged proteins provide a convenient and robust solution for fluorescent imaging of cells undergoing autophagy. Compared to nonviral transfection methods, lentiviral transduction, in many cases, offers higher transfection efficiency and more homogeneous protein expression, particularly for traditionally hard-to-transfect primary cell types. Lentiviral biosensors are ideal for use with fixed and live cell fluorescent microscopy, and are nondisruptive towards cellular function. GFP- or RFP-protein localization matches well with antibody-based immunostaining and demonstrates altered patterns of expression upon treatment with modulators of cell function and phenotype. Lentiviral biosensors provide a broadly effective, convenient method for visualization of cell behavior under a variety of physiological and pathological treatment conditions, in both endpoint and real-time imaging modalities. In this study, we focus on lentiviral biosensors containing GFP-LC3 and RFP-LC3 to study the formation of autophagosomes. PMID:25308268

  14. Measles Virus Transmission from Dendritic Cells to T Cells: Formation of Synapse-Like Interfaces Concentrating Viral and Cellular Components

    PubMed Central

    Koethe, Susanne; Avota, Elita

    2012-01-01

    Transmission of measles virus (MV) to T cells by its early CD150+ target cells is considered to be crucial for viral dissemination within the hematopoietic compartment. Using cocultures involving monocyte-derived dendritic cells (DCs) and T cells, we now show that T cells acquire MV most efficiently from cis-infected DCs rather than DCs having trapped MV (trans-infection). Transmission involves interactions of the viral glycoprotein H with its receptor CD150 and is therefore more efficient to preactivated T cells. In addition to rare association with actin-rich filopodial structures, the formation of contact interfaces consistent with that of virological synapses (VS) was observed where viral proteins accumulated and CD150 was redistributed in an actin-dependent manner. In addition to these molecules, activated LFA-1, DC-SIGN, CD81, and phosphorylated ezrin-radixin-moesin proteins, which also mark the HIV VS, redistributed toward the MV VS. Most interestingly, moesin and substance P receptor, both implicated earlier in assisting MV entry or cell-to-cell transmission, also partitioned to the transmission structure. Altogether, the MV VS shares important similarities to the HIV VS in concentrating cellular components potentially regulating actin dynamics, conjugate stability, and membrane fusion as required for efficient entry of MV into target T cells. PMID:22761368

  15. The impact of formative assessment techniques on the instruction of the high school biology units of photosynthesis and cellular respiration

    NASA Astrophysics Data System (ADS)

    Tury, Shanna Fawn

    The effect of formative assessment on student learning during student-centered, inquiry-based instruction was studied in a high school biology class. The objective of this study was to test whether increasing the level of formative assessment, including feedback to students and reflection on laboratory activities, would make an impact on the learning of concepts related to cellular metabolism, such as cellular respiration and photosynthesis. Two units of instruction were evaluated, one utilizing active learning strategies along with formative assessment techniques, and the other taught in a more teacher-centered manner. The revised methodology showed a statistically significant increase in student learning gains as compared to the unimproved technique. The increased amount of hands-on activities for students, observation of students in an informal context, student and teacher interaction, immediate feedback to students, public discussion and reflection on lab activities and results, and modification of instruction by the teacher is implicated in the trend found in these data. The results suggest that the combined effect of active, inquiry-based instruction and a variety of formative assessments can have a significant positive effect on student learning of topics related to cellular metabolism, such as photosynthesis and cellular respiration.

  16. Electrospun cellular microenvironments: Understanding controlled release and scaffold structure.

    PubMed

    Szentivanyi, Andreas; Chakradeo, Tanmay; Zernetsch, Holger; Glasmacher, Birgit

    2011-04-30

    Electrospinning is a versatile technique in tissue engineering for the production of scaffolds. To guide tissue development, scaffolds must provide specific biochemical, structural and mechanical cues to cells and deliver them in a controlled fashion over time. Electrospun scaffold design thus includes aspects of both controlled release and structural cues. Controlled multicomponent and multiphasic drug delivery can be achieved by the careful application and combination of novel electrospinning techniques, i.e., emulsion and co-axial electrospinning. Drug distribution and polymer properties influence the resulting release kinetics. Pore size is far more relevant as a structural parameter than previously recognized. It enables cell proliferation and ingrowth, whereas fiber diameter predominantly influences cell fate. Both parameters can be exploited by combining multiple fiber types in the form of multifiber and multilayer scaffolds. Such scaffolds are required to reproduce more complex tissue structures. PMID:21145932

  17. Structural and cellular changes during bone growth in healthy children.

    PubMed

    Parfitt, A M; Travers, R; Rauch, F; Glorieux, F H

    2000-10-01

    Normal postnatal bone growth is essential for the health of adults as well as children but has never been studied histologically in human subjects. Accordingly, we analyzed iliac bone histomorphometric data from 58 healthy white subjects, aged 1.5-23 years, 33 females and 25 males, of whom 48 had undergone double tetracycline labeling. The results were compared with similar data from 109 healthy white women, aged 20-76 years, including both young adult reference ranges and regressions on age. There was a significant increase with age in core width, with corresponding increases in both cortical width and cancellous width. In cancellous bone there were increases in bone volume and trabecular thickness, but not trabecular number, wall thickness, interstitial thickness, and inferred erosion depth. Mineral apposition rates declined on the periosteal envelope and on all subdivisions of the endosteal envelope. Because of the concomitant increase in wall thickness, active osteoblast lifespan increased substantially. Bone formation rate was almost eight times higher on the outer than on the inner periosteum, and more than four times higher on the inner than on the outer endocortical surface. On the cancellous surface, bone formation rate and activation frequency declined in accordance with a fifth order polynomial that matched previously published biochemical indices of bone turnover. The analysis suggested the following conclusions: (1) Between 2 and 20 years the ilium grows in width by periosteal apposition (3.8 mm) and endocortical resorption (3.2 mm) on the outer cortex, and net periosteal resorption (0.4 mm) and net endocortical formation (1.0 mm) on the inner cortex. (2) Cortical width increases from 0.52 mm at age 2 years to 1.14 mm by age 20 years. To attain adult values there must be further endocortical apposition of 0.25 mm by age 30 years, at a time when cancellous bone mass is declining. (3) Lateral modeling drift of the outer cortex enlarges the marrow cavity

  18. Myxospore formation in Myxococcus xanthus: chemical changes in the cell wall during cellular morphogenesis.

    PubMed

    Johnson, R Y; White, D

    1972-11-01

    Vegetative cells of Myxococcus xanthus (strain FB) were induced to form myxospores by the glycerol induction technique. Several structural changes took place in the peptidoglycan during myxospore formation. The percent of the peptidoglycan comprised of monomer (disaccharide peptide) decreased from about 20% to approximately 7%. The proportion of the total diaminopimelic acid possessing a free amino group decreased about 11%. A carbohydrate containing only glucose was found to be bound, possibly covalently, to the vegetative cell and myxospore peptidoglycan. The amount of carbohydrate relative to peptidoglycan decreased by two-thirds during myxospore formation. None of the above changes in the peptidoglycan were observed in a mutant (strain GNI) of M. xanthus which was unable to convert to myxospores when incubated in the glycerol induction medium, or in the parental wild type (FB) when it was incubated in induction medium lacking the myxospore inducer, glycerol. PMID:5086662

  19. Minkowski tensor shape analysis of cellular, granular and porous structures.

    PubMed

    Schröder-Turk, G E; Mickel, W; Kapfer, S C; Klatt, M A; Schaller, F M; Hoffmann, M J F; Kleppmann, N; Armstrong, P; Inayat, A; Hug, D; Reichelsdorfer, M; Peukert, W; Schwieger, W; Mecke, K

    2011-06-17

    Predicting physical properties of materials with spatially complex structures is one of the most challenging problems in material science. One key to a better understanding of such materials is the geometric characterization of their spatial structure. Minkowski tensors are tensorial shape indices that allow quantitative characterization of the anisotropy of complex materials and are particularly well suited for developing structure-property relationships for tensor-valued or orientation-dependent physical properties. They are fundamental shape indices, in some sense being the simplest generalization of the concepts of volume, surface and integral curvatures to tensor-valued quantities. Minkowski tensors are based on a solid mathematical foundation provided by integral and stochastic geometry, and are endowed with strong robustness and completeness theorems. The versatile definition of Minkowski tensors applies widely to different types of morphologies, including ordered and disordered structures. Fast linear-time algorithms are available for their computation. This article provides a practical overview of the different uses of Minkowski tensors to extract quantitative physically-relevant spatial structure information from experimental and simulated data, both in 2D and 3D. Applications are presented that quantify (a) alignment of co-polymer films by an electric field imaged by surface force microscopy; (b) local cell anisotropy of spherical bead pack models for granular matter and of closed-cell liquid foam models; (c) surface orientation in open-cell solid foams studied by X-ray tomography; and (d) defect densities and locations in molecular dynamics simulations of crystalline copper. PMID:21681830

  20. Model of intermittent zonal flow structure formation

    SciTech Connect

    Anderson, Johan; Kim, Eun-jin

    2008-11-01

    We present a theory the PDF tails of the zonal flow formation by assuming that a modon (a bipolar vortex) drives a zonal flow through the generalized Reynolds stress. We show that the PDF tails of zonal flow formation have exponential behavior {approx_equal}e{sup -{xi}}{sup {phi}{sub Z}{sub F}{sup 3}}, with the overall amplitude {xi} severely quenched by strong flow shear. It is found that stronger zonal flows are generated in ITG turbulence than Hasegawa-Mima (HM) turbulence as well as further from marginal stability. This suggests that although ITG turbulence has a higher level of heat flux, it also more likely generates stronger zonal flows, leading to a self-regulating system. It is also shown that shear flows can significantly reduce the PDF tails of structure formation.

  1. The structure and formation of natural categories

    NASA Technical Reports Server (NTRS)

    Fisher, Douglas; Langley, Pat

    1990-01-01

    Categorization and concept formation are critical activities of intelligence. These processes and the conceptual structures that support them raise important issues at the interface of cognitive psychology and artificial intelligence. The work presumes that advances in these and other areas are best facilitated by research methodologies that reward interdisciplinary interaction. In particular, a computational model is described of concept formation and categorization that exploits a rational analysis of basic level effects by Gluck and Corter. Their work provides a clean prescription of human category preferences that is adapted to the task of concept learning. Also, their analysis was extended to account for typicality and fan effects, and speculate on how the concept formation strategies might be extended to other facets of intelligence, such as problem solving.

  2. Topology optimization of adaptive fluid-actuated cellular structures with arbitrary polygonal motor cells

    NASA Astrophysics Data System (ADS)

    Lv, Jun; Tang, Liang; Li, Wenbo; Liu, Lei; Zhang, Hongwu

    2016-05-01

    This paper mainly focuses on the fast and efficient design method for plant bioinspired fluidic cellular materials and structures composed of polygonal motor cells. Here we developed a novel structural optimization method with arbitrary polygonal coarse-grid elements based on multiscale finite element frameworks. The fluidic cellular structures are meshed with irregular polygonal coarse-grid elements according to their natural size and the shape of the imbedded motor cells. The multiscale base functions of solid displacement and hydraulic pressure are then constructed to bring the small-scale information of the irregular motor cells to the large-scale simulations on the polygonal coarse-grid elements. On this basis, a new topology optimization method based on the resulting polygonal coarse-grid elements is proposed to determine the optimal distributions or number of motor cells in the smart cellular structures. Three types of optimization problems are solved according to the usages of the fluidic cellular structures. Firstly, the proposed optimization method is utilized to minimize the system compliance of the load-bearing fluidic cellular structures. Second, the method is further extended to design biomimetic compliant actuators of the fluidic cellular materials due to the fact that non-uniform volume expansions of fluid in the cells can induce elastic action. Third, the optimization problem focuses on the weight minimization of the cellular structure under the constraints for the compliance of the whole system. Several representative examples are investigated to validate the effectiveness of the proposed polygon-based topology optimization method of the smart materials.

  3. Simulating the formation of cosmic structure.

    PubMed

    Frenk, C S

    2002-06-15

    A timely combination of new theoretical ideas and observational discoveries has brought about significant advances in our understanding of cosmic evolution. Computer simulations have played a key role in these developments by providing the means to interpret astronomical data in the context of physical and cosmological theory. In the current paradigm, our Universe has a flat geometry, is undergoing accelerated expansion and is gravitationally dominated by elementary particles that make up cold dark matter. Within this framework, it is possible to simulate in a computer the emergence of galaxies and other structures from small quantum fluctuations imprinted during an epoch of inflationary expansion shortly after the Big Bang. The simulations must take into account the evolution of the dark matter as well as the gaseous processes involved in the formation of stars and other visible components. Although many unresolved questions remain, a coherent picture for the formation of cosmic structure is now beginning to emerge. PMID:12804279

  4. Structural Basis of Cargo Recognition by Unconventional Myosins in Cellular Trafficking.

    PubMed

    Li, Jianchao; Lu, Qing; Zhang, Mingjie

    2016-08-01

    Unconventional myosins are a superfamily of actin-based molecular motors playing diverse roles including cellular trafficking, mechanical supports, force sensing and transmission, etc. The variable neck and tail domains of unconventional myosins function to bind to specific cargoes including proteins and lipid vesicles and thus are largely responsible for the diverse cellular functions of myosins in vivo. In addition, the tail regions, together with their cognate cargoes, can regulate activities of the motor heads. This review outlines the advances made in recent years on cargo recognition and cargo binding-induced regulation of the activity of several unconventional myosins including myosin-I, V, VI and X in cellular trafficking. We approach this topic by describing a series of high-resolution structures of the neck and tail domains of these unconventional myosins either alone or in complex with their specific cargoes, and by discussing potential implications of these structural studies on cellular trafficking of these myosin motors. PMID:26842936

  5. General relativity and cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Adamek, Julian; Daverio, David; Durrer, Ruth; Kunz, Martin

    2016-04-01

    Numerical simulations are a versatile tool for providing insight into the complicated process of structure formation in cosmology. This process is mainly governed by gravity, which is the dominant force on large scales. At present, a century after the formulation of general relativity, numerical codes for structure formation still employ Newton’s law of gravitation. This approximation relies on the two assumptions that gravitational fields are weak and that they originate from non-relativistic matter. Whereas the former seems well justified on cosmological scales, the latter imposes restrictions on the nature of the `dark’ components of the Universe (dark matter and dark energy), which are, however, poorly understood. Here we present the first simulations of cosmic structure formation using equations consistently derived from general relativity. We study in detail the small relativistic effects for a standard lambda cold dark matter cosmology that cannot be obtained within a purely Newtonian framework. Our particle-mesh N-body code computes all six degrees of freedom of the metric and consistently solves the geodesic equation for particles, taking into account the relativistic potentials and the frame-dragging force. This conceptually clean approach is very general and can be applied to various settings where the Newtonian approximation fails or becomes inaccurate, ranging from simulations of models with dynamical dark energy or warm/hot dark matter to core collapse supernova explosions.

  6. Multicompartmentalized polymeric systems: towards biomimetic cellular structure and function.

    PubMed

    Marguet, Maïté; Bonduelle, Colin; Lecommandoux, Sébastien

    2013-01-21

    The cell is certainly one of the most complex and exciting systems in Nature that scientists are still trying to fully understand. Such a challenge pushes material scientists to seek to reproduce its perfection by building biomimetic materials with high-added value and previously unmatched properties. Thanks to their versatility, their robustness and the current state of polymer chemistry science, we believe polymer-based materials to constitute or represent ideal candidates when addressing the challenge of biomimicry, which defines the focus of this review. The first step consists in mimicking the structure of the cell: its inner compartments, the organelles, with a multicompartmentalized structure, and the rest, i.e. the cytoplasm minus the organelles (mainly cytoskeleton/cytosol) with gels or particular solutions (highly concentrated for example) in one compartment, and finally the combination of both. Achieving this first structural step enables us to considerably widen the gap of possibilities in drug delivery systems. Another powerful property of the cell lies in its metabolic function. The second step is therefore to achieve enzymatic reactions in a compartment, as occurs in the organelles, in a highly controlled, selective and efficient manner. We classify the most exciting polymersome nanoreactors reported in our opinion into two different subsections, depending on their very final concept or purpose of design. We also highlight in a thorough table the experimental sections crucial to such work. Finally, after achieving control over these prerequisites, scientists are able to combine them and push the frontiers of biomimicry further: from cell structure mimics towards a controlled biofunctionality. Such a biomimetic approach in material design and the future research it will stimulate, are believed to bring considerable enrichments to the fields of drug delivery, (bio)sensors, (bio)catalysis and (bio)technology. PMID:23073077

  7. Silicateins, silicatein interactors and cellular interplay in sponge skeletogenesis: formation of glass fiber-like spicules.

    PubMed

    Wang, Xiaohong; Schloßmacher, Ute; Wiens, Matthias; Batel, Renato; Schröder, Heinz C; Müller, Werner E G

    2012-05-01

    Biomineralization processes are characterized by controlled deposition of inorganic polymers/minerals mediated by functional groups linked to organic templates. One metazoan taxon, the siliceous sponges, has utilized these principles and even gained the ability to form these polymers/minerals by an enzymatic mechanism using silicateins. Silicateins are the dominant protein species present in the axial canal of the skeletal elements of the siliceous sponges, the spicules, where they form the axial filament. Silicateins also represent a major part of the organic components of the silica lamellae, which are cylindrically arranged around the axial canal. With the demosponge Suberites domuncula as a model, quantitative enzymatic studies revealed that both the native and the recombinant enzyme display in vitro the same biosilica-forming activity as the enzyme involved in spicule formation in vivo. Monomeric silicatein molecules assemble into filaments via fractal intermediates, which are stabilized by the silicatein-interacting protein silintaphin-1. Besides the silicateins, a silica-degrading enzyme silicase acting as a catabolic enzyme has been identified. Growth of spicules proceeds in vivo in two directions: first, by axial growth, a process that is controlled by evagination of cell protrusions and mediated by the axial filament-associated silicateins; and second, by appositional growth, which is driven by the extraspicular silicateins, a process that provides the spicules with their final size and morphology. This radial layer-by-layer accretion is directed by organic cylinders that are formed around the growing spicule and consist of galectin and silicatein. The cellular interplay that controls the morphogenetic processes during spiculogenesis is outlined. PMID:22340505

  8. Formation of a Protein Corona on Silver Nanoparticles Mediates Cellular Toxicity via Scavenger Receptors

    PubMed Central

    Shannahan, Jonathan H.; Podila, Ramakrishna; Aldossari, Abdullah A.; Emerson, Hilary; Powell, Brian A.; Ke, Pu Chun; Rao, Apparao M.; Brown, Jared M.

    2015-01-01

    Addition of a protein corona (PC) or protein adsorption layer on the surface of nanomaterials following their introduction into physiological environments may modify their activity, bio-distribution, cellular uptake, clearance, and toxicity. We hypothesize that silver nanoparticles (AgNPs) will associate with proteins common to human serum and cell culture media forming a PC that will impact cell activation and cytotoxicity. Furthermore, the role of scavenger receptor BI (SR-BI) in mediating this toxicity was evaluated. Citrate-suspended 20 nm AgNPs were incubated with human serum albumin (HSA), bovine serum albumin (BSA), high-density lipoprotein (HDL), or water (control) to form a PC. AgNPs associated with each protein (HSA, BSA, and HDL) forming PCs as assessed by electron microscopy, hyperspectral analysis, ζ-potential, and hydrodynamic size. Addition of the PC decreased uptake of AgNPs by rat lung epithelial and rat aortic endothelial cells. Hyperspectral analysis demonstrated a loss of the AgNP PC following internalization. Cells demonstrated concentration-dependent cytotoxicity following exposure to AgNPs with or without PCs (0, 6.25, 12.5, 25 or 50 μg/ml). All PC-coated AgNPs were found to activate cells by inducing IL-6 mRNA expression. A small molecule SR-BI inhibitor was utilized to determine the role of SR-BI in the observed effects. Pretreatment with the SR-BI inhibitor decreased internalization of AgNPs with or without PCs, and reduced both cytotoxicity and IL-6 mRNA expression. This study characterizes the formation of a PC on AgNPs and demonstrates its influence on cytotoxicity and cell activation through a cell surface receptor. PMID:25326241

  9. Analysis of information gain and Kolmogorov complexity for structural evaluation of cellular automata configurations

    NASA Astrophysics Data System (ADS)

    Javaheri Javid, Mohammad Ali; Blackwell, Tim; Zimmer, Robert; Majid al-Rifaie, Mohammad

    2016-04-01

    Shannon entropy fails to discriminate structurally different patterns in two-dimensional images. We have adapted information gain measure and Kolmogorov complexity to overcome the shortcomings of entropy as a measure of image structure. The measures are customised to robustly quantify the complexity of images resulting from multi-state cellular automata (CA). Experiments with a two-dimensional multi-state cellular automaton demonstrate that these measures are able to predict some of the structural characteristics, symmetry and orientation of CA generated patterns.

  10. Localization-Based Super-Resolution Imaging of Cellular Structures

    PubMed Central

    Kanchanawong, Pakorn; Waterman, Clare M.

    2013-01-01

    Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures. PMID:23868582

  11. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

  12. VDAC2-specific cellular functions and the underlying structure.

    PubMed

    Naghdi, Shamim; Hajnóczky, György

    2016-10-01

    Voltage Dependent Anion-selective Channel 2 (VDAC2) contributes to oxidative metabolism by sharing a role in solute transport across the outer mitochondrial membrane (OMM) with other isoforms of the VDAC family, VDAC1 and VDAC3. Recent studies revealed that VDAC2 also has a distinctive role in mediating sarcoplasmic reticulum to mitochondria local Ca(2+) transport at least in cardiomyocytes, which is unlikely to be explained simply by the expression level of VDAC2. Furthermore, a strictly isoform-dependent VDAC2 function was revealed in the mitochondrial import and OMM-permeabilizing function of pro-apoptotic Bcl-2 family proteins, primarily Bak in many cell types. In addition, emerging evidence indicates a variety of other isoform-specific engagements for VDAC2. Since VDAC isoforms display 75% sequence similarity, the distinctive structure underlying VDAC2-specific functions is an intriguing problem. In this paper we summarize studies of VDAC2 structure and functions, which suggest a fundamental and exclusive role for VDAC2 in health and disease. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou. PMID:27116927

  13. Ru(ii)-polypyridyl surface functionalised gold nanoparticles as DNA targeting supramolecular structures and luminescent cellular imaging agents

    NASA Astrophysics Data System (ADS)

    Martínez-Calvo, Miguel; Orange, Kim N.; Elmes, Robert B. P.; La Cour Poulsen, Bjørn; Williams, D. Clive; Gunnlaugsson, Thorfinnur

    2015-12-01

    The development of Ru(ii) functionalized gold nanoparticles 1-3.AuNP is described. These systems were found to be mono-disperse with a hydrodynamic radius of ca. 15 nm in water but gave rise to the formation of higher order structures in buffered solution. The interaction of 1-3.AuNP with DNA was also studied by spectroscopic and microscopic methods and suggested the formation of large self-assembly structures in solution. The uptake of 1-3.AuNP by cancer cells was studied using both confocal fluorescence as well as transmission electron microscopy (TEM), with the aim of investigating their potential as tools for cellular biology. These systems displaying a non-toxic profile with favourable photophysical properties may have application across various biological fields including diagnostics and therapeutics.The development of Ru(ii) functionalized gold nanoparticles 1-3.AuNP is described. These systems were found to be mono-disperse with a hydrodynamic radius of ca. 15 nm in water but gave rise to the formation of higher order structures in buffered solution. The interaction of 1-3.AuNP with DNA was also studied by spectroscopic and microscopic methods and suggested the formation of large self-assembly structures in solution. The uptake of 1-3.AuNP by cancer cells was studied using both confocal fluorescence as well as transmission electron microscopy (TEM), with the aim of investigating their potential as tools for cellular biology. These systems displaying a non-toxic profile with favourable photophysical properties may have application across various biological fields including diagnostics and therapeutics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05598a

  14. Stochastic structure formation in random media

    NASA Astrophysics Data System (ADS)

    Klyatskin, V. I.

