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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. 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

  4. 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.

  5. Cellular Disulfide Bond Formation in Bioactive Peptides and Proteins

    PubMed Central

    Patil, Nitin A.; Tailhades, Julien; Hughes, Richard Anthony; Separovic, Frances; Wade, John D.; Hossain, Mohammed Akhter

    2015-01-01

    Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes—a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor—that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery. PMID:25594871

  6. 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

  7. 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.

  8. Circular structures in retroviral and cellular genomes.

    PubMed

    Albert, F G; Bronson, E C; Fitzgerald, D J; Anderson, J N

    1995-10-01

    A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830-base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I). This unusual structure displayed relatively smooth planar bending throughout its length. The structure is conserved in diverse isolates of HIV-I, HIV-II, and simian immunodeficiency viruses, which implies that it is under selective constraints. A search of all sequences in the GenBank data base was carried out in order to identify similar circular structures in cellular DNA. The results revealed that the structures are associated with a wide range of sequences that undergo recombination, including most known examples of DNA inversion and subtelomeric translocation systems. Circular structures were also associated with replication and transposition systems where DNA looping has been implicated in the generation of large protein-DNA complexes. Experimental evidence for the structures was provided by studies which demonstrated that two sequences detected as circular by computer preferentially formed covalently closed circles during ligation reactions in vitro when compared to nonbent fragments, bent fragments with noncircular shapes, and total genomic DNA. In addition, a single T-->C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization. These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes. PMID:7559522

  9. [Cellular structure of propionibacteria during their multiplication].

    PubMed

    Sobczak, E; Kocoń, J

    1983-01-01

    The aim of the present study was to determine the structure of bacterial cells from Propionibacterium genus as well as their structure during the cellular division. On the basis of the observations made in the electron transmission microscope, in uranyl-acetates-tained preparations of ultra-thin specimens of bacteria, it was stated that propionic bacteria appeared in a shape of short rods, possessing regular profiles of cell walls as opposed to Gram-negative bacteria with a very creased edge line. Besides, it was observed that division of cells had place by formation of septum, most probably preceded by the division of mezosome, which is a signal for creating the divisional wall. In the conducted studies, the following phenomena were started: presence of membraneous structure of mezosomes, which is linked with the chain of circular DNA in bacterial cell, appearance of numerous ribosomes in the regions of tangled threads of nucleic acids, and existence of other undefinite elements. Mezosome present in the cell of propionic bacteria is probably linked with the cell wall at least in two places and on the surface of external cell wall at the site of its linking; it causes the change in electronic density, demonstrated by the undefined holes or scars in cell wall. This finding gives the possibility of distinguishing this genus of Propionibacterium, in the respect of morphology, from other bacteria what, in the opinion of the authors, is a new achievement in the studies on the structure of propionic bacteria.

  10. 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

  11. 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

  12. 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.

  13. Crack propagation in bamboo's hierarchical cellular structure.

    PubMed

    Habibi, Meisam K; Lu, Yang

    2014-07-07

    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.

  14. 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.

  15. 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.

  16. Observations on cellular structures of Porphyridium cruentum.

    PubMed

    BRODY, M; VATTER, A E

    1959-03-25

    The cellular structure of Porphyridium cruentum was studied with both light and electron microscope. The photosynthetic plastid in this red alga was found to be structurally similar to that in the Chlorophyceae and higher green plants. The phycobilins, as well as the chlorophyll, seem to be associated with the lamellae of the plastid. The pyrenoid, a region of low lamellar density, contains no tubules, and does not appear to function in synthesis or storage of reserve material. Grains of floridean starch are located in the cytoplasm, outside the plastid. Typical mitochondrial organelles were not observed. The nucleus is eccentric, and contains a nucleolus located on the inner face of the nucleus, nearest the plastid. The schedule for staining the nucleus is given in detail. Other cell structures (sheath, dictyosomes, etc.) are described. Growing cells in light of intensity leads to disruption of the parallel arrangement of the lamellar characteristic of cells grown in moderate light.

  17. 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

  18. 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).

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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.

  4. 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

  5. pH-sensitive tubular polymersomes: formation and applications in cellular delivery.

    PubMed

    Robertson, James D; Yealland, Guy; Avila-Olias, Milagros; Chierico, Luca; Bandmann, Oliver; Renshaw, Stephen A; Battaglia, Giuseppe

    2014-05-27

    Optimizing the shape of a nanovector influences its interaction with a cell and determines the internalization kinetics. Block copolymer amphiphiles self-assemble into monodisperse structures in aqueous solutions and have been explored extensively as drug delivery vectors. However, the structure of self-assembled block copolymers has mainly been limited to spherical vesicles or spherical and worm-like micelles. Here we show the controlled formation and purification of tubular polymersomes, long cylindrical vesicles. Tubular polymersomes are purified from other structures, and their formation is manipulated by incorporating the biocompatible membrane components cholesterol and phospholipids. Finally we show that these tubular polymersomes have different cellular internalization kinetics compared with spherical polymersomes and can successfully encapsulate and deliver fluorescent bovine serum albumin protein intracellularly.

  6. Structural modeling of sandwich structures with lightweight cellular cores

    NASA Astrophysics Data System (ADS)

    Liu, T.; Deng, Z. C.; Lu, T. J.

    2007-10-01

    An effective single layered finite element (FE) computational model is proposed to predict the structural behavior of lightweight sandwich panels having two dimensional (2D) prismatic or three dimensional (3D) truss cores. Three different types of cellular core topology are considered: pyramidal truss core (3D), Kagome truss core (3D) and corrugated core (2D), representing three kinds of material anisotropy: orthotropic, monoclinic and general anisotropic. A homogenization technique is developed to obtain the homogenized macroscopic stiffness properties of the cellular core. In comparison with the results obtained by using detailed FE model, the single layered computational model can give acceptable predictions for both the static and dynamic behaviors of orthotropic truss core sandwich panels. However, for non-orthotropic 3D truss cores, the predictions are not so well. For both static and dynamic behaviors of a 2D corrugated core sandwich panel, the predictions derived by the single layered computational model is generally acceptable when the size of the unit cell varies within a certain range, with the predictions for moderately strong or strong corrugated cores more accurate than those for weak cores.

  7. Modelling polymersomes: a prototype for complex cellular structures

    NASA Astrophysics Data System (ADS)

    Sevink, G. J. A.; Fraaije, J. G. E. M.

    2004-04-01

    Self-organisation of small amphiphilic molecules is a key technique in many applications of modern nanotechnology. Thin polymer films have been extensively studied theoretically and experimentally because of their rich phase behaviour and use as templates in lithographic processes, optical devices and surfaces with molecular recognition capabilities. Encapsulating polymeric vesicles or polymersomes can be applied in very diverse applications ranging from drug delivery, templates for heterogeneous catalysts, aerosols and personal care products. Moreover, there is some understanding that polymersomes with internal structures can serve as a scaffold for the understanding of complex biological structures, such as the mitochondrium and other (sub-)cellular stuctures. The experimental technique of making polymersomes is relatively new, and the kinetics of their formation delicate, and often not well understood. As a result, the internal and external structures of experimental polymersomes are very diverse, and often highly depend on the method of preparation. Here we report the results of field-theoretic computer simulations of remarkable structures in dispersed droplets of a polymer surfactant. The preparation method is that of quenching a homogenous droplet of polymer surfactant in an aqueous bath. In the discussion part we shortly discuss the road ahead: the use of our method as a tool for understanding complex biological systems.

  8. Charged Group Surface Accessibility Determines Micelleplexes Formation and Cellular Interaction

    PubMed Central

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

    2015-01-01

    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. In this article, we investigated charged group presentation on the micelle surfaces and their interaction with miRNA using thermodynamics, biochemistry, and molecular dynamics simulation. Charged group accessibility on cationic micelle surfaces was shown as a mechanism to alter micelleplex formation and stability. PMID:25866141

  9. 52. CONCRETE FORMWORK FOR THE VAL CELLULAR 'A' FRAME STRUCTURE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    52. CONCRETE FORMWORK FOR THE VAL CELLULAR 'A' FRAME STRUCTURE LOOKING SOUTH, Date unknown, circa December 1946. - Variable Angle Launcher Complex, Variable Angle Launcher, CA State Highway 39 at Morris Reservior, Azusa, Los Angeles County, CA

  10. 51. CONCRETE FORMWORK FOR THE VAL CELLULAR 'A' FRAME STRUCTURE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    51. CONCRETE FORMWORK FOR THE VAL CELLULAR 'A' FRAME STRUCTURE LOOKING NORTHWEST, Date unknown, circa December 1946. - Variable Angle Launcher Complex, Variable Angle Launcher, CA State Highway 39 at Morris Reservior, Azusa, Los Angeles County, CA

  11. Cellular structures in the high-latitude thermosphere

    SciTech Connect

    Crowley, G.; Schoendorf, J.; Roble, R.G.

    1996-01-01

    An organized density (and pressure) structure was recently discovered in the neutral thermosphere at high-latitudes. The structure consists of two to four high- and low-density regions having diameters of 1000 to 2000 km. The density in each region is enhanced or depleted from the hemispheric average by up to 30%. The structure is thus a significant feature of the near-Earth space environment at high-latitudes. The authors refer to each distinct region of enhanced or depleted density as a density {open_quotes}cell.{close_quotes} The cells extend upward from about 120 km into the upper thermosphere, and once formed they remain approximately fixed with respect to the geomagnetic pole. A parametric study of the density cell morphology for different magnetic activity levels is described for equinox solar minimum using the National Center for Atmospheric Research thermosphere ionosphere general circulation model (NCAR model). The TIGCM simulations were used to predict the large density perturbations observed by the S85-1 satellite in a circular sun-synchronous orbit near 200 km altitudes. The most obvious manifestations of the cells was the presence of density peaks located near 70{degrees}{Lambda} on the dayside and nightside, and a density minimum near the magnetic pole. Since high-latitude densities are generally expected to increase during magnetic activity, the low densities over the pole are perhaps the most interesting feature of the cell structure discussed here. The satellite data confirm the existence of the cellular structure over a range of magnetic activity levels. The discovery of the cells is important because the structure provides a unifying framework for the analysis and interpretation of high-latitude data from both past and future experiments. The cells result from various forms of coupling between the ionosphere and thermosphere. The cell formation is quantitatively consistent with concepts from dynamic meteorology. 34 refs., 11 figs.

  12. 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)

  13. 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

  14. 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.

  15. Cellular structural biology as revealed by cryo-electron tomography.

    PubMed

    Irobalieva, Rossitza N; Martins, Bruno; Medalia, Ohad

    2016-02-01

    Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.

  16. Scaling analysis of 2D fractal cellular structures

    NASA Astrophysics Data System (ADS)

    Schliecker, Gudrun

    2001-01-01

    The correlations between topological and metric properties of fractal tessellations are analysed. To this end, Sierpinski cellular structures are constructed for different geometries related to Sierpinski gaskets and to the Apollonian packing of discs. For these geometries, the properties of the distribution of the cells' areas and topologies can be derived analytically. In all cases, an algebraic increase of the cell's average area with its number of neighbours is obtained. This property, unknown from natural cellular structures, confirms previous observations in numerical studies of Voronoi tessellations generated by fractal point sets. In addition, a simple rigorous scaling resp. multiscaling properties relating the shapes and the sizes of the cells are found.

  17. Viral and Cellular Proteins Containing FGDF Motifs Bind G3BP to Block Stress Granule Formation

    PubMed Central

    Panas, Marc D.; Schulte, Tim; Thaa, Bastian; Sandalova, Tatiana; Kedersha, Nancy; Achour, Adnane; McInerney, Gerald M.

    2015-01-01

    The Ras-GAP SH3 domain–binding proteins (G3BP) are essential regulators of the formation of stress granules (SG), cytosolic aggregates of proteins and RNA that are induced upon cellular stress, such as virus infection. Many viruses, including Semliki Forest virus (SFV), block SG induction by targeting G3BP. In this work, we demonstrate that the G3BP-binding motif of SFV nsP3 consists of two FGDF motifs, in which both phenylalanine and the glycine residue are essential for binding. In addition, we show that binding of the cellular G3BP-binding partner USP10 is also mediated by an FGDF motif. Overexpression of wt USP10, but not a mutant lacking the FGDF-motif, blocks SG assembly. Further, we identified FGDF-mediated G3BP binding site in herpes simplex virus (HSV) protein ICP8, and show that ICP8 binding to G3BP also inhibits SG formation, which is a novel function of HSV ICP8. We present a model of the three-dimensional structure of G3BP bound to an FGDF-containing peptide, likely representing a binding mode shared by many proteins to target G3BP. PMID:25658430

  18. Viral and cellular proteins containing FGDF motifs bind G3BP to block stress granule formation.

    PubMed

    Panas, Marc D; Schulte, Tim; Thaa, Bastian; Sandalova, Tatiana; Kedersha, Nancy; Achour, Adnane; McInerney, Gerald M

    2015-02-01

    The Ras-GAP SH3 domain-binding proteins (G3BP) are essential regulators of the formation of stress granules (SG), cytosolic aggregates of proteins and RNA that are induced upon cellular stress, such as virus infection. Many viruses, including Semliki Forest virus (SFV), block SG induction by targeting G3BP. In this work, we demonstrate that the G3BP-binding motif of SFV nsP3 consists of two FGDF motifs, in which both phenylalanine and the glycine residue are essential for binding. In addition, we show that binding of the cellular G3BP-binding partner USP10 is also mediated by an FGDF motif. Overexpression of wt USP10, but not a mutant lacking the FGDF-motif, blocks SG assembly. Further, we identified FGDF-mediated G3BP binding site in herpes simplex virus (HSV) protein ICP8, and show that ICP8 binding to G3BP also inhibits SG formation, which is a novel function of HSV ICP8. We present a model of the three-dimensional structure of G3BP bound to an FGDF-containing peptide, likely representing a binding mode shared by many proteins to target G3BP.

  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. 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.

  3. [Reparative and neoplastic spheroid cellular structures and their mathematical model].

    PubMed

    Kogan, E A; Namiot, V A; Demura, T A; Faĭzullina, N M; Sukhikh, G T

    2014-01-01

    Spheroid cell structures in the cell cultures have been described and are used for studying cell-cell and cell- matrix interactions. At the same time, spheroid cell structure participation in the repair and development of cancer in vivo remains unexplored. The aim of this study was to investigate the cellular composition of spherical structures and their functional significance in the repair of squamous epithelium in human papilloma virus-associated cervical pathology--chronic cervicitis and cervical intraepithelial neoplasia 1-3 degree, and also construct a mathematical model to explain the development and behavior of such spheroid cell structure.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. Statistical properties of cellular automata in the context of learning and recognition: Part 2, inverting local structure theory equations to find cellular automata with specified properties

    SciTech Connect

    Gutowitz, H.A.

    1988-11-18

    This is the second of two lectures. In the first lecture the map from a cellular automaton to a sequence of analytical approximations called the local structure theory was described. In this lecture the inverse map from approximation to the class of cellular automata approximated is constructed. The key matter is formatting the local structure theory equations in terms of block probability estimates weighted by coefficients. The inverse mapping relies on this format. Each possible assignment of values to the coefficients defines a class of automata with related statistical properties. It is suggested that these coefficients serve to smoothly parameterize the space of cellular automata. By varying the values of the parameters a cellular automaton network may be designed so that it has a specified invariant measure. If an invariant measure is considered a ''memory'' of the network, then this variation of parameters to specify the invariant measure must be considered ''learning.'' It is important to note that in this view learning is not the storage of patterns in a network, but rather the tailoring of the dynamics of a network. 7 figs.

  15. 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.

  16. The endoplasmic reticulum: structure, function and response to cellular signaling.

    PubMed

    Schwarz, Dianne S; Blower, Michael D

    2016-01-01

    The endoplasmic reticulum (ER) is a large, dynamic structure that serves many roles in the cell including calcium storage, protein synthesis and lipid metabolism. The diverse functions of the ER are performed by distinct domains; consisting of tubules, sheets and the nuclear envelope. Several proteins that contribute to the overall architecture and dynamics of the ER have been identified, but many questions remain as to how the ER changes shape in response to cellular cues, cell type, cell cycle state and during development of the organism. Here we discuss what is known about the dynamics of the ER, what questions remain, and how coordinated responses add to the layers of regulation in this dynamic organelle. PMID:26433683

  17. A structural and functional homolog supports a general role for frataxin in cellular iron chemistry.

    PubMed

    Qi, Wenbin; Cowan, J A

    2010-02-01

    Bacillus subtilis YdhG lacks sequence homology, but demonstrates structural and functional similarity to the frataxin family, supporting a general cellular role for frataxin-type proteins in cellular iron homeostasis.

  18. 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

  19. Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins

    PubMed Central

    Hegyi, Hedi; Buday, László; Tompa, Peter

    2009-01-01

    Chromosomal translocations, which often generate chimeric proteins by fusing segments of two distinct genes, represent the single major genetic aberration leading to cancer. We suggest that the unifying theme of these events is a high level of intrinsic structural disorder, enabling fusion proteins to evade cellular surveillance mechanisms that eliminate misfolded proteins. Predictions in 406 translocation-related human proteins show that they are significantly enriched in disorder (43.3% vs. 20.7% in all human proteins), they have fewer Pfam domains, and their translocation breakpoints tend to avoid domain splitting. The vicinity of the breakpoint is significantly more disordered than the rest of these already highly disordered fusion proteins. In the unlikely event of domain splitting in fusion it usually spares much of the domain or splits at locations where the newly exposed hydrophobic surface area approximates that of an intact domain. The mechanisms of action of fusion proteins suggest that in most cases their structural disorder is also essential to the acquired oncogenic function, enabling the long-range structural communication of remote binding and/or catalytic elements. In this respect, there are three major mechanisms that contribute to generating an oncogenic signal: (i) a phosphorylation site and a tyrosine-kinase domain are fused, and structural disorder of the intervening region enables intramolecular phosphorylation (e.g., BCR-ABL); (ii) a dimerisation domain fuses with a tyrosine kinase domain and disorder enables the two subunits within the homodimer to engage in permanent intermolecular phosphorylations (e.g., TFG-ALK); (iii) the fusion of a DNA-binding element to a transactivator domain results in an aberrant transcription factor that causes severe misregulation of transcription (e.g. EWS-ATF). Our findings also suggest novel strategies of intervention against the ensuing neoplastic transformations. PMID:19888473

  20. 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.

  1. Real-time 3D visualization of cellular rearrangements during cardiac valve formation.

    PubMed

    Pestel, Jenny; Ramadass, Radhan; Gauvrit, Sebastien; Helker, Christian; Herzog, Wiebke; Stainier, Didier Y R

    2016-06-15

    During cardiac valve development, the single-layered endocardial sheet at the atrioventricular canal (AVC) is remodeled into multilayered immature valve leaflets. Most of our knowledge about this process comes from examining fixed samples that do not allow a real-time appreciation of the intricacies of valve formation. Here, we exploit non-invasive in vivo imaging techniques to identify the dynamic cell behaviors that lead to the formation of the immature valve leaflets. We find that in zebrafish, the valve leaflets consist of two sets of endocardial cells at the luminal and abluminal side, which we refer to as luminal cells (LCs) and abluminal cells (ALCs), respectively. By analyzing cellular rearrangements during valve formation, we observed that the LCs and ALCs originate from the atrium and ventricle, respectively. Furthermore, we utilized Wnt/β-catenin and Notch signaling reporter lines to distinguish between the LCs and ALCs, and also found that cardiac contractility and/or blood flow is necessary for the endocardial expression of these signaling reporters. Thus, our 3D analyses of cardiac valve formation in zebrafish provide fundamental insights into the cellular rearrangements underlying this process.

  2. The suppressive role of p38 MAPK in cellular vacuole formation.

    PubMed

    Chen, Run; Duan, Chun-Yan; Chen, Shao-Kun; Zhang, Chun-Yan; He, Tao; Li, Hong; Liu, You-Ping; Dai, Rong-Yang

    2013-08-01

    Vacuolization of the cytoplasm is one of the dramatic and frequently observed phenomena in various cell types. Cellular vacuoles occur spontaneously or via a wide range of inductive stimuli, but the molecular mechanism involved in this process remains largely unknown. In this study, we investigated the role of the p38 and JNK pathways in the formation of cytoplasmic vacuoles. We found that p38 and JNK agonist anisomycin abolishes spontaneous cytoplasmic vacuolization of HepG2 cells through p38 activation, but not through JNK activation. Importantly, blocking the activity of p38 or suppression the expression of p38 elicits cytoplasmic vacuoles formation in various cancer cells. Furthermore, cytoplasmic vacuoles induced by p38 blocking are derived from the perinuclear region. These observations provide direct evidence for a role of p38 signaling in regulating the formation of cytoplasmic vacuoles.

  3. Variable modulus cellular structures using pneumatic artificial muscles

    NASA Astrophysics Data System (ADS)

    Pontecorvo, Michael E.; Niemiec, Robert J.; Gandhi, Farhan S.

    2014-04-01

    This paper presents a novel variable modulus cellular structure based on a hexagonal unit cell with pneumatic artificial muscle (PAM) inclusions. The cell considered is pin-jointed, loaded in the horizontal direction, with three PAMs (one vertical PAM and two horizontal PAMs) oriented in an "H" configuration between the vertices of the cell. A method for calculation of the hexagonal cell modulus is introduced, as is an expression for the balance of tensile forces between the horizontal and vertical PAMs. An aluminum hexagonal unit cell is fabricated and simulation of the hexagonal cell with PAM inclusions is then compared to experimental measurement of the unit cell modulus in the horizontal direction with all three muscles pressurized to the same value over a pressure range up to 758 kPa. A change in cell modulus by a factor of 1.33 and a corresponding change in cell angle of 0.41° are demonstrated experimentally. A design study via simulation predicts that differential pressurization of the PAMs up to 2068 kPa can change the cell modulus in the horizontal direction by a factor of 6.83 with a change in cell angle of only 2.75°. Both experiment and simulation show that this concept provides a way to decouple the length change of a PAM from the change in modulus to create a structural unit cell whose in-plane modulus in a given direction can be tuned based on the orientation of PAMs within the cell and the pressure supplied to the individual muscles.

  4. Cellular dynamics in the early mouse embryo: from axis formation to gastrulation

    PubMed Central

    Nowotschin, Sonja; Hadjantonakis, Anna-Katerina

    2010-01-01

    Summary Coordinated cell movements and reciprocal tissue interactions direct the formation of the definitive germ layers and the elaboration of the major axes of the mouse embryo. Genetic and embryological studies have defined the major molecular pathways that mediate these morphogenetic processes and provided “snapshots” of the morphogenetic program. However it is increasingly clear that this foundation needs to be validated, and can be significantly refined and extended using live imaging approaches. In situ visualization of these processes in living specimens is a major goal, as it provides unprecedented detail of the individual cellular behaviors, which translate into the large-scale tissue rearrangements that shape the embryo. PMID:20566281

  5. 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.

  6. 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.

  7. Controlled formation of biosilica structures in vitro.

    PubMed

    Naik, Rajesh R; Whitlock, Patrick W; Rodriguez, Francisco; Brott, Lawrence L; Glawe, Diana D; Clarson, Stephen J; Stone, Morley O

    2003-01-21

    Herein we describe the controlled formation of biosilica structures by manipulation of the physical reaction environment; we were able to synthesize arched and elongated silica structures using a synthetic peptide; the results presented here are evidence that in vitro biocatalysis may be controlled in order to form desired silica structures.

  8. Cellular and morphological aspects of fibrodysplasia ossificans progressiva. Lessons of formation, repair, and bone bioengineering.

    PubMed

    Martelli, Anderson; Santos, Arnaldo Rodrigues

    2014-01-01

    Fibrodysplasia ossificans progressiva (FOP) is a rare congenital disease that causes bone formation within the muscles, tendons, ligaments and connective tissues. There is no cure for this disorder and only treatment of the symptoms is available. The purpose of this study was to review the literature and describe the clinical, cellular and molecular aspects of FOP. The material used for the study was obtained by reviewing scientific articles published in various literature-indexed databases. In view of its rarity and of the lack of insightful information and the unpredictability of its course, FOP is a challenging disorder for professionals who are confronted by it. However, this rare disease raises a great deal of interest because understanding the mechanism of mature bone formation can encourage research lines related to bone regeneration and the prevention of heterotopic ossification.

  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. Filament formation by metabolic enzymes is a specific adaptation to an advanced state of cellular starvation

    PubMed Central

    Petrovska, Ivana; Nüske, Elisabeth; Munder, Matthias C; Kulasegaran, Gayathrie; Malinovska, Liliana; Kroschwald, Sonja; Richter, Doris; Fahmy, Karim; Gibson, Kimberley; Verbavatz, Jean-Marc; Alberti, Simon

    2014-01-01

    One of the key questions in biology is how the metabolism of a cell responds to changes in the environment. In budding yeast, starvation causes a drop in intracellular pH, but the functional role of this pH change is not well understood. Here, we show that the enzyme glutamine synthetase (Gln1) forms filaments at low pH and that filament formation leads to enzymatic inactivation. Filament formation by Gln1 is a highly cooperative process, strongly dependent on macromolecular crowding, and involves back-to-back stacking of cylindrical homo-decamers into filaments that associate laterally to form higher order fibrils. Other metabolic enzymes also assemble into filaments at low pH. Hence, we propose that filament formation is a general mechanism to inactivate and store key metabolic enzymes during a state of advanced cellular starvation. These findings have broad implications for understanding the interplay between nutritional stress, the metabolism and the physical organization of a cell. DOI: http://dx.doi.org/10.7554/eLife.02409.001 PMID:24771766

  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. The Biermann Battery and Early Structure Formation

    NASA Astrophysics Data System (ADS)

    Zhao, Fen; Alvarez, Marcelo; Abel, Tom

    2008-03-01

    Using ENZO, a 3D adaptive mesh cosmological simulation code, we look at the characteristics of magnetic fields generated in early structure formation by the Biermann battery process. Tracking six species (H, H+, He, He+, He++ and e-), we follow the formation of structure from multiple independent realizations of cosmological initial conditions to better understand how magnetic fields are generated by non aligned pressure and density gradients. These efforts aim at adding ideal MHD to the ENZO framework which will enable the study of the build up and evolution of cosmic magnetic fields.

  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. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Understanding cochleate formation: insights into structural development.

    PubMed

    Nagarsekar, Kalpa; Ashtikar, Mukul; Steiniger, Frank; Thamm, Jana; Schacher, Felix; Fahr, Alfred

    2016-04-20

    Understanding the structure and the self-assembly process of cochleates has become increasingly necessary considering the advances of this drug delivery system towards the pharmaceutical industry. It is well known that the addition of cations like calcium to a dispersion of anionic lipids such as phosphatidylserines results in stable, multilamellar cochleates through a spontaneous assembly. In the current investigation we have studied the intermediate structures generated during this self-assembly of cochleates. To achieve this, we have varied the process temperature for altering the rate of cochleate formation. Our findings from electron microscopy studies showed the formation of ribbonlike structures, which with proceeding interaction associate to form lipid stacks, networks and eventually cochleates. We also observed that the variation in lipid acyl chains did not make a remarkable difference to the type of structure evolved during the formation of cochleates. More generally, our observations provide a new insight into the self-assembly process of cochleates based on which we have proposed a pathway for cochleate formation from phosphatidylserine and calcium. This knowledge could be employed in using cochleates for a variety of possible biomedical applications in the future.

  3. Neutrophil String Formation: Hydrodynamic Thresholding and Cellular Deformation during Cell Collisions

    PubMed Central

    Kadash, K. E.; Lawrence, M. B.; Diamond, S. L.