    2016-01-01

    Stochastic structure formation in random media is considered using examples of elementary dynamical systems related to the two-dimensional geophysical fluid dynamics (Gaussian random fields) and to stochastically excited dynamical systems described by partial differential equations (lognormal random fields). In the latter case, spatial structures (clusters) may form with a probability of one in almost every system realization due to rare events happening with vanishing probability. Problems involving stochastic parametric excitation occur in fluid dynamics, magnetohydrodynamics, plasma physics, astrophysics, and radiophysics. A more complicated stochastic problem dealing with anomalous structures on the sea surface (rogue waves) is also considered, where the random Gaussian generation of sea surface roughness is accompanied by parametric excitation.

  15. Cerium Oxyhydroxide Clusters: Formation, Structure and Reactivity

    SciTech Connect

    Aubriet, F.; Gaumet, Jean-Jacques; De Jong, Wibe A.; Groenewold, G. S.; Gianotto, Anita K.; McIIwain, Michael E.; Van Stipdonk, Michael J.; Leavitt, Christopher M.

    2009-05-11

    Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [CexOy] ions and neutrals. These initially-formed species react with water, principally forming closed-shell (c-s) oxohydroxy species that are described by the general formula [CexOy(OH)z]-. In general, the extent of hydroxylation varies from a value of 3 OH per Ce atom when x = 1 to a value slightly greater than 1 for x > 8. The Ce3 and Ce6 species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and x = 4. Conversely, the x = 6 cluster is significantly less hydroxylated. Density functional theory (DFT) modeling of the cluster structures show that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce3 oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce6 oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the c-s clusters, open-shell (o-s) oxyhydroxides and superoxides are also formed, and they become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to stabilize a non-bonding electron. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases, however this trend is interrupted at Ce13, which is significantly more stable compared to neighboring congeners, suggesting formation of

  16. Cerium Oxyhydroxide Clusters: Formation, Structure and Reactivity

    SciTech Connect

    Frederic Aubriet; Jean-Jacques Gaumet; Wibe A de Jong; Groenewold, Gary S; Gianotto, Anita K; McIlwain, Michael E; Michael J. Van Stipdonk; Christopher M. Leavitt

    2009-06-01

    Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [CexOy] ions and neutrals. These initially-formed species react with water, principally forming closed-shell (c-s) oxohydroxy species that are described by the general formula [CexOy(OH)z]-. In general, the extent of hydroxylation varies from a value of 3 OH per Ce atom when x = 1 to a value slightly greater than 1 for x > 8. The Ce3 and Ce6 species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and x = 4. Conversely, the x = 6 cluster is significantly less hydroxylated. Density functional theory (DFT) modeling of the cluster structures show that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce3 oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce6 oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the c-s clusters, open-shell (o-s) oxyhydroxides and superoxides are also formed, and they become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to stabilize a non-bonding electron. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases, however this trend is interrupted at Ce13, which is significantly more stable compared to neighboring congeners, suggesting formation of

  17. Structure of adenovirus bound to cellular receptor car

    DOEpatents

    Freimuth, Paul I.

    2004-05-18

    Disclosed is a mutant adenovirus which has a genome comprising one or more mutations in sequences which encode the fiber protein knob domain wherein the mutation causes the encoded viral particle to have significantly weakened binding affinity for CARD1 relative to wild-type adenovirus. Such mutations may be in sequences which encode either the AB loop, or the HI loop of the fiber protein knob domain. Specific residues and mutations are described. Also disclosed is a method for generating a mutant adenovirus which is characterized by a receptor binding affinity or specificity which differs substantially from wild type. In the method, residues of the adenovirus fiber protein knob domain which are predicted to alter D1 binding when mutated, are identified from the crystal structure coordinates of the AD12knob:CAR-D1 complex. A mutation which alters one or more of the identified residues is introduced into the genome of the adenovirus to generate a mutant adenovirus. Whether or not the mutant produced exhibits altered adenovirus-CAR binding properties is then determined.

  18. Secondary structure formation in peptide amphiphile micelles

    NASA Astrophysics Data System (ADS)

    Tirrell, Matthew

    2012-02-01

    Peptide amphiphiles (PAs) are capable of self-assembly into micelles for use in the targeted delivery of peptide therapeutics and diagnostics. PA micelles exhibit a structural resemblance to proteins by having folded bioactive peptides displayed on the exterior of a hydrophobic core. We have studied two factors that influence PA secondary structure in micellar assemblies: the length of the peptide headgroup and amino acids closest to the micelle core. Peptide length was systematically varied using a heptad repeat PA. For all PAs the addition of a C12 tail induced micellization and secondary structure. PAs with 9 amino acids formed beta-sheet interactions upon aggregation, whereas the 23 and 30 residue peptides were displayed in an apha-helical conformation. The 16 amino acid PA experienced a structural transition from helix to sheet, indicating that kinetics play a role in secondary structure formation. A p53 peptide was conjugated to a C16 tail via various linkers to study the effect of linker chemistry on PA headgroup conformation. With no linker the p53 headgroup was predominantly alpha helix and a four alanine linker drastically changed the structure of the peptide headgroup to beta-sheet, highlighting the importance of hydrogen boding potential near the micelle core.

  19. Second harmonic generation imaging microscopy of cellular structure and function

    NASA Astrophysics Data System (ADS)

    Millard, Andrew C.; Jin, Lei; Loew, Leslie M.

    2005-03-01

    Second harmonic generation (SHG) imaging microscopy is an important emerging technique for biological research, with many advantages over existing one- or two-photon fluorescence techniques. A non-linear phenomenon employing mode-locked Ti:sapphire or fiber-based lasers, SHG results in intrinsic optical sectioning without the need for a confocal aperture. Furthermore, as a second-order process SHG is confined to loci lacking a center of symmetry. Many important structural proteins such as collagen and cellulose show intrinsic SHG, thus providing access to sub-resolution information on symmetry. However, we are particularly interested here in "resonance-enhanced" SHG from styryl dyes. In general SHG is a combination of a true second-order process and a third-order process dependent on a static electric field, such that SHG from membrane-bound dyes depends on a cell's trans-membrane potential. With simultaneous patch-clamping and non-linear imaging of cells, we have found that SHG is a sensitive probe of trans-membrane potential with sensitivities that are up to four times better than those obtained under optimal conditions using one-photon fluorescence imaging. With the sensitivity of SHG to local electric fields from other sources such as the membrane dipole potential as well as the quadratic dependence of SHG on concentration, we have found that SHG imaging of styryl dyes is also a powerful technique for the investigation of lipid phases and rafts and for the visualization of the dynamics of membrane-vesicle fusion following fertilization of an ovum.

  20. Adaptive cellular structures and devices with internal features for enhanced structural performance

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael Eugene

    This dissertation aims to develop a family of cellular and repeatable devices that exhibit a variety of force-displacement behaviors. It is envisioned that these cellular structures might be used either as stand-alone elements, or combined and repeated to create multiple types of structures (i.e. buildings, ship hulls, vehicle subfloors, etc.) with the ability to passively or actively perform multiple functions (harmonic energy dissipation, impact mitigation, modulus change) over a range of loading types, amplitudes, and frequencies. To accomplish this goal, this work combines repeatable structural frameworks, such as that provided by a hexagonal cellular structure, with internal structural elements such as springs, viscous dampers, buckling plates, bi-stable von Mises trusses (VMTs), and pneumatic artificial muscles (PAMs). The repeatable framework serves to position damping and load carrying elements throughout the structure, and the configuration of the internal elements allow each cell to be tuned to exhibit a desired force-displacement response. Therefore, gradient structures or structures with variable load paths can be created for an optimal global response to a range of loads. This dissertation focuses on the development of cellular structures for three functions: combined load-carrying capability with harmonic energy dissipation, impact mitigation, and cell modulus variation. One or more conceptual designs are presented for devices that can perform each of these functions, and both experimental measurements and simulations are used to gain a fundamental understanding of each device. Chapter 2 begins with a presentation of a VMT model that is the basis for many of the elements. The equations of motion for the VMT are derived and the static and dynamic behavior of the VMT are discussed in detail. Next, two metrics for the energy dissipation of the VMT - hysteresis loop area and loss factor - are presented. The responses of the VMT to harmonic displacement

  1. Modulating Cellular Recombination Potential through Alterations in RecA Structure and Regulation

    PubMed Central

    Bakhlanova, Irina V.; Dudkina, Alexandra V.; Baitin, Dima M.; Knight, Kendall L.; Cox, Michael M.; Lanzov, Vladislav A.

    2010-01-01

    The wild type E. coli RecA protein is a recombinase platform with unrealized recombination potential. We have explored the factors affecting recombination during conjugation with a quantitative assay. Regulatory proteins that affect RecA function have the capacity to increase or decrease recombination frequencies by factors up to 6 fold. Autoinhibition by the RecA C-terminus can affect recombination frequency by factors up to 4 fold. The greatest changes in recombination frequency measured here are brought about by point mutations in the recA gene. RecA variants can increase recombination frequencies by more than 50 fold. The RecA protein thus possesses an inherently broad functional range. The RecA protein of Escherichia coli (EcRecA) is not optimized for recombination function. Instead, much of the recombination potential of EcRecA is structurally suppressed, probably reflecting cellular requirements. One point mutation in EcRecA with a particularly dramatic effect on recombination frequency, D112R, exhibits an enhanced capacity to load onto SSB-coated ssDNA, overcome the effects of regulatory proteins such as PsiB and RecX, and to pair homologous DNAs. Comparisons of key RecA protein mutants reveal two components to RecA recombination function – filament formation and the inherent DNA pairing activity of the formed filaments. PMID:21143322

  2. Processing and modeling of cellular solids for light-weight structures

    SciTech Connect

    Nieh, T.G.

    1997-12-01

    Cellular solids (also known as porous solids) comprise a special class of materials. Such materials are common in nature; wood, cork, sponge and coral are examples. Recently man has also made his own cellular solids. For example, many honeycomb-like materials, made up of parallel, prismatic cells, are used for lightweight aerospace structural components. Polymeric foams have been used in everything from disposable coffee cups, packaging materials, to the crash padding of an aircraft cockpit. Advanced techniques now exist for foaming not only polymers, but metals and ceramics as well. These newer foams are increasingly used for catalysts (chemical), preforms for metal-matrix composites, thermal insulators and thermal shock resistant materials (thermal), acoustic dampers (acoustic), cushions, vibration reducers, and systems for absorbing the kinetic energy from impacts (mechanical). Their uses exploit the special combination of properties offered by cellular solids, properties which, ultimately, derive from their cellular structure. The objective of this proposed research is to develop processing techniques to produce metallic foams with controlled cellular structures and to understand and model the mechanical behavior of this special class of materials.

  3. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

    PubMed

    Watters, Kyle E; Abbott, Timothy R; Lucks, Julius B

    2016-01-29

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure-function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA-RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA-RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  4. Cosmological structure formation from soft topological defects

    NASA Technical Reports Server (NTRS)

    Hill, Christopher T.; Schramm, David N.; Fry, J. N.

    1988-01-01

    Some models have extremely low-mass pseudo-Goldstone bosons that can lead to vacuum phase transitions at late times, after the decoupling of the microwave background.. This can generate structure formation at redshifts z greater than or approx 10 on mass scales as large as M approx 10 to the 18th solar masses. Such low energy transitions can lead to large but phenomenologically acceptable density inhomogeneities in soft topological defects (e.g., domain walls) with minimal variations in the microwave anisotropy, as small as delta Y/T less than or approx 10 to the minus 6 power. This mechanism is independent of the existence of hot, cold, or baryonic dark matter. It is a novel alternative to both cosmic string and to inflationary quantum fluctuations as the origin of structure in the Universe.

  5. The formation and structure of Olympic gels

    NASA Astrophysics Data System (ADS)

    Fischer, J.; Lang, M.; Sommer, J.-U.

    2015-12-01

    Different methods for creating Olympic gels are analyzed using computer simulations. First ideal reference samples are obtained from freely interpenetrating semi-dilute solutions and melts of cyclic polymers. The distribution of pairwise concatenations per cyclic molecule is given by a Poisson-distribution and can be used to describe the elastic structure of the gels. Several batches of linear chains decorated with different selectively binding groups at their ends are mixed in the "DNA Origami" technique and network formation is realized. While the formation of cyclic molecules follows mean field predictions below overlap of the precursor molecules, an enhanced ring formation above overlap is found that is not explained by mean field arguments. The "progressive construction" method allows to create Olympic gels with a single reaction step from a concentrated mixture of large compressed rings with a low weight fraction of short chains that are below overlap concentration. This method, however, is limited by the difficulty to obtain a sufficiently high degree of polymerization of the large rings.

  6. The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods.

    PubMed

    McCusker, Catherine; Bryant, Susan V; Gardiner, David M

    2015-04-01

    The axolotl is one of the few tetrapods that are capable of regenerating complicated biological structures, such as complete limbs, throughout adulthood. Upon injury the axolotl generates a population of regeneration-competent limb progenitor cells known as the blastema, which will grow, establish pattern, and differentiate into the missing limb structures. In this review we focus on the crucial early events that occur during wound healing, the neural-epithelial interactions that drive the formation of the early blastema, and how these mechanisms differ from those of other species that have restricted regenerative potential, such as humans. We also discuss how the presence of cells from the different axes of the limb is required for the continued growth and establishment of pattern in the blastema as described in the polar coordinate model, and how this positional information is reprogrammed in blastema cells during regeneration. Multiple cell types from the mature limb stump contribute to the blastema at different stages of regeneration, and we discuss the contribution of these types to the regenerate with reference to whether they are "pattern-forming" or "pattern-following" cells. Lastly, we explain how an engineering approach will help resolve unanswered questions in limb regeneration, with the goal of translating these concepts to developing better human regenerative therapies. PMID:27499868

  7. The axolotl limb blastema: cellular and molecular mechanisms driving blastema formation and limb regeneration in tetrapods

    PubMed Central

    McCusker, Catherine; Bryant, Susan V.

    2015-01-01

    Abstract The axolotl is one of the few tetrapods that are capable of regenerating complicated biological structures, such as complete limbs, throughout adulthood. Upon injury the axolotl generates a population of regeneration‐competent limb progenitor cells known as the blastema, which will grow, establish pattern, and differentiate into the missing limb structures. In this review we focus on the crucial early events that occur during wound healing, the neural−epithelial interactions that drive the formation of the early blastema, and how these mechanisms differ from those of other species that have restricted regenerative potential, such as humans. We also discuss how the presence of cells from the different axes of the limb is required for the continued growth and establishment of pattern in the blastema as described in the polar coordinate model, and how this positional information is reprogrammed in blastema cells during regeneration. Multiple cell types from the mature limb stump contribute to the blastema at different stages of regeneration, and we discuss the contribution of these types to the regenerate with reference to whether they are “pattern‐forming” or “pattern‐following” cells. Lastly, we explain how an engineering approach will help resolve unanswered questions in limb regeneration, with the goal of translating these concepts to developing better human regenerative therapies.

  8. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq

    PubMed Central

    Watters, Kyle E.; Abbott, Timothy R.; Lucks, Julius B.

    2016-01-01

    Many non-coding RNAs form structures that interact with cellular machinery to control gene expression. A central goal of molecular and synthetic biology is to uncover design principles linking RNA structure to function to understand and engineer this relationship. Here we report a simple, high-throughput method called in-cell SHAPE-Seq that combines in-cell probing of RNA structure with a measurement of gene expression to simultaneously characterize RNA structure and function in bacterial cells. We use in-cell SHAPE-Seq to study the structure–function relationship of two RNA mechanisms that regulate translation in Escherichia coli. We find that nucleotides that participate in RNA–RNA interactions are highly accessible when their binding partner is absent and that changes in RNA structure due to RNA–RNA interactions can be quantitatively correlated to changes in gene expression. We also characterize the cellular structures of three endogenously expressed non-coding RNAs: 5S rRNA, RNase P and the btuB riboswitch. Finally, a comparison between in-cell and in vitro folded RNA structures revealed remarkable similarities for synthetic RNAs, but significant differences for RNAs that participate in complex cellular interactions. Thus, in-cell SHAPE-Seq represents an easily approachable tool for biologists and engineers to uncover relationships between sequence, structure and function of RNAs in the cell. PMID:26350218

  9. Regulation of biofilm formation and cellular buoyancy through modulating intracellular cyclic di-GMP levels in engineered cyanobacteria.

    PubMed

    Agostoni, Marco; Waters, Christopher M; Montgomery, Beronda L

    2016-02-01

    The second messenger cyclic dimeric (3'→5') GMP (cyclic di-GMP or c-di-GMP) has been implicated in the transition between motile and sessile lifestyles in bacteria. In this study, we demonstrate that biofilm formation, cellular aggregation or flocculation, and cellular buoyancy are under the control of c-di-GMP in Synechocystis sp. PCC 6803 (Synechocystis) and Fremyella diplosiphon. Synechocystis is a unicellular cyanobacterium and displays lower levels of c-di-GMP; F. diplosiphon is filamentous and displays higher intracellular c-di-GMP levels. We transformed Synechocystis and F. diplosiphon with a plasmid for constitutive expression of genes encoding diguanylate cylase (DGC) and phosphodiesterase (PDE) proteins from Vibrio cholerae or Escherichia coli, respectively. These engineered strains allowed us to modulate intracellular c-di-GMP levels. Biofilm formation and cellular deposition were induced in the DGC-expressing Synechocystis strain which exhibited high intracellular levels of c-di-GMP; whereas strains expressing PDE in Synechocystis and F. diplosiphon to drive low intracellular levels of c-di-GMP exhibited enhanced cellular buoyancy. In addition, the PDE-expressing F. diplosiphon strain showed elevated chlorophyll levels. These results imply roles for coordinating c-di-GMP homeostasis in regulating native cyanobacterial phenotypes. Engineering exogenous DGC or PDE proteins to regulate intracellular c-di-GMP levels represents an effective tool for uncovering cryptic phenotypes or modulating phenotypes in cyanobacteria for practical applications in biotechnology applicable in photobioreactors and in green biotechnologies, such as energy-efficient harvesting of cellular biomass or the treatment of metal-containing wastewaters. PMID:26192200

  10. The Crystalline Structure of Escherichia Coli Derived, - and Holo-Rat Cellular Retinol Binding Protein II

    NASA Astrophysics Data System (ADS)

    Winter, Nathan Shoup

    1993-01-01

    Crystal of apo- and holo-rat cellular retinol binding protein II from the recombinant protein isolated from E. coli were grown. X-ray data to about 2A resolution for both crystal forms were collected. The phases for both data sets were determined by the molecular replacement technique using cellular retinol binding protein. The structures were then refined. The electron density from bound retinol was observed in the holo-form. Other than the presence or absence of bound retinol, little difference was noted in the structures of the apo- and holo-protein. The retinol was bound in a interior cavity with the hydroxyl group in the center of the protein, and the ionone ring near the surface. The hydroxyl group of the retinol made a hydrogen bond to glutamine 108, and the amine group of lysine 40 came into Van der Waals contact with the isoprene chain. The structure of cellular retinol binding protein II was then compared with the structures of five other intracellular lipid binding proteins: adipocyte lipid binding protein, cellular retinol binding protein, intestinal fatty acid binding protein, p2 protein from myelin sheaths, and a midgut fatty acid binding protein.

  11. Final Report - Modeling the Physics of Damage Cluster Formation in a Cellular Environment Modeling the Physics of Damage Cluster Formation in a Cellular Environment

    SciTech Connect

    L.H. Toburen, Principal Investigator; J.L. Shinpaugh; M. Dingfelder; and G. Lapicki; Co-Investigators

    2007-01-07

    Modern tools of radiobiology are leading to many new discoveries regarding how cells and tissues respond to radiation exposure. We can now irradiate single cells and observe responses in adjacent cells. We can also measure clusters of radiation damage produced in DNA. Our primary objective has been to understand the underling physics associated with these new biological responses. The primary tools available to describe the initial spatial pattern of damage formed by the absorption of ionizing radiation are based on Monte Carlo simulation of the structure of charged particle tracks. Although many Monte Carlo codes exist and considerable progress is being made in the incorporation of detailed macromolecular target structures into these codes, much of the interaction physics is still based on gas phase measurements and/or untested theoretical calculations that focus on water as the transport medium. Our objectives were threefold, (1) to expand the applicability of Monte Carlo track structure simulation to tissue-like material beyond the current focus on water, (2) to incorporate the most recent experimental information on electron interactions in biologically relevant material, and (3) to compare recent measurements of electron emissions induced by charged particles in thin foils with Monte Carlo predictions. We addressed these research objectives in three ways. First we applied theoretical techniques, similar to those used to derive data for water, to obtain cross sections for other condensed phase materials. This served two purposes. One was to provide testability of the theoretical technique by comparison to existing experimental data for electron transport (similar data does not exist for water), and the other was to expand the target database for use in modeling tissue. Second, we carefully reviewed published data, and ongoing experiments, for electron interaction cross-sections in biologically relevant condensed phase material. Results for low-energy electron

  12. Point process models for localization and interdependence of punctate cellular structures.

    PubMed

    Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

    2016-07-01

    Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures.

  13. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions

    PubMed Central

    Guan, Lirui

    2013-01-01

    Won’t let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by ≈2500-fold but also enables cell-wide profiling of its RNA targets. PMID:23913698

  14. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions.

    PubMed

    Guan, Lirui; Disney, Matthew D

    2013-09-16

    Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets. PMID:23913698

  15. Formation of cellular projections in neural progenitor cells depends on SK3 channel activity.

    PubMed

    Liebau, Stefan; Vaida, Bianca; Proepper, Christian; Grissmer, Stephan; Storch, Alexander; Boeckers, Tobias M; Dietl, Paul; Wittekindt, Oliver H

    2007-06-01

    Ion channels are potent modulators for developmental processes in progenitor cells. In a screening approach for different ion channels in neural progenitor cells (NPCs) we observed a 1-ethyl-2-benzimidazolinone (1-EBIO) activated inward current, which could be blocked by scyllatoxin (ScTX, IC50=2+/- 0.3 nmol/L). This initial evidence for the expression of the small conductance Ca2+ activated K+-channel SK3 was confirmed by the detection of SK3 transcripts and protein in NPCs. Interestingly, SK3 proteins were highly expressed in non-differentiated NPCs with a focused localization in lamellipodia as well as filopodial structures. The activation of SK3 channels using 1-EBIO lead to an immediate filopodial sprouting and the translocation of the protein into these novel filopodial protrusions. Both effects could be prevented by the pre-incubation of NPCs with ScTX. Our study gives first evidence that the formation and prolongation of filopodia in NPCs is, at least in part, effectively induced and regulated by SK3 channels. PMID:17459146

  16. Formation of Structure in the Universe

    NASA Technical Reports Server (NTRS)

    Bahcall, John; Fisher, Karl; Miralda-Escude, Jordi; Strauss, Michael; Weinberg, David

    1997-01-01

    This grant supported research by the investigators through summer salary support for Strauss and Weinberg, support for graduate students at Princeton University and Ohio State University, and travel, visitor, and publication support for the investigators. The grant originally had a duration of 1 year, and it was extended (without additional funding) for an additional year. The impact of the grant was considerable given its relatively modest duration and funding level, in part because it provided 'seed' funding to get Strauss and Weinberg started at new institutions, and in part because it was combined with support from subsequent grants. Here we summarize progress in the three general areas described in the grant proposal: Lyman alpha absorbers and the intergalactic medium, galaxy formation; and large scale structure.