    2004-01-01

    Neutrophils unexpectedly display flow-enhanced adhesion (hydrodynamic thresholding) to L-selectin in rolling or aggregation assays. We report that the primary collision efficiency (ɛ) of flowing neutrophils with preadhered neutrophils on intercellular adhesion molecule-1 (ICAM-1) or fibrinogen also displayed a maximum of ɛ ∼ 0.4–0.45 at a wall shear rate of 100 s−1, an example of thresholding. Primary collision lifetime with no detectable bonding decreased from 130 to 10 ms as wall shear rate increased from 30 to 300 s−1, whereas collision lifetimes with bonding decreased from 300 to 100 ms over this shear range using preadhered neutrophils on ICAM-1, with similar results for fibrinogen. Antibodies against L-selectin, but not against CD11a, CD11b, or CD18, reduced ɛ at 100 s−1 by >85%. High resolution imaging detected large scale deformation of the flowing neutrophil during the collision at 100 s−1 with the apparent contact area increasing up to ∼40 μm2. We observed the formation of long linear string assemblies of neutrophils downstream of neutrophils preadhered to ICAM-1, but not fibrinogen, with a maximum in string formation at 100 s−1. Secondary capture events to the ICAM-1 or fibrinogen coated surfaces after primary collisions were infrequent and short lived, typically lasting from 500 to 3500 ms. Between 5 and 20% of neutrophil interactions with ICAM-1 substrate converted to firm arrest (>3500 ms) and greatly exceeded that observed for fibrinogen, thus defining the root cause of poor string formation on fibrinogen at all shear rates. Additionally, neutrophils mobilized calcium after incorporation into strings. Static adhesion also caused calcium mobilization, as did the subsequent onset of flow. To our knowledge, this is the first report of 1), hydrodynamic thresholding in neutrophil string formation; 2), string formation on ICAM-1 but not on fibrinogen; 3), large cellular deformation due to collisions at a venous shear rate; and 4

  4. 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.

  5. 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

  6. 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

  7. The Temporal Structure of Scientific Consensus Formation.

    PubMed

    Shwed, Uri; Bearman, Peter S

    2010-12-01

    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

  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. 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.

  10. SILICOMB PEEK Kirigami cellular structures: mechanical response and energy dissipation through zero and negative stiffness

    NASA Astrophysics Data System (ADS)

    Virk, K.; Monti, A.; Trehard, T.; Marsh, M.; Hazra, K.; Boba, K.; Remillat, C. D. L.; Scarpa, F.; Farrow, I. R.

    2013-08-01

    The work describes the manufacturing, testing and parametric analysis of cellular structures exhibiting zero Poisson’s ratio-type behaviour, together with zero and negative stiffness effects. The cellular structures are produced in flat panels and curved configurations, using a combination of rapid prototyping techniques and Kirigami (Origami and cutting) procedures for PEEK (Polyether Ether Ketone) thermoplastic composites. The curved cellular configurations show remarkable large deformation behaviours, with zero and negative stiffness regimes depending also on the strain rate applied. These unusual stiffness characteristics lead to a large increase of energy absorption during cyclic tests.

  11. 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.

  12. 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

    2016-07-19

    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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. Cellular mechanisms of Müllerian duct formation in the mouse.

    PubMed

    Orvis, Grant D; Behringer, Richard R

    2007-06-15

    Regardless of their sex chromosome karyotype, amniotes develop two pairs of genital ducts, the Wolffian and Müllerian ducts. As the Müllerian duct forms, its growing tip is intimately associated with the Wolffian duct as it elongates to the urogenital sinus. Previous studies have shown that the presence of the Wolffian duct is required for the development and maintenance of the Müllerian duct. The Müllerian duct is known to form by invagination of the coelomic epithelium, but the mechanism for its elongation to the urogenital sinus remains to be defined. Using genetic fate mapping, we demonstrate that the Wolffian duct does not contribute cells to the Müllerian duct. Experimental embryological manipulations and molecular studies show that precursor cells at the caudal tip of the Müllerian duct proliferate to deposit a cord of cells along the length of the urogenital ridge. Furthermore, immunohistochemical analysis reveals that the cells of the developing Müllerian duct are mesoepithelial when deposited, and subsequently differentiate into an epithelial tube and eventually the female reproductive tract. Our studies define cellular and molecular mechanisms for Müllerian duct formation.

  18. 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

  19. 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

  20. Nano hydroxyapatite structures influence early bone formation.

    PubMed

    Meirelles, Luiz; Arvidsson, Anna; Andersson, Martin; Kjellin, Per; Albrektsson, Tomas; Wennerberg, Ann

    2008-11-01

    In a study model that aims to evaluate the effect of nanotopography on bone formation, micrometer structures known to alter bone formation, should be removed. Electropolished titanium implants were prepared to obtain a surface topography in the absence of micro structures, thereafter the implants were divided in two groups. The test group was modified with nanosize hydroxyapatite particles; the other group was left uncoated and served as control for the experiment. Topographical evaluation demonstrated increased nanoroughness parameters for the nano-HA implant and higher surface porosity compared to the control implant. The detected features had increased size and diameter equivalent to the nano-HA crystals present in the solution and the relative frequency of the feature size and diameter was very similar. Furthermore, feature density per microm(2) showed a decrease of 13.5% on the nano-HA implant. Chemical characterization revealed calcium and phosphorous ions on the modified implants, whereas the control implants consisted of pure titanium oxide. Histological evaluation demonstrated significantly increased bone formation to the coated (p < 0.05) compared to uncoated implants after 4 weeks of healing. These findings indicate for the first time that early bone formation is dependent on the nanosize hydroxyapatite features, but we are unaware if we see an isolated effect of the chemistry or of the nanotopography or a combination of both.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  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.

  7. 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

  8. 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.

  9. Thermal stability of the cellular structure of an austenitic alloy after selective laser melting

    NASA Astrophysics Data System (ADS)

    Bazaleeva, K. O.; Tsvetkova, E. V.; Balakirev, E. V.; Yadroitsev, I. A.; Smurov, I. Yu.

    2016-05-01

    The thermal stability of the cellular structure of an austenitic Fe-17% Cr-12% Ni-2% Mo-1% Mn-0.7% Si-0.02% C alloy produced by selective laser melting in the temperature range 20-1200°C is investigated. Metallographic analysis, transmission electron microscopy, and scanning electron microscopy show that structural changes in the alloy begin at 600-700°C and are fully completed at ~1150°C. Differential scanning calorimetry of the alloy with a cellular structure reveals three exothermic processes occurring upon annealing within the temperature ranges 450-650, 800-1000, and 1050-1200°C.

  10. 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.

  11. Nitrosothiol formation and protection against Fenton chemistry by nitric oxide-induced dinitrosyliron complex formation from anoxia-initiated cellular chelatable iron increase.

    PubMed

    Li, Qian; Li, Chuanyu; Mahtani, Harry K; Du, Jian; Patel, Aashka R; Lancaster, Jack R

    2014-07-18

    Dinitrosyliron complexes (DNIC) have been found in a variety of pathological settings associated with (•)NO. However, the iron source of cellular DNIC is unknown. Previous studies on this question using prolonged (•)NO exposure could be misleading due to the movement of intracellular iron among different sources. We here report that brief (•)NO exposure results in only barely detectable DNIC, but levels increase dramatically after 1-2 h of anoxia. This increase is similar quantitatively and temporally with increases in the chelatable iron, and brief (•)NO treatment prevents detection of this anoxia-induced increased chelatable iron by deferoxamine. DNIC formation is so rapid that it is limited by the availability of (•)NO and chelatable iron. We utilize this ability to selectively manipulate cellular chelatable iron levels and provide evidence for two cellular functions of endogenous DNIC formation, protection against anoxia-induced reactive oxygen chemistry from the Fenton reaction and formation by transnitrosation of protein nitrosothiols (RSNO). The levels of RSNO under these high chelatable iron levels are comparable with DNIC levels and suggest that under these conditions, both DNIC and RSNO are the most abundant cellular adducts of (•)NO.

  12. 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.

  13. 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.

  14. 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

  15. High-Temperature Structure Formation in Metals

    NASA Astrophysics Data System (ADS)

    Filippov, E. S.

    2014-04-01

    Using a non-conventional theoretical approach relying on the electronic density (its probability) distribution in the coordinate space between ion cores rather than on the analysis of P = hk in the momentum space, volumetric and linear atomic relations are formulated, which control the mechanisms of structure formation (bcc, fcc, hcp, hexagonal, etc.) at Т ≈ Т melt. Based on an assumption of electronic density fluctuation in the course of energy gap smearing, the design variable (radius) of the half width value of the probability distribution is derived using coordinate R for the maximum electronic density fluctuation (at the maximum of the Gaussian function).

  16. 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.

  17. 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

  18. Advances in high-resolution imaging – techniques for three-dimensional imaging of cellular structures

    PubMed Central

    Lidke, Diane S.; Lidke, Keith A.

    2012-01-01

    A fundamental goal in biology is to determine how cellular organization is coupled to function. To achieve this goal, a better understanding of organelle composition and structure is needed. Although visualization of cellular organelles using fluorescence or electron microscopy (EM) has become a common tool for the cell biologist, recent advances are providing a clearer picture of the cell than ever before. In particular, advanced light-microscopy techniques are achieving resolutions below the diffraction limit and EM tomography provides high-resolution three-dimensional (3D) images of cellular structures. The ability to perform both fluorescence and electron microscopy on the same sample (correlative light and electron microscopy, CLEM) makes it possible to identify where a fluorescently labeled protein is located with respect to organelle structures visualized by EM. Here, we review the current state of the art in 3D biological imaging techniques with a focus on recent advances in electron microscopy and fluorescence super-resolution techniques. PMID:22685332

  19. 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

  20. 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.

  1. 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.

  2. 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.

  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. 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

  5. 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. PMID:27499868

  6. Nanostructured cellular networks.

    PubMed

    Moriarty, P; Taylor, M D R; Brust, M

    2002-12-01

    Au nanocrystals spin-coated onto silicon from toluene form cellular networks. A quantitative statistical crystallography analysis shows that intercellular correlations drive the networks far from statistical equilibrium. Spin-coating from hexane does not produce cellular structure, yet a strong correlation is retained in the positions of nanocrystal aggregates. Mechanisms based on Marangoni convection alone cannot account for the variety of patterns observed, and we argue that spinodal decomposition plays an important role in foam formation.

  7. Structure Formation Cosmic Rays: Identifying Observational Constraints

    NASA Astrophysics Data System (ADS)

    Prodanovic, T.; Fields, B. D.

    2005-06-01

    Shocks that arise from baryonic in-fall and merger events during the structure formation are believed to be a source of cosmic rays. These "structure formation cosmic rays" (SFCRs) would essentially be primordial in composition, namely, mostly made of protons and alpha particles. However, very little is known about this population of cosmic rays. One way to test the level of its presence is to look at the products of hadronic reactions between SFCRs and the ISM. A perfect probe of these reactions would be 6Li. The rare isotope 6Li is produced only by cosmic rays, dominantly in alpha alpha rightarrow 6Li fusion reactions with the ISM helium. Consequently, this nuclide provides a unique diagnostic of the history of cosmic rays. Exactly because of this unique property is 6Li affected most by the presence of an additional cosmic ray population. In turn, this could have profound consequences for the Big-Bang nucleosynthesis: cosmic rays created during cosmic structure formation would lead to pre-Galactic Li production, which would act as a "contaminant" to the primordial 7Li content of metal-poor halo stars. Given the already existing problem of establishing the concordance between 7Li observed in halo stars and primordial 7Li as predicted by the WMAP, it is crucial to set limits to the level of this "contamination". However, the history of SFCRs is not very well known. Thus we propose a few model- independent ways of testing the SFCR species and their history, as well as the existing lithium problem: 1) we establish the connection between gamma-ray and 6Li production, which enables us to place constraints on the SFCR-made lithium by using the observed Extragalactic Gamma-Ray Background (EGRB); 2) we propose a new site for testing the primordial and SFCR-made lithium, namely, low-metalicity High-Velocity Clouds (HVCs), which retain the pre-Galactic composition without any significant depletion. Although using one method alone may not give us strong constraints, using

  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.

  10. 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.

  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. Distinct BimBH3 (BimSAHB) Stapled Peptides for Structural and Cellular Studies

    PubMed Central

    Bird, Greg H.; Gavathiotis, Evripidis; LaBelle, James L.; Katz, Samuel G.; Walensky, Loren D.

    2014-01-01

    Hydrocarbon stapling is a chemical approach to restoring and fortifying the natural α-helical structure of peptides that otherwise unfold when taken out of context from the host protein. By iterating the peptide sequence, staple type, and sites of insertion, discrete compositions can be generated to suit a diversity of biochemical, structural, proteomic, cellular, and drug development applications. Here, we reinforce key design considerations to avoid pitfalls and maximize progress when applying stapled peptides in chemistry and biology research. PMID:24358963

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Three-dimensional cellular and subcellular structures of human brain tissue determined by microtomography

    NASA Astrophysics Data System (ADS)

    Mizutani, Ryuta; Takeuchi, Akihisa; Takekoshi, Susumu; Yoshiyuki Osamura, R.; Uesugi, Kentaro; Suzuki, Yoshio

    2009-09-01

    We report here x-ray microtomographic studies of human cerebral cortex stained with high-Z elements. Brain tissues were stained with metal elements by the Golgi and Bodian impregnation methods and subjected to x-ray microtomographic analysis. Axons and dendrites arising from cell bodies were visualized as three-dimensional networks. Spherical structures of cellular nuclei were observed in the interiors of cell bodies, indicating that hard x-ray microtomography can reveal the intracellular structure. High-Z element microcontrasting in conjunction with microtomographic analysis can be applied to any soft tissues. Our results show that the metal contrasting facilitates the three-dimensional microtomographic visualization of cellular and subcellular structures of soft tissues.

  19. Heat shock cognate 71 (HSC71) regulates cellular antiviral response by impairing formation of VISA aggregates.

    PubMed

    Liu, Zhigang; Wu, Shu-Wen; Lei, Cao-Qi; Zhou, Qian; Li, Shu; Shu, Hong-Bing; Wang, Yan-Yi

    2013-05-01

    In response to viral infection, RIG-I-like RNA helicases detect viral RNA and signal through the mitochondrial adapter protein VISA. VISA activation leads to rapid activation of transcription factors IRF3 and NF-κB, which collaborate to induce transcription of type I interferon (IFN) genes and cellular antiviral response. It has been demonstrated that VISA is activated by forming prion-like aggregates. However, how this process is regulated remains unknown. Here we show that overexpression of HSC71 resulted in potent inhibition of virus-triggered transcription of IFNB1 gene and cellular antiviral response. Consistently, knockdown of HSC71 had opposite effects. HSC71 interacted with VISA, and negatively regulated virus-triggered VISA aggregation. These findings suggest that HSC71 functions as a check against VISA-mediated antiviral response.

  20. 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

  1. Cellular Automata for Spatiotemporal Pattern Formation from Reaction-Diffusion Partial Differential Equations

    NASA Astrophysics Data System (ADS)

    Ohmori, Shousuke; Yamazaki, Yoshihiro

    2016-01-01

    Ultradiscrete equations are derived from a set of reaction-diffusion partial differential equations, and cellular automaton rules are obtained on the basis of the ultradiscrete equations. Some rules reproduce the dynamical properties of the original reaction-diffusion equations, namely, bistability and pulse annihilation. Furthermore, other rules bring about soliton-like preservation and periodic pulse generation with a pacemaker, which are not obtained from the original reaction-diffusion equations.

  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. 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.

  4. Silicene oxides: formation, structures and electronic properties.

    PubMed

    Wang, Rong; Pi, Xiaodong; Ni, Zhenyi; Liu, Yong; Lin, Shisheng; Xu, Mingsheng; Yang, Deren

    2013-12-16

    Understanding the oxidation of silicon has been critical to the success of all types of silicon materials, which are the cornerstones of modern silicon technologies. For the recent experimentally obtained two-dimensional silicene, oxidation should also be addressed to enable the development of silicene-based devices. Here we focus on silicene oxides (SOs) that result from the partial or full oxidation of silicene in the framework of density functional theory. It is found that the formation of SOs greatly depends on oxidation conditions, which concern the oxidizing agents of oxygen and hydroxyl. The honeycomb lattice of silicene may be preserved, distorted or destroyed after oxidation. The charge state of Si in partially oxidized silicene ranges from +1 to +3, while that in fully oxidized silicene is +4. Metals, semimetals, semiconductors and insulators can all be found among the SOs, which show a wide spectrum of electronic structures. Our work indicates that the oxidation of silicene should be exquisitely controlled to obtain specific SOs with desired electronic properties.

  5. A Single Chance to Contact Multiple Targets: Distinct Osteocyte Morphotypes Shed Light on the Cellular Mechanism Ensuring the Robust Formation of Osteocytic Networks.

    PubMed

    Fritz, Alan; Bertin, Ariana; Hanna, Patricia; Nualart, Francisco; Marcellini, Sylvain

    2016-07-01

    The formation of the complex osteocytic network relies on the emission of long cellular processes involved in communication, mechanical strain sensing, and bone turnover control. Newly deposited osteocytic processes rapidly become trapped within the calcifying matrix, and, therefore, they must adopt their definitive conformation and contact their targets in a single morphogenetic event. However, the cellular mechanisms ensuring the robustness of this unique mode of morphogenesis remain unknown. To address this issue, we examined the developing calvaria of the amphibian Xenopus tropicalis by confocal, two-photon, and super-resolution imaging, and described flattened osteocytes lying within a woven bone structured in lamellae of randomly oriented collagen fibers. While most cells emit peripheral and perpendicular processes, we report two osteocytes morphotypes, located at different depth within the bone matrix and exhibiting distinct number and orientation of perpendicular cell processes. We show that this pattern is conserved with the chick Gallus gallus and suggest that the cellular microenvironment, and more particularly cell-cell contact, plays a fundamental role in the induction and stabilization of osteocytic processes. We propose that this intrinsic property might have been evolutionarily selected for its ability to robustly generate self-organizing osteocytic networks harbored by the wide variety of bone shapes and architectures found in extant and extinct vertebrates. PMID:27381191

  6. 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.

  7. 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

  8. Relationship between sodium-dependent phosphate transporter (NaPi-IIc) function and cellular vacuole formation in opossum kidney cells.

    PubMed

    Shiozaki, Yuji; Segawa, Hiroko; Ohnishi, Saori; Ohi, Akiko; Ito, Mikiko; Kaneko, Ichiro; Kido, Shinsuke; Tatsumi, Sawako; Miyamoto, Ken-ichi

    2015-01-01

    NaPi-IIc/SLC34A3 is a sodium-dependent inorganic phosphate (Pi) transporter in the renal proximal tubules and its mutations cause hereditary hypophosphatemic rickets with hypercalciuria (HHRH). In the present study, we created a specific antibody for opossum SLC34A3, NaPi-IIc (oNaPi-IIc), and analyzed its localization and regulation in opossum kidney cells (a tissue culture model of proximal tubular cells). Immunoreactive oNaPi-IIc protein levels increased during the proliferative phase and decreased during differentiation. Moreover, stimulating cell growth upregulated oNaPi-IIc protein levels, whereas suppressing cell proliferation downregulated oNaPi-IIc protein levels. Immunocytochemistry revealed that endogenous and exogenous oNaPi-IIc proteins localized at the protrusion of the plasma membrane, which is a phosphatidylinositol 4,5-bisphosphate (PIP2) rich-membrane, and at the intracellular vacuolar membrane. Exogenous NaPi-IIc also induced cellular vacuoles and localized in the plasma membrane. The ability to form vacuoles is specific to electroneutral NaPi-IIc, and not electrogenic NaPi-IIa or NaPi-IIb. In addition, mutations of NaPi-IIc (S138F and R468W) in HHRH did not cause cellular PIP2-rich vacuoles. In conclusion, our data anticipate that NaPi-IIc may regulate PIP2 production at the plasma membrane and cellular vesicle formation. PMID:26399350

  9. Non-standard structure formation scenarios

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Little, Brett; Islam, Ranty; Devriendt, Julien; Mahmood, Asim; Silk, Joe

    2003-04-01

    Observations on galactic scales seem to be in contradiction with recent high resolution N-body simulations. This so-called cold dark matter (CDM) crisis has been addressed in several ways, ranging from a change in fundamental physics by introducing self-interacting cold dark matter particles to a tuning of complex astrophysical processes such as global and/or local feedback. All these efforts attempt to soften density profiles and reduce the abundance of satellites in simulated galaxy halos. In this contribution we are exploring the differences between a Warm Dark Matter model and a CDM model where the power on a certain scale is reduced by introducing a narrow negative feature (`dip'). This dip is placed in a way so as to mimic the loss of power in the WDM model: both models have the same integrated power out to the scale where the power of the Dip model rises to the level of the unperturbed CDM spectrum again. Using N-body simulations we show that that the new Dip model appears to be a viable alternative to WDM while being based on different physics: where WDM requires the introduction of a new particle species the Dip stems from anon-standard inflationary period. If we are looking for an alternative to the currently challenged standard ΛCDM structure formation scenario, neither the ΛWDM nor the new Dip model can be ruled out with respect to the analysis presented in this contribution. They both make very similar predictions and the degeneracy between them can only be broken with observations yet to come.

  10. 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

  11. DNA Polymerase κ Is a Key Cellular Factor for the Formation of Covalently Closed Circular DNA of Hepatitis B Virus

    PubMed Central

    Qi, Yonghe; Gao, Zhenchao; Peng, Bo; Yan, Huan; Tang, Dingbin; Song, Zilin; He, Wenhui; Sun, Yinyan; Guo, Ju-Tao; Li, Wenhui

    2016-01-01

    Hepatitis B virus (HBV) infection of hepatocytes begins by binding to its cellular receptor sodium taurocholate cotransporting polypeptide (NTCP), followed by the internalization of viral nucleocapsid into the cytoplasm. The viral relaxed circular (rc) DNA genome in nucleocapsid is transported into the nucleus and converted into covalently closed circular (ccc) DNA to serve as a viral persistence reservoir that is refractory to current antiviral therapies. Host DNA repair enzymes have been speculated to catalyze the conversion of rcDNA to cccDNA, however, the DNA polymerase(s) that fills the gap in the plus strand of rcDNA remains to be determined. Here we conducted targeted genetic screening in combination with chemical inhibition to identify the cellular DNA polymerase(s) responsible for cccDNA formation, and exploited recombinant HBV with capsid coding deficiency which infects HepG2-NTCP cells with similar efficiency of wild-type HBV to assure cccDNA synthesis is exclusively from de novo HBV infection. We found that DNA polymerase κ (POLK), a Y-family DNA polymerase with maximum activity in non-dividing cells, substantially contributes to cccDNA formation during de novo HBV infection. Depleting gene expression of POLK in HepG2-NTCP cells by either siRNA knockdown or CRISPR/Cas9 knockout inhibited the conversion of rcDNA into cccDNA, while the diminished cccDNA formation in, and hence the viral infection of, the knockout cells could be effectively rescued by ectopic expression of POLK. These studies revealed that POLK is a crucial host factor required for cccDNA formation during a de novo HBV infection and suggest that POLK may be a potential target for developing antivirals against HBV. PMID:27783675

  12. 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.

  13. 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.

  14. 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.

  15. Structure-property relationship for cellular accumulation of macrolones in human polymorphonuclear leukocytes (PMNs).

    PubMed

    Munić Kos, Vesna; Koštrun, Sanja; Fajdetić, Andrea; Bosnar, Martina; Kelnerić, Željko; Stepanić, Višnja; Eraković Haber, Vesna

    2013-05-13

    Macrolones are a new class of antimicrobial compounds consisting of a macrolide scaffold linked to a 4-quinolone-3-carboxylic acid moiety via C(4″) position of a macrolide. As macrolides are known to possess favorable pharmacokinetic properties by accumulating in inflammatory cells, in this study we determined the intensity of accumulation in human polymorphonuclear leukocytes (PMNs) of 57 compounds of the macrolone class and analyzed the relationship between the molecular structure and this cellular pharmacokinetic property. Accumulation of macrolones ranged from 0 to 5.5-fold higher than the standard macrolide azithromycin. Distinct structural features in all three considered molecule parts: the macrolide scaffold, quinolone moiety and the linker, affect cellular accumulation. Interestingly, while the parent macrolide, azithromycin, accumulates approximately 3-fold more than clarithromycin, among macrolones all clarithromycin derivatives accumulated in PMNs significantly more than their azithromycin counterparts. Modeling cellular accumulation of macrolones with simple molecular descriptors, as well as with the measured octanol-water distribution coefficient, revealed that the number of hydrogen bond donors and secondary amide groups negatively contribute to macrolone accumulation, while lipophilicity makes a positive contribution.

  16. 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.

  17. 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

  18. 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

  19. Functional connectivity estimation over large networks at cellular resolution based on electrophysiological recordings and structural prior

    PubMed Central

    Ullo, Simona; Nieus, Thierry R.; Sona, Diego; Maccione, Alessandro; Berdondini, Luca; Murino, Vittorio

    2014-01-01

    Despite many structural and functional aspects of the brain organization have been extensively studied in neuroscience, we are still far from a clear understanding of the intricate structure-function interactions occurring in the multi-layered brain architecture, where billions of different neurons are involved. Although structure and function can individually convey a large amount of information, only a combined study of these two aspects can probably shade light on how brain circuits develop and operate at the cellular scale. Here, we propose a novel approach for refining functional connectivity estimates within neuronal networks using the structural connectivity as prior. This is done at the mesoscale, dealing with thousands of neurons while reaching, at the microscale, an unprecedented cellular resolution. The High-Density Micro Electrode Array (HD-MEA) technology, combined with fluorescence microscopy, offers the unique opportunity to acquire structural and functional data from large neuronal cultures approaching the granularity of the single cell. In this work, an advanced method based on probabilistic directional features and heat propagation is introduced to estimate the structural connectivity from the fluorescence image while functional connectivity graphs are obtained from the cross-correlation analysis of the spiking activity. Structural and functional information are then integrated by reweighting the functional connectivity graph based on the structural prior. Results show that the resulting functional connectivity estimates are more coherent with the network topology, as compared to standard measures purely based on cross-correlations and spatio-temporal filters. We finally use the obtained results to gain some insights on which features of the functional activity are more relevant to characterize actual neuronal interactions. PMID:25477790

  20. Functional connectivity estimation over large networks at cellular resolution based on electrophysiological recordings and structural prior.

    PubMed

    Ullo, Simona; Nieus, Thierry R; Sona, Diego; Maccione, Alessandro; Berdondini, Luca; Murino, Vittorio

    2014-01-01

    Despite many structural and functional aspects of the brain organization have been extensively studied in neuroscience, we are still far from a clear understanding of the intricate structure-function interactions occurring in the multi-layered brain architecture, where billions of different neurons are involved. Although structure and function can individually convey a large amount of information, only a combined study of these two aspects can probably shade light on how brain circuits develop and operate at the cellular scale. Here, we propose a novel approach for refining functional connectivity estimates within neuronal networks using the structural connectivity as prior. This is done at the mesoscale, dealing with thousands of neurons while reaching, at the microscale, an unprecedented cellular resolution. The High-Density Micro Electrode Array (HD-MEA) technology, combined with fluorescence microscopy, offers the unique opportunity to acquire structural and functional data from large neuronal cultures approaching the granularity of the single cell. In this work, an advanced method based on probabilistic directional features and heat propagation is introduced to estimate the structural connectivity from the fluorescence image while functional connectivity graphs are obtained from the cross-correlation analysis of the spiking activity. Structural and functional information are then integrated by reweighting the functional connectivity graph based on the structural prior. Results show that the resulting functional connectivity estimates are more coherent with the network topology, as compared to standard measures purely based on cross-correlations and spatio-temporal filters. We finally use the obtained results to gain some insights on which features of the functional activity are more relevant to characterize actual neuronal interactions. PMID:25477790

  1. Cellular and Molecular Mechanisms of Synovial Joint and Articular Cartilage Formation

    PubMed Central

    Pacifici, Maurizio; Koyama, Eiki; Shibukawa, Yoshihiro; Wu, Changshan; Tamamura, Yoshihiro; Enomoto-Iwamoto, Motomi; Iwamoto, Masahiro

    2009-01-01

    Synovial joints and articular cartilage play crucial roles in skeletal function, but relatively little is actually known about their embryonic development. Here we first focused on the interzone, a thin mesenchymal cell layer forming at future joint sites that is widely thought to be critical for joint and articular cartilage development. To determine interzone cell origin and fate, we microinjected the vital fluorescent dye DiI at several peri-joint sites in chick limbs and monitored behavior and fate of labeled cells over time. Peri-joint mesenchymal cells located immediately adjacent to incipient joints migrated, became part of the interzone, and were eventually found in epiphyseal articular layer and joint capsule. Interzone cells isolated and reared in vitro expressed typical phenotypic markers, including GDF-5, Wnt-14 and CD-44, and differentiated into chondrocytes over time. To determine the molecular mechanisms of articular chondrocyte formation, we carried out additional studies on the ets transcription factor family member ERG and its alternatively-spliced variant C-1-1 that we previously found to be expressed in developing avian articular chondrocytes. We cloned the human counterpart of avian C-1-1 (ERGp55Δ81) and conditionally expressed it in transgenic mice under cartilage-specific Col2 gene promoter-enhancer control. The entire transgenic mouse limb chondrocyte population exhibited an immature articular-like phenotype and a virtual lack of growth plate formation and chondrocyte maturation compared to wild type littermate. Together, our studies reveal that peri-joint mesenchymal cells take part in interzone and articular layer formation, interzone cells can differentiate into chondrocytes, and acquisition of a permanent articular chondrocyte phenotype is aided and perhaps dictated by ets transcription factor ERG. PMID:16831907

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Cardiac Troponin and Tropomyosin: Structural and Cellular Perspectives to Unveil the Hypertrophic Cardiomyopathy Phenotype

    PubMed Central

    Marques, Mayra de A.; de Oliveira, Guilherme A. P.

    2016-01-01

    Inherited myopathies affect both skeletal and cardiac muscle and are commonly associated with genetic dysfunctions, leading to the production of anomalous proteins. In cardiomyopathies, mutations frequently occur in sarcomeric genes, but the cause-effect scenario between genetic alterations and pathological processes remains elusive. Hypertrophic cardiomyopathy (HCM) was the first cardiac disease associated with a genetic background. Since the discovery of the first mutation in the β-myosin heavy chain, more than 1400 new mutations in 11 sarcomeric genes have been reported, awarding HCM the title of the “disease of the sarcomere.” The most common macroscopic phenotypes are left ventricle and interventricular septal thickening, but because the clinical profile of this disease is quite heterogeneous, these phenotypes are not suitable for an accurate diagnosis. The development of genomic approaches for clinical investigation allows for diagnostic progress and understanding at the molecular level. Meanwhile, the lack of accurate in vivo models to better comprehend the cellular events triggered by this pathology has become a challenge. Notwithstanding, the imbalance of Ca2+ concentrations, altered signaling pathways, induction of apoptotic factors, and heart remodeling leading to abnormal anatomy have already been reported. Of note, a misbalance of signaling biomolecules, such as kinases and tumor suppressors (e.g., Akt and p53), seems to participate in apoptotic and fibrotic events. In HCM, structural and cellular information about defective sarcomeric proteins and their altered interactome is emerging but still represents a bottleneck for developing new concepts in basic research and for future therapeutic interventions. This review focuses on the structural and cellular alterations triggered by HCM-causing mutations in troponin and tropomyosin proteins and how structural biology can aid in the discovery of new platforms for therapeutics. We highlight the

  7. Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM.

    PubMed

    Hashiguchi, Takao; Ose, Toyoyuki; Kubota, Marie; Maita, Nobuo; Kamishikiryo, Jun; Maenaka, Katsumi; Yanagi, Yusuke

    2011-02-01

    Measles virus, a major cause of childhood morbidity and mortality worldwide, predominantly infects immune cells using signaling lymphocyte activation molecule (SLAM) as a cellular receptor. Here we present crystal structures of measles virus hemagglutinin (MV-H), the receptor-binding glycoprotein, in complex with SLAM. The MV-H head domain binds to a β-sheet of the membrane-distal ectodomain of SLAM using the side of its β-propeller fold. This is distinct from attachment proteins of other paramyxoviruses that bind receptors using the top of their β-propeller. The structure provides templates for antiviral drug design, an explanation for the effectiveness of the measles virus vaccine, and a model of the homophilic SLAM-SLAM interaction involved in immune modulations. Notably, the crystal structures obtained show two forms of the MV-H-SLAM tetrameric assembly (dimer of dimers), which may have implications for the mechanism of fusion triggering.

  8. Structural insights into the extra cellular segment of integrinβ5 and molecular interaction studies.

    PubMed

    Setti, Aravind; Sankati, Harsha Sagar; Devi, T A Phazna; Sekhar, A Chandra; Rao, J Venkateshwar; Pawar, Smita C

    2013-10-01

    Primary tumor cells often spread to other organs by metastasis. Despite of it, primary tumor cells break their surrounding extra cellular matrix (ECM) proteins and reach the destination organ by the process of intravasation and extravasation. Metastasized tumor cells induce the process of angiogenesis, this highly regulated process involves several ECM proteins. However, integrins are primarily involved in the blood vessel growth and repair. Therefore, integrins are promising angiogenesis targets. Integrins are receptors on cell surface, involved in signal transduction and attachments in extra cellular matrix (ECM). IntegrinαVβ3 and αVβ5 are implicated in tumor angiogenesis, metastasis, inflammation and bone resorption. The crystal structure of integrinαvβ5 is not available in protein structural databases, therefore; molecular model of integrinβ5 structure was prepared and stereo chemical model quality was checked. Integrin β5 active sites were identified based on insilico analysis tools. Further, molecular level interactions between integrinβ5 and ECM proteins were predicted. In the present study ECM proteins such as focal adhesion kinase 1 (FAK1), annexin A5 and P21 activated kinase 4 (PAK4) were considered for protein-protein docking, to understand inter molecular interactions. The predicted model is conceived to be stereo chemically good and can be used for molecular interaction studies of angiogenic inhibitors. PMID:23962022

  9. 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.

  10. 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.

  11. On the importance of cotranscriptional RNA structure formation.

    PubMed

    Lai, Daniel; Proctor, Jeff R; Meyer, Irmtraud M

    2013-11-01

    The expression of genes, both coding and noncoding, can be significantly influenced by RNA structural features of their corresponding transcripts. There is by now mounting experimental and some theoretical evidence that structure formation in vivo starts during transcription and that this cotranscriptional folding determines the functional RNA structural features that are being formed. Several decades of research in bioinformatics have resulted in a wide range of computational methods for predicting RNA secondary structures. Almost all state-of-the-art methods in terms of prediction accuracy, however, completely ignore the process of structure formation and focus exclusively on the final RNA structure. This review hopes to bridge this gap. We summarize the existing evidence for cotranscriptional folding and then review the different, currently used strategies for RNA secondary-structure prediction. Finally, we propose a range of ideas on how state-of-the-art methods could be potentially improved by explicitly capturing the process of cotranscriptional structure formation.

  12. 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.

  13. Heterocomplex formation of 5-HT2A-mGlu2 and its relevance for cellular signaling cascades.

    PubMed

    Delille, Hannah K; Becker, Judith M; Burkhardt, Sabrina; Bleher, Barbara; Terstappen, Georg C; Schmidt, Martin; Meyer, Axel H; Unger, Liliane; Marek, Gerard J; Mezler, Mario

    2012-06-01

    Dopamine, serotonin and glutamate play a role in the pathophysiology of schizophrenia. In the brain a functional crosstalk between the serotonin receptor 5-HT(2A) and the metabotropic glutamate receptor mGlu(2) has been demonstrated. Such a crosstalk may be mediated indirectly through neuronal networks or directly by receptor oligomerization. A direct link of the 5-HT(2A)-mGlu(2) heterocomplex formation to receptor function, i.e. to intracellular signaling, has not been fully demonstrated yet. Here we confirm the formation of 5-HT(2A)-mGlu(2) heterocomplexes using quantitative Snap/Clip-tag based HTRF methods. Additionally, mGlu(2) formed complexes with 5-HT(2B) and mGlu(5) but not 5-HT(2C) indicating that complex formation is not specific to the 5-HT(2A)-mGlu(2) pair. We studied the functional consequences of the 5-HT(2A)-mGlu(2) heterocomplex addressing cellular signaling pathways. Co-expression of receptors in HEK-293 cells had no relevant effects on signaling mediated by the individual receptors when mGlu(2) agonists, antagonists and PAMs, or 5-HT(2A) hallucinogenic and non-hallucinogenic agonists and antagonists were used. Hallucinogenic 5-HT(2A) agonists induced signaling through G(q/11), but not G(i) and thus did not lead to modulation of intracellular cAMP levels. In membranes of the medial prefrontal cortex [(3)H]-LY341495 binding competition of mGlu(2/3) agonist LY354740 was not influenced by 2,5-dimethoxy-4-iodoamphetamine (DOI). Taken together, the formation of GPCR heterocomplexes does not necessarily translate into second messenger effects. These results do not put into question the well-documented functional cross-talk of the two receptors in the brain, but do challenge the biological relevance of the 5-HT(2A)-mGlu(2) heterocomplex.

  14. 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.

  15. Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor

    PubMed Central

    Lilyestrom, Wayne; Klein, Michael G.; Zhang, Rongguang; Joachimiak, Andrzej; Chen, Xiaojiang S.

    2006-01-01

    The transformation potential of Simian Virus 40 depends on the activities of large T-antigen (LTag), which interacts with several cellular tumor suppressors including the important “guardian” of the genome, p53. Inhibition of p53 function by LTag is necessary for both efficient viral replication and cellular transformation. We determined the crystal structure of LTag in complex with p53. The structure reveals an unexpected hexameric complex of LTag binding six p53 monomers. Structure-guided mutagenesis of LTag and p53 residues supported the p53–LTag interface defined by the complex structure. The structure also shows that LTag binding induces dramatic conformational changes at the DNA-binding area of p53, which is achieved partially through an unusual “methionine switch” within p53. In the complex structure, LTag occupies the whole p53 DNA-binding surface and likely interferes with formation of a functional p53 tetramer. In addition, we showed that p53 inhibited LTag helicase function through direct complex formation. PMID:16951253

  16. Discovery during Hydrogen Annealing: Formation of Nanoscale Fluorocarbon Tubular Structures

    NASA Astrophysics Data System (ADS)

    Hao, Xiuchun; Tanaka, Sinya; Masuda, Atsuhiko; Maenaka, Kazusuke; Higuchi, Kohei

    2013-09-01

    A novel fabrication method for nanoscale tubular structures is presented in this paper. The tubular structures can be obtained by heating single-crystal silicon trenches or pillars formed by the inductively coupled plasma reactive-ion etching (ICP-RIE) Bosch process in hydrogen ambient. The importance of initial vacuum in the reaction chamber for tube formation and the tube formation mechanism were discussed. The components and sidewall size of the tubular structure were also studied to verify that the tube is made of the fluorocarbon (CF) passivation layer deposited by the Bosch process. The CF tubular structure would be a promising structure for BioMEMS.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Structuring Classroom Discourse Using Formative Assessment Rubrics

    NASA Astrophysics Data System (ADS)

    Brookes, David T.; Lin, Yuhfen

    2010-10-01

    There has been substantial attention paid to students' abilities to engage in a scientific discussion and think critically in a science class. But what constitutes critical thinking in physics? We will discuss a view that critical thinking involves participants (students) becoming increasingly involved in a specialized form of argument that has fixed epistemic rules, but whose rules are seldom made explicit within the physics community that uses them. We will then discuss one method of making the epistemic rules of physics explicit for students by using formative assessment rubrics. We will provide some examples of how these rubrics can be implemented in a physics class and how students were able to transfer critical thinking abilities beyond the physics classroom.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. A new approach to the structural features of the Aegean Sea: Cellular neural network

    NASA Astrophysics Data System (ADS)

    Aydogan, Davut; Elmas, Ali; Albora, A. Muhittin; Ucan, Osman N.

    2005-03-01

    In this study, structural features in the Aegean Sea were investigated by application of Cellular Neural Network (CNN) and Cross-Correlation methods to the gravity anomaly map. CNN is a stochastic image processing technique, which is based on template optimization using neighbourhood relationships of pixels, and probabilistic properties of two-Dimensional (2-D) input data. The performance of CNN can be evaluated by various interesting real applications in geophysics such as edge detection, data enhancement and separation of regional/residual potential anomaly maps. In this study, CNN is used in edge detection of geological bodies closer to the surface, which are masked by other structures with various depths and dimensions. CNN was first tested for (prismatic) synthetic examples and satisfactory results were obtained. Subsequently, CNN/Cross-Correlation maps and bathymetric features were evaluated together to obtain a new structural map for most of the Aegean Sea. In our structural map, the locations of the faults and basins are generally in accordance with the previous maps from restricted areas based on seismic data. In the southern and southeastern parts of the Aegean Sea, E-W trending faults cut NE-SW trending basins and faults, similar to on-shore Western Anatolia. Also, in the western, central and northern parts of the Aegean Sea, all of these structures are truncated by NE-trending faults.

  10. Coherent structure formation in turbulent thermal superfluids.

    PubMed

    Kivotides, Demosthenes

    2006-05-01

    By means of numerical calculations, we show that in turbulent thermal superfluids the normal fluid induces coherent bundles of quantized line vortices in the superfluid. These filamentary structures are formed in between the normal fluid vortices, acquiring eventually comparable circulation. They are self-stretched and evolve according to self-regulating dynamics. Their spectrum mimics the normal fluid spectrum with the mutual friction force exciting the large scales and damping the small scales. Strongly interacting triads of them merge sporadically into stronger, braided vortex filaments, inducing strong fluctuations in the system's energetics. A theoretical account of the system's statistical mechanics is proposed. PMID:16712309

  11. 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.

  12. 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.

  13. 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.

  14. Nonthermal histories and implications for structure formation

    NASA Astrophysics Data System (ADS)

    Fan, JiJi; Özsoy, Ogan; Watson, Scott

    2014-08-01

    We examine the evolution of cosmological perturbations in a nonthermal inflationary history with a late-time matter domination period prior to big bang nucleosynthesis. Such a cosmology could arise naturally in the well-motivated moduli scenario in the context of supersymmetry (SUSY)—in particular in models of split SUSY. Subhorizon dark matter perturbations grow linearly during the matter dominated phase before reheating and can lead to an enhancement in the growth of substructure on small scales, even in the presence of dark matter annihilations. This suggests that a new scale (the horizon size at reheating) could be important for determining the primordial matter power spectrum. However, we find that in many nonthermal models free-streaming effects or kinetic decoupling after reheating can completely erase the enhancement leading to small-scale structures. In particular, in the moduli scenario with wino or Higgsino dark matter we find that the dark matter particles produced from moduli decays would thermalize with radiation and kinetically decouple below the reheating temperature. Thus, the growth of dark matter perturbations is not sustained, and the predictions for the matter power spectrum are similar to a standard thermal history. We comment on possible exceptions, but these appear difficult to realize within standard moduli scenarios. We conclude that although enhanced structure does not provide a new probe for investigating the cosmic dark ages within these models, it does suggest that nonthermal histories offer a robust alternative to a strictly thermal post inflationary history.

  15. 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

  16. 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.

  17. 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

  18. BICD2, dynactin, and LIS1 cooperate in regulating dynein recruitment to cellular structures

    PubMed Central

    Splinter, Daniël; Razafsky, David S.; Schlager, Max A.; Serra-Marques, Andrea; Grigoriev, Ilya; Demmers, Jeroen; Keijzer, Nanda; Jiang, Kai; Poser, Ina; Hyman, Anthony A.; Hoogenraad, Casper C.; King, Stephen J.; Akhmanova, Anna

    2012-01-01

    Cytoplasmic dynein is the major microtubule minus-end–directed cellular motor. Most dynein activities require dynactin, but the mechanisms regulating cargo-dependent dynein–dynactin interaction are poorly understood. In this study, we focus on dynein–dynactin recruitment to cargo by the conserved motor adaptor Bicaudal D2 (BICD2). We show that dynein and dynactin depend on each other for BICD2-mediated targeting to cargo and that BICD2 N-terminus (BICD2-N) strongly promotes stable interaction between dynein and dynactin both in vitro and in vivo. Direct visualization of dynein in live cells indicates that by itself the triple BICD2-N–dynein–dynactin complex is unable to interact with either cargo or microtubules. However, tethering of BICD2-N to different membranes promotes their microtubule minus-end–directed motility. We further show that LIS1 is required for dynein-mediated transport induced by membrane tethering of BICD2-N and that LIS1 contributes to dynein accumulation at microtubule plus ends and BICD2-positive cellular structures. Our results demonstrate that dynein recruitment to cargo requires concerted action of multiple dynein cofactors. PMID:22956769

  19. 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.

  20. Lipid Microdomains: Structural Correlations, Fluctuations, and Formation Mechanisms

    NASA Astrophysics Data System (ADS)

    Fan, Jun; Sammalkorpi, Maria; Haataja, Mikko

    2010-03-01

    Compositional lipid microdomains (“lipid rafts”) in mammalian plasma membranes are believed to facilitate many important cellular processes. While several physically distinct scenarios predicting the presence of finite-sized microdomains in vivo have been proposed in the past, direct experimental verification or falsification of model predictions has remained elusive. Herein, we demonstrate that the combination of the spatial correlation and temporal fluctuation spectra of the lipid domains can be employed to unambiguously differentiate between the existing theoretical scenarios. Furthermore, the differentiation of the raft formation mechanisms using this methodology can be achieved by collecting data at physiologically relevant conditions without the need to tune control parameters.

  1. 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.

  2. 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.

  3. 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).

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

    PubMed

    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

  5. 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.

  6. 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.

  7. Melanin is required for the formation of the multi-cellular conidia in the endophytic fungus Pestalotiopsis microspora.

    PubMed

    Yu, Xi; Huo, Liang; Liu, Heng; Chen, Longfei; Wang, Yu; Zhu, Xudong

    2015-10-01

    Melanin plays an important role in regulating various biological processes in many fungi. However, its biological role in conidiation remains largely elusive. We report here that conidia production, morphogenesis, integrity, germination and their viability in Pestalotiopsis microspora require the polyketide-derived melanin. A polyketide synthase gene, pks1, was identified and demonstrated responsible for melanin biosynthesis in this fungus. A targeted deletion mutant strain Δpks1 displayed a defect in pigmentation of conidia and had an albino colonial phenotype. Interestingly, Δpks1 produced approximately 6-fold as many conidia as the wild type did, suggesting a negative modulation of melanin on conidia production in this fungus. Moreover, the conidia failed to develop into the normal five-cell morphology, rather the three main-body cells separated via constriction at the original septum position to generate three independent mutant conidia. This result suggests a novel role of melanin in the formation of the multi-cellular conidia. Germ tubes could develop from the three different types of mutant conidia and kept elongating, despite a significantly lower germination rate was observed for them. Still more, the unpigmented conidia became permeable to Calcofluor White and DAPI, suggesting the integrity of the conidia was impaired. Deliberate inhibition of melanin biosynthesis by a specific inhibitor, tricyclazole, led to a similar phenotypes. This work demonstrates a new function of fungal melanin in conidial development.

  8. 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.

  9. 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.

  10. Chlorination of Microcystis aeruginosa: toxin release and oxidation, cellular chlorine demand and disinfection by-products formation.

    PubMed

    Zamyadi, Arash; Fan, Yan; Daly, Rob I; Prévost, Michèle

    2013-03-01

    Direct chlorination of toxic cyanobacteria cells can occur at various stages of treatment. The objectives of this work are to determine and model the extent of Microcystis aeruginosa cells lysis, toxins and organic compounds release and oxidation, and quantify the subsequent disinfection by-products formation. Chlorine exposure (CT) values of 296 and 100 mg min/L were required to obtain 76% cell lysis and oxidation of released cell-bound toxins at levels below the provisional World Health Organisation guideline value (1 μg/L MC-LR). Toxin oxidation rates were similar or faster than cell lysis rates in ultrapure water. This work presents much needed unit M. aeruginosa cellular chlorine demand (5.6 ± 0.2 pgCl(2)/cell) which could be used to adjust the chlorination capacity to satisfy the total chlorine demand associated with the presence of cells. Furthermore, a novel successive reaction kinetics model is developed using the kinetics of the chlorine reaction with cyanobacterial cells and cell-bound toxins. Chlorination of dense cell suspensions (500,000 cells/mL) in ultrapure water at CT up to 3051 mg min/L resulted in modest concentrations of trihalomethanes (13 μg/L) and haloacetic acids (below detection limit).

  11. Cellular nucleic-acid-binding protein, a transcriptional enhancer of c-Myc, promotes the formation of parallel G-quadruplexes.

    PubMed

    Borgognone, Mariana; Armas, Pablo; Calcaterra, Nora B

    2010-06-15

    G-rich sequences that contain stretches of tandem guanines can form four-stranded, intramolecular stable DNA structures called G-quadruplexes (termed G4s). Regulation of the equilibrium between single-stranded and G4 DNA in promoter regions is essential for control of gene expression in the cell. G4s are highly stable structures; however, their folding kinetics are slow under physiological conditions. CNBP (cellular nucleic-acid-binding protein) is a nucleic acid chaperone that binds the G4-forming G-rich sequence located within the NHE (nuclease hypersensitivity element) III of the c-Myc proto-oncogene promoter. Several reports have demonstrated that CNBP enhances the transcription of c-Myc in vitro and in vivo; however, none of these reports have assessed the molecular mechanisms responsible for this control. In the present study, by means of Taq polymerase stop assays, electrophoretic mobility-shift assays and CD spectroscopy, we show that CNBP promotes the formation of parallel G4s to the detriment of anti-parallel G4s, and its nucleic acid chaperone activity is required for this effect. These findings are the first to implicate CNBP as a G4-folding modulator and, furthermore, assign CNBP a novel mode-of-action during c-Myc transcriptional regulation.

  12. Optimized parallel computing for cellular automaton-finite element modeling of solidification grain structures

    NASA Astrophysics Data System (ADS)

    Carozzani, T.; Gandin, Ch-A.; Digonnet, H.

    2014-01-01

    A numerical implementation of a three-dimensional (3D) cellular automaton (CA)-finite element (FE) model has been developed for the prediction of solidification grain structures. For the first time, it relies on optimized parallel computation to solve industrial-scale problems (centimeter to meter long) while using a sufficiently small CA grid size to predict representative structures. Several algorithm modifications and strategies to maximize parallel efficiency are introduced. Improvements on a real case simulation are measured and discussed. The CA-FE implementation here is demonstrated using 32 computing units to predict grain structure in a 2.08 m × 0.382 m × 0.382 m ingot involving 4.9 billion cells and 1.6 million grains. These numerical improvements permit tracking of local changes in texture and grain size over real-cast parts while integrating interactions with macrosegregation, heat flow and fluid flow. Full 3D is essential in all these analyses, and can be dealt with successfully using the implementation presented here.

  13. [Neurofibromin - protein structure and cellular functions in the context of neurofibromatosis type I pathogenesis].

    PubMed

    Abramowicz, Anna; Gos, Monika

    2015-12-09

    Neurofibromatosis type I (NF1) is multisystemic disease characterized by pigmentary skin changes, increased susceptibility to tumor formation, neurological deficits and skeletal defects. The disease is a monogenic, autosomal dominant disorder, caused by the presence of mutations in the NF1 gene encoding neurofibromin - a multifunctional regulatory protein. The basic function of neurofibromin protein is modulation of the RAS protein activity necessary for regulation of cell proliferation and differentiation by the RAS/MAPK and RAS/PI3K/AKT signal transduction pathways. In addition, neurofibromin is a regulator of adenylate cyclase activity and therefore may interfere with signaling by the cAMP/protein kinase A pathway that regulates cell cycle progression or learning and memory formation processes. Neurofibromin also interacts with many other proteins that are engaged in intracellular transport (tubulin, kinesin), actin cytoskeleton rearrangements (LIMK2, Rho and Rac) or morphogenesis of neural cells (syndecans, CRMP proteins). The activity of neurofibromin is strictly regulated by the expression of different NF1 mRNA isoforms depending on tissue type or period in organism development, the protein localization, posttranslational modifications (phosphorylation, ubiquitination) or interactions with other proteins (e.g. 14-3-3). The fact that neurofibromin is engaged in many cellular processes has significant consequences when the proper protein functioning is impaired due to decreased protein level or activity. It affects the normal cell function and results in disturbances of organism development that lead to the occurrence of clinical signs specific for NF1. In the article, the basic neurofibromin functions are presented in the context of the molecular pathogenesis of NF1.

  14. 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

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

    PubMed

    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

    2015-12-17

    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.

  16. 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.

  17. Structural and functional cellular alterations underlying the toxicity of methamphetamine in rat retina and prefrontal cortex.

    PubMed

    Prudêncio, Cristina; Abrantes, Bruno; Lopes, Isabel; Tavares, Maria Amélia

    2002-06-01

    The consumption of illicit drugs is an increasing problem in contemporary societies, and is one of the major causes of death and illness all over the world. Methamphetamine is among the drugs more widely used. Although evidence for a role of reactive species--especially reactive oxygen species (ROS) and apoptotic events--has been shown, the mechanism(s) underlying the cellular toxicity induced by this drug is not yet fully identified. In this context the elucidation of the cytotoxic effects induced by methamphetamine in rat frontal cortex and retina, which compromise cell viability and ultimately result in cell death, can further contribute to the understanding of its mechanism of action. This knowledge may provide new insights into the development of new therapeutic approaches to prevent or ameliorate deleterious alterations of the nervous system. The use of epifluorescence microscopy associated with different fluorescent probes, markers of structural and/or functional cell parameters, can be used as a powerful tool to carry out those studies, in particular, the viability probes propidium iodide (PI) to assess plasma membrane integrity and fluorescein diacetate (FDA), which can monitor intracellular esterase activity and/or pH. In a preliminary study, the kinetic assessment of cellular changes induced by different drug concentrations (0, 1.2, 3, and 6 mM) allowed detection of dose-dependent alterations that are observed earlier in the retina. In fact, in the retina it was possible to monitor alterations (at 4 h of incubation) both in plasma membrane integrity and in esterase activity and/or pH for the lowest drug concentration (1.2 mM). In the prefrontal cortex these changes were only visible for drug concentrations > or = 3 mM. This work is a novel approach to the mechanisms of action of illicit drugs in the central nervous system and will provide the foundations and guidelines for further investigations in the context of tolerance, dependence, and addiction.

  18. 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.

  19. In silico analyses of dystrophin Dp40 cellular distribution, nuclear export signals and structure modeling

    PubMed Central

    Martínez-Herrera, Alejandro; Aragón, Jorge; Bermúdez-Cruz, Rosa Ma.; Bazán, Ma. Luisa; Soid-Raggi, Gabriela; Ceja, Víctor; Santos Coy-Arechavaleta, Andrea; Alemán, Víctor; Depardón, Francisco; Montañez, Cecilia

    2015-01-01

    Dystrophin Dp40 is the shortest protein encoded by the DMD (Duchenne muscular dystrophy) gene. This protein is unique since it lacks the C-terminal end of dystrophins. In this data article, we describe the subcellular localization, nuclear export signals and the three-dimensional structure modeling of putative Dp40 proteins using bioinformatics tools. The Dp40 wild type protein was predicted as a cytoplasmic protein while the Dp40n4 was predicted to be nuclear. Changes L93P and L170P are involved in the nuclear localization of Dp40n4 protein. A close analysis of Dp40 protein scored that amino acids 93LEQEHNNLV101 and 168LLLHDSIQI176 could function as NES sequences and the scores are lost in Dp40n4. In addition, the changes L93/170P modify the tertiary structure of putative Dp40 mutants. The analysis showed that changes of residues 93 and 170 from leucine to proline allow the nuclear localization of Dp40 proteins. The data described here are related to the research article entitled “EF-hand domains are involved in the differential cellular distribution of dystrophin Dp40” (J. Aragón et al. Neurosci. Lett. 600 (2015) 115–120) [1]. PMID:26217814

  20. Zebrafish cellular nucleic acid-binding protein: gene structure and developmental behaviour.

    PubMed

    Armas, Pablo; Cachero, Sebastián; Lombardo, Verónica A; Weiner, Andrea; Allende, Miguel L; Calcaterra, Nora B

    2004-08-01

    Here we analyse the structural organisation and expression of the zebrafish cellular nucleic acid-binding protein (zCNBP) gene and protein. The gene is organised in five exons and four introns. A noteworthy feature of the gene is the absence of a predicted promoter region. The coding region encodes a 163-amino acid polypeptide with the highly conserved general structural organisation of seven CCHC Zn knuckle domains and an RGG box between the first and the second Zn knuckles. Although theoretical alternative splicing is possible, only one form of zCNBP is actually detected. This form is able to bind to single-stranded DNA and RNA probes in vitro. The analysis of zCNBP developmental expression shows a high amount of CNBP-mRNA in ovary and during the first developmental stages. CNBP-mRNA levels decrease while early development progresses until the midblastula transition (MBT) stage and increases again thereafter. The protein is localised in the cytoplasm of blastomeres whereas it is mainly nuclear in developmental stages after the MBT. These findings suggest that CNBP is a strikingly conserved single-stranded nucleic acid-binding protein which might interact with maternal mRNA during its storage in the embryo cell cytoplasm. It becomes nuclear once MBT takes place possibly in order to modulate zygotic transcription and/or to associate with newly synthesised transcripts.