  17. Beta Cell Formation in vivo Through Cellular Networking, Integration and Processing (CNIP) in Wild Type Adult Mice.

    PubMed

    Doiron, Bruno; Hu, Wenchao; DeFronzo, Ralph A

    2016-01-01

    Insulin replacement therapy is essential in type 1 diabetic individuals and is required in ~40- 50% of type 2 diabetics during their lifetime. Prior attempts at beta cell regeneration have relied upon pancreatic injury to induce beta cell proliferation, dedifferentiation and activation of the embryonic pathway, or stem cell replacement. We report an alternative method to transform adult non-stem (somatic) cells into pancreatic beta cells. The Cellular Networking, Integration and Processing (CNIP) approach targets cellular mechanisms involved in pancreatic function in the organ's adult state and utilizes a synergistic mechanism that integrates three important levels of cellular regulation to induce beta cell formation: (i) glucose metabolism, (ii) membrane receptor function, and (iii) gene transcription. The aim of the present study was to induce pancreatic beta cell formation in vivo in adult animals without stem cells and without dedifferentiating cells to recapitulate the embryonic pathway as previously published (1-3). Our results employing CNIP demonstrate that: (i) insulin secreting cells can be generated in adult pancreatic tissue in vivo and circumvent the problem of generating endocrine (glucagon and somatostatin) cells that exert deleterious effects on glucose homeostasis, and (ii) longterm normalization of glucose tolerance and insulin secretion can be achieved in a wild type diabetic mouse model. The CNIP cocktail has the potential to be used as a preventative or therapeutic treatment or cure for both type 1 and type 2 diabetes. PMID:26696016

  18. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

    SciTech Connect

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  19. Quantitative structure-activity relationships for cellular uptake of surface-modified nanoparticles.

    PubMed

    Liu, Rong; Rallo, Robert; Bilal, Muhammad; Cohen, Yoram

    2015-01-01

    Quantitative structure-activity relationships (QSARs) were developed, for cellular uptake of nanoparticles (NPs) of the same iron oxide core but with different surface-modifying organic molecules, based on linear and non-linear (epsilon support vector regression (ε-SVR)). A linear QSAR provided high prediction accuracy of R2=0.751 (coefficient of determination) using 11 descriptors selected from an initial pool of 184 descriptors calculated for the NP surfacemodifying molecules, while a ε-SVR based QSAR with only 6 descriptors improved prediction accuracy to R2=0.806. The linear and ε-SVR based QSARs both demonstrated good robustness and well spanned applicability domains. It is suggested that the approach of evaluating pertinent descriptors and their significance, via QSAR analysis, to cellular NP uptake could support planning and interpretation of toxicity studies as well as provide guidance for the tailor-design NPs with respect to targeted cellular uptake for various applications. PMID:25747434

  20. Physiological enzymology: The next frontier in understanding protein structure and function at the cellular level.

    PubMed

    Lee, Irene; Berdis, Anthony J

    2016-01-01

    Historically, the study of proteins has relied heavily on characterizing the activity of a single purified protein isolated from other cellular components. This classic approach allowed scientists to unambiguously define the intrinsic kinetic and chemical properties of that protein. The ultimate hope was to extrapolate this information toward understanding how the enzyme or receptor behaves within its native cellular context. These types of detailed in vitro analyses were necessary to reduce the innate complexities of measuring the singular activity and biochemical properties of a specific enzyme without interference from other enzymes and potential competing substrates. However, recent developments in fields encompassing cell biology, molecular imaging, and chemical biology now provide the unique chemical tools and instrumentation to study protein structure, function, and regulation in their native cellular environment. These advancements provide the foundation for a new field, coined physiological enzymology, which quantifies the function and regulation of enzymes and proteins at the cellular level. In this Special Edition, we explore the area of Physiological Enzymology and Protein Function through a series of review articles that focus on the tools and techniques used to measure the cellular activity of proteins inside living cells. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions. PMID:26277093

  1. Electrically induced structure formation and pattern transfer

    NASA Astrophysics Data System (ADS)

    Schäffer, Erik; Thurn-Albrecht, Thomas; Russell, Thomas P.; Steiner, Ullrich

    2000-02-01

    The wavelength of light represents a fundamental technological barrier to the production of increasingly smaller features on integrated circuits. New technologies that allow the replication of patterns on scales less than 100nm need to be developed if increases in computing power are to continue at the present rate. Here we report a simple electrostatic technique that creates and replicates lateral structures in polymer films on a submicrometre length scale. Our method is based on the fact that dielectric media experience a force in an electric field gradient. Strong field gradients can produce forces that overcome the surface tension in thin liquid films, inducing an instability that features a characteristic hexagonal order. In our experiments, pattern formation takes place in polymer films at elevated temperatures, and is fixed by cooling the sample to room temperature. The application of a laterally varying electric field causes the instability to be focused in the direction of the highest electric field. This results in the replication of a topographically structured electrode. We report patterns with lateral dimensions of 140nm, but the extension of the technique to pattern replication on scales smaller than 100nm seems feasible.

  2. Advances in the formation, use and understanding of multi-cellular spheroids

    PubMed Central

    Achilli, Toni-Marie; Meyer, Julia; Morgan, Jeffrey R

    2015-01-01

    Introduction Developing in vitro models for studying cell biology and cell physiology is of great importance to the fields of biotechnology, cancer research, drug discovery, toxicity testing, as well as the emerging fields of tissue engineering and regenerative medicine. Traditional two dimensional (2D) methods of mammalian cell culture have several limitations and it is increasingly recognized that cells grown in a three dimensional (3D) environment more closely represent normal cellular function due to the increased cell-to-cell interactions, and by mimicking the in vivo architecture of natural organs and tissues. Areas Covered In this review, we discuss the methods to form 3D multi-cellular spheroids, the advantages and limitations of these methods, and assays used to characterize the function of spheroids. The use of spheroids has led to many advances in basic cell sciences, including understanding cancer cell interactions, creating models for drug discovery and cancer metastasis, and they are being investigated as basic units for engineering tissue constructs. As so, this review will focus on contributions made to each of these fields using spheroid models. Expert Opinion Multi-cellular spheroids are rich in biological content and mimic better the in vivo environment than 2D cell culture. New technologies to form and analyze spheroids are rapidly increasing their adoption and expanding their applications. PMID:22784238

  3. Diagnosing delayed ettringite formation in concrete structures

    SciTech Connect

    Thomas, Michael Folliard, Kevin Drimalas, Thano Ramlochan, Terry

    2008-06-15

    There has been a number of cases involving deteriorated concrete structures in North America where there has been considerable controversy surrounding the respective contributions of alkali-silica reaction (ASR) and delayed ettringite formation (DEF) to the observed damage. The problem arises because the macroscopic symptoms of distress are not unequivocal and microscopical examinations of field samples often reveal evidence of both processes making it difficult to separate the individual contributions. This paper presents the results of an investigation of a number of concrete columns carrying a raised expressway in North America; prior studies had implicated both DEF and ASR as possible causes of deterioration. Although the columns were not deliberately heat-cured, it is estimated that the peak internal temperature would have exceeded 70 deg. C and perhaps even 80 deg. C, in some cases. The forensic investigation included scanning electron microscopy with energy-dispersive X-ray analysis and expansion testing of cores extracted from the structure. Small-diameter cores stored in limewater expanded significantly (0.3 to 1.3%) and on the basis of supplementary tests on laboratory-produced concrete specimens it was concluded that expansion under such conditions is caused by DEF as the conditions of the test will not sustain ASR. In at least one column, DEF was diagnosed as the sole contributory cause of damage with no evidence of any contribution from ASR or any other deterioration process. In other cases, both ASR and DEF were observed to have contributed to the apparent damage. Of the columns examined, only concrete containing fly ash appeared to be undamaged. The results of this study confirm that, under certain conditions, the process of DEF (acting in isolation of other processes) can result in significant deterioration of cast-in-place reinforced concrete structures.

  4. Linear and nonlinear effects in detonation wave structure formation

    NASA Astrophysics Data System (ADS)

    Borisov, S. P.; Kudryavtsev, A. N.

    2016-06-01

    The role of linear and nonlinear effects in the process of formation of detonation wave structure is investigated using linear stability analysis and direct numerical simulation. A simple model with a one-step irreversible chemical reaction is considered. For linear stability computations, both the local iterative shooting procedure and the global Chebyshev pseudospectral method are employed. Numerical simulations of 1D pulsating instability are performed using a shock fitting approach based on a 5th order upwind-biased compact-difference discretization and a shock acceleration equation deduced from the Rankine-Hugoniot conditions. A shock capturing WENO scheme of the 5th order is used to simulate propagation of detonation wave in a plane channel. It is shown that the linear analysis predicts correctly the mode dominating on early stages of flow evolution and the size of detonation cells which emerge during these stages. Later, however, when a developed self-reproducing cellular structure forms, the cell size is approximately doubled due to nonlinear effects.

  5. Use of Lightweight Cellular Mats to Reduce the Settlement of Structure on Soft Soil

    NASA Astrophysics Data System (ADS)

    Ganasan, R.; Lim, A. J. M. S.; Wijeyesekera, D. C.

    2016-07-01

    Construction of structures on soft soils gives rise to some difficulties in Malaysia and other country especially in settlement both in short and long term. The focus of this research is to minimize the differential and non-uniform settlement on peat soil with the use of an innovative cellular mat. The behaviour and performance of the lightweight geo-material (in block form) is critically investigated and in particular the use as a fill in embankment on soft ground. Hemic peat soil, sponge and innovative cellular mat will be used as the main material in this study. The monitoring in settlement behavior from this part of research will be done as laboratory testing only. The uneven settlement in this problem was uniquely monitored photographically using spot markers. In the end of the research, it is seen that the innovative cellular mat has reduce the excessive and differential settlement up to 50% compare to flexible and rigid foundations. This had improve the stiffness of soils as well as the porous contain in cellular structure which help in allowing water/moisture to flow through in or out thus resulting in prevent the condition of floating.

  6. Ultraviolet background radiation from cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Miniati, Francesco; Ferrara, Andrea; White, Simon D. M.; Bianchi, Simone

    2004-03-01

    We calculate the contribution to the ultraviolet background (UVB) from thermal emission from gas shock heated during cosmic structure formation. Our main calculation is based on an updated version of Press-Schechter theory. It is consistent with a more empirical estimate based on the observed properties of galaxies and the observed cosmic star formation history. Thermal UVB emission is characterized by a hard spectrum extending well beyond 4 Ryd. The bulk of the radiation is produced by objects in the mass range 1011-1013 Msolar, i.e. large galaxies and small groups. We compute a composite UVB spectrum due to quasi-stellar object (QSO), stellar and thermal components. The ratio of the UVB intensities at the H and He Lyman limits increases from 60 at z= 2 to more than 300 at z= 6. A comparison of the resulting photoionization rates to the observed Gunn-Peterson effect at high redshifts constrains the escape fraction of ionizing photons from galaxies to be less than a few per cent. Near 1 Ryd, thermal and stellar emission are comparable, amounting to about 10, 20 and 35 per cent of the total flux at redshifts of 3, 4.5 and higher, respectively. However, near the ionization threshold for He II, the thermal contribution is much stronger. It is comparable to the QSO intensity already at redshift ~3 and dominates at redshifts above 4. Thermal photons alone are enough to produce and sustain He II reionization already at z~ 6. We discuss the possible implications of our results for the thermal history of the intergalactic medium, in particular for He II reionization.

  7. Structure, Affinity, and Availability of Estrogen Receptor Complexes in the Cellular Environment*

    PubMed Central

    Kofoed, Eric M.; Guerbadot, Martin; Schaufele, Fred

    2010-01-01

    An ability to measure the biochemical parameters and structures of protein complexes at defined locations within the cellular environment would improve our understanding of cellular function. We describe widely applicable, calibrated Förster resonance energy transfer methods that quantify structural and biochemical parameters for interaction of the human estrogen receptor α-isoform (ERα) with the receptor interacting domains (RIDs) of three cofactors (SRC1, SRC2, SRC3) in living cells. The interactions of ERα with all three SRC-RIDs, measured throughout the cell nucleus, transitioned from structurally similar, high affinity complexes containing two ERαs at low free SRC-RID concentrations (<2 nm) to lower affinity complexes with an ERα monomer at higher SRC-RID concentrations (∼10 nm). The methods also showed that only a subpopulation of ERα was available to form complexes with the SRC-RIDs in the cell. These methods represent a template for extracting unprecedented details of the biochemistry and structure of any complex that is capable of being measured by Förster resonance energy transfer in the cellular environment. PMID:19926790

  8. Structural control on karst collapse sinkhole formation

    NASA Astrophysics Data System (ADS)

    Santo, Antonio; Ascione, Alessandra; Mazzoli, Stefano; Santangelo, Nicoletta

    2013-04-01

    Collapse sinkholes owing their formation to erosion and deformation phenomena caused by subsurface karstification are widespread in the carbonate massifs of peninsular Italy. In contrast with solution dolines, which are densely distributed on the subplanar top surfaces of the carbonate massifs, the collapse sinkholes (hereinafter labelled karst collapse sinkholes) generally occur as isolated landforms and mostly affect the slopes and piedmont areas. In the latter instances, the sinkholes also affect alluvial fan conglomerates, or slope debris, overlying the carbonate rocks. We investigated the karst collapse sinkholes of the southern-central Apennines mountain belt (Italy), which is representative of a young orogenic system, characterised by recent tectonic activity and strong seismicity. The aim of the study is the identification of the causative factors which control the occurrence of such hazardous phenomena. The study was based on a regional scale analysis on sinkhole distribution in relation to the local geological-structural, geomorphological and hydrogeological contexts, and was paralleled with field analysis of some selected areas. The regional scale analysis indicates that the karst collapse sinkholes are not the mere response to the concurrence of the climatic and lithological conditions which commonly favour the development of karst processes, the occurrence of such landforms appearing strongly influenced by distinctive structural and hydrogeological conditions. In particular, a close relationship between the karst collapse sinkholes and the main extensional faults showing evidence of late Quaternary activity may be envisaged. This is inferred from the spatial distribution of the karst collapse sinkholes, which is strikingly uneven, the sinkholes generally occurring in alignments following large late Quaternary fault zones, or being clustered at the terminations of those faults. In addition, areas affected by the occurrence of groups of sinkholes, are

  9. Nanoparticle-cell interactions: molecular structure of the protein corona and cellular outcomes.

    PubMed

    Fleischer, Candace C; Payne, Christine K

    2014-08-19

    The use of nanoparticles (NPs) in biology and medicine requires a molecular-level understanding of how NPs interact with cells in a physiological environment. A critical difference between well-controlled in vitro experiments and in vivo applications is the presence of a complex mixture of extracellular proteins. It has been established that extracellular serum proteins present in blood will adsorb onto the surface of NPs, forming a "protein corona". Our goal was to understand how this protein layer affected cellular-level events, including NP binding, internalization, and transport. A combination of microscopy, which provides spatial resolution, and spectroscopy, which provides molecular information, is necessary to probe protein-NP-cell interactions. Initial experiments used a model system composed of polystyrene NPs functionalized with either amine or carboxylate groups to provide a cationic or anionic surface, respectively. Serum proteins adsorb onto the surface of both cationic and anionic NPs, forming a net anionic protein-NP complex. Although these protein-NP complexes have similar diameters and effective surface charges, they show the exact opposite behavior in terms of cellular binding. In the presence of bovine serum albumin (BSA), the cellular binding of BSA-NP complexes formed from cationic NPs is enhanced, whereas the cellular binding of BSA-NP complexes formed from anionic NPs is inhibited. These trends are independent of NP diameter or cell type. Similar results were obtained for anionic quantum dots and colloidal gold nanospheres. Using competition assays, we determined that BSA-NP complexes formed from anionic NPs bind to albumin receptors on the cell surface. BSA-NP complexes formed from cationic NPs are redirected to scavenger receptors. The observation that similar NPs with identical protein corona compositions bind to different cellular receptors suggested that a difference in the structure of the adsorbed protein may be responsible for the

  10. Association of p60src with Triton X-100-Resistant Cellular Structure Correlates with Morphological Transformation

    NASA Astrophysics Data System (ADS)

    Hamaguchi, Michinari; Hanafusa, Hidesaburo

    1987-04-01

    More than 70% of wild-type Rous sarcoma virus p60v-src was found to be associated with a cellular structure resistant to nonionic detergent extraction that consists primarily of cytoskeletal proteins. On the other hand, nontransforming src proteins, including cellular p60c-src, nonmyristoylated forms, and those inactive in protein kinase, were found in the fraction solubilized by the detergent extraction. p60c-src was detergent-soluble even in transformed cells, suggesting that the association of p60v-src is not a result of cell transformation. Analyses with a variety of Rous sarcoma virus mutants showed a good correlation between the degree of association with the detergent-resistant structure and the extent of cell transformation caused by mutant src proteins, suggesting that this association may be significant for the process of cell transformation by Rous sarcoma virus.

  11. Role of Viral RNA and Co-opted Cellular ESCRT-I and ESCRT-III Factors in Formation of Tombusvirus Spherules Harboring the Tombusvirus Replicase

    PubMed Central

    Kovalev, Nikolay; de Castro Martín, Isabel Fernández; Pogany, Judit; Barajas, Daniel; Pathak, Kunj; Risco, Cristina

    2016-01-01

    ABSTRACT Plus-stranded RNA viruses induce membrane deformations in infected cells in order to build viral replication complexes (VRCs). Tomato bushy stunt virus (TBSV) co-opts cellular ESCRT (endosomal sorting complexes required for transport) proteins to induce the formation of vesicle (spherule)-like structures in the peroxisomal membrane with tight openings toward the cytosol. In this study, using a yeast (Saccharomyces cerevisiae) vps23Δ bro1Δ double-deletion mutant, we showed that the Vps23p ESCRT-I protein (Tsg101 in mammals) and Bro1p (ALIX) ESCRT-associated protein, both of which bind to the viral p33 replication protein, play partially complementary roles in TBSV replication in cells and in cell extracts. Dual expression of dominant-negative versions of Arabidopsis homologs of Vps23p and Bro1p inhibited tombusvirus replication to greater extent than individual expression in Nicotiana benthamiana leaves. We also demonstrated the critical role of Snf7p (CHMP4), Vps20p, and Vps24p ESCRT-III proteins in tombusvirus replication in yeast and in vitro. Electron microscopic imaging of vps23Δ yeast revealed the lack of tombusvirus-induced spherule-like structures, while crescent-like structures are formed in ESCRT-III deletion yeasts replicating TBSV RNA. In addition, we also showed that the length of the viral RNA affects the sizes of spherules formed in N. benthamiana cells. The 4.8-kb genomic RNA is needed for the formation of spherules 66 nm in diameter, while spherules formed during the replication of the ∼600-nucleotide (nt)-long defective interfering RNA in the presence of p33 and p92 replication proteins are 42 nm. We propose that the viral RNA serves as a “measuring string” during VRC assembly and spherule formation. IMPORTANCE Plant positive-strand RNA viruses, similarly to animal positive-strand RNA viruses, replicate in membrane-bound viral replicase complexes in the cytoplasm of infected cells. Identification of cellular and viral factors

  12. Dysfunctional telomeres induce p53-dependent and independent apoptosis to compromise cellular proliferation and inhibit tumor formation.

    PubMed

    Wang, Yang; Wang, Xinwei; Flores, Elsa R; Yu, Jian; Chang, Sandy

    2016-08-01

    Aging is associated with progressive telomere shortening, resulting in the formation of dysfunctional telomeres that compromise tissue proliferation. However, dysfunctional telomeres can limit tumorigenesis by activating p53-dependent cellular senescence and apoptosis. While activation of both senescence and apoptosis is required for repress tumor formation, it is not clear which pathway is the major tumor suppressive pathway in vivo. In this study, we generated Eμ-myc; Pot1b(∆/∆) mouse to directly compare tumor formation under conditions in which either p53-dependent apoptosis or senescence is activated by telomeres devoid of the shelterin component Pot1b. We found that activation of p53-dependent apoptosis plays a more critical role in suppressing lymphoma formation than p53-dependent senescence. In addition, we found that telomeres in Pot1b(∆/∆) ; p53(-/-) mice activate an ATR-Chk1-dependent DNA damage response to initiate a robust p53-independent, p73-dependent apoptotic pathway that limited stem cell proliferation but suppressed B-cell lymphomagenesis. Our results demonstrate that in mouse models, both p53-dependent and p53-independent apoptosis are important to suppressing tumor formation. PMID:27113195

  13. Heterozygous inactivation of the Nf1 gene in myeloid cells enhances neointima formation via a rosuvastatin-sensitive cellular pathway.

    PubMed

    Stansfield, Brian K; Bessler, Waylan K; Mali, Raghuveer; Mund, Julie A; Downing, Brandon; Li, Fang; Sarchet, Kara N; DiStasi, Matthew R; Conway, Simon J; Kapur, Reuben; Ingram, David A

    2013-03-01

    Mutations in the NF1 tumor suppressor gene cause Neurofibromatosis type 1 (NF1). Neurofibromin, the protein product of NF1, functions as a negative regulator of Ras activity. Some NF1 patients develop cardiovascular disease, which represents an underrecognized disease complication and contributes to excess morbidity and mortality. Specifically, NF1 patients develop arterial occlusion resulting in tissue ischemia and sudden death. Murine studies demonstrate that heterozygous inactivation of Nf1 (Nf1(+/-)) in bone marrow cells enhances neointima formation following arterial injury. Macrophages infiltrate Nf1(+/-) neointimas, and NF1 patients have increased circulating inflammatory monocytes in their peripheral blood. Therefore, we tested the hypothesis that heterozygous inactivation of Nf1 in myeloid cells is sufficient for neointima formation. Specific ablation of a single copy of the Nf1 gene in myeloid cells alone mobilizes a discrete pro-inflammatory murine monocyte population via a cell autonomous and gene-dosage dependent mechanism. Furthermore, lineage-restricted heterozygous inactivation of Nf1 in myeloid cells is sufficient to reproduce the enhanced neointima formation observed in Nf1(+/-) mice when compared with wild-type controls, and homozygous inactivation of Nf1 in myeloid cells amplified the degree of arterial stenosis after arterial injury. Treatment of Nf1(+/-) mice with rosuvastatin, a stain with anti-inflammatory properties, significantly reduced neointima formation when compared with control. These studies identify neurofibromin-deficient myeloid cells as critical cellular effectors of Nf1(+/-) neointima formation and propose a potential therapeutic for NF1 cardiovascular disease. PMID:23197650

  14. Simulation Based Optimization of Complex Monolithic Composite Structures Using Cellular Core Technology

    NASA Astrophysics Data System (ADS)

    Hickmott, Curtis W.