  1. [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

  2. [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.

  3. Formation of coherent structures in 3D laminar mixing flows

    NASA Astrophysics Data System (ADS)

    Speetjens, Michel; Clercx, Herman

    2009-11-01

    Mixing under laminar flow conditions is key to a wide variety of industrial systems of size extending from microns to meters. Examples range from the traditional (and still very relevant) mixing of viscous fluids via compact processing equipment down to emerging micro-fluidics applications. Profound insight into laminar mixing mechanisms is imperative for further advancement of mixing technology (particularly for complex micro-fluidics systems) yet remains limited to date. The present study concentrates on a fundamental transport phenomenon of potential relevance to laminar mixing: the formation of coherent structures in the web of 3D fluid trajectories due to fluid inertia. Such coherent structures geometrically determine the transport properties of the flow and better understanding of their formation and characteristics may offer ways to control and manipulate the mixing properties of laminar flows. The formation of coherent structures and its impact upon 3D transport properties is demonstrated by way of examples.

  4. 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.

  5. 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

  6. 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.

  7. Genes and structural patterns in ciliates: Vance Tartar and the "cellular architects".

    PubMed

    Frankel, J

    1992-01-01

    The one form of cytoplasmic inheritance that has not been assimilated into the Central Dogma is the inheritance of surface structural patterns, a phenomenon most clearly expressed in ciliates. Vance Tartar, although he worked with a genetically undomesticated organism (Stentor coeruleus), provided early evidence for the crucial role of clonally propagated features of the cell cortex. He showed that the capacity for development of cortical organelle systems is associated with a particular relational feature, the "locus of stripe contrast" (LSC), and that clonally inherited cortical variants (homopolar doublets) could be created at will by microsurgical operations that duplicated the LSC. Tartar also hoped to demonstrate the existence of what David Nanney called "cellular architects" by provoking stentors to carry out entirely novel types of morphogenetic performances. He eventually acknowledged failure, although the bizarre juxtapositions by which he attempted to elicit such novel performances did bring about specific and illuminating defects in cortical development. Subsequent analyses of similar defects in other ciliates revealed not the unitary "pattern factor" postulated by Tartar, but rather a hierarchy of distinct patterning mechanisms. Nonetheless, by pursuing an embryological approach toward morphogenesis in a highly regulative ciliate, Tartar uncovered relational aspects of pattern-determination; this, in my view, delineates the major problem that we must solve to gain understanding of intracellular patterning. PMID:1499161

  8. 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.

  9. 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.

  10. SPT genes: key players in the regulation of transcription, chromatin structure and other cellular processes.

    PubMed

    Yamaguchi, Y; Narita, T; Inukai, N; Wada, T; Handa, H

    2001-02-01

    Suppressor of Ty (SPT) genes were originally identified through a genetic screen for mutations in the yeast Saccharomyces cerevisiae that restore gene expression disrupted by the insertion of the transposon Ty. Classic members of the SPT gene family, SPT11, SPT12, and SPT15, encode for the histones H2A and H2B, and for TATA-binding protein (TBP), respectively. Over the past few years, molecular complexes and cellular functions in which other SPT gene products involve have been discovered through genetic and biochemical studies in yeast and several other organisms: Key regulators of transcription and chromatin structure, such as DSIF, SAGA, and FACT, all contain SPT gene products as essential subunits. In addition, accumulating evidence suggests that SPT gene products play more diverse roles, including roles in DNA replication, DNA recombination and developmental regulation. Here we review the current understanding of the functions and roles of the SPT genes, with special emphasis on the role of SPT5 in transcript elongation and in neuronal development in vertebrates.

  11. 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.

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

    PubMed

    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.

  13. 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

  14. Personality Development at Preadolescence; Explorations of Structure Formation.

    ERIC Educational Resources Information Center

    Gardner, Riley W.; Moriarty, Alice

    Personality development and structure formation were studied in 60 preadolescent children (aged 9 to 13). Six major aspects of preadolescent individuality were assessed: cognitive controls, performance on the Holtzman Inkblot Test, intellectual abilities, general response to clinical testing, general response to laboratory testing, and defense…

  15. 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

  16. Structural Development, Cellular Differentiation and Proliferation of the Respiratory Epithelium in the Bovine Fetal Lung.

    PubMed

    Drozdowska, J; Cousens, C; Finlayson, J; Collie, D; Dagleish, M P

    2016-01-01

    Fetal bovine lung samples of 11 different gestational ages were assigned to a classical developmental stage based on histological morphology. Immunohistochemistry was used to characterize the morphology of forming airways, proliferation rate of airway epithelium and the presence of epithelial cell types (i.e. ciliated cells, club cells, neuroepithelial cells (NECs) and type II pneumocytes). Typical structural organization of pseudoglandular (84-98 days gestational age [DGA]), canalicular (154-168 DGA) and alveolar (224-266 DGA) stages was recognized. In addition, transitional pseudoglandular-canalicular (112-126 DGA) and canalicular-saccular (182 DGA) morphologies were present. The embryonic stage was not observed. A significantly (P <0.05) higher proliferation rate of pulmonary epithelium, on average 5.5% and 4.4% in bronchi and bronchioles, respectively, was present in the transitional pseudoglandular-canalicular phase (112-126 DGA) compared with all other phases, while from 8 weeks before term (224-266 DGA) proliferation had almost ceased. The first epithelial cells identified by specific marker proteins in the earliest samples available for study (84 DGA) were ciliated cells and NECs. Club cells were present initially at 112 DGA and type II pneumocytes at 224 DGA. At the latest time points (224-226 DGA) these latter cell types were still present at a much lower percentage compared with adult cattle. This study characterized bovine fetal lung development by histological morphology and cellular composition of the respiratory epithelium and suggests that the apparent structural anatomical maturity of the bovine lung at term is not matched by functional maturity of the respiratory epithelium.

  17. Benzothiophene inhibitors of MK2. Part 1: structure-activity relationships, assessments of selectivity and cellular potency.

    PubMed

    Anderson, David R; Meyers, Marvin J; Kurumbail, Ravi G; Caspers, Nicole; Poda, Gennadiy I; Long, Scott A; Pierce, Betsy S; Mahoney, Matthew W; Mourey, Robert J

    2009-08-15

    Identification of potent benzothiophene inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK2), structure-activity relationship (SAR) studies, selectivity assessments against CDK2, cellular potency and mechanism of action are presented. Crystallographic data provide a rationale for the observed MK2 potency as well as selectivity over CDK2 for this class of inhibitors.

  18. Regulatory effects of cotranscriptional RNA structure formation and transitions.

    PubMed

    Liu, Sheng-Rui; Hu, Chun-Gen; Zhang, Jin-Zhi

    2016-09-01

    RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website. PMID:27028291

  19. Orogenic structural inheritance and rifted passive margin formation

    NASA Astrophysics Data System (ADS)

    Salazar Mora, Claudio A.; Huismans, Ritske S.

    2016-04-01

    Structural inheritance is related to mechanical weaknesses in the lithosphere due to previous tectonic events, e.g. rifting, subduction and collision. The North and South Atlantic rifted passive margins that formed during the breakup of Western Gondwana, are parallel to the older Caledonide and the Brasiliano-Pan-African orogenic belts. In the South Atlantic, 'old' mantle lithospheric fabric resulting from crystallographic preferred orientation of olivine is suggested to play a role during rifted margin formation (Tommasi and Vauchez, 2001). Magnetometric and gravimetric mapping of onshore structures in the Camamu and Almada basins suggest that extensional faults are controlled by two different directions of inherited older Brasiliano structures in the upper lithosphere (Ferreira et al., 2009). In the South Atlantic Campos Basin, 3D seismic data indicate that inherited basement structures provide a first order control on basin structure (Fetter, 2009). Here we investigate the role of structural inheritance on the formation of rifted passive margins with high-resolution 2D thermo-mechanical numerical experiments. The numerical domain is 1200 km long and 600 km deep and represents the lithosphere and the sublithospheric mantle. Model experiments were carried out by creating self-consistent orogenic inheritance where a first phase of orogen formation is followed by extension. We focus in particular on the role of varying amount of orogenic shortening, crustal rheology, contrasting styles of orogen formation on rifted margin style, and the time delay between orogeny and subsequent rifted passive formation. Model results are compared to contrasting structural styles of rifted passive margin formation as observed in the South Atlantic. Ferreira, T.S., Caixeta, J.M., Lima, F.D., 2009. Basement control in Camamu and Almada rift basins. Boletim de Geociências da Petrobrás 17, 69-88. Fetter, M., 2009. The role of basement tectonic reactivation on the structural evolution

  20. Mechanisms underlying structural variant formation in genomic disorders

    PubMed Central

    Carvalho, Claudia M. B.; Lupski, James R.

    2016-01-01

    With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility. PMID:26924765

  1. Hysteresis-driven structure formation in biochemical networks

    PubMed

    Klein

    1998-09-21

    A mechanism of structure formation, based on hysteresis behaviour is presented. A bisubstrate kinetic system with substrate inhibition, discussed previously in the context of Turing structure formation, may show hysteresis behaviour, when embedded in a metabolic network: the system may possess multiple steady states and may be switched from one stable fixpoint to the other. When cells containing this type of system are diffusively coupled, under certain conditions patterns result, which, as is demonstrated, are not of the Turing type. The main difference to diffusion-driven (Turing) structures is the fact that the hysteresis-driven patterns emerge under diffusive conditions, under which both the homogeneous and the asymmetrical steady state is stable. The resulting special properties and biological implications are discussed.Copyright 1998 Academic Press Limited PMID:9778438

  2. 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

  3. 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.

  4. 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

  5. Hierarchical Structure Formation of Nanoparticulate Spray-Dried Composite Aggregates.

    PubMed

    Zellmer, Sabrina; Garnweitner, Georg; Breinlinger, Thomas; Kraft, Torsten; Schilde, Carsten

    2015-11-24

    The design of hierarchically structured nano- and microparticles of different sizes, porosities, surface areas, compositions, and internal structures from nanoparticle building blocks is important for new or enhanced application properties of high-quality products in a variety of industries. Spray-drying processes are well-suited for the design of hierarchical structures of multicomponent products. This structure design using various nanoparticles as building blocks is one of the most important challenges for the future to create products with optimized or completely new properties. Furthermore, the transfer of designed nanomaterials to large-scale products with favorable handling and processing can be achieved. The resultant aggregate structure depends on the utilized nanoparticle building blocks as well as on a large number of process and formulation parameters. In this study, structure formation and segregation phenomena during the spray drying process were investigated to enable the synthesis of tailor-made nanostructures with defined properties. Moreover, a theoretical model of this segregation and structure formation in nanosuspensions is presented using a discrete element method simulation. PMID:26505280

  6. Sub-cellular structure studied by combined atomic force-fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Trache, Andreea

    2009-03-01

    A novel experimental technique that integrates atomic force microscopy (AFM) with fluorescence imaging was used to study the role of extracellular matrix proteins in cellular organization. To understand the mechanism by which living cells sense mechanical forces, and how they respond and adapt to their environment, we developed a new technology able to investigate cellular behavior at sub-cellular level that integrates an AFM with total internal reflection fluorescence (TIRF) microscopy and fast-spinning disk (FSD) confocal microscopy. Live smooth muscle cells exhibited differences in focal adhesions and actin pattern depending on the extracellular matrix used for substrate coating. Data obtained by using the AFM-optical imaging integrated technique offer novel quantitative information that allows understanding the fundamental processes of cellular reorganization in response to extracellular matrix modulation. The integrated microscope presented here is broadly applicable across a wide range of molecular dynamic studies in any adherent live cells.

  7. 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.

  8. Manifestation of the shape-memory effect in polyetherurethane cellular plastics, fabric composites, and sandwich structures under microgravity

    NASA Astrophysics Data System (ADS)

    Babaevskii, P. G.; Kozlov, N. A.; Agapov, I. G.; Reznichenko, G. M.; Churilo, N. V.; Churilo, I. V.

    2016-09-01

    The results of experiments that were performed to test the feasibility of creating sandwich structures (consisting of thin-layer sheaths of polymer composites and a cellular polymer core) with the shapememory effect as models of the transformable components of space structures have been given. The data obtained indicate that samples of sandwich structures under microgravity conditions on board the International Space Station have recovered their shape to almost the same degree as under terrestrial conditions, which makes it possible to recommend them for creating components of transformable space structures on their basis.

  9. Correlating metrics of community structure with cellular indicators of stress in an Arkansas bayou

    SciTech Connect

    Schlenk, D.; Leus, J.; Lahyer, W.G.; Zhang, Y.S. ||

    1994-12-31

    A major disadvantage of using cellular indicators of stress or biomarkers to evaluate ecosystem health is the lack of a documented relationship between the cellular response and detrimental changes to an ecosystem. In an attempt to correlate ecosystem health with cellular stress, a Shannon-Weaver Index was constructed to assess fish species diversity at 13 sites in Bayou Barthalamew. With the exception of site 8, urban sites 1--4 possessed the lowest D-bar values than other sites on the Bayou. White Crappie (Pomoxis anularus), common grass carp (Cyprinus carpio) and large mouth bass (Micropteris salmoides) were sampled from each site, analyzed for expression of the cellular stress protein, metallothionein and compared with fish collected from another waterway of pristine nature. Initial findings from 3 sites indicated that metallothionein induction correlated with D-bar values (r{sup 2} = .985). Other stress proteins and cellular markers are currently being examined at the remaining sites in an attempt to correlate cellular effects and potential changes in species diversity.

  10. Three-dimensional cellular structure of detonations in suspensions of aluminium particles

    NASA Astrophysics Data System (ADS)

    Khasainov, B.; Virot, F.; Veyssière, B.

    2013-05-01

    Recently, we have used scarce available data on the detonation cell size in suspensions of aluminium particles in air and oxygen to adjust the kinetic parameters of our two-phase model of detonations in these mixtures. The calculated detonation cell width was derived by means of two-dimensional (2D) unsteady simulations using an assumption of cylindrical symmetry of the flow in the tube. However, in reality, the detonation cells are three-dimensional (3D). In this work, we have applied the same detonation model which is based on the continuous mechanics of two-phase flows, for 3D numerical simulations of cellular detonation structures in aluminium particle suspensions in oxygen. Reasonable agreement on the detonation cell width was obtained with the aforementioned 2D results. The range of tube diameters where detonations in { Al/O}_2 mixture at a given particle size and concentration would propagate in the spinning mode has been estimated (these results make a complement to our previous analysis of spinning detonations in Al/air mixtures). Coupling these results with the dependencies of detonation cell size on the mean particle diameter is of great interest for the understanding of fundamental mechanisms of detonation propagation in solid particle suspensions in gas and can help to better guide the experimental studies of detonations in aluminium suspensions. It is shown that the part of detonation wave energy used for transverse kinetic energy of both gas and particles is quite small, which explains why the propagation velocity of spinning and multi-headed detonations reasonably agrees with the ideal CJ values.

  11. Excitonic gap formation and condensation in the bilayer graphene structure

    NASA Astrophysics Data System (ADS)

    Apinyan, V.; Kopeć, T. K.

    2016-09-01

    We have studied the excitonic gap formation in the Bernal Stacked, bilayer graphene (BLG) structures at half-filling. Considering the local Coulomb interaction between the layers, we calculate the excitonic gap parameter and we discuss the role of the interlayer and intralayer Coulomb interactions and the interlayer hopping on the excitonic pair formation in the BLG. Particularly, we predict the origin of excitonic gap formation and condensation, in relation to the furthermost interband optical transition spectrum. The general diagram of excitonic phase transition is given, explaining different interlayer correlation regimes. The temperature dependence of the excitonic gap parameter is shown and the role of the chemical potential, in the BLG, is discussed in details.

  12. Neural pattern formation in networks with dendritic structure

    NASA Astrophysics Data System (ADS)

    Bressloff, P. C.; De Souza, B.

    1998-04-01

    We present a detailed analysis of a recently proposed model of neural pattern formation that is based on the combined effect of diffusion along a neuron's dendritic tree and recurrent interactions along axo-dendritic synaptic connections. For concreteness, we consider a one-dimensional array of analog neurons with the dendritic tree idealized as a one-dimensional cable. Linear stability analysis and bifurcation theory together with numerical simulations are used to establish conditions for the onset of a Turing instability leading to the formation of stable spatial patterns of network output activity. It is shown that the presence of dendritic structure can induce dynamic (time-periodic) spatial pattern formation. Moreover, correlations between the dendritic location of a synapse and the relative positions of neurons in the network are shown to result in spatially oscillating patterns of activity along the dendrites of each neuron.

  13. Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef

    SciTech Connect

    Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie; Yang, Haitao; Guatelli, John; Xiong, Yong

    2012-10-24

    The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the {mu}1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-{mu}1 interface, which encompasses the cargo-recognition site of {mu}1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in {mu}1, whereas the N terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on {mu}1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity.

  14. Structural Basis of Evasion of Cellular Adaptive Immunity by HIV-1 Nef

    PubMed Central

    Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie; Yang, Haitao; Guatelli, John; Xiong, Yong

    2012-01-01

    The HIV-1 protein Nef inhibits antigen presentation by class I MHC (MHC-I). Here the mechanism of this activity is revealed by the crystal structure of a protein complex consisting of Nef, the MHC-I cytoplasmic domain (MHC-I CD), and the μ1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-μ1 interface encompassing the cargo-recognition site of μ1 and the proline rich strand of Nef. The Nef C-terminus induces a novel conformational change in μ1, while the N-terminus binds the Nef core to position it optimally for complex formation. Positively charged patches on μ1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity. PMID:22705789

  15. Analysis of the Particle Formation Process of Structured Microparticles.

    PubMed

    Baldelli, Alberto; Boraey, Mohammed A; Nobes, David S; Vehring, Reinhard

    2015-08-01

    The particle formation process for microparticles of cellulose acetate butyrate dried from an acetone solution was investigated experimentally and theoretically. A monodisperse droplet chain was used to produce solution microdroplets in a size range of 55-70 μm with solution concentrations of 0.37 and 10 mg/mL. As the droplets dried in a laminar air flow with a temperature of 30, 40, or 55 °C, the particle formation process was recorded by two independent optical methods. Dried particles in a size range of 10-30 μm were collected for morphology analysis, showing hollow, elongated particles whose structure was dependent on the drying gas temperature and initial solution concentration. The setup allowed comprehensive measurements of the particle formation process to be made, including the period after initial shell formation. The early particle formation process for this system was controlled by the diffusion of cellulose acetate butyrate in the liquid phase, whereas later stages of the process were dominated by shell buckling and folding. PMID:25685865

  16. Gravitationally induced particle production and its impact on structure formation

    NASA Astrophysics Data System (ADS)

    Nunes, Rafael C.

    2016-08-01

    In this paper we investigate the influence of a continuous particles creation processes on the linear and nonlinear matter clustering, and its consequences on the weak lensing effect induced by structure formation. We study the line of sight behavior of the contribution to the bispectrum signal at a given angular multipole l, showing that the scale where the nonlinear growth overcomes the linear effect depends strongly of particles creation rate.

  17. Nonlinear structure formation in gravity theories beyond general relativity

    NASA Astrophysics Data System (ADS)

    Mota, David F.

    2016-07-01

    We investigate the effects of modified gravity theories, in particular, the symmetron and f(R) gravity, on the nonlinear regime of structure formation. In particular, we investigate the velocity dispersion of galaxy clusters as a function of the halo masses, how the matter power spectra depend on the coupling, range and screening scale of the fifth force, and on possible ways of detecting violations of the equivalence principle using the mass inferred via lensing methods versus the mass inferred via dynamical methods.

  18. Hierarchical structure formation of cylindrical brush polymer-surfactant complexes.

    PubMed

    Cong, Yang; Gunari, Nikhil; Zhang, Bin; Janshoff, Andreas; Schmidt, Manfred

    2009-06-01

    The complex formation of cylindrical brush polymers with poly(l-lysine) side chains (PLL) and sodium dodecyl sulfate (SDS) can induce a helical conformation of the cylindrical brush polymer in aqueous solution (Gunari, N.; Cong, Y.; Zhang, B.; Fischer, K.; Janshoff, A.; Schmidt, M. Macromol. Rapid Commun. 2008, 29, 821-825). Herein, we have systematically investigated the influence of surfactant, salt, and pH on the supramolecular structure formation. The cylindrical brush polymers and their complexes with surfactants were directly visualized by atomic force microscopy in air and in aqueous solution. The alkyl chain length (measured by the carbon number, n) of the surfactant plays a key role. While helical structures were formed with n=10, 11, and 12, no helices were observed with n<10 and n>13. Addition of salt destroys the helical structures as do pH conditions below 4 and above 6, most probably because the polymer-surfactant complexes start to disintegrate. Circular dichroism was utilized to monitor the PLL side chain conformation and clearly revealed that beta-sheet formation of the side chains induces the helical conformation of the atactic main chain. PMID:19326944

  19. Structure Formation in Planetary Disk and Laboratory Plasma

    NASA Astrophysics Data System (ADS)

    Noguchi, Koichi; Tajima, Toshiki; Horton, Wendell

    2000-10-01

    The shear flow instabilities under the presence of magnetic fields in the protoplanetary disk can greatly facilitate the formation of density structures that serve prior to the onset of the gravitational Jeans instability as a seed for the faster formation of planetesimals. Such a process may explain several puzzles in the planetary genesis. We evaluate the effects of the Parker, magnetorotational, and kinematic dynamo instabilities, and calculate the mass spectra of coagulated density structures by the above mechanism in the radial direction for two typical models. The mass spectrum of the magnetorotational instability may describe the origin of giant planets away from central star. Our local three-dimentional MHD simulation indicates that the coupling of those instabilities creates spiral arms and gas blobs in the accretion disk, reinforcing our theory. Such a mechanism for the early structure formation may be tested in a laboratory. The recent progress in experiments invloving shear flows in tokamak and laser plasmas may become a key in this regard. * The work is supported by NSF and DoE.

  20. Tuning of the electro-mechanical behavior of the cellular carbon nanotube structures with nanoparticle dispersions

    SciTech Connect

    Gowda, Prarthana; Misra, Abha; Ramamurty, Upadrasta

    2014-03-10

    The mechanical and electrical characteristics of cellular network of the carbon nanotubes (CNT) impregnated with metallic and nonmetallic nanoparticles were examined simultaneously by employing the nanoindentation technique. Experimental results show that the nanoparticle dispersion not only enhances the mechanical strength of the cellular CNT by two orders of magnitude but also imparts variable nonlinear electrical characteristics; the latter depends on the contact resistance between nanoparticles and CNT, which is shown to depend on the applied load while indentation. Impregnation with silver nanoparticles enhances the electrical conductance, the dispersion with copper oxide and zinc oxide nanoparticles reduces the conductance of CNT network. In all cases, a power law behavior with suppression in the differential conductivity at zero bias was noted, indicating electron tunneling through the channels formed at the CNT-nanoparticle interfaces. These results open avenues for designing cellular CNT foams with desired electro-mechanical properties and coupling.

  1. Transition from a planar interface to cellular and dendritic structures during rapid solidification processing

    NASA Technical Reports Server (NTRS)

    Laxmanan, V.

    1986-01-01

    The development of theoretical models which characterize the planar-cellular and cell-dendrite transitions is described. The transitions are analyzed in terms of the Chalmers number, the solute Peclet number, and the tip stability parameter, which correlate microstructural features and processing conditions. The planar-cellular transition is examined using the constitutional supercooling theory of Chalmers et al., (1953) and it is observed that the Chalmers number is between 0 and 1 during dendritic and cellular growth. Analysis of cell-dendrite transition data reveal that the transition occurs when the solute Peclet number goes through a minimum, the primary arm spacings go through a maximum, and the Chalmers number is equal to 1/2. The relation between the tip stability parameter and the solute Peclet number is investigated and it is noted that the tip stability parameter is useful for studying dendritic growth in alloys.

  2. Morphological aspects of the ectopic granule-like cellular populations in the albino rat hippocampal formation: a Golgi study.

    PubMed

    Martí-Subirana, A; Soriano, E; García-Verdugo, J M

    1986-02-01

    Rat hippocampal formation was examined by the Golgi impregnation method. Three different ectopic granule-like populations of cells were differentiated: (1) Ectopic granule-like cells of the regio inferior, located in the stratum radiatum; one or two dendrites arose from the cell body and ran towards either the molecular layer of the fascia dentata or the stratum lacunosum-moleculare of the hippocampus, where they branched into secondary and tertiary dendrites. (2) Ectopic granule-like cells of the hilar region; this cell population showed bipolar and monopolar types of dendritic tree. Unipolar cells had dendrites oriented towards the granular layer where they branched profusely. Dendritic arborisation of bipolar cells was confined to the hilus. (3) Ectopic granule-like cells of the molecular layer; they showed several structural appearances depending on their location within the layer. Axonal tracts of ectopic granule-like cells gave rise to numerous collaterals; the main branch ran to the CA4 and CA3 hippocampal subregions. Several 'en passant' and mossy-like boutons were shown along this path.

  3. Morphological aspects of the ectopic granule-like cellular populations in the albino rat hippocampal formation: a Golgi study.

    PubMed Central

    Martí-Subirana, A; Soriano, E; García-Verdugo, J M

    1986-01-01

    Rat hippocampal formation was examined by the Golgi impregnation method. Three different ectopic granule-like populations of cells were differentiated: (1) Ectopic granule-like cells of the regio inferior, located in the stratum radiatum; one or two dendrites arose from the cell body and ran towards either the molecular layer of the fascia dentata or the stratum lacunosum-moleculare of the hippocampus, where they branched into secondary and tertiary dendrites. (2) Ectopic granule-like cells of the hilar region; this cell population showed bipolar and monopolar types of dendritic tree. Unipolar cells had dendrites oriented towards the granular layer where they branched profusely. Dendritic arborisation of bipolar cells was confined to the hilus. (3) Ectopic granule-like cells of the molecular layer; they showed several structural appearances depending on their location within the layer. Axonal tracts of ectopic granule-like cells gave rise to numerous collaterals; the main branch ran to the CA4 and CA3 hippocampal subregions. Several 'en passant' and mossy-like boutons were shown along this path. Images Figs. 2-7 Figs. 9-12 Figs. 14-16 PMID:2447048

  4. Glycan structure determinants for cation-independent mannose 6-phosphate receptor binding and cellular uptake of a recombinant protein.

    PubMed

    Zhou, Qun; Avila, Luis Z; Konowicz, Paul A; Harrahy, John; Finn, Patrick; Kim, Jennifer; Reardon, Michael R; Kyazike, Josephine; Brunyak, Elizabeth; Zheng, Xiaoyang; Patten, Scott M Van; Miller, Robert J; Pan, Clark Q

    2013-12-18

    The cation-independent mannose 6-phosphate receptor (CI-MPR) plays a critical role in intracellular transport of lysosomal enzymes as well as the uptake of recombinant proteins. To define the minimal glycan structure determinants necessary for receptor binding and cellular uptake, we synthesized a series of glycans containing mono-, di-, tri-, tetra-, and hexamannoses terminated with either one or two phosphates for conjugating to a model protein, recombinant human acid α-glucosidase. A high affinity interaction with the CI-MPR can be achieved for the enzyme conjugated to a dimannose glycan with a single phosphate. However, tightest binding to a CI-MPR affinity column was observed with a hexamannose structure containing two phosphates. Moreover, maximal cellular uptake and a 5-fold improvement in in vivo potency were achieved when the bisphosphorylated hexamannose glycan is conjugated to the protein by a β linker. Nevertheless, even a monophosphorylated dimannose glycan conjugate showed stronger binding to the receptor affinity column, higher cellular uptake, and significantly greater in vivo efficacy compared to the unconjugated protein which contains a low level of high affinity glycan structure. These results demonstrate that the phosphorylated dimannose moiety appears to be the minimal structure determinant for enhanced CI-MPR binding and that the orientation of the glycan is critical for maximum receptor interaction. In summary, we have improved the understanding of the mechanism of CI-MPR binding and developed a simple alternative for CI-MPR targeting.