    Cellular core tooling is a new technology which has the capability to manufacture complex integrated monolithic composite structures. This novel tooling method utilizes thermoplastic cellular cores as inner tooling. The semi-rigid nature of the cellular cores makes them convenient for lay-up, and under autoclave temperature and pressure they soften and expand providing uniform compaction on all surfaces including internal features such as ribs and spar tubes. This process has the capability of developing fully optimized aerospace structures by reducing or eliminating assembly using fasteners or bonded joints. The technology is studied in the context of evaluating its capabilities, advantages, and limitations in developing high quality structures. The complex nature of these parts has led to development of a model using the Finite Element Analysis (FEA) software Abaqus and the plug-in COMPRO Common Component Architecture (CCA) provided by Convergent Manufacturing Technologies. This model utilizes a "virtual autoclave" technique to simulate temperature profiles, resin flow paths, and ultimately deformation from residual stress. A model has been developed simulating the temperature profile during curing of composite parts made with the cellular core technology. While modeling of composites has been performed in the past, this project will look to take this existing knowledge and apply it to this new manufacturing method capable of building more complex parts and develop a model designed specifically for building large, complex components with a high degree of accuracy. The model development has been carried out in conjunction with experimental validation. A double box beam structure was chosen for analysis to determine the effects of the technology on internal ribs and joints. Double box beams were manufactured and sectioned into T-joints for characterization. Mechanical behavior of T-joints was performed using the T-joint pull-off test and compared to traditional

  15. Coxsackievirus B3-Induced Cellular Protrusions: Structural Characteristics and Functional Competence▿†

    PubMed Central

    Paloheimo, Outi; Ihalainen, Teemu O.; Tauriainen, Sisko; Välilehto, Outi; Kirjavainen, Sanna; Niskanen, Einari A.; Laakkonen, Johanna P.; Hyöty, Heikki; Vihinen-Ranta, Maija

    2011-01-01

    Virus-induced alterations in cell morphology play important roles in the viral life cycle. To examine the intracellular events of coxsackievirus B3 (CVB3) infection, green monkey kidney (GMK) cells were either inoculated with the virus or transfected with the viral RNA. Various microscopic and flow cytometric approaches demonstrated the emergence of CVB3 capsid proteins at 8 h posttransfection, followed by morphological transformation of the cells. The morphological changes included formation of membranous protrusions containing viral capsids, together with microtubules and actin. Translocation of viral capsids into these protrusions was sensitive to cytochalasin D, suggesting the importance of actin in the process. Three-dimensional (3D) live-cell imaging demonstrated frequent contacts between cellular protrusions and adjacent cells. Markedly, in spite of an increase in the cellular viral protein content starting 8 h postinfection, no significant decrease in cell viability or increase in the amount of early apoptotic markers was observed by flow cytometry by 28 h postinfection. Comicroinjection of viral RNA and fluorescent dextran in the presence of neutralizing virus antibody suggested that these protrusions mediated the spread of infection from one cell to another prior to virus-induced cell lysis. Altogether, the CVB3-induced cellular protrusions could function as a hitherto-unknown nonlytic mechanism of cell-to-cell transmission exploited by enteroviruses. PMID:21525342

  16. Cellular origin and developmental mechanisms during the formation of skin melanocytes

    SciTech Connect

    Ernfors, Patrik

    2010-05-01

    Melanocytes are derived from the neural crest (NC), which are transient multipotent cells arising by delamination from the developing dorsal neural tube. During recent years, signaling systems and molecular mechanisms of melanocyte development have been studied in detail, but the exact diversification of the NC into melanocytes and how they migrate, expand and disperse in the skin have not been fully understood. The recent finding that Schwann cell precursors (SCPs) of the growing nerve represents a stem cell niche from which various cell types, including Schwann cells, endoneural fibroblasts and melanocytes arise has exposed new knowledge on the cellular basis for melanocyte development. This opens for the identification of new factors and reinterpretation of old data on cell fate instructive, proliferative, survival and cell homing factors participating in melanocyte development.

  17. Cellular Trafficking of Phospholamban and Formation of Functional Sarcoplasmic Reticulum During Myocyte DIfferentiation

    SciTech Connect

    Stenoien, David L.; Knyushko, Tatyana V.; Londono, Monica P.; Opresko, Lee; Mayer, M. Uljana; Brady, Scott T.; Squier, Thomas C.; Bigelow, Diana J.

    2007-06-01

    The sarco/endoplasmic reticulum Ca-ATPase (SERCA) family members are transmembrane proteins that play an essential role in regulating intracellular calcium levels. Phospholamban (PLB), a 52 amino acid phosphoprotein, regulates SERCA activity in adult heart and skeletal muscle. Using the C2C12 myocyte cell line, we find endogenous PLB constitutively expressed in both myoblasts and myotubes, whereas SERCA expression coincides with activation of the differentiation program. PLB has a punctuate distribution in myoblasts changing to a reticular distribution in myotubes where it colocalizes with SERCAs. To examine the distribution and dynamics of PLB and SERCA, we expressed fluorescent fusion proteins (GFP, CFP, and YFP) of PLB and SERCA in myoblasts. Coexpressed PLB and SERCA localize to distinct cellular compartments in myoblasts but begin to colocalize as cells differentiate. Fluorescence Recovery After Photobleaching (FRAP) studies show different recovery patterns for each protein in myoblasts confirming their localization to distinct compartments. To extend these studies, we created stable cell lines expressing O6-alkylguanine-DNA alkyltransferase (AGT) fusions with PLB or SERCA to track their localization as myocytes differentiate. These experiments demonstrate that PLB localizes to punctate vesicles in myoblasts and adopts a reticular distribution that coincides with SERCA distribution after differentiation. Colocalization experiments indicate that a subset of PLB in myoblasts colocalizes with endosomes, Golgi, and the plasma membrane however PLB also localizes to other, as yet unidentified vesicles. Our results indicate that differentiation plays a critical role in regulating PLB distribution to ensure its colocalization within the same cellular compartment as SERCA in differentiated cells. The presence and altered distribution of PLB in undifferentiated myoblasts raises the possibility that this protein has additional functions distinct from SERCA regulation.

  18. 2D-CELL: image processing software for extraction and analysis of 2-dimensional cellular structures

    NASA Astrophysics Data System (ADS)

    Righetti, F.; Telley, H.; Leibling, Th. M.; Mocellin, A.

    1992-01-01

    2D-CELL is a software package for the processing and analyzing of photographic images of cellular structures in a largely interactive way. Starting from a binary digitized image, the programs extract the line network (skeleton) of the structure and determine the graph representation that best models it. Provision is made for manually correcting defects such as incorrect node positions or dangling bonds. Then a suitable algorithm retrieves polygonal contours which define individual cells — local boundary curvatures are neglected for simplicity. Using elementary analytical geometry relations, a range of metric and topological parameters describing the population are then computed, organized into statistical distributions and graphically displayed.

  19. Structure Formation of Block Copolymer Membranes

    NASA Astrophysics Data System (ADS)

    Abetz, Volker

    2013-03-01

    Isoporous membranes have received increasing attention during the last couple of years. The advantage of these materials is to give access to membranes with a very high number density of pores with controlled diameters, thus leading to ultrafiltration membranes with a very high permeability, and simultaneously also with a very high selectivity in terms of size exclusion. Different approaches have been reported, which typically involve the transfer of a thin block copolymer film from a solid to a porous support, eventually followed by an edging step. An alternative strategy is to form integral asymmetric membranes, where the thin top layer is continuously changing into a spongy support layer, thus avoiding the build-up of mechanical stresses. This happens by subjecting the cast polymer solution film into a precipitant, inducing the so-called phase inversion by exchange of solvent with the non-solvent. Here it is important to have a system where solvent and nonsolvent are fully miscible. This strategy also enables the direct formation of open pores without a subsequent edging step, if the solvents and nonsolvents are appropriately chosen. Different types of amphiphilic block copolymers based on styrene, 2- or 4-vinyl pyridine, and ethylene oxide with various compositions and molecular weights will be discussed. These block copolymers were dissolved at different concentrations in various solvent mixtures, and then cast on a non-woven support, which was either pretreated with a liquid, or not. Varying the time before the cast solution was subjected to phase inversion, as well as choosing the temperature of the precipitation bath, are further parameters having strong influence on the obtained membrane film structure. Membranes with pore forming blocks showing pH or temperature sensitive behaviour can be reversibly switched from an open state to a closed state. The size of the pores can be controlled by both molecular weight and composition of the block copolymers.

  20. Investigating lipid interactions and the process of raft formation in cellular membranes using ToF-SIMS

    NASA Astrophysics Data System (ADS)

    McQuaw, Carolyn M.; Sostarecz, Audra G.; Zheng, Leiliang; Ewing, Andrew G.; Winograd, Nicholas

    2006-07-01

    There is an increased interest in how lipids interact with each other, especially in the lateral separation of lipids into coexisting liquid phases as this is believed to be an attribute of raft formation in cell membranes. ToF-SIMS has shown itself to be an excellent tool for investigating cellular and model membrane systems and will be perhaps the most powerful one for investigating raft formation. Results from our laboratory show the capability of ToF-SIMS at identifying unequivocally the content of coexisting liquid lipid phases. Using supported lipid monolayers we find that the inclusion of dipalmitoylphosphatidylethanolamine (DPPE) to a homogeneous dipalmitoyl-phosphatidylcholine (DPPC)/cholesterol phase results in the formation of cholesterol-rich domains [A.G. Sostarecz, C.M. McQuaw, A.G. Ewing, N. Winograd, J. Am. Chem. Soc. 126 (2004) 13882]. Also, for DPPE/cholesterol systems a single homogeneous DPPE/cholesterol phase is formed at ˜50 mol% cholesterol, whereas DPPC/cholesterol systems form a single phase at 30 mol% cholesterol [C.M. McQuaw, A. Sostarecz, L. Zheng, A.G. Ewing, N. Winograd, Langmuir 21 (2005) 807]. Currently we are exploring the incorporation of sphingomyelin into phospholipid-cholesterol mixtures in an effort to gain a better understanding of its role in raft formation.

  1. Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes.

    PubMed Central

    Dougherty, W G; Semler, B L

    1993-01-01

    Many viruses express their genome, or part of their genome, initially as a polyprotein precursor that undergoes proteolytic processing. Molecular genetic analyses of viral gene expression have revealed that many of these processing events are mediated by virus-encoded proteinases. Biochemical activity studies and structural analyses of these viral enzymes reveal that they have remarkable similarities to cellular proteinases. However, the viral proteinases have evolved unique features that permit them to function in a cellular environment. In this article, the current status of plant and animal virus proteinases is described along with their role in the viral replication cycle. The reactions catalyzed by viral proteinases are not simple enzyme-substrate interactions; rather, the processing steps are highly regulated, are coordinated with other viral processes, and frequently involve the participation of other factors. Images PMID:8302216

  2. Nonlinear structure formation in flat cosmological models

    NASA Technical Reports Server (NTRS)

    Martel, Hugo

    1995-01-01

    This paper describes the formation of nonlinear structure in flat (zero curvature) Friedmann cosmological models. We consider models with two components: the usual nonrelativistic component that evolves under gravity and eventually forms the large-scale structure of the universe, and a uniform dark matter component that does not clump under gravity, and whose energy density varies with the scale factor a(t) like a(t)(sup -n), where n is a free parameter. Each model is characterized by two parameters: the exponent n and the present density parameter Omega(sub 0) of the nonrelativistic component. The linear perturbation equations are derived and solved for these models, for the three different cases n = 3, n is greater than 3, and n is less than 3. The case n = 3 is relevant to model with massive neutrinos. The presence of the uniform component strongly reduces the growth of the perturbation compared with the Einstein-de Sitter model. We show that the Meszaros effect (suppression of growth at high redshift) holds not only for n = 4, radiation-dominated models, but for all models with n is greater than 3. This essentially rules out any such model. For the case n is less than 3, we numerically integrate the perturbation equations from the big bang to the present, for 620 different models with various values of Omega(sub 0) and n. Using these solutions, we show that the function f(Omega(sub 0), n) = (a/delta(sub +))d(delta)(sub +)/da, which enters in the relationship between the present density contrast delta(sub 0) and peculiar velocity field u(sub 0) is essentially independent of n. We derive approximate solutions for the second-order perturbation equations. These second-order solutions are tested against the exact solutions and the Zel'dovich approximation for spherically symmetric perturbations in the marginally nonlinear regime (the absolute value of delta is less than or approximately 1). The second-order and Zel'dovich solutions have comparable accuracy

  3. Structural Analysis of Dusty Plasma Formations Based on Spatial Spectra

    SciTech Connect

    Khakhaev, A. D.; Luizova, L. A.; Piskunov, A. A.; Podryadchikov, S. F.; Soloviev, A. V.

    2008-09-07

    Some advantages of studying the structure of dusty plasma formations using spatial spectra are illustrated by simulated experiments and by processing actual images of dusty structures in dc glow discharge in inert and molecular gases.

  4. Heterozygous inactivation of the Nf1 gene in myeloid cells enhances neointima formation via a rosuvastatin-sensitive cellular pathway

    PubMed Central

    Stansfield, Brian K.; Bessler, Waylan K.; Mali, Raghuveer; Mund, Julie A.; Downing, Brandon; Li, Fang; Sarchet, Kara N.; DiStasi, Matthew R.; Conway, Simon J.; Kapur, Reuben; Ingram, David A.

    2013-01-01

    Mutations in the NF1 tumor suppressor gene cause Neurofibromatosis type 1 (NF1). Neurofibromin, the protein product of NF1, functions as a negative regulator of Ras activity. Some NF1 patients develop cardiovascular disease, which represents an underrecognized disease complication and contributes to excess morbidity and mortality. Specifically, NF1 patients develop arterial occlusion resulting in tissue ischemia and sudden death. Murine studies demonstrate that heterozygous inactivation of Nf1 (Nf1+/−) in bone marrow cells enhances neointima formation following arterial injury. Macrophages infiltrate Nf1+/− neointimas, and NF1 patients have increased circulating inflammatory monocytes in their peripheral blood. Therefore, we tested the hypothesis that heterozygous inactivation of Nf1 in myeloid cells is sufficient for neointima formation. Specific ablation of a single copy of the Nf1 gene in myeloid cells alone mobilizes a discrete pro-inflammatory murine monocyte population via a cell autonomous and gene-dosage dependent mechanism. Furthermore, lineage-restricted heterozygous inactivation of Nf1 in myeloid cells is sufficient to reproduce the enhanced neointima formation observed in Nf1+/− mice when compared with wild-type controls, and homozygous inactivation of Nf1 in myeloid cells amplified the degree of arterial stenosis after arterial injury. Treatment of Nf1+/− mice with rosuvastatin, a stain with anti-inflammatory properties, significantly reduced neointima formation when compared with control. These studies identify neurofibromin-deficient myeloid cells as critical cellular effectors of Nf1+/− neointima formation and propose a potential therapeutic for NF1 cardiovascular disease. PMID:23197650

  5. The reversal phase of the bone-remodeling cycle: cellular prerequisites for coupling resorption and formation

    PubMed Central

    Delaisse, Jean-Marie

    2014-01-01

    The reversal phase couples bone resorption to bone formation by generating an osteogenic environment at remodeling sites. The coupling mechanism remains poorly understood, despite the identification of a number of ‘coupling' osteogenic molecules. A possible reason is the poor attention for the cells leading to osteogenesis during the reversal phase. This review aims at creating awareness of these cells and their activities in adult cancellous bone. It relates cell events (i) on the bone surface, (ii) in the mesenchymal envelope surrounding the bone marrow and appearing as a canopy above remodeling surfaces and (iii) in the bone marrow itself within a 50-μm distance of this canopy. When bone remodeling is initiated, osteoprogenitors at these three different levels are activated, likely as a result of a rearrangement of cell–cell and cell–matrix interactions. Notably, canopies are brought under the osteogenic influence of capillaries and osteoclasts, whereas bone surface cells become exposed to the eroded matrix and other osteoclast products. In several diverse pathophysiological situations, including osteoporosis, a decreased availability of osteoprogenitors from these local reservoirs coincides with decreased osteoblast recruitment and impaired initiation of bone formation, that is, uncoupling. Overall, this review stresses that coupling does not only depend on molecules able to activate osteogenesis, but that it also demands the presence of osteoprogenitors and ordered cell rearrangements at the remodeling site. It points to protection of local osteoprogenitors as a critical strategy to prevent bone loss. PMID:25120911

  6. Visualizing Escherichia coli sub-cellular structure using sparse deconvolution Spatial Light Interference Tomography.

    PubMed

    Mir, Mustafa; Babacan, S Derin; Bednarz, Michael; Do, Minh N; Golding, Ido; Popescu, Gabriel

    2012-01-01

    Studying the 3D sub-cellular structure of living cells is essential to our understanding of biological function. However, tomographic imaging of live cells is challenging mainly because they are transparent, i.e., weakly scattering structures. Therefore, this type of imaging has been implemented largely using fluorescence techniques. While confocal fluorescence imaging is a common approach to achieve sectioning, it requires fluorescence probes that are often harmful to the living specimen. On the other hand, by using the intrinsic contrast of the structures it is possible to study living cells in a non-invasive manner. One method that provides high-resolution quantitative information about nanoscale structures is a broadband interferometric technique known as Spatial Light Interference Microscopy (SLIM). In addition to rendering quantitative phase information, when combined with a high numerical aperture objective, SLIM also provides excellent depth sectioning capabilities. However, like in all linear optical systems, SLIM's resolution is limited by diffraction. Here we present a novel 3D field deconvolution algorithm that exploits the sparsity of phase images and renders images with resolution beyond the diffraction limit. We employ this label-free method, called deconvolution Spatial Light Interference Tomography (dSLIT), to visualize coiled sub-cellular structures in E. coli cells which are most likely the cytoskeletal MreB protein and the division site regulating MinCDE proteins. Previously these structures have only been observed using specialized strains and plasmids and fluorescence techniques. Our results indicate that dSLIT can be employed to study such structures in a practical and non-invasive manner. PMID:22761910

  7. Dielectric properties modelling of cellular structures with PDMS for micro-sensor applications

    NASA Astrophysics Data System (ADS)

    Kachroudi, Achraf; Basrour, Skandar; Rufer, Libor; Sylvestre, Alain; Jomni, Fathi

    2015-12-01

    Electro-active polymers are emerging in the fields of actuators and micro-sensors because their good dielectric and mechanical properties makes them suitable for such applications. In this work, we focus on micro-structured (cellular) polymer materials (referred as piezoelectrets or ferroelectrets) that need prior charging to attain piezoelectric behaviour. The development of such applications requires an in-depth knowledge of the intrinsic dielectric properties of such structures and models to enable the accurate prediction of a given micro-structured material’s dielectric properties. Various polymers including polypropylene, polytetrafluoroethylene, fluoroethylenepropylene, cyclo-olefines and poly(ethylene terephthalate) in a cellular form have been studied by researchers over the last fifteen years. However, there is still a lack of information on the intrinsic dielectric properties of the most recently used dielectric polymer (polydimethylsiloxane, PDMS) over wide frequency and temperature ranges. In this work, we shall propose an exhaustive equivalent electrical circuit model and explain how it can be used to predict the micro-structured PDMS complex permittivity versus frequency and temperature. The results obtained from the model were found to be in good agreement with experimental data for various micro-structured PDMS materials. Typically, for micro-sensor applications, the dielectric constant and dielectric losses are key factors which need to be minimized. We have developed a configuration which enables both to be strongly reduced with a reduction of 16% in the dielectric constant of a micro-structured PDMS compared with the bulk material. In addition, the phenomena responsible for dielectric losses variations with frequency and temperature are discussed and correlated with the theoretical model. Our model is thus proved to be a powerful tool for the control of the dielectric properties of micro-structured PDMS material for micro-sensor applications.

  8. Simple and Flexible Self-Reproducing Structures in Asynchronous Cellular Automata and Their Dynamics

    NASA Astrophysics Data System (ADS)

    Huang, Xin; Lee, Jia; Yang, Rui-Long; Zhu, Qing-Sheng

    2013-03-01

    Self-reproduction on asynchronous cellular automata (ACAs) has attracted wide attention due to the evident artifacts induced by synchronous updating. Asynchronous updating, which allows cells to undergo transitions independently at random times, might be more compatible with the natural processes occurring at micro-scale, but the dark side of the coin is the increment in the complexity of an ACA in order to accomplish stable self-reproduction. This paper proposes a novel model of self-timed cellular automata (STCAs), a special type of ACAs, where unsheathed loops are able to duplicate themselves reliably in parallel. The removal of sheath cannot only allow various loops with more flexible and compact structures to replicate themselves, but also reduce the number of cell states of the STCA as compared to the previous model adopting sheathed loops [Y. Takada, T. Isokawa, F. Peper and N. Matsui, Physica D227, 26 (2007)]. The lack of sheath, on the other hand, often tends to cause much more complicated interactions among loops, when all of them struggle independently to stretch out their constructing arms at the same time. In particular, such intense collisions may even cause the emergence of a mess of twisted constructing arms in the cellular space. By using a simple and natural method, our self-reproducing loops (SRLs) are able to retract their arms successively, thereby disentangling from the mess successfully.

  9. [Construction and structural analysis of integrated cellular network of Corynebacterium glutamicum].

    PubMed

    Jiang, Jinguo; Song, Lifu; Zheng, Ping; Jia, Shiru; Sun, Jibin

    2012-05-01

    Corynebacterium glutamicum is one of the most important traditional industrial microorganisms and receiving more and more attention towards a novel cellular factory due to the recently rapid development in genomics and genetic operation toolboxes for Corynebacterium. However, compared to other model organisms such as Escherichia coli, there were few studies on its metabolic regulation, especially a genome-scale integrated cellular network model currently missing for Corynebacterium, which hindered the systematic study of Corynebacterium glutamicum and large-scale rational design and optimization for strains. Here, by gathering relevant information from a number of public databases, we successfully constructed an integrated cellular network, which was composed of 1384 reactions, 1276 metabolites, 88 transcriptional factors and 999 pairs of transcriptional regulatory relationships. The transcriptional regulatory sub-network could be arranged into five layers and the metabolic sub-network presented a clear bow-tie structure. We proposed a new method to extract complex metabolic and regulatory sub-network for product-orientated study taking lysine biosynthesis as an example. The metabolic and regulatory sub-network extracted by our method was more close to the real functional network than the simplex biochemical pathways. The results would be greatly helpful for understanding the high-yielding biomechanism for amino acids and the re-design of the industrial strains. PMID:22916496

  10. A Computationally Efficient Modeling Approach for Predicting Mechanical Behavior of Cellular Lattice Structures

    NASA Astrophysics Data System (ADS)

    Karamooz Ravari, M. R.; Kadkhodaei, M.

    2015-01-01

    As the fabrication and characterization of cellular lattice structures are time consuming and expensive, development of simple models is vital. In this paper, a new approach is presented to model the mechanical stress-strain curve of cellular lattices with low computational efforts. To do so, first, a single strut of the lattice is modeled with its imperfections and defects. The stress-strain of a specimen fabricated with the same processing parameters as those used for the lattice is used as the base material. Then, this strut is simulated in simple tension, and its stress-strain curve is obtained. After that, a unit cell of the lattice is simulated without any imperfections, and the material parameters of the single strut are attributed to the bulk material. Using this method, the stress-strain behavior of the lattice is obtained and shown to be in a good agreement with the experimental result. Accordingly, this paper presents a computationally efficient method for modeling the mechanical properties of cellular lattices with a reasonable accuracy using the material parameters of simple tension tests. The effects of the single strut's length and its micropores on its mechanical properties are also assessed.

  11. Fluorescent protein-based cellular assays analyzed by laser-scanning microplate cytometry in 1536-well plate format.

    PubMed

    Auld, Douglas S; Johnson, Ronald L; Zhang, Ya-qin; Veith, Henrike; Jadhav, Ajit; Yasgar, Adam; Simeonov, Anton; Zheng, Wei; Martinez, Elisabeth D; Westwick, John K; Austin, Christopher P; Inglese, James

    2006-01-01

    Microtiter plate readers have evolved from photomultiplier and charged-coupled device-based readers, where a population-averaged signal is detected from each well, to microscope-based imaging systems, where cellular characteristics from individual cells are measured. For these systems, speed and ease of data analysis are inversely proportional to the amount of data collected from each well. Microplate laser cytometry is a technology compatible with a 1536-well plate format and capable of population distribution analysis. Microplate cytometers such as the Acumen Explorer can monitor up to four fluorescent signals from single objects in microtiter plates with densities as high as 1536 wells. These instruments can measure changes in fluorescent protein expression, cell shape, or simple cellular redistribution events such as cytoplasmic to nuclear translocation. To develop high-throughput screening applications using laser-scanning microplate cytometry, we used green fluorescent protein- and yellow fluorescent protein-expressing cell lines designed to measure diverse biological functions such as nuclear translocation, epigenetic signaling, and G protein-coupled receptor activation. This chapter illustrates the application of microplate laser cytometry to these assays in a manner that is suitable for screening large compound collections in high throughput. PMID:17110211

  12. Vanadium pentoxide-coated ultrafine titanium dioxide particles induce cellular damage and micronucleus formation in V79 cells.

    PubMed

    Bhattacharya, K; Cramer, H; Albrecht, C; Schins, R; Rahman, Q; Zimmermann, U; Dopp, E

    2008-01-01

    Surface-treated titanium dioxide (TiO(2)) particles coated with vanadium pentoxide (V(2)O(5)) are used industrially for selective catalytic reactions such as the removal of nitrous oxide from exhaust gases of combustion power plants (SCR process) and in biomaterials for increasing the strength of implants. In the present study, untreated ultrafine TiO(2) particles (anatase, diameter: 30-50 nm) and vanadium pentoxide (V(2)O(5))-treated anatase particles were tested for their cyto- and genotoxic effects in V79 cells (hamster lung fibroblasts). Cytotoxic effects of the particles were assessed by trypan blue exclusion, while genotoxic effects were investigated by micronucleus (MN) assay. In addition, the generation of reactive oxygen species (ROS) was determined by the acellular method of electron spin resonance technique (ESR) and by the cellular technique of determination of thiobarbituric acid-reactive substances (TBARS). Our results demonstrate that V(2)O(5)-treated TiO(2) particles induce more potent cyto- and genotoxic effects than untreated particles. Further, acellular and cellular radical formation was more pronounced with V(2)O(5)-anatase than untreated anatase. Thus, data indicate that V(2)O(5)-treated TiO(2) particles were more reactive than natural anatase and capable of inducing DNA damage in mammalian cells through production of free radicals. PMID:18569605

  13. The group A streptococcal collagen-like protein 1, Scl1, mediates biofilm formation by targeting the EDA-containing variant of cellular fibronectin expressed in wounded tissue

    PubMed Central

    Oliver-Kozup, Heaven; Martin, Karen H.; Schwegler-Berry, Diane; Green, Brett J.; Betts, Courtney; Shinde, Arti V.; Van De Water, Livingston; Lukomski, Slawomir

    2012-01-01

    Summary Wounds are known to serve as portals of entry for group A Streptococcus (GAS). Subsequent tissue colonization is mediated by interactions between GAS surface proteins and host extracellular matrix components. We recently reported that the streptococcal collagen-like protein-1, Scl1, selectively binds the cellular form of fibronectin (cFn) and also contributes to GAS biofilm formation on abiotic surfaces. One structural feature of cFn, which is predominantly expressed in response to tissue injury, is the presence of a spliced variant containing extra domain A (EDA/EIIIA). We now report that GAS biofilm formation is mediated by the Scl1 interaction with EDA-containing cFn. Recombinant Scl1 proteins that bound cFn also bound recombinant EDA within the C-C′ loop region recognized by the α9β1 integrin. The extracellular 2-D matrix derived from human dermal fibroblasts supports GAS adherence and biofilm formation. Altogether, this work identifies and characterizes a novel molecular mechanism by which GAS utilizes Scl1 to specifically target an extracellular matrix component that is predominantly expressed at the site of injury in order to secure host tissue colonization. PMID:23217101

  14. Extra- and intra-cellular ice formation in Stage I and II Xenopus laevis oocytes.

    PubMed

    Guenther, James F; Seki, Shinsuke; Kleinhans, F W; Edashige, Keisuke; Roberts, Daniel M; Mazur, Peter

    2006-06-01

    We are currently investigating factors that influence intracellular ice formation (IIF) in mouse oocytes and oocytes of the frog Xenopus. A major reason for choosing these two species is that while their eggs normally do not possess aquaporin channels in their plasma membranes, these channels can be made to express. We wish to see whether IIF is affected by the presence of these channels. The present Xenopus study deals with control eggs not expressing aquaporins. The main factor studied has been the effect of a cryoprotective agent [ethylene glycol (EG) or glycerol] and its concentration. The general procedure was to (a) cool the oocytes on a cryostage to slightly below the temperatures at which extracellular ice formation occurs, (b) warm them to just below the melting point, and (c) then re-cool them to -50 degrees C at 10 degrees C/min. In the majority of cases, IIF occurs well into step (c), but a sizeable minority undergo IIF in steps (a) or (b). The former group we refer to as low-temperature flashers; the latter as high-temperature flashers. IIF is manifested as abrupt blackening of the egg, which we refer to as "flashing." Observations on the Linkam cryostage are restricted to Stage I and II oocytes, which have diameters of 200 300 microm. In the absence of a cryoprotective agent, that is in frog Ringers, the mean flash temperature for the low-temperature freezers is -11.4 degrees C, although a sizeable percentage flash at temperatures much closer to that of the EIF (-3.9 degrees C). When EG is present, the flash temperature for the low-temperatures freezers drops significantly to approximately -20 degrees C for EG concentrations ranging from 0.5 to 1.5 M. The presence of 1.5 M glycerol also substantially reduces the IIF temperature of the low-temperature freezers; namely, to -29 degrees C, but 0.5 and 1 M glycerol exert little or no effect. The IIF temperatures observed using the Linkam cryostage agree well with those estimated by calorimetry [F

  15. Structure and formation of ant transportation networks

    PubMed Central

    Latty, Tanya; Ramsch, Kai; Ito, Kentaro; Nakagaki, Toshiyuki; Sumpter, David J. T.; Middendorf, Martin; Beekman, Madeleine

    2011-01-01

    Many biological systems use extensive networks for the transport of resources and information. Ants are no exception. How do biological systems achieve efficient transportation networks in the absence of centralized control and without global knowledge of the environment? Here, we address this question by studying the formation and properties of inter-nest transportation networks in the Argentine ant (Linepithema humile). We find that the formation of inter-nest networks depends on the number of ants involved in the construction process. When the number of ants is sufficient and networks do form, they tend to have short total length but a low level of robustness. These networks are topologically similar to either minimum spanning trees or Steiner networks. The process of network formation involves an initial construction of multiple links followed by a pruning process that reduces the number of trails. Our study thus illuminates the conditions under and the process by which minimal biological transport networks can be constructed. PMID:21288958

  16. NMDA-R inhibition affects cellular process formation in Tilapia melanocytes; a model for pigmented adrenergic neurons in process formation and retraction.

    PubMed

    Ogundele, Olalekan Michael; Okunnuga, Adetokunbo Adedotun; Fabiyi, Temitope Deborah; Olajide, Olayemi Joseph; Akinrinade, Ibukun Dorcas; Adeniyi, Philip Adeyemi; Ojo, Abiodun Ayodele

    2014-06-01

    Parkinson's disease has long been described to be a product of dopamine and (or) melanin loss in the substanstia nigra (SN). Although most studies have focused on dopaminergic neurons, it is important to consider the role of pigment cells in the etiology of the disease and to create an in vitro live cell model for studies involving pigmented adrenergic cells of the SN in Parkinsonism. The Melanocytes share specific features with the pigmented adrenergic neurons as both cells are pigmented, contain adrenergic receptors and have cellular processes. Although the melanocyte cellular processes are relatively short and observable only when stimulated appropriately by epinephrine and other factors or molecules. This study employs the manipulation of N-Methyl-D-Aspartate Receptor (NMDA-R), a major receptor in neuronal development, in the process formation pattern of the melanocyte in order to create a suitable model to depict cellular process elongation and shortening in pigmented adrenergic cells. NMDA-R is an important glutamate receptor implicated in neurogenesis, neuronal migration, maturation and cell death, thus we investigated the role of NMDA-R potentiation by glutamate/KCN and its inhibition by ketamine in the behavior of fish scale melanocytes in vitro. This is aimed at establishing the regulatory role of NMDA-R in this cell type (melanocytes isolated form Tilapia) in a similar manner to what is observable in the mammalian neurons. In vitro live cell culture was prepared in modified Ringer's solution following which the cells were treated as follows; Control, Glutamate, Ketamine, Glutamate + Ketamine, KCN + Ketamine and KCN. The culture was maintained for 10 min and the changes were captured in 3D-Time frame at 0, 5 and 10 min for the control and 5, 7 and 10 min for each of the treatment category. Glutamate treatment caused formation of short cellular processes localized directly on the cell body while ketamine treatment (inhibition of NMDA-R) facilitated

  17. On the effects of geometry, defects, and material asymmetry on the mechanical response of shape memory alloy cellular lattice structures

    NASA Astrophysics Data System (ADS)

    Karamooz Ravari, M. R.; Nasr Esfahani, S.; Taheri Andani, M.; Kadkhodaei, M.; Ghaei, A.; Karaca, H.; Elahinia, M.

    2016-02-01

    Shape memory alloy (such as NiTi) cellular lattice structures are a new class of advanced materials with many potential applications. The cost of fabrication of these structures however is high. It is therefore necessary to develop modeling methods to predict the functional behavior of these alloys before fabrication. The main aim of the present study is to assess the effects of geometry, microstructural imperfections and material asymmetric response of dense shape memory alloys on the mechanical response of cellular structures. To this end, several cellular and dense NiTi samples are fabricated using a selective laser melting process. Both cellular and dense specimens were tested in compression in order to obtain their stress-strain response. For modeling purposes, a three -dimensional (3D) constitutive model based on microplane theory which is able to describe the material asymmetry was employed. Five finite element models based on unit cell and multi-cell methods were generated to predict the mechanical response of cellular lattices. The results show the considerable effects of the microstructural imperfections on the mechanical response of the cellular lattice structures. The asymmetric material response of the bulk material also affects the mechanical response of the corresponding cellular structure.

  18. Formation and structure of neutrino astronomical objects

    NASA Astrophysics Data System (ADS)

    Lu, Tan; Luo, Liao-fu; Yang, Gou-chen

    1981-12-01

    Neutrinos with non-zero mass could gather to form a new kind of astronomical bodies: the Neutrino Astronomical Objects (NAO). We have investigated the mechanism of their formation and the relation of this formation to that of the galaxies, ascertained their e, p, He 4 content, whose presence should produce a series of observable effects. NAOs are a peculiar kind of heavenly bodies with many new properties. They have a linear size of the order of 100 pc, a total neutrino content of the order of 10 14M⊙ and an e, p, He 4 content of the order of 10 9M⊙.

  19. Turbulence effects on cellular burning structures in lean premixed hydrogen flames

    SciTech Connect

    Day, Marc; Bell, John; Beckner, Vince; Lijewski, Michael; Bremer, Peer-Timo; Pascucci, Valerio

    2009-05-15

    We present numerical simulations of lean hydrogen flames interacting with turbulence. The simulations are performed in an idealized setting using an adaptive low Mach number model with a numerical feedback control algorithm to stabilize the flame. At the conditions considered here, hydrogen flames are thermodiffusively unstable, and burn in cellular structures. For that reason, we consider two levels of turbulence intensity and a case without turbulence whose dynamics is driven by the natural flame instability. An overview of the flame structure shows that the burning in the cellular structures is quite intense, with the burning patches separated by regions in which the flame is effectively extinguished. We explore the geometry of the flame surface in detail, quantifying the mean and Gaussian curvature distributions and the distribution of the cell sizes. We next characterize the local flame speed to quantify the effect of flame intensification on local propagation speed. We then introduce several diagnostics aimed at quantifying both the level of intensification and diffusive mechanisms that lead to the intensification. (author)

  20. The formation, function and regulation of amyloids: insights from structural biology.

    PubMed

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. PMID:27237473

  1. Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

    SciTech Connect

    Sievers, Stuart A.; Karanicolas, John; Chang, Howard W.; Zhao, Anni; Jiang, Lin; Zirafi, Onofrio; Stevens, Jason T.; Münch, Jan; Baker, David; Eisenberg, David

    2011-09-20

    Many globular and natively disordered proteins can convert into amyloid fibrils. These fibrils are associated with numerous pathologies as well as with normal cellular functions, and frequently form during protein denaturation. Inhibitors of pathological amyloid fibril formation could be useful in the development of therapeutics, provided that the inhibitors were specific enough to avoid interfering with normal processes. Here we show that computer-aided, structure-based design can yield highly specific peptide inhibitors of amyloid formation. Using known atomic structures of segments of amyloid fibrils as templates, we have designed and characterized an all-D-amino-acid inhibitor of the fibril formation of the tau protein associated with Alzheimer's disease, and a non-natural L-amino-acid inhibitor of an amyloid fibril that enhances sexual transmission of human immunodeficiency virus. Our results indicate that peptides from structure-based designs can disrupt the fibril formation of full-length proteins, including those, such as tau protein, that lack fully ordered native structures. Because the inhibiting peptides have been designed on structures of dual-{beta}-sheet 'steric zippers', the successful inhibition of amyloid fibril formation strengthens the hypothesis that amyloid spines contain steric zippers.

  2. Structural basis of lentiviral subversion of a cellular protein degradation pathway

    NASA Astrophysics Data System (ADS)

    Schwefel, David; Groom, Harriet C. T.; Boucherit, Virginie C.; Christodoulou, Evangelos; Walker, Philip A.; Stoye, Jonathan P.; Bishop, Kate N.; Taylor, Ian A.

    2014-01-01

    Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits human immunodeficiency virus (HIV)-1 infection of myeloid-lineage cells as well as resting CD4+ T cells by reducing the cellular deoxynucleoside 5'-triphosphate (dNTP) concentration to a level at which the viral reverse transcriptase cannot function. In other lentiviruses, including HIV-2 and related simian immunodeficiency viruses (SIVs), SAMHD1 restriction is overcome by the action of viral accessory protein x (Vpx) or the related viral protein r (Vpr) that target and recruit SAMHD1 for proteasomal degradation. The molecular mechanism by which these viral proteins are able to usurp the host cell's ubiquitination machinery to destroy the cell's protection against these viruses has not been defined. Here we present the crystal structure of a ternary complex of Vpx with the human E3 ligase substrate adaptor DCAF1 and the carboxy-terminal region of human SAMHD1. Vpx is made up of a three-helical bundle stabilized by a zinc finger motif, and wraps tightly around the disc-shaped DCAF1 molecule to present a new molecular surface. This adapted surface is then able to recruit SAMHD1 via its C terminus, making it a competent substrate for the E3 ligase to mark for proteasomal degradation. The structure reported here provides a molecular description of how a lentiviral accessory protein is able to subvert the cell's normal protein degradation pathway to inactivate the cellular viral defence system.

  3. Structural basis of lentiviral subversion of a cellular protein degradation pathway

    PubMed Central

    Schwefel, David; Groom, Harriet C. T.; Boucherit, Virginie C.; Christodoulou, Evangelos; Walker, Philip A.; Stoye, Jonathan P.; Bishop, Kate N.; Taylor, Ian A.

    2013-01-01

    Lentiviruses contain accessory genes that have evolved to counteract the effects of host cellular defence proteins that inhibit productive infection. One such restriction factor, SAMHD1, inhibits HIV-1 infection of myeloid-lineage cells 1,2 as well as resting CD4+ T cells 3,4 by reducing the cellular dNTP concentration to a level where the viral reverse transcriptase cannot function 5,6. In other lentiviruses, including HIV-2 and related SIVs, SAMHD1 restriction is overcome by the action of viral accessory protein x (Vpx) or the related viral protein r (Vpr) that target and recruit SAMHD1 for proteasomal degradation 7,8. The molecular mechanism by which these viral proteins are able to usurp the host cell’s ubiquitination machinery to destroy the cell’s protection against these viruses has not been defined. We present here the crystal structure of a ternary complex of Vpx with the host cell’s E3 ligase substrate adaptor DCAF1 and the C-terminal region of SAMHD1. Vpx is made up of a three-helical bundle, stabilised by a zinc finger motif and wraps tightly around the disc-shaped DCAF1 molecule to present a new molecular surface. This adapted surface is then able to recruit SAMHD1 via its C-terminus making it a competent substrate for the E3 ligase to mark for proteasomal degradation. The structure provides the first description of how a lentiviral accessory protein is able to subvert the cell’s normal protein degradation pathway to inactivate the cellular viral defence system. PMID:24336198

  4. Multilayer structure formation via homophily and homeostasis

    NASA Astrophysics Data System (ADS)

    Makarov, Vladimir V.; Koronovskii, Alexey A.; Maksimenko, Vladimir A.; Khramova, Marina V.; Hramov, Alexander E.; Pavlov, Alexey N.; Moskalenko, Olga I.; Buldú, Javier M.; Boccaletti, Stefano

    2016-03-01

    The competition of homophily and homeostasis mechanisms taking place in the multilayer network where several layers of connection topologies are simultaneously present as well as the interaction between layers is considered. We have shown that the competition of homophily and homeostasis leads in such networks to the formation of synchronous patterns within the different layers of the network, which may be both the distinct and identical.

  5. Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2)

    SciTech Connect

    McDonough,M.; Li, V.; Flashman, E.; Chowdhury, R.; Mohr, C.; Lienard, B.; Zondlo, J.; Oldham, N.; Clifton, I.; et al.

    2006-01-01

    Cellular and physiological responses to changes in dioxygen levels in metazoans are mediated via the posttranslational oxidation of hypoxia-inducible transcription factor (HIF). Hydroxylation of conserved prolyl residues in the HIF-{alpha} subunit, catalyzed by HIF prolyl-hydroxylases (PHDs), signals for its proteasomal degradation. The requirement of the PHDs for dioxygen links changes in dioxygen levels with the transcriptional regulation of the gene array that enables the cellular response to chronic hypoxia; the PHDs thus act as an oxygen-sensing component of the HIF system, and their inhibition mimics the hypoxic response. We describe crystal structures of the catalytic domain of human PHD2, an important prolyl-4-hydroxylase in the human hypoxic response in normal cells, in complex with Fe(II) and an inhibitor to 1.7 Angstroms resolution. PHD2 crystallizes as a homotrimer and contains a double-stranded {beta}-helix core fold common to the Fe(II) and 2-oxoglutarate-dependant dioxygenase family, the residues of which are well conserved in the three human PHD enzymes (PHD 1-3). The structure provides insights into the hypoxic response, helps to rationalize a clinically observed mutation leading to familial erythrocytosis, and will aid in the design of PHD selective inhibitors for the treatment of anemia and ischemic disease.

  6. TRPV1 mediates cellular uptake of anandamide and thus promotes endothelial cell proliferation and network-formation

    PubMed Central

    Hofmann, Nicole A.; Barth, Sonja; Waldeck-Weiermair, Markus; Klec, Christiane; Strunk, Dirk; Malli, Roland; Graier, Wolfgang F.

    2014-01-01

    ABSTRACT Anandamide (N-arachidonyl ethanolamide, AEA) is an endogenous cannabinoid that is involved in various pathological conditions, including cardiovascular diseases and tumor-angiogenesis. Herein, we tested the involvement of classical cannabinoid receptors (CBRs) and the Ca2+-channel transient receptor potential vanilloid 1 (TRPV1) on cellular AEA uptake and its effect on endothelial cell proliferation and network-formation. Uptake of the fluorescence-labeled anandamide (SKM4-45-1) was monitored in human endothelial colony-forming cells (ECFCs) and a human endothelial-vein cell line (EA.hy926). Involvement of the receptors during AEA translocation was determined by selective pharmacological inhibition (AM251, SR144528, CID16020046, SB366791) and molecular interference by TRPV1-selective siRNA-mediated knock-down and TRPV1 overexpression. We show that exclusively TRPV1 contributes essentially to AEA transport into endothelial cells in a Ca2+-independent manner. This TRPV1 function is a prerequisite for AEA-induced endothelial cell proliferation and network-formation. Our findings point to a so far unknown moonlighting function of TRPV1 as Ca2+-independent contributor/regulator of AEA uptake. We propose TRPV1 as representing a promising target for development of pharmacological therapies against AEA-triggered endothelial cell functions, including their stimulatory effect on tumor-angiogenesis. PMID:25395667

  7. The extracellular matrix of Volvox carteri: molecular structure of the cellular compartment.

    PubMed

    Ertl, H; Mengele, R; Wenzl, S; Engel, J; Sumper, M

    1989-12-01

    The extracellular matrix (ECM) of Volvox contains insoluble fibrous layers that surround individual cells at a distance to form contiguous cellular compartments. Using immunological techniques, we identified a sulfated surface glycoprotein (SSG 185) as the monomeric precursor of this substructure within the ECM. The primary structure of the SSG 185 poly-peptide chain has been derived from cDNA and genomic DNA. A central domain of the protein, 80 amino acid residues long, consists almost exclusively of hydroxyproline residues. The chemical structure of the highly sulfated polysaccharide covalently attached to SSG 185 has been determined by permethylation analysis. As revealed by EM, SSG 185 is a rod-shaped molecule with a 21-nm-long polysaccharide strand protruding from its central region. The chemical nature of the cross-links between SSG 185 monomers is discussed. PMID:2689458

  8. Structure and biochemical characterization of proliferating cellular nuclear antigen from a parasitic protozoon

    SciTech Connect

    Cardona-Felix, Cesar S.; Lara-Gonzalez, Samuel; Brieba, Luis G.

    2012-02-08

    Proliferating cellular nuclear antigen (PCNA) is a toroidal-shaped protein that is involved in cell-cycle control, DNA replication and DNA repair. Parasitic protozoa are early-diverged eukaryotes that are responsible for neglected diseases. In this work, a PCNA from a parasitic protozoon was identified, cloned and biochemically characterized and its crystal structure was determined. Structural and biochemical studies demonstrate that PCNA from Entamoeba histolytica assembles as a homotrimer that is able to interact with and stimulate the activity of a PCNA-interacting peptide-motif protein from E. histolytica, EhDNAligI. The data indicate a conservation of the biochemical mechanisms of PCNA-mediated interactions between metazoa, yeast and parasitic protozoa.

  9. Topometry optimization of sheet metal structures for crashworthiness design using hybrid cellular automata

    NASA Astrophysics Data System (ADS)

    Mozumder, Chandan K.

    The objective in crashworthiness design is to generate plastically deformable energy absorbing structures which can satisfy the prescribed force-displacement (FD) response. The FD behavior determines the reaction force, displacement and the internal energy that the structure should withstand. However, attempts to include this requirement in structural optimization problems remain scarce. The existing commercial optimization tools utilize models under static loading conditions because of the complexities associated with dynamic/impact loading. Due to the complexity of a crash event and the consequent time required to numerically analyze the dynamic response of the structure, classical methods (i.e., gradient-based and direct) are not well developed to solve this undertaking. This work presents an approach under the framework of the hybrid cellular automaton (HCA) method to solve the above challenge. The HCA method has been successfully applied to nonlinear transient topology optimization for crashworthiness design. In this work, the HCA algorithm has been utilized to develop an efficient methodology for synthesizing shell-based sheet metal structures with optimal material thickness distribution under a dynamic loading event using topometry optimization. This method utilizes the cellular automata (CA) computing paradigm and nonlinear transient finite element analysis (FEA) via ls-dyna. In this method, a set field variables is driven to their target states by changing a convenient set of design variables (e.g., thickness). These rules operate locally in cells within a lattice that only know local conditions. The field variables associated with the cells are driven to a setpoint to obtain the desired structure. This methodology is used to design for structures with controlled energy absorption with specified buckling zones. The peak reaction force and the maximum displacement are also constrained to meet the desired safety level according to passenger safety

  10. Structural-mechanical model of wax crystal networks—a mesoscale cellular solid approach

    NASA Astrophysics Data System (ADS)

    Miyazaki, Yukihiro; Marangoni, Alejandro G.