  5. A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding

    PubMed Central

    2013-01-01

    Background A tandem technique of hard equipment is often used for the chemical analysis of a single cell to first isolate and then detect the wanted identities. The first part is the separation of wanted chemicals from the bulk of a cell; the second part is the actual detection of the important identities. To identify the key structural modifications around ligand binding, the present study aims to develop a counterpart of tandem technique for cheminformatics. A statistical regression and its outliers act as a computational technique for separation. Results A PPARγ (peroxisome proliferator-activated receptor gamma) agonist cellular system was subjected to such an investigation. Results show that this tandem regression-outlier analysis, or the prioritization of the context equations tagged with features of the outliers, is an effective regression technique of cheminformatics to detect key structural modifications, as well as their tendency of impact to ligand binding. Conclusions The key structural modifications around ligand binding are effectively extracted or characterized out of cellular reactions. This is because molecular binding is the paramount factor in such ligand cellular system and key structural modifications around ligand binding are expected to create outliers. Therefore, such outliers can be captured by this tandem regression-outlier analysis. PMID:23627990

  6. Steric interactions in cellular structures formed in a water/oil/surfactant/cosurfactant mixture.

    PubMed

    Molle, B; de Geyer, A; Guillermo, A; Farago, B

    2003-02-14

    Dynamics of dense microemulsion droplets forming ordered cellular phases as temperature increases are investigated by neutron spin echo spectroscopy (NSE). The shape fluctuations of droplets are shown using a specific contrast. Their relaxation time tau(f) is obtained by analysis of the NSE curves, which also reveals the short-range Brownian motion (diffusion constant D0) of the "caged" droplets. The thermal dependence of D0 and tau(f) supports the notion of entropically driven interdroplet steric repulsion stabilizing the cellular phases.

  7. Steric Interactions in Cellular Structures Formed in a Water/Oil/Surfactant/Cosurfactant Mixture

    NASA Astrophysics Data System (ADS)

    Molle, B.; de Geyer, A.; Guillermo, A.; Farago, B.

    2003-02-01

    Dynamics of dense microemulsion droplets forming ordered cellular phases as temperature increases are investigated by neutron spin echo spectroscopy (NSE). The shape fluctuations of droplets are shown using a specific contrast. Their relaxation time τf is obtained by analysis of the NSE curves, which also reveals the short-range Brownian motion (diffusion constant D0) of the “caged” droplets. The thermal dependence of D0 and τf supports the notion of entropically driven interdroplet steric repulsion stabilizing the cellular phases.

  8. Terasaki Ramps in the Endoplasmic Reticulum: Structure, Function and Formation

    NASA Astrophysics Data System (ADS)

    Huber, Greg; Guven, Jemal; Valencia, Dulce-Maria

    2015-03-01

    The endoplasmic reticulum (ER) has long been considered an exceedingly important and complex cellular organelle in eukaryotes (like you). It is a membrane structure, part folded lamellae, part tubular network, that both envelopes the nucleus and threads its way outward, all the way to the cell's periphery. Despite the elegant mechanics of bilayer membranes offered by the work of Helfrich and Canham, as far as the ER is concerned, theory has mostly sat on the sidelines. However, refined imaging of the ER has recently revealed beautiful and subtle geometrical forms - simple geometries, from the mathematical point of view - which some have called a ``parking garage for ribosomes.'' I'll review the discovery and physics of Terasaki ramps and discuss their relation to cell-biological questions, such as ER and nuclear-membrane re-organization during mitosis. Rather than being a footnote in a textbook on differential geometry, these structures suggest answers to a number of the ER's structure-function problems.

  9. Synthesis, cellular uptake and structure-activity relationships for potent cytotoxic trichloridoiridium(III) polypyridyl complexes.

    PubMed

    Scharwitz, Michael A; Ott, Ingo; Gust, Ronald; Kromm, Anna; Sheldrick, William S

    2008-08-01

    The complexes fac-[IrCl(3)(DMSO)(pp)] 1a-5a may be prepared by stepwise reaction of IrCl(3) x 3H(2)O with the appropriate polypyridyl ligand (pp=bpy, phen, dpq, dppz, dppn) and DMSO in CH(3)OH solution in the dark. The fac isomers of 1a-5a are stable in light-protected CD(2)Cl(2) solution but, with the exception of 5a, isomerize rapidly to a mixture of the fac and mer isomers in the presence of light. In contrast, solutions of the fac isomers in the polar solvents D(2)O and CD(3)OD are stable under such conditions. The isomer mer-[IrCl(3)(DMSO-kappa S)(phen)] 2b was, however, isolated by slow evaporation of an H(2)O/CH(3)OH solution of 2a and characterized by X-ray structural analysis. UV/Vis and CD studies of the interaction of 1a-5a with calf thymus DNA are in accordance with an effective absence of intercalation. (1)H NMR studies indicate that the complexes react slowly with compounds containing soft S donor atoms (e. g. N-acetylmethionine) but do not react with the guanine base of 5'-GMP(2-). The complexes 2a-5a are potent in vitro cytotoxic agents toward the human cell lines MCF-7 and HT-29 and their IC(50) values are dependent on the size of the polypyridyl ligand in the order phen, dpq>dppz>dppn. For instance IC(50) values of 5.5 (0.9), 0.8 (0.3) and 0.21 (0.11)microM were established for 3a-5a against MCF-7 cells and 6.1 (0.7), 1.5 (0.2) and 1.3 (0.4)microM against HT-29 cells. These values correlate with the cellular uptake efficiency which, on exposure to 10 microM solutions, reaches its highest levels (19.3(0.8) and 37.4(8.9) ng Ir/mg protein for MCF-7 and HT-29, respectively) for the dppn compound 5a. PMID:18472166

  10. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    PubMed

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-01

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  11. Chinese lexical networks: The structure, function and formation

    NASA Astrophysics Data System (ADS)

    Li, Jianyu; Zhou, Jie; Luo, Xiaoyue; Yang, Zhanxin

    2012-11-01

    In this paper Chinese phrases are modeled using complex networks theory. We analyze statistical properties of the networks and find that phrase networks display some important features: not only small world and the power-law distribution, but also hierarchical structure and disassortative mixing. These statistical traits display the global organization of Chinese phrases. The origin and formation of such traits are analyzed from a macroscopic Chinese culture and philosophy perspective. It is interesting to find that Chinese culture and philosophy may shape the formation and structure of Chinese phrases. To uncover the structural design principles of networks, network motif patterns are studied. It is shown that they serve as basic building blocks to form the whole phrase networks, especially triad 38 (feed forward loop) plays a more important role in forming most of the phrases and other motifs. The distinct structure may not only keep the networks stable and robust, but also be helpful for information processing. The results of the paper can give some insight into Chinese language learning and language acquisition. It strengthens the idea that learning the phrases helps to understand Chinese culture. On the other side, understanding Chinese culture and philosophy does help to learn Chinese phrases. The hub nodes in the networks show the close relationship with Chinese culture and philosophy. Learning or teaching the hub characters, hub-linking phrases and phrases which are meaning related based on motif feature should be very useful and important for Chinese learning and acquisition.

  12. Centromere protein B of African green monkey cells: gene structure, cellular expression, and centromeric localization.

    PubMed Central

    Yoda, K; Nakamura, T; Masumoto, H; Suzuki, N; Kitagawa, K; Nakano, M; Shinjo, A; Okazaki, T

    1996-01-01

    Centromere protein B (CENP-B) is a centromeric DNA-binding protein which recognizes a 17-bp sequence (CENP-B box) in human and mouse centromeric satellite DNA. The African green monkey (AGM) is phylogenetically closer to humans than mice and is known to contain large amounts of alpha-satellite DNA, but there has been no report of CENP-B boxes or CENP-B in the centromere domains of its chromosomes. To elucidate the AGM CENP-B-CENP-B box interaction, we have analyzed the gene structure, expression, biochemical properties, and centromeric localization of its CENP-B. The amino acid sequence deduced from the cloned AGM CENP-B gene was established to be highly homologous to that of human and mouse CENP-B. In particular, the DNA binding and homodimer formation domains demonstrated 100% identity to their human and mouse counterparts. Immunoblotting and DNA mobility shift analyses revealed CENP-B to be expressed in AGM cell lines. As predicted from the gene structure, the AGM CENP-B in the cell extracts exhibited the same DNA binding specificity and homodimer forming activity as human CENP-B. By indirect immunofluorescent staining of AGM mitotic cells with anti-CENP-B antibodies, a centromere-specific localization of AGM CENP-B could be demonstrated. We also isolated AGM alpha-satellite DNA with a CENP-B box-like sequence with CENP-B affinity. These results not only prove that CENP-B functionally persists in AGM cells but also suggest that the AGM genome contains the recognition sequences for CENP-B (CENP-B boxes with the core recognition sequence or CENP-B box variants) in centromeric satellite DNA. PMID:8756674

  13. Electron microscopic examination of wastewater biofilm formation and structural components.

    PubMed Central

    Eighmy, T T; Maratea, D; Bishop, P L

    1983-01-01

    This research documents in situ wastewater biofilm formation, structure, and physiochemical properties as revealed by scanning and transmission electron microscopy. Cationized ferritin was used to label anionic sites of the biofilm glycocalyx for viewing in thin section. Wastewater biofilm formation paralleled the processes involved in marine biofilm formation. Scanning electron microscopy revealed a dramatic increase in cell colonization and growth over a 144-h period. Constituents included a variety of actively dividing morphological types. Many of the colonizing bacteria were flagellated. Filaments were seen after primary colonization of the surface. Transmission electron microscopy revealed a dominant gram-negative cell wall structure in the biofilm constituents. At least three types of glycocalyces were observed. The predominant glycocalyx possessed interstices and was densely labeled with cationized ferritin. Two of the glycocalyces appeared to mediate biofilm adhesion to the substratum. The results suggest that the predominant glycocalyx of this thin wastewater biofilm serves, in part, to: (i) enclose the bacteria in a matrix and anchor the biofilm to the substratum and (ii) provide an extensive surface area with polyanionic properties. Images PMID:6881965

  14. Structure and formation of the lunar farside highlands.

    PubMed

    Garrick-Bethell, Ian; Nimmo, Francis; Wieczorek, Mark A

    2010-11-12

    The formation of the lunar farside highlands has long been an open problem in lunar science. We show that much of the topography and crustal thickness in this terrain can be described by a degree-2 harmonic. No other portion of the Moon exhibits comparable degree-2 structure. The quantified structure of the farside highlands unites them with the nearside and suggests a relation between lunar crustal structure, nearside volcanism, and heat-producing elements. The farside topography cannot be explained by a frozen-in tidal bulge. However, the farside crustal thickness and the topography it produces may have been caused by spatial variations in tidal heating when the ancient crust was decoupled from the mantle by a liquid magma ocean, similar to Europa's present ice shell. PMID:21071665

  15. Formation of electrostatic solitons and hole structures in pair plasmas.

    PubMed

    Jao, C-S; Hau, L-N

    2012-11-01

    In an electron-proton plasma, electrostatic solitary waves and hole structures can easily be generated by streaming instability due to the asymmetric inertia between ions and electrons. It has been argued theoretically whether electrostatic solitons and/or hole structures can form in a pair plasma. This paper presents results on the formation of pair electrostatic hole structure in an electron-positron plasma based on one-dimensional electrostatic particle-in-cell simulations. In particular, we show the feature of interlacing electron and positron holes in phase space generated by current-free electron and positron beams streaming in a stationary electron-positron background plasma. The coexistent electron and positron holes are associated with periodic interlacing of positive and negative potentials, respectively. Detailed comparisons between simulation results and linear theory of streaming instability in pair plasmas are made and the thermodynamic state is inferred. PMID:23214890

  16. FORMATION OF COLD FILAMENTARY STRUCTURE FROM WIND-BLOWN SUPERBUBBLES

    SciTech Connect

    Ntormousi, Evangelia; Burkert, Andreas; Fierlinger, Katharina; Heitsch, Fabian

    2011-04-10

    The expansion and collision of two wind-blown superbubbles is investigated numerically. Our models go beyond previous simulations of molecular cloud formation from converging gas flows by exploring this process with realistic flow parameters, sizes, and timescales. The superbubbles are blown by time-dependent winds and supernova explosions, calculated from population synthesis models. They expand into a uniform or turbulent diffuse medium. We find that dense, cold gas clumps and filaments form naturally in the compressed collision zone of the two superbubbles. Their shapes resemble the elongated, irregular structure of observed cold, molecular gas filaments, and clumps. At the end of the simulations, between 65% and 80% of the total gas mass in our simulation box is contained in these structures. The clumps are found in a variety of physical states, ranging from pressure equilibrium with the surrounding medium to highly underpressured clumps with large irregular internal motions and structures which are rotationally supported.

  17. DNA-Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes.

    PubMed

    Tretyakova, Natalia Y; Groehler, Arnold; Ji, Shaofei

    2015-06-16

    Noncovalent DNA-protein interactions are at the heart of normal cell function. In eukaryotic cells, genomic DNA is wrapped around histone octamers to allow for chromosomal packaging in the nucleus. Binding of regulatory protein factors to DNA directs replication, controls transcription, and mediates cellular responses to DNA damage. Because of their fundamental significance in all cellular processes involving DNA, dynamic DNA-protein interactions are required for cell survival, and their disruption is likely to have serious biological consequences. DNA-protein cross-links (DPCs) form when cellular proteins become covalently trapped on DNA strands upon exposure to various endogenous, environmental and chemotherapeutic agents. DPCs progressively accumulate in the brain and heart tissues as a result of endogenous exposure to reactive oxygen species and lipid peroxidation products, as well as normal cellular metabolism. A range of structurally diverse DPCs are found following treatment with chemotherapeutic drugs, transition metal ions, and metabolically activated carcinogens. Because of their considerable size and their helix-distorting nature, DPCs interfere with the progression of replication and transcription machineries and hence hamper the faithful expression of genetic information, potentially contributing to mutagenesis and carcinogenesis. Mass spectrometry-based studies have identified hundreds of proteins that can become cross-linked to nuclear DNA in the presence of reactive oxygen species, carcinogen metabolites, and antitumor drugs. While many of these proteins including histones, transcription factors, and repair proteins are known DNA binding partners, other gene products with no documented affinity for DNA also participate in DPC formation. Furthermore, multiple sites within DNA can be targeted for cross-linking including the N7 of guanine, the C-5 methyl group of thymine, and the exocyclic amino groups of guanine, cytosine, and adenine. This structural

  18. Constraints on the Cosmic Structure Formation Models from Early Formation of Giant Galaxies

    NASA Astrophysics Data System (ADS)

    Mo, H. J.; Fukugita, M.

    1996-08-01

    A recent observation of Steidel and coworkers indicates that a substantial fraction of giant galaxies were formed at an epoch as early as redshift z > 3--3.5. We show that this early formation gives strong constraints on models of cosmic structure formation. Adopting the COBE normalization for the density perturbation spectrum, we argue that the following models do not have large enough power on galactic scales to yield the observed abundance: (1) standard cold dark matter (CDM) models (where mass density Omega 0 = 1 and power index n = 1) with the Hubble constant h <~ 0.35; (2) tilted CDM models with h = 0.5 and n <~ 0.75; (3) open CDM models with h <~ 0.8 and Omega 0 <~ 0.3; and (4) mixed dark matter models with h = 0.5 and Omega nu >~ 0.2. Flat CDM models with a cosmological constant lambda 0 ~ 0.7 are consistent with the observation, provided that h >~ 0.6. Combined with constraints from large-scale structure formation, these results imply that the flat CDM model with a low Omega 0 is the one fully consistent with observations. We predict that these high-redshift galaxies are more strongly clustered today than normal galaxies.

  19. Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells

    PubMed Central

    Liang, Jie; Cao, Youfang; Gürsoy, Gamze; Naveed, Hammad; Terebus, Anna; Zhao, Jieling

    2016-01-01

    Genome sequences provide the overall genetic blueprint of cells, but cells possessing the same genome can exhibit diverse phenotypes. There is a multitude of mechanisms controlling cellular epigenetic states and that dictate the behavior of cells. Among these, networks of interacting molecules, often under stochastic control, depending on the specific wirings of molecular components and the physiological conditions, can have a different landscape of cellular states. In addition, chromosome folding in three-dimensional space provides another important control mechanism for selective activation and repression of gene expression. Fully differentiated cells with different properties grow, divide, and interact through mechanical forces and communicate through signal transduction, resulting in the formation of complex tissue patterns. Developing quantitative models to study these multi-scale phenomena and to identify opportunities for improving human health requires development of theoretical models, algorithms, and computational tools. Here we review recent progress made in these important directions. PMID:27480462

  20. Multiscale Modeling of Cellular Epigenetic States: Stochasticity in Molecular Networks, Chromatin Folding in Cell Nuclei, and Tissue Pattern Formation of Cells.

    PubMed

    Liang, Jie; Cao, Youfang; Gursoy, Gamze; Naveed, Hammad; Terebus, Anna; Zhao, Jieling

    2015-01-01

    Genome sequences provide the overall genetic blueprint of cells, but cells possessing the same genome can exhibit diverse phenotypes. There is a multitude of mechanisms controlling cellular epigenetic states and that dictate the behavior of cells. Among these, networks of interacting molecules, often under stochastic control, depending on the specific wirings of molecular components and the physiological conditions, can have a different landscape of cellular states. In addition, chromosome folding in three-dimensional space provides another important control mechanism for selective activation and repression of gene expression. Fully differentiated cells with different properties grow, divide, and interact through mechanical forces and communicate through signal transduction, resulting in the formation of complex tissue patterns. Developing quantitative models to study these multi-scale phenomena and to identify opportunities for improving human health requires development of theoretical models, algorithms, and computational tools. Here we review recent progress made in these important directions.

  1. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented. PMID:27100912

  2. Structural and Kinetic Studies of Formate Dehydrogenase from Candida boidinii.

    PubMed

    Guo, Qi; Gakhar, Lokesh; Wickersham, Kyle; Francis, Kevin; Vardi-Kilshtain, Alexandra; Major, Dan T; Cheatum, Christopher M; Kohen, Amnon

    2016-05-17

    The structure of formate dehydrogenase from Candida boidinii (CbFDH) is of both academic and practical interests. First, this enzyme represents a unique model system for studies on the role of protein dynamics in catalysis, but so far these studies have been limited by the availability of structural information. Second, CbFDH and its mutants can be used in various industrial applications (e.g., CO2 fixation or nicotinamide recycling systems), and the lack of structural information has been a limiting factor in commercial development. Here, we report the crystallization and structural determination of both holo- and apo-CbFDH. The free-energy barrier for the catalyzed reaction was computed and indicates that this structure indeed represents a catalytically competent form of the enzyme. Complementing kinetic examinations demonstrate that the recombinant CbFDH has a well-organized reactive state. Finally, a fortuitous observation has been made: the apoenzyme crystal was obtained under cocrystallization conditions with a saturating concentration of both the cofactor (NAD(+)) and inhibitor (azide), which has a nanomolar dissociation constant. It was found that the fraction of the apoenzyme present in the solution is less than 1.7 × 10(-7) (i.e., the solution is 99.9999% holoenzyme). This is an extreme case where the crystal structure represents an insignificant fraction of the enzyme in solution, and a mechanism rationalizing this phenomenon is presented.

  3. Formation of plasma dust structures at atmospheric pressure

    SciTech Connect

    Filippov, A. V. Babichev, V. N.; Dyatko, N. A.; Pal', A. F.; Starostin, A. N.; Taran, M. D.; Fortov, V. E.

    2006-02-15

    The formation of strongly coupled stable dust structures in the plasma produced by an electron beam at atmospheric pressure was detected experimentally. Analytical expressions were derived for the ionization rate of a gas by an electron beam in an axially symmetric geometry by comparing experimental data with Monte Carlo calculations. Self-consistent one-dimensional simulations of the beam plasma were performed in the diffusion drift approximation of charged plasma particle transport with electron diffusion to determine the dust particle levitation conditions. Since almost all of the applied voltage drops on the cathode layer in the Thomson glow regime of a non-self-sustained gas discharge, a distribution of the electric field that grows toward the cathode is produced in it; this field together with the gravity produces a potential well in which the dust particles levitate to form a stable disk-shaped structure. The nonideality parameters of the dust component in the formation region of a highly ordered quasi-crystalline structure calculated using computational data for the dust particle charging problem were found to be higher than the critical value after exceeding which an ensemble of particles with a Yukawa interaction should pass to the crystalline state.

  4. Improving the Factor Structure of Psychological Scales: The Expanded Format as an Alternative to the Likert Scale Format

    ERIC Educational Resources Information Center

    Zhang, Xijuan; Savalei, Victoria

    2016-01-01

    Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format,…

  5. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2008-01-01

    Intense structure formation and reionization occur at high redshift, yet there is currently little observational information about this very important epoch. Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the formation of structures in the early universe. Past efforts have been limited to calculating merger rates using different models in which many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span a very wide range (0.1 - 104 mergers/year). Here we develop a semi-analytical, phenomenological model of MBH mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z 5 - 30 structure formation era. We do this by generating synthetic LISA observable data (total BH mass, BH mass ratio, redshift, merger rates), which are then analyzed using a Markov Chain Monte Carlo method. This allows us to constrain the physical parameters of the mergers. We find that our methodology works well at estimating merger parameters, consistently giving results within 1- of the input parameter values. We also discover that the number of merger events is a key discriminant among models. This helps our method be robust against observational uncertainties. Our approach, which at this stage constitutes a proof of principle, can be readily extended to physical models and to more general problems in cosmology and gravitational wave astrophysics.

  6. Studying GPCR/cAMP pharmacology from the perspective of cellular structure

    PubMed Central

    Wright, Peter T.; Schobesberger, Sophie; Gorelik, Julia

    2015-01-01

    Signal transduction via G-protein coupled receptors (GPCRs) relies upon the production of cAMP and other signaling cascades. A given receptor and agonist pair, produce multiple effects upon cellular physiology which can be opposite in different cell types. The production of variable cellular effects via the signaling of the same GPCR in different cell types is a result of signal organization in space and time (compartmentation). This organization is usually based upon the physical and chemical properties of the membranes in which the GPCRs reside and the repertoire of downstream effectors and co-factors that are available at that location. In this review we explore mechanisms of GPCR signal compartmentation and broadly review the state-of-the-art methodologies which can be utilized to study them. We provide a clear rationale for a “localized” approach to the study of the pharmacology and physiology of GPCRs and particularly the secondary messenger cAMP. PMID:26236239

  7. Star formation along the Hubble sequence. Radial structure of the star formation of CALIFA galaxies

    NASA Astrophysics Data System (ADS)

    González Delgado, R. M.; Cid Fernandes, R.; Pérez, E.; García-Benito, R.; López Fernández, R.; Lacerda, E. A. D.; Cortijo-Ferrero, C.; de Amorim, A. L.; Vale Asari, N.; Sánchez, S. F.; Walcher, C. J.; Wisotzki, L.; Mast, D.; Alves, J.; Ascasibar, Y.; Bland-Hawthorn, J.; Galbany, L.; Kennicutt, R. C.; Márquez, I.; Masegosa, J.; Mollá, M.; Sánchez-Blázquez, P.; Vílchez, J. M.

    2016-05-01

    The spatially resolved stellar population content of today's galaxies holds important information for understanding the different processes that contribute to the star formation and mass assembly histories of galaxies. The aim of this paper is to characterize the radial structure of the star formation rate (SFR) in galaxies in the nearby Universe as represented by a uniquely rich and diverse data set drawn from the CALIFA survey. The sample under study contains 416 galaxies observed with integral field spectroscopy, covering a wide range of Hubble types and stellar masses ranging from M⋆ ~ 109 to 7 × 1011 M⊙. Spectral synthesis techniques are applied to the datacubes to derive 2D maps and radial profiles of the intensity of the star formation rate in the recent past (ΣSFR), as well as related properties, such as the local specific star formation rate (sSFR), defined as the ratio between ΣSFR and the stellar mass surface density (μ⋆). To emphasize the behavior of these properties for galaxies that are on and off the main sequence of star formation (MSSF), we stack the individual radial profiles in seven bins of galaxy morphology (E, S0, Sa, Sb, Sbc, Sc, and Sd), and several stellar masses. Our main results are: (a) the intensity of the star formation rate shows declining profiles that exhibit very small differences between spirals with values at R = 1 half light radius (HLR) within a factor two of ΣSFR ~ 20 M⊙Gyr-1pc-2. The dispersion in the ΣSFR(R) profiles is significantly smaller in late type spirals (Sbc, Sc, Sd). This confirms that the MSSF is a sequence of galaxies with nearly constant ΣSFR. (b) sSFR values scale with Hubble type and increase radially outward with a steeper slope in the inner 1 HLR. This behavior suggests that galaxies are quenched inside-out and that this process is faster in the central, bulge-dominated part than in the disks. (c) As a whole and at all radii, E and S0 are off the MSSF with SFR much smaller than spirals of the

  8. Effective myotube formation in human adipose tissue-derived stem cells expressing dystrophin and myosin heavy chain by cellular fusion with mouse C2C12 myoblasts

    SciTech Connect

    Eom, Young Woo; Lee, Jong Eun; Yang, Mal Sook; Jang, In Keun; Kim, Hyo Eun; Lee, Doo Hoon; Kim, Young Jin; Park, Won Jin; Kong, Jee Hyun; Shim, Kwang Yong; Lee, Jong In; Kim, Hyun Soo

    2011-04-29

    Highlights: {yields} hASCs were differentiated into skeletal muscle cells by treatment with 5-azacytidine, FGF-2, and the supernatant of cultured hASCs. {yields} Dystrophin and MyHC were expressed in late differentiation step by treatment with the supernatant of cultured hASCs. {yields} hASCs expressing dystrophin and MyHC contributed to myotube formation during co-culture with mouse myoblast C2C12 cells. -- Abstract: Stem cell therapy for muscular dystrophies requires stem cells that are able to participate in the formation of new muscle fibers. However, the differentiation steps that are the most critical for this process are not clear. We investigated the myogenic phases of human adipose tissue-derived stem cells (hASCs) step by step and the capability of myotube formation according to the differentiation phase by cellular fusion with mouse myoblast C2C12 cells. In hASCs treated with 5-azacytidine and fibroblast growth factor-2 (FGF-2) for 1 day, the early differentiation step to express MyoD and myogenin was induced by FGF-2 treatment for 6 days. Dystrophin and myosin heavy chain (MyHC) expression was induced by hASC conditioned medium in the late differentiation step. Myotubes were observed only in hASCs undergoing the late differentiation step by cellular fusion with C2C12 cells. In contrast, hASCs that were normal or in the early stage were not involved in myotube formation. Our results indicate that stem cells expressing dystrophin and MyHC are more suitable for myotube formation by co-culture with myoblasts than normal or early differentiated stem cells expressing MyoD and myogenin.

  9. Structural elucidation and cellular antioxidant activity evaluation of major antioxidant phenolics in lychee pulp.

    PubMed

    Su, Dongxiao; Ti, Huihui; Zhang, Ruifen; Zhang, Mingwei; Wei, Zhengchen; Deng, Yuanyuan; Guo, Jinxin

    2014-09-01

    Lychee pulp contains phenolic compounds that are strong antioxidants, but the identities of the major antioxidants present are unknown. In the present study, the major contributors to the antioxidant activity of fresh lychee pulp were identified and their cellular antioxidant activities were investigated. Aqueous acetone extracts of lychee pulp were fractionated on polyamide resin, and those fractions with the largest antioxidant and radical scavenging activities were selected using cellular antioxidant activity and oxygen radical absorbance capacity assays. Three compounds that were major contributors to the antioxidant activity in these fractions were obtained by reverse-phase preparative HPLC and identified as quercetin 3-O-rutinoside-7-O-α-L-rhamnosidase (quercetin 3-rut-7-rha), quercetin 3-O-rutinoside (rutin) and (-)-epicatechin using NMR spectroscopy, HMBC, and ESI-MS spectrometry. The concentration of quercetin 3-rut-7-rha was 17.25mg per 100g of lychee pulp fresh weight. This is the first report of the identification and cellular antioxidant activity of quercetin 3-rut-7-rha from lychee pulp.

  10. Fractal structure formation from Ag nanoparticle films on insulating substrates.

    PubMed

    Tang, Jing; Li, Zhiyong; Xia, Qiangfei; Williams, R Stanley

    2009-07-01

    Two dimensional (2D) fractal structures were observed to form from fairly uniform Ag island films (equivalent mass thicknesses of 1.5 and 5 nm) on insulating silicon dioxide surfaces (thermally grown silicon oxide on Si or quartz) upon immersion in deionized water. This result is distinctly different from the previously observed three-dimensional (3D) growth of faceted Ag nanocrystals on conductive surfaces (ITO and graphite) as the result of an electrochemical Ostwald ripening process, which also occurs on native oxide covered silicon surfaces as reported here. The fractal structures formed by diffusion-limited aggregation (DLA) of Ag species on the insulating surfaces. We present the experimental observation of this phenomenon and discuss some possible mechanisms for the DLA formation. PMID:19496573

  11. Giant planet formation in radially structured protoplanetary discs

    NASA Astrophysics Data System (ADS)

    Coleman, Gavin A. L.; Nelson, Richard P.

    2016-08-01

    Our recent N-body simulations of planetary system formation, incorporating models for the main physical processes thought to be important during the building of planets (i.e. gas disc evolution, migration, planetesimal/boulder accretion, gas accretion on to cores, etc.), have been successful in reproducing some of the broad features of the observed exoplanet population (e.g. compact systems of low-mass planets, hot Jupiters), but fail completely to form any surviving cold Jupiters. The primary reason for this failure is rapid inward migration of growing protoplanets during the gas accretion phase, resulting in the delivery of these bodies on to orbits close to the star. Here, we present the results of simulations that examine the formation of gas giant planets in protoplanetary discs that are radially structured due to spatial and temporal variations in the effective viscous stresses, and show that such a model results in the formation of a population of cold gas giants. Furthermore, when combined with models for disc photoevaporation and a central magnetospheric cavity, the simulations reproduce the well-known hot-Jupiter/cold-Jupiter dichotomy in the observed period distribution of giant exoplanets, with a period valley between 10 and 100 d.

  12. The role of cellular structure on increasing the detonability limits of three-step chain-branching detonations

    SciTech Connect

    Short, Mark; Kiyanda, Charles B; Quirk, James J; Sharpe, Gary J

    2011-01-27

    In [1], the dynamics of a pulsating three-step chain-branching detonation were studied. The reaction model consists of, sequentially, chain-initiation, chain-branching and chain-termination steps. The chain-initiation and chain-branching steps are taken to be thermally neutral, with chemical energy release occuring in the chain-termination stage. The purpose of the present study is to examine whether cellular detonation structure can increase the value of the chain-branching cross-over temperature T{sub b} at which fully coupled detonation solutions are observed over those in 1 D. The basic concept is straightforward and has been discussed in [1] and [3]; if T{sub s} drops below T{sub b} at the lead shock, the passage of a transverse shock can increase both the lead shock temperature and the temperature behind the transverse wave back above T{sub b}, thus sustaining an unstable cellular detonation for values of T{sub b} for which a one-dimensional pulsating detonation will fail. Experiments potentially supporting this hypothesis with irregular detonations have been shown in [3] in a shock tube with acoustically absorbing walls. Removal of the transverse waves results in detonation failure, giving way to a decoupled shock-flame complex. A number of questions remain to be addressed regarding the possibility of such a mechanism, and, if so, about the precise mechanisms driving the cellular structure for large T{sub b}. For instance, one might ask what sets the cell size in a chain-branching detonation, particularly could the characteristic cell size be set by the chain-branching cross-over temperature T{sub b}: after a transverse wave shock collision, the strength of the transverse wave weakens as it propagates along the front. If the spacing between shock collisions is too large (cell size), then the transverse shocks may weaken to the extent that the lead shock temperature or that behind the transverse waves is not raised above T{sub b}, losing chemical energy to

  13. The evolution and cellular structure of a detonation subsequent to a head-on interaction with a shock wave

    SciTech Connect

    Botros, Barbara B.; Zhu, YuJian; Lee, John H.S.; Ng, Hoi Dick; Ju, Yiguang

    2007-12-15

    This paper analyzes the results of a head-on collision between a detonation and a planar shock wave. The evolution of the detonation cellular structure subsequent to the frontal collision was examined through smoked foil experiments. It is shown that a large reduction in cell size is observed following the frontal collision, and that the detonation cell widths are correlated well with the chemical kinetic calculations from the ZND model. From chemical kinetic calculations, the density increase caused by shock compression appears to be the main factor leading to the significant reduction in cell size. It was found that depending on the initial conditions, the transition to the final cellular pattern can be either smooth or spotty. This phenomenon appears to be equivalent to Oppenheim's strong and mild reflected shock ignition experiments. The difference between these two transitions is, however, more related to the stability of the incident detonation and the strength of the perturbation generated by the incident shock. (author)

  14. Modulation of nanotube formation by structural modifications of sphingolipids.

    PubMed Central

    Kulkarni, V S; Boggs, J M; Brown, R E

    1999-01-01

    Galactosylceramides (GalCers) containing nervonoyl (24:1(Delta15(cis))) acyl chains have the capacity to assemble into nanotubular microstructures in excess water (. Biophys. J. 69:1976-1986). To define the structural parameters that modulate nanotube formation, GalCer derivatives were synthesized that contained cis monounsaturated acyl chains with the formula X:1((X-9)). X indicates the total acyl carbon number (24, 22, 20, or 18), and 1 indicates a single cis double bond, the location of which is designated by the superscript (X-9). Deep etching of freeze-fractured 24:1(Delta15(cis)) GalCer dispersions followed by replica production and transmission electron microscopic analysis confirmed nanotube morphology (25-30-nm diameter). Control experiments revealed that tubule formation was promoted by cooling through the main enthalpic phase transition coupled with repetitive freeze-thaw cycling. Imparting a negative charge to the sugar headgroup of 24:1(Delta15)GalCer via sulfate dramatically altered mesomorpholgy and resulted in myelinic-like, multilamellar structures. Removal of the sugar headgroup (24:1(Delta15)Cer) resulted in flattened cylindrical structures with a cochleate appearance. Compared to these large-scale changes in morphology, more subtle changes were induced by structural changes in the acyl chain of 24:1(Delta15)GalCer. 22:1(Delta13)GalCer dispersions consisted of long, smooth tubules (35-40-nm diameters) with a strong tendency to self-align into bundle-like aggregates. In contrast, the microstructures formed by 20:1(Delta11)GalCer resembled helical ribbons with a right-handed twist. Ribbon widths averaged 30-35 nm, with helical pitches of 80-90 nm. 18:1(Delta9)GalCer displayed a variety of morphologies, including large-diameter multilamellar cylinders and liposome-like structures, as well as stacked, plate-like arrays. The results are discussed within the context of current theories of lipid tubule formation. PMID:10388760

  15. Formation of Coronae Structures on Venus by Thermochemical Diapirs

    NASA Astrophysics Data System (ADS)

    Golabek, G. J.; Kaus, B. J. P.; Tackley, P. J.

    2009-04-01

    One of the most prominent features on the surface of Venus are the coronae. They are large scale volcano-tectonic structures, which are approximately circular with a mean diameter of 200 - 300 km [Dombard et al., 2007], with extrema ranging from 60 km to about 2000 km diameter. A total of 515 coronae were found on Venus in the Magellan data [Stofan et al., 2001]. The intruiging point about corona is that there is no counterpart on the other terrestrial planets for these structures. Nine different groups of coronae have been observed on Venus [Smrekar and Stofan, 1997]. Smrekar and Stofan [1997] suggested that these different groups can stand for different steps in the time evolution of coronae. Several mechanisms have been proposed to explain their formation: Dombard et al. [2007] suggested that coronae form in response to magmatic loading of the crust over zones of partial melting above thermally buoyant heads of transient mantle plumes that impinge on the base of the thermal lithosphere. On the other side, the potential importance of crust delamination induced by mantle upwellings as formation mechanisms for coronae was pointed out by Smrekar and Stofan [1997]. Here, we present results on coronae formation using the recently developed 2D finite element code MILAMIN_VEP, which employs MILAMIN technology [Dabrowski et al., 2008]. We apply a temperature and stress-dependent visco-elasto-plastic rheology in a rectangular box, which includes a rising thermochemical diapir beneath the Venusian crust and lithosphere. The rheological parameters are taken from results inferred for Venusian materials [Mackwell et al., 1998]. A free surface is used in our calculations, which allows for the self-consistent computation of topography induced by the buoyant diapir. A hybrid particle-in-cell approach allows remeshing of strongly deformed grid cells. A systematic investigation of the physical conditions under which coronae can form is being performed in 2D. Initial results

  16. Perineuronal net formation and structure in aggrecan knockout mice.

    PubMed

    Giamanco, K A; Morawski, M; Matthews, R T

    2010-11-10

    Perineuronal nets (PNNs) are specialized substructures of the neural extracellular matrix (ECM) which envelop the cell soma and proximal neurites of particular sets of neurons with apertures at sites of synaptic contact. Previous studies have shown that PNNs are enriched with chondroitin sulfate proteoglycans (CSPGs) and hyaluronan, however, a complete understanding of their precise molecular composition has been elusive. In addition, identifying which specific PNN components are critical to the formation of this structure has not been demonstrated. Previous work in our laboratory has demonstrated that the CSPG, aggrecan, is a key activity-dependent component of PNNs in vivo. In order to assess the contribution of aggrecan to PNN formation, we utilized cartilage matrix deficiency (cmd) mice, which lack aggrecan. Herein, we utilized an in vitro model, dissociated cortical culture, and an ex vivo model, organotypic slice culture, to specifically investigate the role aggrecan plays in PNN formation. Our work demonstrates that staining with the lectin, Wisteria floribunda agglutinin (WFA), considered a broad PNN marker, is eliminated in the absence of aggrecan, suggesting the loss of PNNs. However, in contrast, we found that the expression patterns of other PNN markers, including hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R, brevican, and hyaluronan are unaffected by the absence of aggrecan. Lastly, we determined that while all PNN components are bound to the surface in a hyaluronan-dependent manner, only HAPLN1 remains attached to the cell surface when neurons are treated with chondroitinase. These results suggest a different model for the molecular association of PNNs to the cell surface. Together our work has served to assess the contribution of aggrecan to PNN formation while providing key evidence concerning the molecular composition of PNNs in addition to determining how these components ultimately form PNNs.

  17. Perineuronal net formation and structure in aggrecan knockout mice.

    PubMed

    Giamanco, K A; Morawski, M; Matthews, R T

    2010-11-10

    Perineuronal nets (PNNs) are specialized substructures of the neural extracellular matrix (ECM) which envelop the cell soma and proximal neurites of particular sets of neurons with apertures at sites of synaptic contact. Previous studies have shown that PNNs are enriched with chondroitin sulfate proteoglycans (CSPGs) and hyaluronan, however, a complete understanding of their precise molecular composition has been elusive. In addition, identifying which specific PNN components are critical to the formation of this structure has not been demonstrated. Previous work in our laboratory has demonstrated that the CSPG, aggrecan, is a key activity-dependent component of PNNs in vivo. In order to assess the contribution of aggrecan to PNN formation, we utilized cartilage matrix deficiency (cmd) mice, which lack aggrecan. Herein, we utilized an in vitro model, dissociated cortical culture, and an ex vivo model, organotypic slice culture, to specifically investigate the role aggrecan plays in PNN formation. Our work demonstrates that staining with the lectin, Wisteria floribunda agglutinin (WFA), considered a broad PNN marker, is eliminated in the absence of aggrecan, suggesting the loss of PNNs. However, in contrast, we found that the expression patterns of other PNN markers, including hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R, brevican, and hyaluronan are unaffected by the absence of aggrecan. Lastly, we determined that while all PNN components are bound to the surface in a hyaluronan-dependent manner, only HAPLN1 remains attached to the cell surface when neurons are treated with chondroitinase. These results suggest a different model for the molecular association of PNNs to the cell surface. Together our work has served to assess the contribution of aggrecan to PNN formation while providing key evidence concerning the molecular composition of PNNs in addition to determining how these components ultimately form PNNs. PMID:20732394

  18. Towards the mathematical model of rim structure formation

    NASA Astrophysics Data System (ADS)

    Kinoshita, M.

    1997-09-01

    The high burnup LWR UO 2 fuels show a notable micro-structural change around the pellet outer zone which is called the rim structure. It is observed at temperatures as low as 400°C so that fission track and cascade mixing could be the key mechanism. SEM observation revealed that the structure primarily appears on free surfaces of UO 2, indicating that strong sink for point defects may play a big role. And as generic observations, increase of lattice parameter indicates extensive amounts of vacancies are stored in high burnup fuel, which may induce the restructuring interacting with dislocations of high density at high burnup. Considering these observations a model of reaction-diffusion process of defects with irradiation induced transport is proposed. The equations are investigated numerically. The model indicates that an instability starts when the dislocation network starts intensive interaction with vacancy flux which is modified by interstitial diffusion between spatial segments. It appeared to be similar to the Turing type instability which indicates that the rim structure formation is one kind of the self-organizing processes of open reaction-diffusion systems.

  19. Structural Basis of Clostridium perfringens Toxin Complex Formation

    SciTech Connect

    Adams,J.; Gregg, K.; Bayer, E.; Boraston, A.; Smith, S.

    2008-01-01

    The virulent properties of the common human and livestock pathogen Clostridium perfringens are attributable to a formidable battery of toxins. Among these are a number of large and highly modular carbohydrate-active enzymes, including the {mu}-toxin and sialidases, whose catalytic properties are consistent with degradation of the mucosal layer of the human gut, glycosaminoglycans, and other cellular glycans found throughout the body. The conservation of noncatalytic ancillary modules among these enzymes suggests they make significant contributions to the overall functionality of the toxins. Here, we describe the structural basis of an ultra-tight interaction (Ka = 1.44 x 1011 M-1) between the X82 and dockerin modules, which are found throughout numerous C. perfringens carbohydrate-active enzymes. Extensive hydrogen-bonding and van der Waals contacts between the X82 and dockerin modules give rise to the observed high affinity. The {mu}-toxin dockerin module in this complex is positioned {approx}180 relative to the orientation of the dockerin modules on the cohesin module surface within cellulolytic complexes. These observations represent a unique property of these clostridial toxins whereby they can associate into large, noncovalent multitoxin complexes that allow potentiation of the activities of the individual toxins by combining complementary toxin specificities.

  20. Label-free cellular structure imaging with 82 nm lateral resolution using an electron-beam excitation-assisted optical microscope.

    PubMed

    Fukuta, Masahiro; Masuda, Yuriko; Inami, Wataru; Kawata, Yoshimasa

    2016-07-25

    We present label-free and high spatial-resolution imaging for specific cellular structures using an electron-beam excitation-assisted optical microscope (EXA microscope). Images of the actin filament and mitochondria of stained HeLa cells, obtained by fluorescence and EXA microscopy, were compared to identify cellular structures. Based on these results, we demonstrated the feasibility of identifying label-free cellular structures at a spatial resolution of 82 nm. Using numerical analysis, we calculated the imaging depth region and determined the spot size of a cathodoluminescent (CL) light source to be 83 nm at the membrane surface.

  1. The Large-scale Structure of the Universe: Probes of Cosmology and Structure Formation

    NASA Astrophysics Data System (ADS)

    Noh, Yookyung

    The usefulness of large-scale structure as a probe of cosmology and structure formation is increasing as large deep surveys in multi-wavelength bands are becoming possible. The observational analysis of large-scale structure guided by large volume numerical simulations are beginning to offer us complementary information and crosschecks of cosmological parameters estimated from the anisotropies in Cosmic Microwave Background (CMB) radiation. Understanding structure formation and evolution and even galaxy formation history is also being aided by observations of different redshift snapshots of the Universe, using various tracers of large-scale structure. This dissertation work covers aspects of large-scale structure from the baryon acoustic oscillation scale, to that of large scale filaments and galaxy clusters. First, I discuss a large- scale structure use for high precision cosmology. I investigate the reconstruction of Baryon Acoustic Oscillation (BAO) peak within the context of Lagrangian perturbation theory, testing its validity in a large suite of cosmological volume N-body simulations. Then I consider galaxy clusters and the large scale filaments surrounding them in a high resolution N-body simulation. I investigate the geometrical properties of galaxy cluster neighborhoods, focusing on the filaments connected to clusters. Using mock observations of galaxy clusters, I explore the correlations of scatter in galaxy cluster mass estimates from multi-wavelength observations and different measurement techniques. I also examine the sources of the correlated scatter by considering the intrinsic and environmental properties of clusters.

  2. Pronounced alterations of cellular metabolism and structure due to hyper- or hypo-osmosis.

    PubMed

    Mao, Lei; Hartl, Daniela; Nolden, Tobias; Koppelstätter, Andrea; Klose, Joachim; Himmelbauer, Heinz; Zabel, Claus

    2008-09-01

    Cell volume alteration represents an important factor contributing to the pathology of late-onset diseases. Previously, it was reported that protein biosynthesis and degradation are inversely (trans) regulated during cell volume regulation. Upon cell shrinkage, protein biosynthesis was up-regulated and protein degradation down-regulated. Cell swelling showed opposite regulation. Recent evidence suggests a decrease of protein biodegradation activity in many neurodegenerative diseases and even during aging; both also show prominent cell shrinkage. To clarify the effect of cell volume regulation on the overall protein turnover dynamics, we investigated mouse embryonic stem cells under hyper- and hypotonic osmotic conditions using a 2-D gel based proteomics approach. These conditions cause cell swelling and shrinkage, respectively. Our results demonstrate that the adaption to altered osmotic conditions and therefore cell volume alterations affects a broad spectrum of cellular pathways, including stress response, cytoskeleton remodeling and importantly, cellular metabolism and protein degradation. Interestingly, protein synthesis and degradation appears to be cis-regulated (same direction) on a global level. Our findings also support the hypothesis that protein alterations due to osmotic stress contribute to the pathology of neurodegenerative diseases due to a 60% expression overlap with proteins found altered in Alzheimer's, Huntington's, or Parkinson's disease. Eighteen percent of the proteins altered are even shared with all three disorders. PMID:18646788

  3. The cellular RNA helicase UAP56 is required for prevention of double-stranded RNA formation during influenza A virus infection.

    PubMed

    Wisskirchen, Christian; Ludersdorfer, Thomas H; Müller, Dominik A; Moritz, Eva; Pavlovic, Jovan

    2011-09-01

    The cellular DEAD box RNA helicase UAP56 plays a pivotal role in the efficient transcription/replication of influenza A virus. UAP56 is recruited by the nucleoprotein (NP) of influenza A viruses, and recent data revealed that the RNA helicase is required for the nuclear export of a subset of spliced and unspliced viral mRNAs. The fact that influenza viruses do not produce detectable amounts of double-stranded RNA (dsRNA) intermediates during transcription/replication suggests the involvement of cellular RNA helicases. Hence, we examined whether the RNA-unwinding activity of UAP56 or its paralog URH49 plays a role in preventing the accumulation of dsRNA during infection. First, our data showed that not only UAP56 but also its paralog URH49 can interact with NPs of avian and human influenza A viruses. The small interfering RNA (siRNA)-mediated depletion of either RNA helicase reduced the transport of M1 and hemagglutinin (HA) mRNAs and, to a lesser extent, NP and NS1 mRNAs into the cytoplasm. Moreover, we found that virus infection of UAP56-depleted cells leads to the rapid accumulation of dsRNA in the perinuclear region. In parallel, we observed a robust virus-mediated activation of dsRNA-dependent protein kinase R (PKR), indicating that the cellular RNA helicase UAP56 may be recruited by influenza virus to prevent dsRNA formation. The accumulation of dsRNA was blocked when actinomycin D or cycloheximide was used to inhibit viral transcription/replication or translation, respectively. In summary, we demonstrate that UAP56 is utilized by influenza A viruses to prevent the formation of dsRNA and, hence, the activation of the innate immune response.

  4. Aldehyde Oxidase Functions as a Superoxide Generating NADH Oxidase: An Important Redox Regulated Pathway of Cellular Oxygen Radical Formation

    PubMed Central

    Kundu, Tapan K.; Velayutham, Murugesan; Zweier, Jay L.

    2012-01-01

    The enzyme aldehyde oxidase (AO) is a member of the molybdenum hydroxylase family that includes xanthine oxidoreductase (XOR); however, its physiological substrates and functions remain unclear. Moreover, little is known about its role in cellular redox stress. Utilizing electron paramagnetic resonance spin trapping we measured the role of AO in the generation of reactive oxygen species (ROS) through the oxidation of NADH, and the effects of inhibitors of AO on NADH-mediated superoxide ( O2•−) generation. NADH was found to be a good substrate for AO with apparent Km and Vmax values of 29μM and 12 nmol min−1 mg−1, respectively. From O2•− generation measurements by cytochrome c reduction the apparent Km and Vmax values of NADH for AO were 11 μM and 15 nmol min−1 mg−1, respectively. With NADH oxidation by AO, ≥65% of the total electron flux led to O2•− generation. Diphenyleneiodonium completely inhibited AO-mediated O2•− production confirming that this occurs at the FAD site. Inhibitors of this NADH-derived O2•− generation were studied with amidone the most potent exerting complete inhibition at 100 μM concentration, while 150 μM menadione, raloxifene or β-estradiol led to 81%, 46% or 26% inhibition, respectively. From the kinetic data, the levels of AO and NADH, O2•− production was estimated to be ~89 and ~4 nM/s in liver and heart, respectively, much higher than that estimated for XOR under similar conditions. Owing to the ubiquitous distribution of NADH, aldehydes, and other endogenous AO substrates, AO is predicted to have an important role in cellular redox stress and related disease pathogenesis. PMID:22404107

  5. Locally Biased Galaxy Formation and Large-Scale Structure

    NASA Astrophysics Data System (ADS)

    Narayanan, Vijay K.; Berlind, Andreas A.; Weinberg, David H.

    2000-01-01

    We examine the influence of the morphology-density relation and a wide range of simple models for biased galaxy formation on statistical measures of large-scale structure. We contrast the behavior of local biasing models, in which the efficiency of galaxy formation is determined by the density, geometry, or velocity dispersion of the local mass distribution, with that of nonlocal biasing models, in which galaxy formation is modulated coherently over scales larger than the galaxy correlation length. If morphological segregation of galaxies is governed by a local morphology-density relation, then the correlation function of E/S0 galaxies should be steeper and stronger than that of spiral galaxies on small scales, as observed, while on large scales the E/S0 and spiral galaxies should have correlation functions with the same shape but different amplitudes. Similarly, all of our local bias models produce scale-independent amplification of the correlation function and power spectrum in the linear and mildly nonlinear regimes; only a nonlocal biasing mechanism can alter the shape of the power spectrum on large scales. Moments of the biased galaxy distribution retain the hierarchical pattern of the mass moments, but biasing alters the values and scale dependence of the hierarchical amplitudes S3 and S4. Pair-weighted moments of the galaxy velocity distribution are sensitive to the details of the bias prescription even if galaxies have the same local velocity distribution as the underlying dark matter. The nonlinearity of the relation between galaxy density and mass density depends on the biasing prescription and the smoothing scale, and the scatter in this relation is a useful diagnostic of the physical parameters that determine the bias. While the assumption that galaxy formation is governed by local physics leads to some important simplifications on large scales, even local biasing is a multifaceted phenomenon whose impact cannot be described by a single parameter or

  6. Changes in protein structure at the interface accompanying complex formation.

    PubMed

    Chakravarty, Devlina; Janin, Joël; Robert, Charles H; Chakrabarti, Pinak

    2015-11-01

    Protein interactions are essential in all biological processes. The changes brought about in the structure when a free component forms a complex with another molecule need to be characterized for a proper understanding of molecular recognition as well as for the successful implementation of docking algorithms. Here, unbound (U) and bound (B) forms of protein structures from the Protein-Protein Interaction Affinity Database are compared in order to enumerate the changes that occur at the interface atoms/residues in terms of the solvent-accessible surface area (ASA), secondary structure, temperature factors (B factors) and disorder-to-order transitions. It is found that the interface atoms optimize contacts with the atoms in the partner protein, which leads to an increase in their ASA in the bound interface in the majority (69%) of the proteins when compared with the unbound interface, and this is independent of the root-mean-square deviation between the U and B forms. Changes in secondary structure during the transition indicate a likely extension of helices and strands at the expense of turns and coils. A reduction in flexibility during complex formation is reflected in the decrease in B factors of the interface residues on going from the U form to the B form. There is, however, no distinction in flexibility between the interface and the surface in the monomeric structure, thereby highlighting the potential problem of using B factors for the prediction of binding sites in the unbound form for docking another protein. 16% of the proteins have missing (disordered) residues in the U form which are observed (ordered) in the B form, mostly with an irregular conformation; the data set also shows differences in the composition of interface and non-interface residues in the disordered polypeptide segments as well as differences in their surface burial.

  7. Innovative design of composite structures: The use of curvilinear fiber format in composite structure design

    NASA Technical Reports Server (NTRS)

    Hyer, M. W.; Charette, R. F.

    1990-01-01

    The gains in structural efficiency are investigated that can be achieved by aligning the fibers in some or all of the layers in a laminate with the principal stress directions in those layers. The name curvilinear fiber format is given to this idea. The problem studied is a plate with a central circular hole subjected to a uniaxial tensile load. An iteration scheme is used to find the fiber directions at each point in the laminate. Two failure criteria are used to evaluate the tensile load capacity of the plates with a curvilinear format, and for comparison, counterpart plates with a conventional straightline fiber format. The curvilinear designs for improved tensile capacity are then checked for buckling resistance. It is concluded that gains in efficiency can be realized with the curvilinear format.

  8. Structural basis of complement membrane attack complex formation

    NASA Astrophysics Data System (ADS)

    Serna, Marina; Giles, Joanna L.; Morgan, B. Paul; Bubeck, Doryen

    2016-02-01

    In response to complement activation, the membrane attack complex (MAC) assembles from fluid-phase proteins to form pores in lipid bilayers. MAC directly lyses pathogens by a `multi-hit' mechanism; however, sublytic MAC pores on host cells activate signalling pathways. Previous studies have described the structures of individual MAC components and subcomplexes; however, the molecular details of its assembly and mechanism of action remain unresolved. Here we report the electron cryo-microscopy structure of human MAC at subnanometre resolution. Structural analyses define the stoichiometry of the complete pore and identify a network of interaction interfaces that determine its assembly mechanism. MAC adopts a `split-washer' configuration, in contrast to the predicted closed ring observed for perforin and cholesterol-dependent cytolysins. Assembly precursors partially penetrate the lipid bilayer, resulting in an irregular β-barrel pore. Our results demonstrate how differences in symmetric and asymmetric components of the MAC underpin a molecular basis for pore formation and suggest a mechanism of action that extends beyond membrane penetration.

  9. Numerical models of sunspot formation and fine structure.

    PubMed

    Rempel, Matthias

    2012-07-13

    Sunspots are central to our understanding of solar (and stellar) magnetism in many respects. On the large scale, they link the magnetic field observable in the photosphere to the dynamo processes operating in the solar interior. Properly interpreting the constraints that sunspots impose on the dynamo process requires a detailed understanding of the processes involved in their formation, dynamical evolution and decay. On the small scale, they give an insight into how convective energy transport interacts with the magnetic field over a wide range of field strengths and inclination angles, leading to sunspot fine structure observed in the form of umbral dots and penumbral filaments. Over the past decade, substantial progress has been made on both observational and theoretical sides. Advanced ground- and space-based observations have resolved, for the first time, the details of umbral dots and penumbral filaments and discovered similarities in their substructures. Numerical models have advanced to the degree that simulations of entire sunspots with sufficient resolution to resolve sunspot fine structure are feasible. A combination of improved helioseismic inversion techniques with seismic forward modelling provides new views on the subsurface structure of sunspots. In this review, we summarize recent progress, with particular focus on numerical modelling. PMID:22665895

  10. Formation, structure and morphology of polyurethane-metal interphases

    NASA Astrophysics Data System (ADS)

    Wehlack, C.; Possart, W.