    2014-04-01

    Mineral waxes are widely used materials in industrial applications; however, the relationship between structure and mechanical properties is poorly understood. In this work, mineral wax-oil networks were characterized as closed-cell cellular solids, and differences in their mechanical response predicted from structural data. The systems studied included straight-chain paraffin wax (SW)-oil mixtures and polyethylene wax (PW)-oil mixtures. Analysis of cryogenic-SEM images of wax-oil networks allowed for the determination of the length (l) and thickness (t) of the wax cell walls as a function of wax mass fraction (Φ). A linear relationship between t/l and Φ (t/l ˜ Φ 0.89) suggested that wax-oil networks were cellular solids of the closed-cell type. However, the scaling behavior of the elastic modulus with the volume fraction of solids did not agree with theoretical predictions, yielding the same scaling exponent, μ = 0.84, for both waxes. This scaling exponent obtained from mechanical measurements could be predicted from the scaling behavior of the effective wax cell size as a function of wax mass fraction in oil obtained by cryogenic scanning electron microscopy. Microscopy studies allowed us to propose that wax-oil networks are structured as an ensemble of close-packed spherical cells filled with oil, and that it is the links between cells that yield under simple uniaxial compression. Thus, the Young’s moduli for the links between cells in SW and PW wax systems could be estimated as E L (SW) = 2.76 × 109 Pa and E L (PW) = 1.64 × 109 Pa, respectively. The structural parameter responsible for the observed differences in the mechanical strength between the two wax-oil systems is the size of the cells. Polyethylene wax has much smaller cell sizes than the straight chain wax and thus displays a higher Young’s modulus and yield stress.

  11. Structural and functional characterization of recombinant human cellular retinaldehyde-binding protein.

    PubMed Central

    Crabb, J. W.; Carlson, A.; Chen, Y.; Goldflam, S.; Intres, R.; West, K. A.; Hulmes, J. D.; Kapron, J. T.; Luck, L. A.; Horwitz, J.; Bok, D.

    1998-01-01

    Cellular retinaldehyde-binding protein (CRALBP) is abundant in the retinal pigment epithelium (RPE) and Müller cells of the retina where it is thought to function in retinoid metabolism and visual pigment regeneration. The protein carries 11-cis-retinal and/or 11-cis-retinol as endogenous ligands in the RPE and retina and mutations in human CRALBP that destroy retinoid binding functionality have been linked to autosomal recessive retinitis pigmentosa. CRALBP is also present in brain without endogenous retinoids, suggesting other ligands and physiological roles exist for the protein. Human recombinant cellular retinaldehyde-binding protein (rCRALBP) has been over expressed as non-fusion and fusion proteins in Escherichia coli from pET3a and pET19b vectors, respectively. The recombinant proteins typically constitute 15-20% of the soluble bacterial lysate protein and after purification, yield about 3-8 mg per liter of bacterial culture. Liquid chromatography electrospray mass spectrometry, amino acid analysis, and Edman degradation were used to demonstrate that rCRALBP exhibits the correct primary structure and mass. Circular dichroism, retinoid HPLC, UV-visible absorption spectroscopy, and solution state 19F-NMR were used to characterize the secondary structure and retinoid binding properties of rCRALBP. Human rCRALBP appears virtually identical to bovine retinal CRALBP in terms of secondary structure, thermal stability, and stereoselective retinoid-binding properties. Ligand-dependent conformational changes appear to influence a newly detected difference in the bathochromic shift exhibited by bovine and human CRALBP when complexed with 9-cis-retinal. These recombinant preparations provide valid models for human CRALBP structure-function studies. PMID:9541407

  12. Formation of the structure of gold nanoclusters during crystallization

    SciTech Connect

    Gafner, Yu. Ya. Goloven'ko, Zh. V.; Gafner, S. L.

    2013-02-15

    The structure formation in gold nanoparticles 1.6-5.0 nm in diameter is studied by molecular dynamics simulation using a tight-binding potential. The simulation shows that the initial fcc phase in small Au clusters transforms into other structural modifications as temperature changes. As the cluster size increases, the transition temperature shifts toward the melting temperature of the cluster. The effect of various crystallization conditions on the formation of the internal structure of gold nanoclusters is studied in terms of microcanonical and canonical ensembles. The stability boundaries of various crystalline isomers are analyzed. The obtained dependences are compared with the corresponding data obtained for copper and nickel nanoparticles. The structure formation during crystallization is found to be characterized by a clear effect of the particle size on the stability of a certain isomer modification. Nickel and copper clusters are shown to exhibit common features in the formation of their structural properties, whereas gold clusters demonstrate much more complex behavior.

  13. Pattern formation in a growing bacterial colony facilitated by extra-cellular polymeric substances

    NASA Astrophysics Data System (ADS)

    Ghosh, Pushpita; Mondal, Jagannath; Ben-Jacob, Eshel; Levine, Herbert

    2015-03-01

    Self-organization in bacterial colony is quite pervasive and diverse phenomena. Bacteria are known to self-organize into multicellular communities, commonly known as biofilms, in which microbial cells live in close association with a solid surface and are embedded in a self-produced extracellular polymeric substances(EPS). In such dense systems mechanical interactions among the structural components can be expected to significantly contribute to the morphological properties. By a simple particle-based simulation model of nonmotile rod-shaped bacterial cells and EPS secreted in a growing colony, we investigate how the combined mechanical effects can give rise naturally spatial heterogeneity observed in a biofilm. In our individual-based simulation model all the components interact mechanically via repulsive forces by pushing each other away as bacterial cells grow and divide consuming diffusing nutrient and produce EPS. We show that mechanical interactions control the collective behavior of the system, particularly, we show that the presence of non-adsorbing EPS leads spontaneous aggregation of bacterial cells by depletion attraction and generates phase separated patterns in a nonequilibrium growing colony.

  14. Increase of Piezoelectric Constant and Thermal Durability of Polypropylene Electret by Introducing SiO2 and Kaolin Filler and Creating a Cellular Structure

    NASA Astrophysics Data System (ADS)

    Klimiec, E.; Królikowski, B.; Machnik, M.; Zaraska, W.; Dzwonkowski, J.

    2015-07-01

    This article presents a method for preparing and testing the piezoelectric properties and stability of cellular electret based on polypropylene (PP). Introducing 5% mineral filler as a mixture of crystalline silica, colloidal silica, and kaolin to isotactic polypropylene followed by a film stretching process resulted in the formation of a composite cellular structure. To manufacture electrets, the films were polarized at a constant electric field in the range from 100 V/ μm to 125 V/ μm, in a climatic chamber heated up to 80°C. The durability of the electrets was determined using thermostimulated discharge currents and approximate calculations of depolarization process activation energy. For electrets made of cellular films, the depolarization temperature T m at which the density of the discharge current assumes the highest value was ˜108°C and the activation energy was 6.25 eV. The response of the polarized composite film to mechanical stress expressed as the piezoelectric constant d 33 was about 3 times higher than for a-PP film of the prevailing atactic phase and poly(vinylidene fluoride) film without a cellular structure. In the range of stress of 1 kPa to 120 kPa it was 135 pC/N for lower stresses and 60 pC/N for higher stresses.

  15. Granular gel support-enabled extrusion of three-dimensional alginate and cellular structures.

    PubMed

    Jin, Yifei; Compaan, Ashley; Bhattacharjee, Tapomoy; Huang, Yong

    2016-06-01

    Freeform fabrication of soft structures has been of great interest in recent years. In particular, it is viewed as a critical step toward the grand vision of organ printing--the on-demand design and fabrication of three-dimensional (3D) human organ constructs for implantation and regenerative medicine. The objective of this study is to develop a novel granular gel support material-enabled, two-step gelation-based 'printing-then-gelation' approach to fabricate 3D alginate structures using filament extrusion. Specifically, a granular Carbopol microgel bath holds the ungelled alginate structure being extruded, avoiding the instantaneous gelation of each printed layer as well as resultant surface tension-induced nozzle clogging. Since Carbopol microgels react with multivalent cations, which are needed for alginate crosslinking, gelatin is introduced as a sacrificial material to make an alginate and gelatin bioink for extrusion, which gels thermally (step-one gelation) to initially stabilize the printed structure for removal from Carbopol. Then gelatin is melted and diffused away while alginate is ionically crosslinked in a 37 °C calcium chloride bath (step-two gelation), resulting in an alginate structure. The proposed 'printing-then-gelation' approach works for alginate structure fabrication, and it is also applicable for the printing of cellular constructs and other similar homogeneous soft structures using a two-step or even multi-step approach. The main conclusions are: (1) 0.8% (w/v) Carbopol bath with a neutral pH value may be most suitable for soft structure printing; (2) it is most effective to use a 0.9% (w/v) NaCl solution to facilitate the removal of residual Carbopol; and (3) alginate structures fabricated using the proposed approach demonstrate better mechanical properties than those fabricated using the conventional 'gelation-while-printing' approach. PMID:27257095

  16. PACS—Realization of an adaptive concept using pressure actuated cellular structures

    NASA Astrophysics Data System (ADS)

    Gramüller, B.; Boblenz, J.; Hühne, C.

    2014-10-01

    A biologically inspired concept is investigated which can be utilized to develop energy efficient, lightweight and applicational flexible adaptive structures. Building a real life morphing unit is an ambitious task as the numerous works in the particular field show. Summarizing fundamental demands and barriers regarding shape changing structures, the basic challenges of designing morphing structures are listed. The concept of Pressure Actuated Cellular Structures (PACS) is arranged within the recent morphing activities and it is shown that it complies with the underlying demands. Systematically divided into energy-related and structural subcomponents the working principle is illuminated and relationships between basic design parameters are expressed. The analytical background describing the physical mechanisms of PACS is presented in concentrated manner. This work focuses on the procedure of dimensioning, realizing and experimental testing of a single cell and a single row cantilever made of PACS. The experimental outcomes as well as the results from the FEM computations are used for evaluating the analytical methods. The functionality of the basic principle is thus validated and open issues are determined pointing the way ahead.

  17. Powder Removal from Ti-6Al-4V Cellular Structures Fabricated via Electron Beam Melting

    NASA Astrophysics Data System (ADS)

    Hasib, Hazman; Harrysson, Ola L. A.; West, Harvey A.

    2015-03-01

    Direct metal fabrication systems like electron beam melting (EBM) and direct metal laser sintering (also called selective laser melting) are gaining popularity. One reason is the design and fabrication freedom that these technologies offer over traditional processes. One specific feature that is of interest is mesh or lattice structures that can be produced using these powder-bed systems. One issue with the EBM process is that the powder trapped within the structure during the fabrication process is sintered and can be hard to remove as the mesh density increases. This is usually not an issue for the laser-based systems since most of them work at a low temperature and the sintering of the powder is less of an issue. Within the scope of this project, a chemical etching process was evaluated for sintered powder removal using three different cellular structures with varying mesh densities. All meshes were fabricated via EBM using Ti6Al4V powder. The results are promising, but the larger the structures, the more difficult it is to completely remove the sintered powder without affecting the integrity of the mesh structure.

  18. Formation and structure of misfit dislocations

    NASA Astrophysics Data System (ADS)

    Nandedkar, A. S.; Srinivasan, G. R.; Murthy, C. S.

    1991-03-01

    We report here theoretical observations of the evolution of core structure of well-defined misfit dislocations arising from the spontaneous decomposition of highly strained coherent interfaces in a fcc bicrystal. We use a finely stepped energy-minimization technique and Lennard-Jones pair potential, which allowed Burgers-circuit construction and core-structure analysis. Simulations were made for (111) and (001) interfaces, which produced 60° and edge dislocations, respectively. The atomic configurations produced were consistent with those expected from the elasticity theory.

  19. Formation of bulk refractive index structures

    DOEpatents

    Potter, Jr., Barrett George; Potter, Kelly Simmons; Wheeler, David R.; Jamison, Gregory M.

    2003-07-15

    A method of making a stacked three-dimensional refractive index structure in photosensitive materials using photo-patterning where first determined is the wavelength at which a photosensitive material film exhibits a change in refractive index upon exposure to optical radiation, a portion of the surfaces of the photosensitive material film is optically irradiated, the film is marked to produce a registry mark. Multiple films are produced and aligned using the registry marks to form a stacked three-dimensional refractive index structure.

  20. Structure and Mechanism of a Pentameric Formate Channel

    SciTech Connect

    Waight, A.; Love, J; Wang, D

    2010-01-01

    Formate transport across the inner membrane is a critical step in anaerobic bacterial respiration. Members of the formate/nitrite transport protein family function to shuttle substrate across the cytoplasmic membrane. In bacterial pathogens, the nitrite transport protein is involved in protecting bacteria from peroxynitrite released by host macrophages. We have determined the 2.13-{angstrom} structure of the formate channel FocA from Vibrio cholerae, which reveals a pentamer in which each monomer possesses its own substrate translocation pore. Unexpectedly, the fold of the FocA monomer resembles that found in water and glycerol channels. The selectivity filter in FocA consists of a cytoplasmic slit and a central constriction ring. A 2.5-{angstrom} high-formate structure shows two formate ions bound to the cytoplasmic slit via both hydrogen bonding and van der Waals interactions, providing a structural basis for the substrate selectivity of the channel.

  1. G-triplex structure and formation propensity

    PubMed Central

    Cerofolini, Linda; Amato, Jussara; Giachetti, Andrea; Limongelli, Vittorio; Novellino, Ettore; Parrinello, Michele; Fragai, Marco; Randazzo, Antonio; Luchinat, Claudio

    2014-01-01

    The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3′ end TBA-truncated 11-mer oligonucleotide (11-mer-3′-t-TBA). Here we present the solution structure of 11-mer-3′-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3′-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3′-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3′ and the 5′ ends show that only the 11-mer-3′-t-TBA yields a relatively stable G-triplex. PMID:25378342

  2. The Novel Plant Protein INAPERTURATE POLLEN1 Marks Distinct Cellular Domains and Controls Formation of Apertures in the Arabidopsis Pollen Exine[C][W

    PubMed Central

    Dobritsa, Anna A.; Coerper, Daniel

    2012-01-01

    Pollen grains protect the sperm cells inside them with the help of the unique cell wall, the exine, which exhibits enormous morphological variation across plant taxa, assembling into intricate and diverse species-specific patterns. How this complex extracellular structure is faithfully deposited at precise sites and acquires precise shape within a species is not understood. Here, we describe the isolation and characterization of the novel Arabidopsis thaliana gene INAPERTURATE POLLEN1 (INP1), which is specifically involved in formation of the pollen surface apertures, which arise by restriction of exine deposition at specific sites. Loss of INP1 leads to the loss of all three apertures in Arabidopsis pollen, and INP1 protein exhibits a unique tripartite localization in developing pollen, indicative of its direct involvement in specification of aperture positions. We also show that aperture length appears to be sensitive to INP1 dosage and INP1 misexpression can affect global exine patterning. Phenotypes of some inp1 mutants indicate that Arabidopsis apertures are initiated at three nonrandom positions around the pollen equator. The identification of INP1 opens up new avenues for studies of how formation of distinct cellular domains results in the production of different extracellular morphologies. PMID:23136373

  3. Selective formation of turbulent structures in magnetized cylindrical plasmas

    SciTech Connect

    Kasuya, Naohiro; Itoh, Kimitaka; Yagi, Masatoshi; Itoh, Sanae-I

    2008-05-15

    The mechanism of nonlinear structural formation has been studied with a three-field reduced fluid model, which is extended to describe the resistive drift wave turbulence in magnetized cylindrical plasmas. In this model, ion-neutral collisions strongly stabilize the resistive drift wave, and the formed structure depends on the collision frequency. If the collision frequency is small, modulational coupling of unstable modes generates a zonal flow. On the other hand, if the collision frequency is large, a streamer, which is a localized vortex in the azimuthal direction, is formed. The structure is generated by nonlinear wave coupling and is sustained for a much longer duration than the drift wave oscillation period. This is a minimal model for analyzing the turbulent structural formation mechanism by mode coupling in cylindrical plasmas, and the competitive nature of structural formation is revealed. These turbulent structures affect particle transport.

  4. A study on the cellular structure during stress solicitation induced by BioMEMS.

    PubMed

    Fior, Raffaella; Maggiolino, Stefano; Codan, Barbara; Lazzarino, Marco; Sbaizero, Orfeo

    2011-01-01

    The investigation of single cells is a topic in continuous evolution. The complexity of the cellular matrix, the huge variety of cells, the interaction of one cell with the other are all factors that must be taken into consideration in the study of the cellular structure and mechanics. In this project, we developed different types of bioMEMS for cell's stretching, both transparent devices based on silicon nitride and non-transparent silicon based. While the use of silicon devices is limited to reflection microscopes, transparent bioMEMS can be used with transmission and reflection microscopes but can also be easily coupled with other tools such as patch clamp analyzers or atomic force microscope. This improvement will open brand new possibilities in the biological investigation field. We used these two BioMEMS to stretch a single cell in a controlled way and, as a first investigation, we focused on its morphology. We noticed that during a controlled stretch, cells react to the applied deformation. A hysteretic behavior on the ratio between area and perimeter has been highlighted. PMID:22254838

  5. Physical principles of genomic regulation through cellular nanoscale structure and implications for initiation of carcinogenesis

    NASA Astrophysics Data System (ADS)

    Backman, Vadim

    2011-03-01

    Although compelling evidence suggests that cellular nanoarchitecture and nanoscale environment where molecular interactions take place would be expected to significantly affect macromolecular processes, biological ramifications of cellular nanoscale organization have been largely unexplored. This understanding has been hampered in part by the diffraction limited resolution of optical microscopy. The talk will discuss a novel optical microscopy technique, partial wave spectroscopic (PWS) microscopy, that is capable of quantifying statistical properties of cell structure at the nanoscale. Animal and human studies demonstrated that an alteration in the statistical properties of the nanoscale mass density distribution in the cell nucleus (e.g. nuclear nanoarchitecture) is one of the earliest and ubiquitous events in carcinogenesis and precedes any other known morphological changes at larger length scales (e.g. microarchitecture). The talk will also discuss the physical principles of how the alteration in nuclear nanoarchitecture may modulate genomic processes and, in particular, gene transcription. Work done in collaboration with Hariharan Subramanian, Prabhakar Pradhan, Dhwanil Damania, Lusik Cherkezyan, Yolanda Stypula, Jun Soo Kim, Igal Szleifer, Northwestern University, Evanston, IL, Hemant K. Roy, Northshore University HealthSystems, Evanston, IL

  6. Development of High-Pressure Structural and Cellular Biophysics at Miami University

    NASA Astrophysics Data System (ADS)

    Urayama, Paul

    2004-04-01

    Pressures found in the biosphere (up to 1200 atm) have large effects on enzyme specificity and activity, molecular associations, protein folding, viral infectivity, and cellular morphology. The importance of pressure in pharmaceuticals, medical, and biomaterials sciences is beginning to be appreciated. Enzyme reactions under high pressure or in supercritical fluids may be promising in the synthesis of pharmaceuticals. High pressure processing of biopolymer networks may be important in producing matrices for biomaterials applications. In medicine, herpes, immunodeficiency viruses, and certain prion proteins are inactivated by pressure, which may be useful in the ex vivo treatment of blood. Even physiologically generated pressures, such as during colon peristalsis, have biological effects, for example, on the adhesion properties of epithelial cells in colon cancer. This presentation describes a new high-pressure structural and cellular biophysics laboratory under development at Miami University. Applications of specific methods, including high-pressure time-resolved fluorescence spectroscopy; high-pressure fluorescence microscopy; and high-pressure x-ray macromolecular crystallography will be discussed.

  7. Adolescent Identity Formation and the Organizational Structure of High Schools.

    ERIC Educational Resources Information Center

    Schmiedeck, Raoul A.

    1979-01-01

    The author describes aspects of the size and organizational structure of high schools which reduce human contact and have a negative influence on the sense of community, the development of relationships, and the formation of personal identity. (Author/SJL)

  8. Structure formation of thermally driven turbulence

    NASA Astrophysics Data System (ADS)

    Kawazura, Yohei; Yoshida, Zensho

    2013-10-01

    Self-organized structures in plasma turbulence, such as zonal flow and streamer, play important roles in terms of confinement in fusion devices. Recently thermodynamical approaches to dictate self-organization are proposed. Yoshida and Mahajan explained the bifurcation to ``High confinement mode'' in magnetically confined fusion device by using thermodynamic model. The nonexact term available to generate vorticity in equation of motion is baroclinicity (T∇S). Assuming circulation of the fluid element as cycle of heat engine, fluid mechanics and thermodynamic laws can be connected. In this study, by solving the fluid equation of motion as specific mechanical process, we investigate the connection between thermal driving of turbulence and self-organization of vortical structures. Grant-in-Aid for JSPS Fellows 241010.

  9. Ultrastructural features of the differentiating thyroid primordium in the sand lizard (Lacerta agilis L.) from the differentiation of the cellular cords to the formation of the follicular lumen.

    PubMed

    Rupik, Weronika; Kowalska, Magdalena; Swadźba, Elwira; Maślak, Robert

    2016-04-01

    The differentiation of the thyroid primordium of lacertilian species is poorly understood. The present study reports on the ultrastructural analysis of the developing thyroid primordium in the sand lizard (Lacerta agilis) during the early stages of differentiation. The early thyroid primordium of sand lizard embryos was composed of cellular cords that contained single cells with a giant lipid droplet, which were eliminated by specific autophagy (lipophagy). The follicular lumens at the periphery of the primordium differentiated even before the division of the cellular cords. When the single cells within the cords started to die through paraptosis, the adjacent cells started to polarise and junctional complexes began to form around them. After polarisation and clearing up after the formation of the lumens, the cellular cords divided into definitive follicles. The cellular cords in the central part of the primordium started to differentiate later than those at the periphery. The cellular cords divided into presumptive follicles first and only later differentiated into definitive follicles. During this process, a population of centrally located cells was removed through apoptosis to form the lumen. Although the follicular lumen in sand lizard embryos is differentiated by cavitation similar to that in the grass snake, there were very important differences during the early stages of the differentiation of the cellular cords and the formation of the thyroid follicles. PMID:26966051

  10. Fluidic origami cellular structure -- combining the plant nastic movements with paper folding art

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2015-04-01

    By combining the physical principles behind the nastic plant movements and the rich designs of paper folding art, we propose a new class of multi-functional adaptive structure called fluidic origami cellular structure. The basic elements of this structure are fluid filled origami "cells", made by connecting two compatible Miura-Ori stripes along their crease lines. These cells are assembled seamlessly into a three dimensional topology, and their internal fluid pressure or volume are strategically controlled just like in plants for nastic movements. Because of the unique geometry of the Miura-Ori, the relationships among origami folding, internal fluid properties, and the crease bending are intricate and highly nonlinear. Fluidic origami can exploit such relationships to provide multiple adaptive functions concurrently and effectively. For example, it can achieve actuation or morphing by actively changing the internal fluid volume, and stillness tuning by constraining the fluid volume. Fluidic origami can also be bistable because of the nonlinear correlation between folding and crease material bending, and such bistable character can be altered significantly by fluid pressurization. These functions are natural and essential companions with respect to each other, so that fluidic origami can holistically exhibit many attractive characteristics of plants and deliver rapid and efficient actuation/morphing while maintaining a high structural stillness. The purpose of this paper is to introduce the design and working principles of the fluidic origami, as well as to explore and demonstrate its performance potential.

  11. Ligand binding PAS domains in a genomic, cellular, and structural context

    PubMed Central

    Henry, Jonathan T.; Crosson, Sean

    2012-01-01

    Per-Arnt-Sim (PAS) domains occur in proteins from all kingdoms of life. In the bacterial kingdom, PAS domains are commonly positioned at the amino terminus of signaling proteins such as sensor histidine kinases, cyclic-di-GMP synthases/hydrolases, and methyl-accepting chemotaxis proteins. Although these domains are highly divergent at the primary sequence level, the structures of dozens of PAS domains across a broad section of sequence space have been solved, revealing a conserved three-dimensional architecture. An all-versus-all alignment of 63 PAS structures demonstrates that the PAS domain family forms structural clades on the basis of two principal variables: (a) topological location inside or outside the plasma membrane and (b) the class of small molecule that they bind. The binding of a chemically diverse range of small-molecule metabolites is a hallmark of the PAS domain family. PAS ligand binding either functions as a primary cue to initiate a cellular signaling response or provides the domain with the capacity to respond to secondary physical or chemical signals such as gas molecules, redox potential, or photons. This review synthesizes the current state of knowledge of the structural foundations and evolution of ligand recognition and binding by PAS domains. PMID:21663441

  12. Crystal structure of listeriolysin O reveals molecular details of oligomerization and pore formation

    NASA Astrophysics Data System (ADS)

    Köster, Stefan; van Pee, Katharina; Hudel, Martina; Leustik, Martin; Rhinow, Daniel; Kühlbrandt, Werner; Chakraborty, Trinad; Yildiz, Özkan

    2014-04-01

    Listeriolysin O (LLO) is an essential virulence factor of Listeria monocytogenes that causes listeriosis. Listeria monocytogenes owes its ability to live within cells to the pH- and temperature-dependent pore-forming activity of LLO, which is unique among cholesterol-dependent cytolysins. LLO enables the bacteria to cross the phagosomal membrane and is also involved in activation of cellular processes, including the modulation of gene expression or intracellular Ca2+ oscillations. Neither the pore-forming mechanism nor the mechanisms triggering the signalling processes in the host cell are known in detail. Here, we report the crystal structure of LLO, in which we identified regions important for oligomerization and pore formation. Mutants were characterized by determining their haemolytic and Ca2+ uptake activity. We analysed the pore formation of LLO and its variants on erythrocyte ghosts by electron microscopy and show that pore formation requires precise interface interactions during toxin oligomerization on the membrane.

  13. A novel, high-efficiency cellular model of fibrillar alpha-synuclein inclusions and the examination of mutations that inhibit amyloid formation.

    PubMed

    Waxman, Elisa A; Giasson, Benoit I

    2010-04-01

    Intracytoplasmic alpha-synuclein (alpha-syn) amyloidogenic inclusions are a major pathological feature of Parkinson's disease, dementia with Lewy body disease and multiple systems atrophy. The mechanisms involved in the formation and inhibition of these aggregates are areas of intense investigation. The present study characterizes a novel cellular model for the study of alpha-syn aggregation, incorporating nucleation-dependent aggregation and a new function for calcium phosphate precipitation. Cultured cells were readily induced to develop large, cytoplasmic alpha-syn filamentous aggregates that were hyperphosphorylated, often ubiquitinated and thioflavin positive. These cellular aggregates formed in the majority of transfected cells and recruited approximately half of endogenously expressed alpha-syn. Using this system, we examined single-point mutations that inhibit alpha-syn amyloid formation in vitro. Three mutations (V66P, T72P and T75P) significantly hindered alpha-syn aggregation in this cell model. The T75P mutant, which could abrogate amyloid formation of wild-type alpha-syn in vitro, did not prevent wild-type alpha-syn cellular aggregates. These studies suggest that the propensity of alpha-syn to form cellular aggregates may be more pronounced than in isolated in vitro studies. This novel high-efficiency cellular model of alpha-syn aggregation is a valuable system that may be used to further understand alpha-syn aggregation and allow for the generation of future therapeutics. PMID:20132485

  14. Formation of cosmic structure by Doppler instability

    NASA Technical Reports Server (NTRS)

    Hogan, Craig J.

    1991-01-01

    A new mechanism is described which can create an instability in homogeneous gaseous matter at very low density. When an isotropic background radiation field has, near an electronic resonance, a spectral feature for which photon occupation number increases with frequency, moving atoms increase their speed by taking energy from the photon distribution. In a cosmological setting, a sufficiently intense spectral feature can interact with neutral atomic gas, after recombination, to generate protogalactic perturbations of the scale and magnitude needed to explain large-scale cosmic structure.

  15. A cellular automaton model for the ventricular myocardium considering the layer structure

    NASA Astrophysics Data System (ADS)

    Deng, Min-Yi; Dai, Jing-Yu; Zhang, Xue-Liang

    2015-09-01

    A cellular automaton model for the ventricular myocardium considering the layer structure has been established. The three types of cells in this model differ principally in the repolarization characteristics. For the normal travelling waves in this model, the computer simulation results show the R, S, and T waves and they are qualitatively in agreement with the standard electrocardiograph. Phenomena such as the potential decline of point J and segment ST and the rise of the potential line after the T wave appear when the ischemia occurs in the endocardium. The spiral wave has also been simulated, and the corresponding potential has a lower amplitude, higher frequency, and wider R wave, which accords with the distinguishing feature of the clinical electrocardiograph. Mechanisms underlying the above phenomena are analyzed briefly. Project supported by the National Natural Science Foundation of China (Grant Nos. 11365003 and 11165004).

  16. Amplitude and phase images of cellular structures with a scanning surface plasmon microscope.

    PubMed

    Berguiga, L; Roland, T; Monier, K; Elezgaray, J; Argoul, F

    2011-03-28

    Imaging cellular internal structure at nanometer scale axial resolution with non invasive microscopy techniques has been a major technical challenge since the nineties. We propose here a complement to fluorescence based microscopies with no need of staining the biological samples, based on a Scanning Surface Plasmon Microscope (SSPM). We describe the advantages of this microscope, namely the possibility of both amplitude and phase imaging and, due to evanescent field enhancement by the surface plasmon resonance, a very high resolution in Z scanning (Z being the axis normal to the sample). We show for fibroblast cells (IMR90) that SSPM offers an enhanced detection of index gradient regions, and we conclude it is very well suited to discriminate regions of variable density in biological media such as cell compartments, nucleus, nucleoli and membranes. PMID:21451685

  17. Competing stability modes in vortex structure formation

    NASA Astrophysics Data System (ADS)

    Garrett, Stephen; Gostelow, J. Paul; Rona, Aldo; McMullan, W. Andrew

    2015-11-01

    Nose cones and turbine blades have rotating components and represent very practical geometries for which the behavior of vortex structures is not completely understood. These two different physical cases demonstrate a common theme of competition between mode and vortex types. The literature concerning boundary-layer transition over rotating cones presents clear evidence of an alternative instability mode leading to counter-rotating vortex pairs, consistent with a centrifugal instability. This is in contrast to co-rotating vortices present over rotating disks that arise from crossflow effects. It is demonstrated analytically that this mode competes with the crossflow mode and is dominant only over slender cones. Predictions are aligned with experimental measurements over slender cones. Concurrent experimental work on the flow over swept cylinders shows that organized fine-scale streamwise vorticity occurs more frequently on convex surfaces than is appreciated. The conventional view of purely two-dimensional laminar boundary layers following blunt leading edges is not realistic and such boundary layers need to be treated three-dimensionally, particularly when sweep is present. The vortical structures are counter-rotating for normal cylinders and co-rotating under high sweep conditions. Crossflow instabilities may have a major role to play in the transition process but the streamline curvature mode is still present, and seemingly unchanged, when the boundary layer becomes turbulent.

  18. Structural template formation with discovery of subclasses

    NASA Astrophysics Data System (ADS)

    Long, Xiaojing; Wyatt, Chris

    2010-03-01

    A major focus of computational anatomy is to extract the most relevant information to identify and characterize anatomical variability within a group of subjects as well as between different groups. The construction of atlases is central to this effort. An atlas is a deterministic or probabilistic model with intensity variance, structural, functional or biochemical information over a population. To date most algorithms to construct atlases have been based on a single subject assuming that the population is best described by a single atlas. However, we believe that in a population with a wide range of subjects multiple atlases may be more representative since they reveal the anatomical differences and similarities within the group. In this work, we propose to use the K-means clustering algorithm to partition a set of images into several subclasses, based on a joint distance which is composed of a distance quantifying the deformation between images and a dissimilarity measured from the registration residual. During clustering, the spatial transformations are averaged rather than images to form cluster centers, to ensure a crisp reference. At the end of this algorithm, the updated centers of the k clusters are our atlases. We demonstrate this algorithm on a subset of a public available database with whole brain volumes of subjects aged 18-96 years. The atlases constructed by this method capture the significant structural differences across the group.

  19. Cellular Dynamics Drives the Emergence of Supracellular Structure in the Cyanobacterium, Phormidium sp. KS

    PubMed Central

    Sato, Naoki; Katsumata, Yutaro; Sato, Kaoru; Tajima, Naoyuki

    2014-01-01

    Motile filamentous cyanobacteria, such as Oscillatoria, Phormidium and Arthrospira, are ubiquitous in terrestrial and aquatic environments. As noted by Nägeli in 1860, many of them form complex three-dimensional or two-dimensional structures, such as biofilm, weed-like thalli, bundles of filaments and spirals, which we call supracellular structures. In all of these structures, individual filaments incessantly move back and forth. The structures are, therefore, macroscopic, dynamic structures that are continuously changing their microscopic arrangement of filaments. In the present study, we analyzed quantitatively the movement of individual filaments of Phormidium sp. KS grown on agar plates. Junctional pores, which have been proposed to drive cell movement by mucilage/slime secretion, were found to align on both sides of each septum. The velocity of movement was highest just after the reversal of direction and, then, attenuated exponentially to a final value before the next reversal of direction. This kinetics is compatible with the “slime gun” model. A higher agar concentration restricts the movement more severely and, thus, resulted in more spiral formation. The spiral is a robust form compatible with non-homogeneous movements of different parts of a long filament. We propose a model of spiral formation based on the microscopic movement of filaments. PMID:25460162

  20. Modeling the fusion of cylindrical bioink particles in post bioprinting structure formation

    NASA Astrophysics Data System (ADS)

    McCune, Matt; Shafiee, Ashkan; Forgacs, Gabor; Kosztin, Ioan

    2015-03-01

    Cellular Particle Dynamics (CPD) is an effective computational method to describe the shape evolution and biomechanical relaxation processes in multicellular systems. Thus, CPD is a useful tool to predict the outcome of post-printing structure formation in bioprinting. The predictive power of CPD has been demonstrated for multicellular systems composed of spherical bioink units. Experiments and computer simulations were related through an independently developed theoretical formalism based on continuum mechanics. Here we generalize the CPD formalism to (i) include cylindrical bioink particles often used in specific bioprinting applications, (ii) describe the more realistic experimental situation in which both the length and the volume of the cylindrical bioink units decrease during post-printing structure formation, and (iii) directly connect CPD simulations to the corresponding experiments without the need of the intermediate continuum theory inherently based on simplifying assumptions. Work supported by NSF [PHY-0957914]. Computer time provided by the University of Missouri Bioinformatics Consortium.

  1. Control of Formation and Cellular Detachment from Shewanella oneidensis MR-1 Biofilms by Cyclic di-GMP

    SciTech Connect

    Thormann, Kai M.; Duttler, Stefanie; Saville, Renee; Hyodo, Mamoru; Shukla, Soni; Hayakawa, Yoshihiro; Spormann, Alfred M.

    2006-04-01

    Stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. Biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. Using Shewanella oneidensis MR-1, an environmentally versatile, Fe(III) and Mn(IV) mineral -reducing microorganism, we identified mxdABCD as a new set of genes essential for formation of a three-dimensional biofilm. Molecular analysis revealed that mxdA encodes a cyclic bis(3',5')guanylic acid (cyclic di-GMP)-forming enzyme with an unusual GGDEF motif, i.e., NVDEF, which is essential for its function. mxdB encodes a putative membrane-associated glycosyl transferase. Both genes are essential for matrix attachment. The attachment-deficient phenotype of a Delta mxdA mutant was rescued by ectopic expression of VCA0956, encoding another diguanylate cyclase. Interestingly, a rapid cellular detachment from the biofilm occurred upon induction of yhjH, a gene encoding an enzyme that has been shown to have phosphodiesterase activity. In this way, it was possible to bypass the previously identified sudden depletion of molecular oxygen as an environmental trigger to induce biofilm dissolution. We propose a model for c-di-GMP as a key intracellular regulator for controlling biofilm stability by shifting the state of a biofilm cell between attachment and detachment in a concentration-dependent manner.

  2. Formation of Soluble Organo-Chromium(III) Complexes after Chromate Reduction in the Presence of Cellular Organics

    SciTech Connect

    Puzon, Geoffrey J.; Roberts, Arthur G.; Kramer, David M.; Xun, Luying

    2005-04-01

    Microbial reduction of hexavalent chromium [Cr(VI)] to trivalent chromium [Cr(III)] has been investigated as a method for bioremediation of Cr(VI) contaminated environments. The produced Cr(III) is thought to be insoluble Cr(OH)3; however, recent reports suggested a more complex fate of Cr(III). A bacterial enzyme system, using NADH as the reductant, converts Cr(VI) to a soluble NAD+-Cr(III) complex, and cytochrome c-mediated Cr(VI) reduction produces cytochrome c-Cr(III) adducts. In this study, Cr(VI) reduction in the presence of cellular organic metabolites formed both soluble and insoluble organo-Cr(III) end-products. Several soluble end-products were characterized by absorbance spectroscopy and electron paramagnetic resonance spectrometry as organo-Cr(III) complexes, similar to the known ascorbate-Cr(III) complex. The complexes remained soluble and stable upon dialysis against distilled H2O and over a broad pH range. The ready formation of stable organo-Cr(III) complexes suggests that organo-Cr(III) complexes are rather common, likely representing an integral part of the natural cycling of chromium. Finally, thus, organo-Cr(III) complexes may account for the mobile form of Cr(III) detected in the environment.

  3. Structural Basis for Glycyl Radical Formation By Pyruvate Formate-Lyase Activating Enzyme

    SciTech Connect

    Vey, J.L.; Yang, J.; Li, M.; Broderick, W.E.; Broderick, J.B.; Drennan, C.L.

    2009-05-26

    Pyruvate formate-lyase activating enzyme generates a stable and catalytically essential glycyl radical on G{sup 734} of pyruvate formate-lyase via the direct, stereospecific abstraction of a hydrogen atom from pyruvate formate-lyase. The activase performs this remarkable feat by using an iron-sulfur cluster and S-adenosylmethionine (AdoMet), thus placing it among the AdoMet radical superfamily of enzymes. We report here structures of the substrate-free and substrate-bound forms of pyruvate formate-lyase-activating enzyme, the first structures of an AdoMet radical activase. To obtain the substrate-bound structure, we have used a peptide substrate, the 7-mer RVSGYAV, which contains the sequence surrounding G{sup 734}. Our structures provide fundamental insights into the interactions between the activase and the G{sup 734} loop of pyruvate formate-lyase and provide a structural basis for direct and stereospecific H atom abstraction from the buried G{sup 734}4 of pyruvate formate-lyase.

  4. The role of Bni5 in the regulation of septin higher-order structure formation.

    PubMed

    Patasi, Csilla; Godočíková, Jana; Michlíková, Soňa; Nie, Yan; Káčeriková, Radka; Kválová, Katarína; Raunser, Stefan; Farkašovský, Marian

    2015-12-01

    Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins. PMID:26351911

  5. Nonlinear structure formation in nonlocal gravity

    SciTech Connect

    Barreira, Alexandre; Li, Baojiu; Hellwing, Wojciech A.; Baugh, Carlton M.; Pascoli, Silvia E-mail: baojiu.li@durham.ac.uk E-mail: c.m.baugh@durham.ac.uk

    2014-09-01

    We study the nonlinear growth of structure in nonlocal gravity models with the aid of N-body simulation and the spherical collapse and halo models. We focus on a model in which the inverse-squared of the d'Alembertian operator acts on the Ricci scalar in the action. For fixed cosmological parameters, this model differs from ΛCDM by having a lower late-time expansion rate and an enhanced and time-dependent gravitational strength ∼ 6% larger today). Compared to ΛCDM today, in the nonlocal model, massive haloes are slightly more abundant (by ∼ 10% at M ∼ 10{sup 14} M{sub ⊙}/h) and concentrated ≈ 8% enhancement over a range of mass scales), but their linear bias remains almost unchanged. We find that the Sheth-Tormen formalism describes the mass function and halo bias very well, with little need for recalibration of free parameters. The fitting of the halo concentrations is however essential to ensure the good performance of the halo model on small scales. For k ∼> 1 h/Mpc, the amplitude of the nonlinear matter and velocity divergence power spectra exhibits a modest enhancement of ∼ 12% to 15%, compared to ΛCDM today. This suggests that this model might only be distinguishable from ΛCDM by future observational missions. We point out that the absence of a screening mechanism may lead to tensions with Solar System tests due to local time variations of the gravitational strength, although this is subject to assumptions about the local time evolution of background averaged quantities.

  6. Extracellular environment modulates the formation and propagation of particular amyloid structures

    PubMed Central

    Westergard, Laura; True, Heather L.

    2016-01-01

    Summary Amyloidogenic proteins, including prions, assemble into multiple forms of structurally distinct fibres. The [PSI+] prion, endogenous to the yeast Saccharomyces cerevisiae, is a dominantly inherited, epigenetic modifier of phenotypes. [PSI+] formation relies on the coexistence of another prion, [RNQ+]. Here, in order to better define the role of amyloid diversity on cellular phenotypes, we investigated how physiological and environmental changes impact the generation and propagation of diverse protein conformations from a single polypeptide. Utilizing the yeast model system, we defined extracellular factors that influence the formation of a spectrum of alternative self-propagating amyloid structures of the Sup35 protein, called [PSI+] variants. Strikingly, exposure to specific stressful environments dramatically altered the variants of [PSI+] that formed de novo. Additionally, we found that stress also influenced the association between the [PSI+] and [RNQ+] prions in a way that it superceded their typical relationship. Furthermore, changing the growth environment modified both the biochemical properties and [PSI+]-inducing capabilities of the [RNQ+] template. These data suggest that the cellular environment contributes to both the generation and the selective propagation of specific amyloid structures, providing insight into a key feature that impacts phenotypic diversity in yeast and the cross-species transmission barriers characteristic of prion diseases. PMID:24628771

  7. Critical evaluation on structural stiffness of porous cellular structure of cobalt chromium alloy

    NASA Astrophysics Data System (ADS)

    Abd Malek, N. M. S.; Mohamed, S. R.; Che Ghani, S. A.; Harun, W. S. Wan

    2015-12-01

    In order to improve the stiffness characteristics of orthopedic devices implants that mimic the mechanical behavior of bone need to be considered. With the capability of Additive layer manufacturing processes to produce orthopedic implants with tailored mechanical properties are needed. This paper discusses finite element (FE) analysis and mechanical characterization of porous medical grade cobalt chromium (CoCr) alloy in cubical structures with volume based porosity ranging between 60% to 80% produced using direct metal laser sintering (DMLS) process. ANSYS 14.0 FE modelling software was used to predict the effective elastic modulus of the samples and comparisons were made with the experimental data. The effective mechanical properties of porous samples that were determined by uniaxial compression testing show exponential decreasing trend with the increase in porosity. Finite element model shows good agreement with experimentally obtained stress-strain curve in the elastic regions. The models prove that numerical analysis of actual prosthesis implant can be computed particularly in load bearing condition

  8. Structural Basis of Vesicle Formation at the Inner Nuclear Membrane

    PubMed Central

    Hagen, Christoph; Dent, Kyle C.; Zeev-Ben-Mordehai, Tzviya; Grange, Michael; Bosse, Jens B.; Whittle, Cathy; Klupp, Barbara G.; Siebert, C. Alistair; Vasishtan, Daven; Bäuerlein, Felix J.B.; Cheleski, Juliana; Werner, Stephan; Guttmann, Peter; Rehbein, Stefan; Henzler, Katja; Demmerle, Justin; Adler, Barbara; Koszinowski, Ulrich; Schermelleh, Lothar; Schneider, Gerd; Enquist, Lynn W.; Plitzko, Jürgen M.; Mettenleiter, Thomas C.; Grünewald, Kay

    2015-01-01

    Summary Vesicular nucleo-cytoplasmic transport is becoming recognized as a general cellular mechanism for translocation of large cargoes across the nuclear envelope. Cargo is recruited, enveloped at the inner nuclear membrane (INM), and delivered by membrane fusion at the outer nuclear membrane. To understand the structural underpinning for this trafficking, we investigated nuclear egress of progeny herpesvirus capsids where capsid envelopment is mediated by two viral proteins, forming the nuclear egress complex (NEC). Using a multi-modal imaging approach, we visualized the NEC in situ forming coated vesicles of defined size. Cellular electron cryo-tomography revealed a protein layer showing two distinct hexagonal lattices at its membrane-proximal and membrane-distant faces, respectively. NEC coat architecture was determined by combining this information with integrative modeling using small-angle X-ray scattering data. The molecular arrangement of the NEC establishes the basic mechanism for budding and scission of tailored vesicles at the INM. PMID:26687357

  9. Amide-Modified Prenylcysteine based Icmt Inhibitors: Structure Activity Relationships, Kinetic Analysis and Cellular Characterization

    PubMed Central

    Majmudar, Jaimeen D.; Hodges-Loaiza, Heather B.; Hahne, Kalub; Donelson, James L.; Song, Jiao; Shrestha, Liza; Harrison, Marietta L.; Hrycyna, Christine A.; Gibbs, Richard A.

    2012-01-01

    Human protein isoprenylcysteine carboxyl methyltransferase (hIcmt) is the enzyme responsible for the α-carboxyl methylation of the C-termimal isoprenylated cysteine of CaaX proteins, including Ras proteins. This specific posttranslational methylation event has been shown to be important for cellular transformation by oncogenic Ras isoforms. This finding led to interest in hIcmt inhibitors as potential anti-cancer agents. Previous analog studies based on N-acetyl-S-farnesylcysteine identified two prenylcysteine-based low micromolar inhibitors (1a and 1b) of hIcmt, each bearing a phenoxyphenyl amide modification. In this study, a focused library of analogs of 1a and 1b was synthesized and screened versus hIcmt, delineating structural features important for inhibition. Kinetic characterization of the most potent analogs 1a and 1b established that both inhibitors exhibited mixed-mode inhibition and that the competitive component predominated. Using the Cheng – Prusoff method, the Ki values were determined from the IC50 values. Analog 1a has a KIC of 1.4 ± 0.2 μM and a KIU of 4.8 ± 0.5 μM while 1b has a KIC of 0.5 ± 0.07 μM and a KIU of 1.9 ± 0.2 μM. Cellular evaluation of 1b revealed that it alters the subcellular localization of GFP-KRas, and also inhibits both Ras activation and Erk phosphorylation in Jurkat cells. PMID:22142613

  10. Overexpression of p49/STRAP alters cellular cytoskeletal structure and gross anatomy in mice

    PubMed Central

    2014-01-01

    Background The protein p49/STRAP (SRFBP1) is a transcription cofactor of serum response factor (SRF) which regulates cytoskeletal and muscle-specific genes. Results Two conserved domains were found in the p49/STRAP protein. The SRF-binding domain was at its N-terminus and was highly conserved among mammalian species, xenopus and zebrafish. A BUD22 domain was found at its C-terminus in three sequence databases. The BUD22 domain was conserved among mammalian p49/STRAP proteins, and yeast cellular morphogenesis proteins, which is involved in ribosome biogenesis that affects growth rate and cell size. The endogenous p49/SRAP protein was localized mainly in the nucleus but also widely distributed in the cytoplasm, and was in close proximity to the actin. Transfected GFP-p49/STRAP protein co-localized with nucleolin within the nucleolus. Overexpression of p49/STRAP reduced actin content in cultured cells and resulted in smaller cell size versus control cells. Increased expression of p49/STRAP in transgenic mice resulted in newborns with malformations, which included asymmetric abdominal and thoracic cavities, and substantial changes in cardiac morphology. p49/STRAP altered the expression of certain muscle-specific genes, including that of the SRF gene, which is a key regulator of cardiac genes at the developmental, structural and maintenance level and has two SRE binding sites. Conclusions Since p49/STRAP is a co-factor of SRF, our data suggest that p49/STRAP likely regulates cell size and morphology through SRF target genes. The function of its BUD22 domain warrants further investigation. The observed increase in p49/STRAP expression during cellular aging may contribute to observed morphological changes in senescence. PMID:25183317

  11. High resolution simulations of energy absorption in dynamically loaded cellular structures

    NASA Astrophysics Data System (ADS)

    Winter, R. E.; Cotton, M.; Harris, E. J.; Eakins, D. E.; McShane, G.