    2009-09-01

    Thin films (few 10 nm to some μm) of different two-part polyurethane adhesive systems (polyether resins and aromatic isocyanate hardener) are characterised on the native metal surfaces of gold, aluminium, copper and steel, thus acting as a model for the interphase in technically relevant material compounds. It is investigated in how far the curing processes, the resulting chemical structure and the morphology of the polymer films differ from the bulk. The comparison of films on the different metals and with the bulk provides conclusions on the properties of the interphase at polymer-metal contacts. The variation of the film thickness gives access to microstructure gradients. The chemical structure of the films is characterised by IR spectroscopy during curing at room temperature (RT kinetics) and in the cured state. Furthermore, microscopic (e.g. SFM) and additional spectroscopic techniques (e.g. XPS) characterise the films and their surface with respect to morphology, composition, homogeneity and topography. The results reveal specific features in the interphase caused by adhesive interactions, catalysis, phase separation and transport phenomena on the different metal surfaces. Remarkable quantitative differences can be seen in the chemical structure formation of thin PU films with respect to reaction rate and final degree of cure.

  11. Investigation of Laser Induced Structure formation and resultant fluorescence

    NASA Astrophysics Data System (ADS)

    Kandpal, Sanjeev Kumar; Otterson, Samantha L.; Bousfield, Douglas W.; Neivandt, David J.; Mason, Michael D.

    2015-04-01

    The formation mechanism of 3D micron-sized fluorescent structures generated in silver nanoparticle containing sodium citrate dihydrate films, during exposure to focused laser radiation, was investigated. Microscopic and thermochemical data indicate that heat accumulates at the nanoparticle surface. The heat causes local melting and an increase in temperature beyond the decomposition point of the immediate surrounding layer. In turn this leads to the rapid release of volatile gases (H2O and CO2). These expanding gases push the melted liquid pool outward, from the center of the focal volume, leaving behind a trough-like structure with elevated edges. It was observed that the edges of the structures were fluorescent. The fluorescence mechanism was investigated using atomic force, scanning electron and Confocal Fluorescence Microscopy. The observed fluorescence was attributed to the decomposition of sodium citrate dihydrate to sodium citrate. The presence of water acts to quench fluorescence in the bulk film, but near regions that experienced heat, the water is driven off.

  12. Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment.

    PubMed

    Yamashita, Hiroko; Kato, Takuma; Oba, Makoto; Misawa, Takashi; Hattori, Takayuki; Ohoka, Nobumichi; Tanaka, Masakazu; Naito, Mikihiko; Kurihara, Masaaki; Demizu, Yosuke

    2016-01-01

    Cell-penetrating peptides (CPP) are received a lot of attention as an intracellular delivery tool for hydrophilic molecules such as drugs, proteins, and DNAs. We designed and synthesized nona-arginine analogues 1-5 [FAM-β-Ala-(l-Arg-l-Arg-l-Pro)3-(Gly)3-NH2 (1), FAM-β-Ala-(l-Arg-l-Arg-l-Pro(NH2))3-(Gly)3-NH2 (2), FAM-β-Ala-(l-Arg-l-Arg-l-Pro(Gu))3-(Gly)3-NH2 (3), FAM-β-Ala-(l-Arg)2-(l-Pro(Gu))2-(l-Arg)4-l-Pro(Gu)-(Gly)3-NH2 (4), and FAM-β-Ala-(l-Arg)6-(l-Pro(Gu))3-(Gly)3-NH2 (5)] containing l-proline (l-Pro) or cationic proline derivatives (l-Pro(NH2) and l-Pro(Gu)), and investigated their cell-penetrating abilities. Interestingly, only peptide 3 having the side-chain guanidinyl l-Pro(Gu) exhibited a secondary structural change in cellular environment. Specifically, peptide 3 formed a random structure in hydrophilic conditions, whereas it formed a helical structure under amphipathic conditions. Furthermore, during cellular permeability tests, peptide 3 demonstrated greater cell-penetrating activity than other peptides and effectively transported plasmid DNA into HeLa cells. Thus, l-Pro(Gu)-containing peptide 3 may be a useful candidate as a gene delivery carrier. PMID:27609319

  13. Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment

    PubMed Central

    Yamashita, Hiroko; Kato, Takuma; Oba, Makoto; Misawa, Takashi; Hattori, Takayuki; Ohoka, Nobumichi; Tanaka, Masakazu; Naito, Mikihiko; Kurihara, Masaaki; Demizu, Yosuke

    2016-01-01

    Cell-penetrating peptides (CPP) are received a lot of attention as an intracellular delivery tool for hydrophilic molecules such as drugs, proteins, and DNAs. We designed and synthesized nona-arginine analogues 1–5 [FAM-β-Ala-(l-Arg-l-Arg-l-Pro)3-(Gly)3-NH2 (1), FAM-β-Ala-(l-Arg-l-Arg-l-ProNH2)3-(Gly)3-NH2 (2), FAM-β-Ala-(l-Arg-l-Arg-l-ProGu)3-(Gly)3-NH2 (3), FAM-β-Ala-(l-Arg)2-(l-ProGu)2-(l-Arg)4-l-ProGu-(Gly)3-NH2 (4), and FAM-β-Ala-(l-Arg)6-(l-ProGu)3-(Gly)3-NH2 (5)] containing l-proline (l-Pro) or cationic proline derivatives (l-ProNH2 and l-ProGu), and investigated their cell-penetrating abilities. Interestingly, only peptide 3 having the side-chain guanidinyl l-ProGu exhibited a secondary structural change in cellular environment. Specifically, peptide 3 formed a random structure in hydrophilic conditions, whereas it formed a helical structure under amphipathic conditions. Furthermore, during cellular permeability tests, peptide 3 demonstrated greater cell-penetrating activity than other peptides and effectively transported plasmid DNA into HeLa cells. Thus, l-ProGu-containing peptide 3 may be a useful candidate as a gene delivery carrier. PMID:27609319

  14. Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment.

    PubMed

    Yamashita, Hiroko; Kato, Takuma; Oba, Makoto; Misawa, Takashi; Hattori, Takayuki; Ohoka, Nobumichi; Tanaka, Masakazu; Naito, Mikihiko; Kurihara, Masaaki; Demizu, Yosuke

    2016-01-01

    Cell-penetrating peptides (CPP) are received a lot of attention as an intracellular delivery tool for hydrophilic molecules such as drugs, proteins, and DNAs. We designed and synthesized nona-arginine analogues 1-5 [FAM-β-Ala-(l-Arg-l-Arg-l-Pro)3-(Gly)3-NH2 (1), FAM-β-Ala-(l-Arg-l-Arg-l-Pro(NH2))3-(Gly)3-NH2 (2), FAM-β-Ala-(l-Arg-l-Arg-l-Pro(Gu))3-(Gly)3-NH2 (3), FAM-β-Ala-(l-Arg)2-(l-Pro(Gu))2-(l-Arg)4-l-Pro(Gu)-(Gly)3-NH2 (4), and FAM-β-Ala-(l-Arg)6-(l-Pro(Gu))3-(Gly)3-NH2 (5)] containing l-proline (l-Pro) or cationic proline derivatives (l-Pro(NH2) and l-Pro(Gu)), and investigated their cell-penetrating abilities. Interestingly, only peptide 3 having the side-chain guanidinyl l-Pro(Gu) exhibited a secondary structural change in cellular environment. Specifically, peptide 3 formed a random structure in hydrophilic conditions, whereas it formed a helical structure under amphipathic conditions. Furthermore, during cellular permeability tests, peptide 3 demonstrated greater cell-penetrating activity than other peptides and effectively transported plasmid DNA into HeLa cells. Thus, l-Pro(Gu)-containing peptide 3 may be a useful candidate as a gene delivery carrier.

  15. A supra-cellular model for coupling of bone resorption to formation during remodeling: lessons from two bone resorption inhibitors affecting bone formation differently.

    PubMed

    Jensen, Pia Rosgaard; Andersen, Thomas Levin; Pennypacker, Brenda L; Duong, Le T; Engelholm, Lars H; Delaissé, Jean-Marie

    2014-01-10

    The bone matrix is maintained functional through the combined action of bone resorbing osteoclasts and bone forming osteoblasts, in so-called bone remodeling units. The coupling of these two activities is critical for securing bone replenishment and involves osteogenic factors released by the osteoclasts. However, the osteoclasts are separated from the mature bone forming osteoblasts in time and space. Therefore the target cell of these osteoclastic factors has remained unknown. Recent explorations of the physical microenvironment of osteoclasts revealed a cell layer lining the bone marrow and forming a canopy over the whole remodeling surface, spanning from the osteoclasts to the bone forming osteoblasts. Several observations show that these canopy cells are a source of osteoblast progenitors, and we hypothesized therefore that they are the likely cells targeted by the osteogenic factors of the osteoclasts. Here we provide evidence supporting this hypothesis, by comparing the osteoclast-canopy interface in response to two types of bone resorption inhibitors in rabbit lumbar vertebrae. The bisphosphonate alendronate, an inhibitor leading to low bone formation levels, reduces the extent of canopy coverage above osteoclasts. This effect is in accordance with its toxic action on periosteoclastic cells. In contrast, odanacatib, an inhibitor preserving bone formation, increases the extent of the osteoclast-canopy interface. Interestingly, these distinct effects correlate with how fast bone formation follows resorption during these respective treatments. Furthermore, canopy cells exhibit uPARAP/Endo180, a receptor able to bind the collagen made available by osteoclasts, and reported to mediate osteoblast recruitment. Overall these observations support a mechanism where the recruitment of bone forming osteoblasts from the canopy is induced by osteoclastic factors, thereby favoring initiation of bone formation. They lead to a model where the osteoclast-canopy interface is

  16. The Influence of Molecular Cooling in Pregalactic Structure Formation

    NASA Astrophysics Data System (ADS)

    Stancil, P. C.; Abel, T.; Lepp, S.; Dalgarno, A.

    1999-12-01

    The detailed chemistry and cooling in collapsing primordial clouds will be presented for total baryonic densities up to 106 cm-3. The model consists of 160 reactions of 23 species including H2, HD, HeH+, and LiH, and accounts for 8 different cooling and heating mechanisms. The hydrodynamic evolution of the gas is modeled under the assumptions of free-fall, isothermal, and isobaric collapse as well as for the central regions of 105 M⊙ objects in hierarchical scenarios. The latter being drawn from three-dimensional cosmological hydrodynamical simulations. The dominant processes in the reaction network are identified and a minimal model that accurately predicts the full chemistry will be presented. It is found that radiative cooling due to collisional excitation of HD can lower the temperature in a primordial cloud below that reachable through H2 cooling alone. Further, the temperature evolution is influenced by the choice of the adopted H2 radiative cooling function. Implications for globular cluster and primordial star formation, as well as structure formation on small scales and the importance of molecular cooling in general will be discussed. The work of P.C.S. was supported by the DoE ORNL LDRD Seed Money Fund. T.A. acknowledges support from NSF Grant ASC--9318185. The work of S.L. and A.D. was supported by NSF Cooperative Agreement OSR-9353227 and Astronomical Sciences Grant AST-93-01099, respectively.

  17. Magnetic Structure and Formation of On-disk Coronal Plumes

    NASA Astrophysics Data System (ADS)

    Antonsson, S.; Tiwari, S. K.; Moore, R. L.; Winebarger, A. R.

    2015-12-01

    "Plumes" are feather-like features found on the solar disk, in the plage-like field concentrations of quiet regions. On-disk plumes are analogous to polar/coronal-hole plumes but have not been studied in detail in the past. We research their formation and characteristics, such as lifetime, intensity and magnetic setting at the feet. Atmospheric Imaging Assembly (AIA) images in the 171 Å filter and Helioseismic and Magnetic Imager (HMI) line-of-sight magnetograms, both from the Solar Dynamics Observatory (SDO), are analyzed with the IDL SolarSoftWare package and used to study the plumes. We find that on-disk plumes form at the places of converging magnetic fields, and disappear when those fields disperse. However, plumes disappear after nearby events, such as flares, or with the emergence of opposite polarity. The lifetime of each plume tends to be several days, although some appear and disappear within several hours. On-disk plumes outline magnetic fields close to the sun, allowing a better understanding of fine magnetic structures than before. Additionally, since plumes must be heated to around 600,000 K to be visible in 171 Å, their formation and characteristics could tell about how they, and therefore the corona, are heated.

  18. Formation of RNA Beads from Various DNA Nanoring Structures.

    PubMed

    Kim, Hyejin; Lee, Jong Bum

    2016-05-01

    By taking advantages of rolling circle transcription, one of the powerful methods to overcome the instability of RNA, we successfully synthesized RNA particles having high copy numbers of RNA strands. To examine dependence of RNA particle formation to template circular DNA strands, we synthesized RNA beads with 65-nt, 92-nt and 200-nt DNA nanoring structures as template circular DNA. Our conclusion is that characteristics of RNA beads could be controlled with various template circular DNA for RCT. It is feasible that our RNA beads could be used for RNAzyme-based metal sensors such as aqueous lead ion sensing. In this case, we expect that multi-metal ion detection would be possible by using 200-nt circular DNA bearing multiple desired functions as a template for RNA bead formation. Furthermore, certain features of RNA beads such as sensitivity to nuclease digestion and maximum loading amount of drugs when used as a carrier are expected to be further adjusted by choosing appropriate porosity and size.

  19. Ocean acidification affects competition for space: projections of community structure using cellular automata.

    PubMed

    McCoy, Sophie J; Allesina, Stefano; Pfister, Catherine A

    2016-03-16

    Historical ecological datasets from a coastal marine community of crustose coralline algae (CCA) enabled the documentation of ecological changes in this community over 30 years in the Northeast Pacific. Data on competitive interactions obtained from field surveys showed concordance between the 1980s and 2013, yet also revealed a reduction in how strongly species interact. Here, we extend these empirical findings with a cellular automaton model to forecast ecological dynamics. Our model suggests the emergence of a new dominant competitor in a global change scenario, with a reduced role of herbivory pressure, or trophic control, in regulating competition among CCA. Ocean acidification, due to its energetic demands, may now instead play this role in mediating competitive interactions and thereby promote species diversity within this guild.

  20. Halo formation and evolution: unification of structure and physical properties

    NASA Astrophysics Data System (ADS)

    Ernest, Allan D.; Collins, Matthew P.

    2016-08-01

    The assembly of matter in the universe proliferates a wide variety of halo structures, often with enigmatic consequences. Giant spiral galaxies, for example, contain both dark matter and hot gas, while dwarf spheroidal galaxies, with weaker gravity, contain much larger fractions of dark matter, but little gas. Globular clusters, superficially resembling these dwarf spheroidals, have little or no dark matter. Halo temperatures are also puzzling: hot cluster halos contain cooler galaxy halos; dwarf galaxies have no hot gas at all despite their similar internal processes. Another mystery is the origin of the gas that galaxies require to maintain their measured star formation rates (SFRs). We outline how gravitational quantum theory solves these problems, and enables baryons to function as weakly-interacting-massive-particles (WIMPs) in Lambda Cold Dark Matter (LCDM) theory. Significantly, these dark-baryon ensembles may also be consistent with primordial nucleosynthesis (BBN) and cosmic microwave background (CMB) anisotropies.

  1. Statistics of Caustics in Large-Scale Structure Formation

    NASA Astrophysics Data System (ADS)

    Feldbrugge, Job L.; Hidding, Johan; van de Weygaert, Rien

    2016-10-01

    The cosmic web is a complex spatial pattern of walls, filaments, cluster nodes and underdense void regions. It emerged through gravitational amplification from the Gaussian primordial density field. Here we infer analytical expressions for the spatial statistics of caustics in the evolving large-scale mass distribution. In our analysis, following the quasi-linear Zel'dovich formalism and confined to the 1D and 2D situation, we compute number density and correlation properties of caustics in cosmic density fields that evolve from Gaussian primordial conditions. The analysis can be straightforwardly extended to the 3D situation. We moreover, are currently extending the approach to the non-linear regime of structure formation by including higher order Lagrangian approximations and Lagrangian effective field theory.

  2. Structural modification in the formation of starch - silver nanocomposites

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    Polymer based nanocomposites have gained wide applications in field of battery technology. Starch is a naturally occurring polysaccharide with sustainable properties such as biodegradable, non toxic, excellent film forming capacity and it also act as reducing agent for the metal nanoparticles. In our research various concentration of silver nitrate (AgNO3) was added to the starch solution and films were obtained using solution casting method. Surface electron microscope (SEM) of the films shows modifications depending upon the concentration of AgNO3. Small angle neutron scattering (SANS) analysis showed that addition of silver nitrate modifies the starch to disc like structures and with increasing the AgNO3 concentration leads to the formation of fractals. This research could benefit battery technology where solid polymer membranes using starch is used.

  3. Structure formation in inhomogeneous Early Dark Energy models

    SciTech Connect

    Batista, R.C.; Pace, F. E-mail: francesco.pace@port.ac.uk

    2013-06-01

    We study the impact of Early Dark Energy fluctuations in the linear and non-linear regimes of structure formation. In these models the energy density of dark energy is non-negligible at high redshifts and the fluctuations in the dark energy component can have the same order of magnitude of dark matter fluctuations. Since two basic approximations usually taken in the standard scenario of quintessence models, that both dark energy density during the matter dominated period and dark energy fluctuations on small scales are negligible, are not valid in such models, we first study approximate analytical solutions for dark matter and dark energy perturbations in the linear regime. This study is helpful to find consistent initial conditions for the system of equations and to analytically understand the effects of Early Dark Energy and its fluctuations, which are also verified numerically. In the linear regime we compute the matter growth and variation of the gravitational potential associated with the Integrated Sachs-Wolf effect, showing that these observables present important modifications due to Early Dark Energy fluctuations, though making them more similar to the ΛCDM model. We also make use of the Spherical Collapse model to study the influence of Early Dark Energy fluctuations in the nonlinear regime of structure formation, especially on δ{sub c} parameter, and their contribution to the halo mass, which we show can be of the order of 10%. We finally compute how the number density of halos is modified in comparison to the ΛCDM model and address the problem of how to correct the mass function in order to take into account the contribution of clustered dark energy. We conclude that the inhomogeneous Early Dark Energy models are more similar to the ΛCDM model than its homogeneous counterparts.

  4. Halo formation and evolution: unifying physical properties with structure

    NASA Astrophysics Data System (ADS)

    Ernest, Alllan David; Collins, Matthew P.

    2015-08-01

    The assembly of matter in the universe proliferates a variety of structures with diverse properties. For example, massive halos of clusters of galaxies have temperatures often an order of magnitude or more higher than the individual galaxy halos within the cluster, or the temperatures of isolated galaxy halos. Giant spiral galaxies contain large quantities of both dark matter and hot gas while other structures like globular clusters appear to have little or no dark matter or gas. Still others, like the dwarf spheroidal galaxies have low gravity and little hot gas, but ironically contain some of the largest fractions of dark matter in the universe. Star forming rates (SFRs) also vary: compare for example the SFRs of giant elliptical galaxies, globular clusters, spiral and starburst galaxies. Furthermore there is evidence that the various structure types have existed over a large fraction of cosmic history. How can this array of variation in properties be reconciled with galaxy halo formation and evolution?We propose a model of halo formation [1] and evolution [2] that is consistent with both primordial nucleosynthesis (BBN) and the isotropies in the cosmic microwave background (CMB). The model uses two simple parameters, the total mass and size of a structure, to (1) explain why galaxies have the fractions of dark matter that they do (including why dwarf spheroidals are so dark matter dominated despite their weak gravity), (2) enable an understanding of the black hole-bulge/black hole-dark halo relations, (3) explain how fully formed massive galaxies can occur so early in cosmic history, (4) understand the connection between spiral and elliptical galaxies (5) unify the nature of globular clusters, dwarf spheroidal galaxies and bulges and (6) predict the temperatures of hot gas halos and understand how cool galaxy halos can remain stable in the hot environments of cluster-galaxy halos.[1] Ernest, A. D., 2012, in Prof. Ion Cotaescu (Ed) Advances in Quantum Theory, pp

  5. Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus.

    PubMed

    Frederick, Kendra K; Michaelis, Vladimir K; Corzilius, Björn; Ong, Ta-Chung; Jacavone, Angela C; Griffin, Robert G; Lindquist, Susan

    2015-10-22

    Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and enable structural studies in biologically complex environments. Here, we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an intrinsically disordered region, the yeast prion protein Sup35. We added an exogenously prepared isotopically labeled protein to deuterated lysates, rendering the biological environment "invisible" and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible, and such contexts can influence protein structure. PMID:26456111

  6. Sensitivity enhanced NMR reveals alterations in protein structure by cellular milieus

    PubMed Central

    Frederick, Kendra K.; Michaelis, Vladimir K.; Corzilius, Björn; Ong, Ta-Chung; Jacavone, Angela C.; Griffin, Robert G.; Lindquist, Susan

    2015-01-01

    Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of NMR spectroscopy and enable structural studies in biologically complex environments. Here we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an instrinsically disordered region, the yeast prion protein Sup35. We added an exogenously-prepared isotopically-labeled protein to deuterated lysates, rendering the biological environment “invisible” and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible and such contexts can influence protein structure. PMID:26456111

  7. Does the tail wag the dog? How the structure of a glycosylphosphatidylinositol anchor affects prion formation.

    PubMed

    Bate, Clive; Nolan, William; Williams, Alun

    2016-03-01

    There is increasing interest in the role of the glycosylphosphatidylinositol (GPI) anchor attached to the cellular prion protein (PrP(C)). Since GPI anchors can alter protein targeting, trafficking and cell signaling, our recent study examined how the structure of the GPI anchor affected prion formation. PrP(C) containing a GPI anchor from which the sialic acid had been removed (desialylated PrP(C)) was not converted to PrP(Sc) in prion-infected neuronal cell lines and in scrapie-infected primary cortical neurons. In uninfected neurons desialylated PrP(C) was associated with greater concentrations of gangliosides and cholesterol than PrP(C). In addition, the targeting of desialylated PrP(C) to lipid rafts showed greater resistance to cholesterol depletion than PrP(C). The presence of desialylated PrP(C) caused the dissociation of cytoplasmic phospholipase A2 (cPLA2) from PrP-containing lipid rafts, reduced the activation of cPLA2 and inhibited PrP(Sc) production. We conclude that the sialic acid moiety of the GPI attached to PrP(C) modifies local membrane microenvironments that are important in PrP-mediated cell signaling and PrP(Sc) formation. PMID:26901126

  8. Cosmological Structure Formation Shocks and Cosmic Rays in Hydrodynamical Simulations

    NASA Astrophysics Data System (ADS)

    Pfrommer, C.; Springel, V.; Enβlin, T. A.; Jubelgas, M.

    Cosmological shock waves during structure formation not only play a decisive role for the thermalization of gas in virializing structures but also for the acceleration of relativistic cosmic rays (CRs) through diffusive shock acceleration. We discuss a novel numerical treatment of the physics of cosmic rays in combination with a formalism for identifying and measuring the shock strength on-the-fly during a smoothed particle hydrodynamics simulation. In our methodology, the non-thermal CR population is treated self-consistently in order to assess its dynamical impact on the thermal gas as well as other implications on cosmological observables. Using this formalism, we study the history of the thermalization process in high-resolution hydrodynamic simulations of the Lambda cold dark matter model. Collapsed cosmological structures are surrounded by shocks with high Mach numbers up to 1000, but they play only a minor role in the energy balance of thermalization. However, this finding has important consequences for our understanding of the spatial distribution of CRs in the large-scale structure. In high resolution simulations of galaxy clusters, we find a low contribution of the averaged CR pressure, due to the small acceleration efficiency of lower Mach numbers of flow shocks inside halos and the softer adiabatic index of CRs. These effects disfavour CRs when a composite of thermal gas and CRs is adiabatically compressed. However, within cool core regions, the CR pressure reaches equipartition with the thermal pressure leading, to a lower effective adiabatic index and thus to an enhanced compressibility of the central intracluster medium. This effect increases the central density and pressure of the cluster, and thus the resulting X-ray emission and the central Sunyaev-Zel'dovich flux decrement. The integrated Sunyaev-Zel'dovich effect, however, is only slightly changed.

  9. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations.

  10. Regulation by mitochondrial superoxide and NADPH oxidase of cellular formation of nitrated cyclic GMP: potential implications for ROS signalling.

    PubMed

    Ahmed, Khandaker Ahtesham; Sawa, Tomohiro; Ihara, Hideshi; Kasamatsu, Shingo; Yoshitake, Jun; Rahaman, Md Mizanur; Okamoto, Tatsuya; Fujii, Shigemoto; Akaike, Takaaki

    2012-01-15

    8-Nitro-cGMP (8-nitroguanosine 3',5'-cyclic monophosphate) is a nitrated derivative of cGMP, which can function as a unique electrophilic second messenger involved in regulation of an antioxidant adaptive response in cells. In the present study, we investigated chemical and biochemical regulatory mechanisms involved in 8-nitro-cGMP formation, with particular focus on the roles of ROS (reactive oxygen species). Chemical analyses demonstrated that peroxynitrite-dependent oxidation and myeloperoxidase-dependent oxidation of nitrite in the presence of H2O2 were two major pathways for guanine nucleotide nitration. Among the guanine nucleotides examined, GTP was the most sensitive to peroxynitrite-mediated nitration. Immunocytochemical and tandem mass spectrometric analyses revealed that formation of 8-nitro-cGMP in rat C6 glioma cells stimulated with lipopolysaccharide plus pro-inflammatory cytokines depended on production of both superoxide and H2O2. Using the mitochondria-targeted chemical probe MitoSOX Red, we found that mitochondria-derived superoxide can act as a direct determinant of 8-nitro-cGMP formation. Furthermore, we demonstrated that Nox2 (NADPH oxidase 2)-generated H2O2 regulated mitochondria-derived superoxide production, which suggests the importance of cross-talk between Nox2-dependent H2O2 production and mitochondrial superoxide production. The results of the present study suggest that 8-nitro-cGMP can serve as a unique second messenger that may be implicated in regulating ROS signalling in the presence of NO.

  11. Structure Formation through Magnetohydrodynamical Instabilities in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Noguchi, K.; Tajima, T.; Horton, W.

    2000-12-01

    The shear flow instabilities under the presence of magnetic fields in the protoplanetary disk can greatly facilitate the formation of density structures that serve as seeds prior to the onset of the gravitational Jeans instability. Such a seeding process may explain several outstanding puzzles in the planetary genesis that are further compounded by the new discoveries of extrasolar planets and a new insight into the equation of state of dense matter. This puzzle also includes the apparent narrow window of the age difference of the Sun and the Earth. We evaluate the effects of the Parker, magnetorotational(Balbus-Hawley), and kinematic dynamo instabilities by comparing the properties of these instabilities. We calculate the mass spectra of aggregated density structures by the above mechanism in the radial direction for an axisymmetric magnetohydrodynamic(MHD) torus equiblium and power-law density profile models. The mass spectrum of the magnetorotational instability may describe the origin of giant planets away from the central star such as Jupiter. Our local three-dimentional MHD simulation indicates that the coupling of the Parker and magnetorotational instabilities creates spiral arms and gas blobs in the accretion disk, reinforcing the theory and model.

  12. CdTe film structure formation in layerwise component sorption

    SciTech Connect

    Murashev, S.V.; Denisova, A.T.; Ezhovskii, Yu.K.

    1988-04-10

    Aleskovskii's insular hypothesis has been used in a new approach to film synthesis, where irreversible reactions occur at surfaces on sequential component treatment, where the components contain the compound units. One can synthesize a film of a strictly defined composition on the basis of the critical condensation temperatures T/sub A/ and T/sub B/ together with the compound decomposition temperature T/sub AB/, i.e., it is necessary to have T/sub A/, T/sub B/ < T/sub s/ < T/sub AB/, where T/sub s/ is substrate temperature. The authors used AGChT-23-17 single-crystal gallium arsenide substrates having (100) orientation. Films up to 15 nm thick were measured by ellipsometry, while thicker films were assessed with an interferometer. The cadmium telluride films were made by alternating treatment in cadmium and tellurium beams made by evaporation from Knudsen cells. The lower limit to monolayer growth is set by the onset of tellurium condensation, and the upper by the transition from irreversible chemisorption to reversible. The growth constant and the diffraction data indicate the mode of film formation, the growth direction, and the relationship to the structure, which is related to the temperature. Films with the best structure are made at substrate temperatures of 498-535 K.