    2016-04-01

    Cellular materials have potential application as absorbers of energy generated by high velocity impact. CTH, a Sandia National Laboratories Code which allows very severe strains to be simulated, has been used to perform very high resolution simulations showing the dynamic crushing of a series of two-dimensional, stainless steel metal structures with varying architectures. The structures are positioned to provide a cushion between a solid stainless steel flyer plate with velocities ranging from 300 to 900 m/s, and an initially stationary stainless steel target. Each of the alternative architectures under consideration was formed by an array of identical cells each of which had a constant volume and a constant density. The resolution of the simulations was maximised by choosing a configuration in which one-dimensional conditions persisted for the full period over which the specimen densified, a condition which is most readily met by impacting high density specimens at high velocity. It was found that the total plastic flow and, therefore, the irreversible energy dissipated in the fully densified energy absorbing cell, increase (a) as the structure becomes more rodlike and less platelike and (b) as the impact velocity increases. Sequential CTH images of the deformation processes show that the flow of the cell material may be broadly divided into macroscopic flow perpendicular to the compression direction and jetting-type processes (microkinetic flow) which tend to predominate in rod and rodlike configurations and also tend to play an increasing role at increased strain rates. A very simple analysis of a configuration in which a solid flyer impacts a solid target provides a baseline against which to compare and explain features seen in the simulations. The work provides a basis for the development of energy absorbing structures for application in the 200-1000 m/s impact regime.

  12. [Motivation and Emotional States: Structural Systemic, Neurochemical, Molecular and Cellular Mechanisms].

    PubMed

    Bazyan, A S

    2016-01-01

    The structural, systemic, neurochemical, molecular and cellular mechanisms of organization and coding motivation and emotional states are describe. The GABA and glutamatergic synaptic systems of basal ganglia form a neural network and participate in the implementation of voluntary behavior. Neuropeptides, neurohormones and paracrine neuromodulators involved in the organization of motivation and emotional states, integrated with synaptic systems, controlled by neural networks and organizing goal-directed behavior. Structural centers for united and integrated of information in voluntary and goal-directed behavior are globus pallidus. Substantia nigra pars reticulata switches the information from corticobasal networks to thalamocortical networks, induces global dopaminergic (DA) signal and organize interaction of mesolimbic and nigostriatnoy DA systems controlled by prefrontal and motor cortex. Together with the motor cortex, substantia nigra displays information in the brainstem and spinal cord to implementation of behavior. Motivation states are formed in the interaction of neurohormonal and neuropeptide systems by monoaminergic systems of brain. Emotional states are formed by monoaminergic systems of the mid-brain, where the leading role belongs to the mesolimbic DA system. The emotional and motivation state of the encoded specific epigenetic molecular and chemical pattern of neuron. PMID:27149821

  13. Femtosecond laser-induced periodic surface structure formation on tungsten

    SciTech Connect

    Vorobyev, A. Y.; Guo Chunlei

    2008-09-15

    In this paper, we demonstrate the generation of periodic surface structures on a technologically important material, tungsten, at both 400 and 800 nm, despite that the table values of dielectric constants for tungsten at these two wavelengths suggest the absence of surface plasmons, a wave necessary for forming periodic structures on metals. Furthermore, we find that the structure periods formed on tungsten are significantly less than the laser wavelengths. We believe that the dielectric constants of tungsten change significantly due to intense laser pulse heating and surface structuring and roughening at nanometer scales, permitting surface plasmon excitation and periodic structure formation.

  14. Internal Structure of Stellar Clusters: Geometry of Star Formation

    NASA Astrophysics Data System (ADS)

    Alfaro, Emilio J.; Sánchez, Néstor

    2011-04-01

    The study of the internal structure of star clusters provides important clues concerning their formation mechanism and dynamical evolution. There are both observational and numerical evidences indicating that open clusters evolve from an initial clumpy structure, presumably a direct consequence of the formation in a fractal medium, toward a centrally condensed state. This simple picture has, however, several drawbacks. There can be very young clusters exhibiting radial patterns maybe reflecting the early effect of gravity on primordial gas. There can be also very evolved clusters showing fractal patterns that either have survived through time or have been generated subsequently by some (unknown) mechanism. Additionally, the fractal structure of some open clusters is much clumpier than the average structure of the interstellar medium in the Milky Way, although in principle a very similar structure should be expected. Here we summarize and discuss observational and numerical results concerning this subject.

  15. Structures in material transference and vitelline envelope formation in Betta splendens follicles.

    PubMed

    Genta, H D

    1996-01-01

    Structures were found by transmission electron microscopy, they were located within follicular cells and the oocyte, and in the interspace between them in follicles of the teleost fish Betta splendens. Some structures with features characteristic or lamellar bodies were found in small follicles. The possible role of these structures in the formation of the vitelline envelope as well as in the material transference is discussed. Vacuoles, vesticles and particles intensely stained were found in the microvilli and the cortical cytoplasm of the oocyte at the onset of vitellogenesis. These results suggest that different substances present in the cellular components of the follicle might be transferred from cell to cell through the extracellular space and through the prolongations that cross the extracellular space. PMID:9369035

  16. Circulating Microparticles Alter Formation, Structure, and Properties of Fibrin Clots

    PubMed Central

    Zubairova, Laily D.; Nabiullina, Roza M.; Nagaswami, Chandrasekaran; Zuev, Yuriy F.; Mustafin, Ilshat G.; Litvinov, Rustem I.; Weisel, John W.

    2015-01-01

    Despite the importance of circulating microparticles in haemostasis and thrombosis, there is limited evidence for potential causative effects of naturally produced cell-derived microparticles on fibrin clot formation and its properties. We studied the significance of blood microparticles for fibrin formation, structure, and susceptibility to fibrinolysis by removing them from platelet-free plasma using filtration. Clots made in platelet-free and microparticle-depleted plasma samples from the same healthy donors were analyzed in parallel. Microparticles accelerate fibrin polymerisation and support formation of more compact clots that resist internal and external fibrinolysis. These variations correlate with faster thrombin generation, suggesting thrombin-mediated kinetic effects of microparticles on fibrin formation, structure, and properties. In addition, clots formed in the presence of microparticles, unlike clots from the microparticle-depleted plasma, contain 0.1–0.5-μm size granular and CD61-positive material on fibres, suggesting that platelet-derived microparticles attach to fibrin. Therefore, the blood of healthy individuals contains functional microparticles at the levels that have a procoagulant potential. They affect the structure and stability of fibrin clots indirectly through acceleration of thrombin generation and through direct physical incorporation into the fibrin network. Both mechanisms underlie a potential role of microparticles in haemostasis and thrombosis as modulators of fibrin formation, structure, and resistance to fibrinolysis. PMID:26635081

  17. Cellular imaging of deep organ using two-photon Bessel light-sheet nonlinear structured illumination microscopy

    PubMed Central

    Zhao, Ming; Zhang, Han; Li, Yu; Ashok, Amit; Liang, Rongguang; Zhou, Weibin; Peng, Leilei

    2014-01-01

    In vivo fluorescent cellular imaging of deep internal organs is highly challenging, because the excitation needs to penetrate through strong scattering tissue and the emission signal is degraded significantly by photon diffusion induced by tissue-scattering. We report that by combining two-photon Bessel light-sheet microscopy with nonlinear structured illumination microscopy (SIM), live samples up to 600 microns wide can be imaged by light-sheet microscopy with 500 microns penetration depth, and diffused background in deep tissue light-sheet imaging can be reduced to obtain clear images at cellular resolution in depth beyond 200 microns. We demonstrate in vivo two-color imaging of pronephric glomeruli and vasculature of zebrafish kidney, whose cellular structures located at the center of the fish body are revealed in high clarity by two-color two-photon Bessel light-sheet SIM. PMID:24876996

  18. Cellular growth in biofilms

    SciTech Connect

    Wood, B.D.; Whitaker, S.

    1999-09-20

    In this paper the authors develop a macroscopic evolutionary equation for the growth of the cellular phase starting from a microscopic description of mass transport and a simple structured model for product formation. The methods of continuum mechanics and volume averaging are used to develop the macroscopic representation by carefully considering the fluxes of chemical species that pertain to cell growth. The concept of structured models is extended to include the transport of reacting chemical species at the microscopic scale. The resulting macroscopic growth model is similar in form to previously published models for the transport of a single substrate and electron donor and for the production of cellular mass and exopolymer. The method of volume averaging indicated under what conditions the developed growth model is valid and provides an explicit connection between the relevant microscopic model parameters and their corresponding macroscopic counterparts.

  19. Structure of tetracarbonylethyleneosmium: ethylene structure changes upon complex formation.

    PubMed

    Karunatilaka, Chandana; Tackett, Brandon S; Washington, John; Kukolich, Stephen G

    2007-08-29

    Rotational spectra of seven isotopomers of tetracarbonylethyleneosmium, Os(CO)4(eta2-C2H4), were measured in the 4-12 GHz range using a Flygare-Balle-type pulsed-beam Fourier transform microwave spectrometer system. Olefin-transition metal complexes of this type occur extensively in recent organic syntheses and serve as important models for transition states in the metal-mediated transformations of alkenes. Three osmium ((192)Os, (190)Os, and (188)Os) and three unique 13C isotopomers (13C in ethylene, axial, and equatorial positions) were observed in natural abundance. Additional spectra were measured for a perdeuterated sample, Os(CO)4(eta2-C2D4). The measured rotational constants for the main osmium isotopomer ((192)Os) are A = 929.3256(6), B = 755.1707(3), and C = 752.7446(3) MHz, indicating a near-prolate asymmetric top molecule. The approximately 140 assigned b-type transitions were fit using a Watson S-reduced Hamiltonian including A, B, C, and five centrifugal distortion constants. A near-complete r0 gas-phase structure has been determined from a least-squares structural fit using eight adjustable structural parameters to fit the 21 measured rotational constants. Changes in the structure of ethylene on coordination to Os(CO)4 are large and well-determined. For the complex, the experimental ethylene C-C bond length is 1.432(5) A, which falls between the free ethylene value of 1.3391(13) A and the ethane value of 1.534(2) A. The angle between the plane of the CH2 group and the extended ethylene C-C bond ( angleout-of-plane) is 26.0(3) degrees , indicating that this complex is better described as a metallacyclopropane than as a pi-bonded olefin-metal complex. The Os-C-C-H dihedral angle is 106.7(2) degrees , indicating that the ethylene carbon atoms have near sp3 character in the complex. Kraitchman analysis of the available rotational constants gave principal axis coordinates for the carbon and hydrogen atoms in excellent agreement with the least-squares fit

  20. The probabilistic mechanism of formation of block structures

    NASA Astrophysics Data System (ADS)

    Ivanov, V. I.

    2012-03-01

    Questions on the formation of block structures are considered. It is shown that the block structure is characteristic of bodies in a wide range of scales from microscopic to astronomic and from the bodies of nonliving nature to living organisms and communities. A scheme of the mechanism of the probabilistic formation of block structures is suggested. The characteristics general for structures of all scales are revealed. Evidence is presented that the hierarchical pattern of element sizes is characteristic of natural structures in which the ratio of linear sizes of elements neighboring by hierarchy is 2-5, while the characteristic scale coefficient is √ N , where N is the total number of elements of which the system is formed. The block-probabilistic approach ensures knowledge of rare catastrophic events, including earthquakes, market crashes, floods, and industrial catastrophes, or creative events such as the formation of hypercomplex systems similar to organisms and communities. The statistics of rare events follows the power distribution (the distribution with a "heavy tail") rather than the exponential one and especially the Poisson distribution, the Gaussian distribution, or the distributions with "light tails" close to them. The expression for the factor of increasing the formation probability of the systems, which is of many orders of magnitude even for the simplest systems, is acquired.

  1. Effects of Ionizing Radiation on Cellular Structures, Induced Instability, and Carcinogenesis

    SciTech Connect

    Resat, Marianne S.; Arthurs, Benjamin J.; Estes, Brian J.; Morgan, William F.

    2006-03-01

    According to the American Cancer Society, the United States can expect 1,368,030 new cases of cancer in 2004 [1]. Among the many carcinogens Americans are exposed to, ionizing radiation will contribute to this statistic. Humans live in a radiation environment. Ionizing radiation is in the air we breathe, the earth we live on, and the food we eat. Man-made radiation adds to this naturally occurring radiation level thereby increasing the chance for human exposure. For many decades the scientific community, governmental regulatory bodies, and concerned citizens have struggled to estimate health risks associated with radiation exposures, particularly at low doses. While cancer induction is the primary concern and the most important somatic effect of exposure to ionizing radiation, potential health risks do not involve neoplastic diseases exclusively but also include somatic mutations that might contribute to birth defects and ocular maladies, and heritable mutations that might impact on disease risks in future generations. Consequently it is important we understand the effect of ionizingradiation on cellular structures and the subsequent long-term health risks associated with exposure to ionizing radiation.

  2. An assessment of galactic cosmic radiation quality considering heavy ion track structures within the cellular environment.

    PubMed

    Craven, P A; Rycroft, M J

    1996-01-01

    Beyond the magnetic influence of the Earth, the flux of galactic cosmic radiation (GCR) represents a radiological concern for long-term manned space missions. Current concepts of radiation quality and equivalent dose are inadequate for accurately specifying the relative biological "efficiency" of low doses of such heavily ionising radiations, based as they are on the single parameter of Linear Energy Transfer (LET). Such methods take no account of the mechanisms, nor of the highly inhomogeneous spatial structure, of energy deposition in radiation tracks. DNA damage in the cell nucleus, which ultimately leads to the death or transformation of the cell, is usually initiated by electrons liberated from surrounding molecules by the incident projectile ion. The characteristics of these emitted "delta-rays", dependent primarily upon the charge and velocity of the ion, are considered in relation to an idealised representation of the cellular environment. Theoretically calculated delta-ray energy spectra are multiplied by a series of weighting algorithms designed to represent the potential for DNA insult in this environment, both in terms of the quantity and quality of damage. By evaluating the resulting curves, and taking into account the energy spectra of heavy ions in space, a relative measure of the biological relevance of the most abundant GCR species is obtained, behind several shielding configurations. It is hoped that this method of assessing the radiation quality of galactic cosmic rays will be of value when considering the safety of long-term manned space missions. PMID:11538985

  3. Cellular automata segmentation of the boundary between the compacta of vertebral bodies and surrounding structures

    NASA Astrophysics Data System (ADS)

    Egger, Jan; Nimsky, Christopher

    2016-03-01

    Due to the aging population, spinal diseases get more and more common nowadays; e.g., lifetime risk of osteoporotic fracture is 40% for white women and 13% for white men in the United States. Thus the numbers of surgical spinal procedures are also increasing with the aging population and precise diagnosis plays a vital role in reducing complication and recurrence of symptoms. Spinal imaging of vertebral column is a tedious process subjected to interpretation errors. In this contribution, we aim to reduce time and error for vertebral interpretation by applying and studying the GrowCut - algorithm for boundary segmentation between vertebral body compacta and surrounding structures. GrowCut is a competitive region growing algorithm using cellular automata. For our study, vertebral T2-weighted Magnetic Resonance Imaging (MRI) scans were first manually outlined by neurosurgeons. Then, the vertebral bodies were segmented in the medical images by a GrowCut-trained physician using the semi-automated GrowCut-algorithm. Afterwards, results of both segmentation processes were compared using the Dice Similarity Coefficient (DSC) and the Hausdorff Distance (HD) which yielded to a DSC of 82.99+/-5.03% and a HD of 18.91+/-7.2 voxel, respectively. In addition, the times have been measured during the manual and the GrowCut segmentations, showing that a GrowCutsegmentation - with an average time of less than six minutes (5.77+/-0.73) - is significantly shorter than a pure manual outlining.

  4. Two-Photon Autofluorescence Imaging Reveals Cellular Structures Throughout the Retina of the Living Primate Eye

    PubMed Central

    Sharma, Robin; Williams, David R.; Palczewska, Grazyna; Palczewski, Krzysztof; Hunter, Jennifer J.

    2016-01-01

    Purpose Although extrinsic fluorophores can be introduced to label specific cell types in the retina, endogenous fluorophores, such as NAD(P)H, FAD, collagen, and others, are present in all retinal layers. These molecules are a potential source of optical contrast and can enable noninvasive visualization of all cellular layers. We used a two-photon fluorescence adaptive optics scanning light ophthalmoscope (TPF-AOSLO) to explore the native autofluorescence of various cell classes spanning several layers in the unlabeled retina of a living primate eye. Methods Three macaques were imaged on separate occasions using a custom TPF-AOSLO. Two-photon fluorescence was evoked by pulsed light at 730 and 920 nm excitation wavelengths, while fluorescence emission was collected in the visible range from several retinal layers and different locations. Backscattered light was recorded simultaneously in confocal modality and images were postprocessed to remove eye motion. Results All retinal layers yielded two-photon signals and the heterogeneous distribution of fluorophores provided optical contrast. Several structural features were observed, such as autofluorescence from vessel walls, Müller cell processes in the nerve fibers, mosaics of cells in the ganglion cell and other nuclear layers of the inner retina, as well as photoreceptor and RPE layers in the outer retina. Conclusions This in vivo survey of two-photon autofluorescence throughout the primate retina demonstrates a wider variety of structural detail in the living eye than is available through conventional imaging methods, and broadens the use of two-photon imaging of normal and diseased eyes. PMID:26903224

  5. Bifurcation of learning and structure formation in neuronal maps

    NASA Astrophysics Data System (ADS)

    Marschler, Christian; Faust-Ellsässer, Carmen; Starke, Jens; van Hemmen, J. Leo

    2014-11-01

    Most learning processes in neuronal networks happen on a much longer time scale than that of the underlying neuronal dynamics. It is therefore useful to analyze slowly varying macroscopic order parameters to explore a network's learning ability. We study the synaptic learning process giving rise to map formation in the laminar nucleus of the barn owl's auditory system. Using equation-free methods, we perform a bifurcation analysis of spatio-temporal structure formation in the associated synaptic-weight matrix. This enables us to analyze learning as a bifurcation process and follow the unstable states as well. A simple time translation of the learning window function shifts the bifurcation point of structure formation and goes along with traveling waves in the map, without changing the animal's sound localization performance.

  6. Food Composition Database Format and Structure: A User Focused Approach

    PubMed Central

    Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

  7. Distinctive expression of extracellular matrix molecules at mRNA and protein levels during formation of cellular and acellular cementum in the rat.

    PubMed

    Sasano, Y; Maruya, Y; Sato, H; Zhu, J X; Takahashi, I; Mizoguchi, I; Kagayama, M

    2001-02-01

    Little is known about differential expression of extracellular matrices secreted by cementoblasts between cellular and acellular cementum. We hypothesize that cementoblasts lining acellular cementum express extracellular matrix genes differently from those lining cellular cementum, thereby forming two distinct types of extracellular matrices. To test this hypothesis, we investigated spatial and temporal gene expression of selected extracellular matrix molecules, that is type I collagen, bone sialoprotein, osteocalcin and osteopontin, during formation of both cellular and acellular cementum using in situ hybridization. In addition, their extracellularly deposited and accumulated proteins were examined immunohistochemically. The mRNA transcripts of pro-alpha1 (I) collagen were primarily localized in cementoblasts of cellular cementum and cementocytes, while those of bone sialoprotein were predominantly seen in cementoblasts lining acellular cementum. In contrast, osteocalcin was expressed by both types of cementoblasts and cementocytes and so was osteopontin but only transiently. Our immunohistochemical examination revealed that translated proteins were localized extracellularly where the genes had been expressed intracellularly. The present study demonstrated the distinctive expression of genes and proteins of the extracellular matrix molecules between cellular and acellular cementum. PMID:11432645

  8. Family Structure: Its Effects on Adolescent Attachment and Identity Formation.

    ERIC Educational Resources Information Center

    Faber, Anthony J.; Edwards, Anne E.; Bauer, Karlin S.; Wetchler, Joseph L.

    2003-01-01

    Examines the association between family structure, attachment, and identity formation. Results partially support the hypotheses and indicate that unresolved spouse conflict is associated with low levels of attachment in adolescents and attachment to father is linked to identity achieved and the diffused identity status. Findings support a link…

  9. High hard magnetic properties and cellular structure of nanocomposite magnet Nd 4.5Fe 73.8B 18.5Cr 0.5Co 1.5Nb 1Cu 0.2

    NASA Astrophysics Data System (ADS)

    The, N. D.; Chau, N.; Vuong, N. V.; Quyen, N. H.

    2006-08-01

    The formation of special nanostructure, cellular structure, in Nd 4.5Fe 73.8B 18.5Cr 0.5Co 1.5Nb 1Cu 0.2 nanocomposite magnet has been observed by means of SEM for the first time. Ultrafine structure of cellules with thickness of 20-25 nm and length in range of 200-300 nm leads to high shape anisotropy of the materials. Therefore, high hard magnetic properties were obtained with ( BH) max up to 17.3 MG Oe in ribbons with very high remanence of 13.5 kG. The role of Cr and Co in the formation and refinement of cellular structure is proposed. Effect of heat treatment on hard magnetic properties is discussed in detail.

  10. Sponge cell reaggregation: Cellular structure and morphogenetic potencies of multicellular aggregates.

    PubMed

    Lavrov, Andrey I; Kosevich, Igor A

    2016-02-01

    Sponges (phylum Porifera) are one of the most ancient extant multicellular animals and can provide valuable insights into origin and early evolution of Metazoa. High plasticity of cell differentiations and anatomical structure is characteristic feature of sponges. Present study deals with sponge cell reaggregation after dissociation as the most outstanding case of sponge plasticity. Dynamic of cell reaggregation and structure of multicellular aggregates of three demosponge species (Halichondria panicea (Pallas, 1766), Haliclona aquaeductus (Sсhmidt, 1862), and Halisarca dujardinii Johnston, 1842) were studied. Sponge tissue dissociation was performed mechanically. Resulting cell suspensions were cultured at 8-10°C for at least 5 days. Structure of multicellular aggregates was studied by light, transmission and scanning electron microscopy. Studied species share common stages of cell reaggregation-primary multicellular aggregates, early-stage primmorphs and primmorphs, but the rate of reaggregation varies considerably among species. Only cells of H. dujardinii are able to reconstruct functional and viable sponge after primmorphs formation. Sponge reconstruction in this species occurs due to active cell locomotion. Development of H. aquaeductus and H. panicea cells ceases at the stages of early primmorphs and primmorphs, respectively. Development of aggregates of these species is most likely arrested due to immobility of the majority of cells inside them. However, the inability of certain sponge species to reconstruct functional and viable individuals during cell reaggregation may be not a permanent species-specific characteristic, but depends on various factors, including the stage of the life cycle and experimental conditions. PMID:26863993