  13. Turbulence driven by structure formation in the circumgalactic medium

    NASA Astrophysics Data System (ADS)

    Iapichino, L.; Viel, M.; Borgani, S.

    2013-07-01

    The injection of turbulence in the circumgalactic medium at redshift z = 2 is investigated using the mesh-based hydrodynamic code ENZO and a sub-grid-scale (SGS) model for unresolved turbulence. Radiative cooling and heating by a uniform Ultraviolet (UV) background are included in our runs and compared with the effect of turbulence modelling. Mechanisms of gas exchange between galaxies and the surrounding medium, as well as metal enrichment, are not taken into account, and turbulence is here driven solely by structure formation (mergers and shocks). We find that turbulence, both at resolved and SGS scales, impacts mostly the warm-hot intergalactic medium (WHIM), with temperature between 105 and 107 K, mainly located around collapsed and shock-heated structures, and in filaments. Typical values of the ratio of turbulent to thermal pressure is 0.1 in the WHIM, corresponding to a volume-weighted average of the SGS turbulent to thermal Doppler broadening bt/btherm = 0.26, on length scales below the grid resolution of 25 kpc h- 1. In the diffuse intergalactic medium, defined in a range of baryon overdensity δ between 1 and 50, the importance of turbulence is smaller, but grows as a function of gas density, and the Doppler broadening ratio is fitted by the function bt/btherm = 0.023 × δ0.58.

  14. Detonation cellular structure in NO{sub 2}/N{sub 2}O{sub 4}-fuel gaseous mixtures

    SciTech Connect

    Joubert, Franckie; Desbordes, Daniel; Presles, Henri-Noel

    2008-03-15

    Experimental and numerical studies of the detonation in NO{sub 2}-N{sub 2}O{sub 4}/fuel (H{sub 2}, CH{sub 4}, and C{sub 2}H{sub 6}) gaseous mixtures show that for equivalence ratio {phi}>0.8-1, (1) the detonation has a double cellular structure, the ratio between the cell size of each net being at least one order of magnitude; (2) inside the detonation reaction zone the chemical energy is released in two successive exothermic steps. Their chemical induction lengths, defined between the leading shock front and each local maximum heat release rate associated with each step, differ by at least one order of magnitude. The chemical reaction NO{sub 2} + H {yields} NO + OH is mainly responsible for the first exothermic step (fast kinetics), NO being the oxidizer on the second one (slow kinetics). Existence of correlations between calculated induction lengths and corresponding cell sizes strengthen the assumption that the cellular structure originates from local strong gradients of chemical heat release inside the detonation reaction zone. (author)

  15. On the synthesis of a bio-inspired dual-cellular fluidic flexible matrix composite adaptive structure based on a non-dimensional dynamics model

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2013-01-01

    A recent study investigated the dynamic characteristics of an adaptive structure concept featuring dual fluidic flexible matrix composite (F2MC) cells inspired by the configuration of plant cells and cell walls. This novel bio-inspired system consists of two F2MC cells with different fiber angles connected through internal fluid circuits. It was discovered that the dual F2MC cellular structure can be characterized as a two degree of freedom damped mass-spring oscillator, and can be utilized as a vibration absorber or an enhanced actuator under different operation conditions. These results demonstrated that the concept is promising and further investigations are needed to develop methodologies for synthesizing future multi-cellular F2MC structural systems. While interesting, the previous study focused on specific case studies and analysis. That is, the outcome did not provide insight that could be generalized, or tools for synthesizing a multiple F2MC cellular structure. This paper attempts to address this important issue by developing a non-dimensional dynamic model, which reveals good physical insights as well as identifying crucial constitutive parameters for F2MC cellular design. Working with these parameters, rather than physical variables, can greatly simplify the mathematics involved in the study. A synthesis tool is then developed for the dual-cellular structure, and it is found that for each set of achievable target poles and zero, there exist multiple F2MC cellular designs, forming a design space. The presented physical insights and synthesis tool for the dual-cellular structure will be the building blocks for future investigation on cellular structures with a larger number of cells.

  16. Withania somnifera attenuates acid production, acid tolerance and extra-cellular polysaccharide formation of Streptococcus mutans biofilms.

    PubMed

    Pandit, Santosh; Song, Kwang-Yeob; Jeon, Jae-Gyu

    2014-01-01

    Withania somnifera (Ashwagandha) is a plant of the Solanaceae family. It has been widely used as a remedy for a variety of ailments in India and Nepal. The plant has also been used as a controlling agent for dental diseases. The aim of the present study was to evaluate the activity of the methanol extract of W. somnifera against the physiological ability of cariogenic biofilms and to identify the components of the extract. To determine the activity of the extract, assays for sucrose-dependent bacterial adherence, glycolytic acid production, acid tolerance, and extracellular polysaccharide formation were performed using Streptococcus mutans biofilms. The viability change of S. mutans biofilms cells was also determined. A phytochemical analysis of the extract was performed using TLC and LC/MS/MS. The extract showed inhibitory effects on sucrose-dependent bacterial adherence (≥ 100 μg/ml), glycolytic acid production (≥ 300 μg/ml), acid tolerance (≥ 300 μg/ml), and extracellular polysaccharide formation (≥ 300 μg/ml) of S. mutans biofilms. However, the extract did not alter the viability of S. mutans biofilms cells in all concentrations tested. Based on the phytochemical analysis, the activity of the extract may be related to the presence of alkaloids, anthrones, coumarines, anthraquinones, terpenoids, flavonoids, and steroid lactones (withanolide A, withaferin A, withanolide B, withanoside IV, and 12-deoxy withastramonolide). These data indicate that W. somnifera may be a potential agent for restraining the physiological ability of cariogenic biofilms.

  17. Cellular automata-based modelling and simulation of biofilm structure on multi-core computers.

    PubMed

    Skoneczny, Szymon

    2015-01-01

    The article presents a mathematical model of biofilm growth for aerobic biodegradation of a toxic carbonaceous substrate. Modelling of biofilm growth has fundamental significance in numerous processes of biotechnology and mathematical modelling of bioreactors. The process following double-substrate kinetics with substrate inhibition proceeding in a biofilm has not been modelled so far by means of cellular automata. Each process in the model proposed, i.e. diffusion of substrates, uptake of substrates, growth and decay of microorganisms and biofilm detachment, is simulated in a discrete manner. It was shown that for flat biofilm of constant thickness, the results of the presented model agree with those of a continuous model. The primary outcome of the study was to propose a mathematical model of biofilm growth; however a considerable amount of focus was also placed on the development of efficient algorithms for its solution. Two parallel algorithms were created, differing in the way computations are distributed. Computer programs were created using OpenMP Application Programming Interface for C++ programming language. Simulations of biofilm growth were performed on three high-performance computers. Speed-up coefficients of computer programs were compared. Both algorithms enabled a significant reduction of computation time. It is important, inter alia, in modelling and simulation of bioreactor dynamics. PMID:26606102

  18. Cellular automata-based modelling and simulation of biofilm structure on multi-core computers.

    PubMed

    Skoneczny, Szymon

    2015-01-01

    The article presents a mathematical model of biofilm growth for aerobic biodegradation of a toxic carbonaceous substrate. Modelling of biofilm growth has fundamental significance in numerous processes of biotechnology and mathematical modelling of bioreactors. The process following double-substrate kinetics with substrate inhibition proceeding in a biofilm has not been modelled so far by means of cellular automata. Each process in the model proposed, i.e. diffusion of substrates, uptake of substrates, growth and decay of microorganisms and biofilm detachment, is simulated in a discrete manner. It was shown that for flat biofilm of constant thickness, the results of the presented model agree with those of a continuous model. The primary outcome of the study was to propose a mathematical model of biofilm growth; however a considerable amount of focus was also placed on the development of efficient algorithms for its solution. Two parallel algorithms were created, differing in the way computations are distributed. Computer programs were created using OpenMP Application Programming Interface for C++ programming language. Simulations of biofilm growth were performed on three high-performance computers. Speed-up coefficients of computer programs were compared. Both algorithms enabled a significant reduction of computation time. It is important, inter alia, in modelling and simulation of bioreactor dynamics.

  19. The solution structure of the FATC domain of the protein kinase target of rapamycin suggests a role for redox-dependent structural and cellular stability.

    PubMed

    Dames, Sonja A; Mulet, José M; Rathgeb-Szabo, Klara; Hall, Michael N; Grzesiek, Stephan

    2005-05-27

    The target of rapamycin (TOR) is a highly conserved Ser/Thr kinase that plays a central role in the control of cellular growth. TOR has a characteristic multidomain structure. Only the kinase domain has catalytic function; the other domains are assumed to mediate interactions with TOR substrates and regulators. Except for the rapamycin-binding domain, there are no high-resolution structural data available for TOR. Here, we present a structural, biophysical, and mutagenesis study of the extremely conserved COOH-terminal FATC domain. The importance of this domain for TOR function has been highlighted in several publications. We show that the FATC domain, in its oxidized form, exhibits a novel structural motif consisting of an alpha-helix and a COOH-terminal disulfide-bonded loop between two completely conserved cysteine residues. Upon reduction, the flexibility of the loop region increases dramatically. The structural data, the redox potential of the disulfide bridge, and the biochemical data of a cysteine to serine mutant indicate that the intracellular redox potential can affect the cellular amount of the TOR protein via the FATC domain. Because the amount of TOR mRNA is not changed, the redox state of the FATC disulfide bond is probably influencing the degradation of TOR. PMID:15772072

  20. Fibres and cellular structures preserved in 75-million–year-old dinosaur specimens

    PubMed Central

    Bertazzo, Sergio; Maidment, Susannah C. R.; Kallepitis, Charalambos; Fearn, Sarah; Stevens, Molly M.; Xie, Hai-nan

    2015-01-01

    Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ∼67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals. PMID:26056764

  1. Fibres and cellular structures preserved in 75-million-year-old dinosaur specimens.

    PubMed

    Bertazzo, Sergio; Maidment, Susannah C R; Kallepitis, Charalambos; Fearn, Sarah; Stevens, Molly M; Xie, Hai-nan

    2015-06-09

    Exceptionally preserved organic remains are known throughout the vertebrate fossil record, and recently, evidence has emerged that such soft tissue might contain original components. We examined samples from eight Cretaceous dinosaur bones using nano-analytical techniques; the bones are not exceptionally preserved and show no external indication of soft tissue. In one sample, we observe structures consistent with endogenous collagen fibre remains displaying ∼ 67 nm banding, indicating the possible preservation of the original quaternary structure. Using ToF-SIMS, we identify amino-acid fragments typical of collagen fibrils. Furthermore, we observe structures consistent with putative erythrocyte remains that exhibit mass spectra similar to emu whole blood. Using advanced material characterization approaches, we find that these putative biological structures can be well preserved over geological timescales, and their preservation is more common than previously thought. The preservation of protein over geological timescales offers the opportunity to investigate relationships, physiology and behaviour of long extinct animals.

  2. 3D Printing: 3D Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures.

    PubMed

    Hong, Sungmin; Sycks, Dalton; Chan, Hon Fai; Lin, Shaoting; Lopez, Gabriel P; Guilak, Farshid; Leong, Kam W; Zhao, Xuanhe

    2015-07-15

    X. Zhao and co-workers develop on page 4035 a new biocompatible hydrogel system that is extremely tough and stretchable and can be 3D printed into complex structures, such as the multilayer mesh shown. Cells encapsulated in the tough and printable hydrogel maintain high viability. 3D-printed structures of the tough hydrogel can sustain high mechanical loads and deformations. PMID:26172844

  3. FORMATION AND STRUCTURE OF LOW-DENSITY EXO-NEPTUNES

    SciTech Connect

    Rogers, Leslie A.; Seager, Sara; Bodenheimer, Peter

    2011-09-01

    Kepler has found hundreds of Neptune-size (2-6 R{sub +}) planet candidates within 0.5 AU of their stars. The nature of the vast majority of these planets is not known because their masses have not been measured. Using theoretical models of planet formation, evolution, and structure, we explore the range of minimum plausible masses for low-density exo-Neptunes. We focus on highly irradiated planets with T{sub eq} {>=} 500 K. We consider two separate formation pathways for low-mass planets with voluminous atmospheres of light gases: core-nucleated accretion and outgassing of hydrogen from dissociated ices. We show that Neptune-size planets at T{sub eq} = 500 K with masses as small as a few times that of Earth can plausibly be formed by core-nucleated accretion coupled with subsequent inward migration. We also derive a limiting low-density mass-radius relation for rocky planets with outgassed hydrogen envelopes but no surface water. Rocky planets with outgassed hydrogen envelopes typically have computed radii well below 3 R{sub +}. For both planets with H/He envelopes from core-nucleated accretion and planets with outgassed hydrogen envelopes, we employ planet interior models to map the range of planet mass-envelope mass-equilibrium temperature parameter space that is consistent with Neptune-size planet radii. Atmospheric mass loss mediates which corners of this parameter space are populated by actual planets and ultimately governs the minimum plausible mass at a specified transit radius. We find that Kepler's 2-6 R{sub +} planet candidates at T{sub eq} = 500-1000 K could potentially have masses {approx}< 4 M{sub +}. Although our quantitative results depend on several assumptions, our qualitative finding that warm Neptune-size planets can have masses substantially smaller than those given by interpolating the masses and radii of planets within our Solar System is robust.

  4. The assembly and properties of protobiological structures - The beginnings of cellular peptide synthesis

    NASA Technical Reports Server (NTRS)

    Fox, S. W.; Nakashima, T.

    1980-01-01

    New data indicate that lysine-rich proteinoids have the ability to catalyze the synthesis of peptide bonds from a variety of amino acids and ATP. This capacity is evident in aqueous solution, in suspension of phase-separated complexes of lysine-rich proteinoid with acidic proteinoids, and in suspension of phase-separated particles composed of lysine-rich proteinoids with polynucleotides. Since the proteinoid complexes can contain other catalytic activities, including ability to catalyze internucleotide bond formation, it is inferred that the first protocells on earth already had a number of biological types of activity.

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

    PubMed

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

    2013-02-01

    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 α(9)β(1) 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.

  6. The Drosophila FHOD1-like formin Knittrig acts through Rok to promote stress fiber formation and directed macrophage migration during the cellular immune response.

    PubMed

    Lammel, Uwe; Bechtold, Meike; Risse, Benjamin; Berh, Dimitri; Fleige, Astrid; Bunse, Ingrid; Jiang, Xiaoyi; Klämbt, Christian; Bogdan, Sven

    2014-03-01

    A tight spatiotemporal control of actin polymerization is important for many cellular processes that shape cells into a multicellular organism. The formation of unbranched F-actin is induced by several members of the formin family. Drosophila encodes six formin genes, representing six of the seven known mammalian subclasses. Knittrig, the Drosophila homolog of mammalian FHOD1, is specifically expressed in the developing central nervous system midline glia, the trachea, the wing and in macrophages. knittrig mutants exhibit mild tracheal defects but survive until late pupal stages and mainly die as pharate adult flies. knittrig mutant macrophages are smaller and show reduced cell spreading and cell migration in in vivo wounding experiments. Rescue experiments further demonstrate a cell-autonomous function of Knittrig in regulating actin dynamics and cell migration. Knittrig localizes at the rear of migrating macrophages in vivo, suggesting a cellular requirement of Knittrig in the retraction of the trailing edge. Supporting this notion, we found that Knittrig is a target of the Rho-dependent kinase Rok. Co-expression with Rok or expression of an activated form of Knittrig induces actin stress fibers in macrophages and in epithelial tissues. Thus, we propose a model in which Rok-induced phosphorylation of residues within the basic region mediates the activation of Knittrig in controlling macrophage migration. PMID:24553290

  7. Microstructure and in vitro cellular response to novel soy protein-based porous structures for tissue regeneration applications.

    PubMed

    Olami, Hilla; Zilberman, Meital

    2016-02-01

    Interest in the development of new bioresorbable structures for various tissue engineering applications is on the rise. In the current study, we developed and studied novel soy protein-based porous blends as potential new scaffolds for such applications. Soy protein has several advantages over the various types of natural proteins employed for biomedical applications due to its low price, non-animal origin and relatively long storage time and stability. In the present study, blends of soy protein with other polymers (gelatin, pectin and alginate) were added and chemically cross-linked using the cross-linking agents carbodiimide or glyoxal, and the porous structure was obtained through lyophilization. The resulting blend porous structures were characterized using environmental scanning microscopy, and the cytotoxicity of these scaffolds was examined in vitro. The biocompatibility of the scaffolds was also evaluated in vitro by seeding and culturing human fibroblasts on these scaffolds. Cell growth morphology and adhesion were examined histologically. The results show that these blends can be assembled into porous three-dimensional structures by combining chemical cross-linking with freeze-drying. The achieved blend structures combine suitable porosity with a large pore size (100-300 µm). The pore structure in the soy-alginate scaffolds possesses adequate interconnectivity compared to that of the soy-gelatin scaffolds. However, porous structure was not observed for the soy-pectin blend, which presented a different structure with significantly lower porosities than all other groups. The in vitro evaluation of these porous soy blends demonstrated that soy-alginate blends are advantageous over soy-gelatin blends and exhibited adequate cytocompatibility along with better cell infiltration and stability. These soy protein scaffolds may be potentially useful as a cellular/acellular platform for skin regeneration applications. PMID:26526932

  8. Formation and Internal Structure of Terrestrial Planets, and Atmospheric Escape

    NASA Astrophysics Data System (ADS)

    Jin, S.

    2014-11-01

    As of 2014 April 21, over 1490 confirmed exoplanets and 3705 Kepler candidates have been detected. This implies that exoplanets may be ubiquitous in the universe. In this paper, we focus on the formation, evolution, and internal structure of terrestrial planets, and the atmospheric escape of close-in planets. In chapter 2, we investigate the dynamical evolution of planetary system after the protoplanetary disk has dissipated. We find that in the final assembly stage, the occurrence of terrestrial planets is quite common and in 40% of our simulations finally at least one planet is formed in the habitable zone. We also find that if there is a highly-inclined giant planet in the system, a great many bodies will be either driven out of the system, or collide with the giant planet or the central star. This will lead to the difficulty in planetary accretion. Moreover, our results show that planetary migration can lead to the formation of close-in planets. Besides migration, close-in terrestrial planets can also be formed by a collision-merger mechanism, which means that planetary embryos can kick terrestrial planets directly into orbits that are extremely close to their parent stars. In chapter 3, we construct numerically an internal structure model for terrestrial planets, and provide three kinds of possible internal structures of Europa (Jupiter's moon) based on this model. Then, we calculate the radii of low-mass exoplanets for various mass combinations of core and mantle, and find that some of them are inconsistent with the observed radius of rocky planets. This phenomenon can be explained only if there exists a large amount of water in the core, or they own gaseous envelopes. In chapter 4, we improve our planetary evolution codes using the semi-gray model of Guillot (2010), which includes the incident flux from the host star as a heating source in planetary atmosphere. The updated codes can solve the structure of the top radiative zone of intensely irradiated

  9. Void lattice formation in electron irradiated CaF2: Statistical analysis of experimental data and cellular automata simulations

    NASA Astrophysics Data System (ADS)

    Zvejnieks, G.; Merzlyakov, P.; Kuzovkov, V. N.; Kotomin, E. A.

    2016-02-01

    Calcium fluoride (CaF2) is an important optical material widely used in both microlithography and deep UV windows. It is known that under certain conditions electron beam irradiation can create therein a superlattice consisting of vacancy clusters (called a void lattice). The goal of this paper is twofold. Firstly, to perform a quantitative analysis of experimental TEM images demonstrating void lattice formation, we developed two distinct image filters. As a result, we can easily calculate vacancy concentration, vacancy cluster distribution function as well as average distances between defect clusters. The results for two suggested filters are similar and demonstrate that experimental void cluster growth is accompanied by a slight increase of the void lattice constant. Secondly, we proposed a microscopic model that allows us to reproduce a macroscopic void ordering, in agreement with experimental data, and to resolve existing theoretical and experimental contradictions. Our computer simulations demonstrate that macroscopic void lattice self-organization can occur only in a narrow parameter range. Moreover, we studied the kinetics of a void lattice ordering, starting from an initial disordered stage, in a good agreement with the TEM experimental data.

  10. Expansion and concatenation of nonmuscle myosin IIA filaments drive cellular contractile system formation during interphase and mitosis

    PubMed Central

    Fenix, Aidan M.; Taneja, Nilay; Buttler, Carmen A.; Lewis, John; Van Engelenburg, Schuyler B.; Ohi, Ryoma; Burnette, Dylan T.

    2016-01-01

    Cell movement and cytokinesis are facilitated by contractile forces generated by the molecular motor, nonmuscle myosin II (NMII). NMII molecules form a filament (NMII-F) through interactions of their C-terminal rod domains, positioning groups of N-terminal motor domains on opposite sides. The NMII motors then bind and pull actin filaments toward the NMII-F, thus driving contraction. Inside of crawling cells, NMIIA-Fs form large macromolecular ensembles (i.e., NMIIA-F stacks), but how this occurs is unknown. Here we show NMIIA-F stacks are formed through two non–mutually exclusive mechanisms: expansion and concatenation. During expansion, NMIIA molecules within the NMIIA-F spread out concurrent with addition of new NMIIA molecules. Concatenation occurs when multiple NMIIA-Fs/NMIIA-F stacks move together and align. We found that NMIIA-F stack formation was regulated by both motor activity and the availability of surrounding actin filaments. Furthermore, our data showed expansion and concatenation also formed the contractile ring in dividing cells. Thus interphase and mitotic cells share similar mechanisms for creating large contractile units, and these are likely to underlie how other myosin II–based contractile systems are assembled. PMID:26960797

  11. Interferon-gamma increases cellular calcium ion concentration and inositol 1,4,5-trisphosphate formation in human renal carcinoma cells: relation to ICAM-1 antigen expression.

    PubMed Central

    Hansen, A. B.; Bouchelouche, P. N.; Lillevang, S. T.; Andersen, C. B.

    1994-01-01

    In the present study, we investigated the effect of interferon-gamma (IFN-gamma) on cellular calcium ion concentration [Ca2+]i and inositol 1,4,5-trisphosphate (Ins 1,4,5-P3) formation in the human renal carcinoma cell line CaKi-1. We also examined the possible role of a Ca(2+)-dependent mechanism during IFN-gamma-induced intercellular adhesion molecule 1 (ICAM-1) antigen expression. IFN-gamma caused a rapid concentration-dependent rise in [Ca2+]i, which was partly inhibited by diltiazem, a calcium channel blocker, TMB-8, an inhibitor of intracellular calcium redistribution, and in calcium-free medium. IFN-gamma caused a fourfold increase in Ins 1,4,5-P3 formation. The induction of ICAM-1 antigen expression was synergistically enhanced by 4-bromocalcium ionophore A23187. Finally, the calcium antagonists diltiazem. TMB-8 and EGTA, as well as two potent inhibitors of Ca(2+)-dependent kinases, calmidazolium (R24571) and W7, had no or only a minor inhibitory effect on IFN-gamma induction. Our data suggest that IFN-gamma increases [Ca2+]i in CaKi-1 cells by stimulating influx of Ca2+ and release of Ca2+ from intracellular stores, probably via Ins 1,4,5-P3 formation. IFN-gamma signal transduction in our model may not be limited to an increase in [Ca2+]i and Ins 1,4,5-P3, since IFN-gamma-induced ICAM-1 antigen expression was abrogated to a minor degree by calcium antagonists and not coupled to Ins 1,4,5-P3 formation. PMID:7905278

  12. Plasma Suppression of Large Scale Structure Formation in the Universe

    SciTech Connect

    Chen, Pisin; Lai, Kwang-Chang

    2007-12-10

    We point out that during the reionization epoch of the cosmic history, the plasma collective effect among the ordinary matter would suppress the large scale structure formation. The imperfect Debye shielding at finite temperature would induce a residual long-range electrostatic potential which, working together with the baryon thermal pressure, would counter the gravitational collapse. As a result the effective Jean's length, {tilde {lambda}}{sub J}, is increased by a factor, {tilde {lambda}}{sub J}/{lambda}{sub J} = {radical}8/5, relative to the conventional one. For scales smaller than the effective Jean's scale the plasma would oscillate at the ion-acoustic frequency. The modes that would be influenced by this effect depend on the starting time and the initial temperature of reionization, but roughly lie in the range 0.5hMpc{sup -1} < k, which corresponds to the region of the Lyman-{alpha} forest from the inter-galactic medium. We predict that in the linear regime of density-contrast growth, the plasma suppression of the matter power spectrum would approach 1 - ({Omega}{sub dm}/{Omega}{sub m}){sup 2} {approx} 1 -(5/6){sup 2} {approx} 30%.

  13. Using Black Hole Mergers to Explore Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2009-01-01

    Observations of gravitational waves from massive black hole mergers will open a new window into the era of structure formation in the early universe. Past efforts have concentrated on calculating merger rates using different physical assumptions, resulting in merger rate estimates that span a wide range (0.1 - 10(exp 4) mergers/year). We develop a semi-analytical, phenomenological model of massive black hole mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 epoch. Our approach involves generating synthetic LISA observable data (total BH masses, BH mass ratios, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo method, thus finding constraints for the physical parameters of the mergers. We find that our method works well at estimating merger parameters and that the number of merger events is a key discriminant among models, therefore making our method robust against observational uncertainties. Our approach can also be extended to more physically-driven models and more general problems in cosmology. This work is supported in part by the Cooperative Education Program at NASA/GSFC.

  14. Using Black Hole Mergers to Explore Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, E.; Miller, M. Coleman

    2008-01-01

    Observations of gravitational waves from massive black hole mergers will open a new window into the era of structure formation in the early universe. Past efforts have concentrated on calculating merger rates using different physical assumptions, resulting in merger rate estimates that span a wide range (0.1 - 1 0A4 mergers/year). We develop a semi-analytical, phenomenological model of massive black hole mergers that includes plausible combinations of several physical parameters, which we then turn around to determine how well observations with the Laser Interferometer Space Antenna (LISA) will be able to enhance our understanding of the universe during the critical z approx. 5 - 30 epoch. Our approach involves generating synthetic LISA observable data (total BH masses, BH mass ratios, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo method, thus finding constraints for the physical parameters of the mergers. We find that our method works well at estimating merger parameters and that the number of merger events is a key discriminant among models, therefore making our method robust against observational uncertainties. Our approach can also be extended to more physically-driven models and more general problems in cosmology.

  15. Renormalizing a viscous fluid model for large scale structure formation

    NASA Astrophysics Data System (ADS)

    Führer, Florian; Rigopoulos, Gerasimos

    2016-02-01

    Using the Stochastic Adhesion Model (SAM) as a simple toy model for cosmic structure formation, we study renormalization and the removal of the cutoff dependence from loop integrals in perturbative calculations. SAM shares the same symmetry with the full system of continuity+Euler equations and includes a viscosity term and a stochastic noise term, similar to the effective theories recently put forward to model CDM clustering. We show in this context that if the viscosity and noise terms are treated as perturbative corrections to the standard eulerian perturbation theory, they are necessarily non-local in time. To ensure Galilean Invariance higher order vertices related to the viscosity and the noise must then be added and we explicitly show at one-loop that these terms act as counter terms for vertex diagrams. The Ward Identities ensure that the non-local-in-time theory can be renormalized consistently. Another possibility is to include the viscosity in the linear propagator, resulting in exponential damping at high wavenumber. The resulting local-in-time theory is then renormalizable to one loop, requiring less free parameters for its renormalization.

  16. Generation of Hierarchically Ordered Structures on a Polymer Film by Electrohydrodynamic Structure Formation.

    PubMed

    Tian, Hongmiao; Shao, Jinyou; Hu, Hong; Wang, Li; Ding, Yucheng

    2016-06-29

    The extensive applications of hierarchical structures in optoelectronics, micro/nanofluidics, energy conservation, etc., have led to the development of a variety of approaches for their fabrication, which can be categorized as bottom-up or top-down strategies. Current bottom-up and top-down strategies bear a complementary relationship to each other due to their processing characteristics, i.e., the advantages of one method correspond to the disadvantages of the other, and vice versa. Here we propose a novel method based on electrohydrodynamic structure formation, aimed at combining the main advantages of the two strategies. The method allows the fabrication of a hierarchically ordered structure with well-defined geometry and high mechanical durability on a polymer film, through a simple and low-cost process also suitable for mass-production. In this approach, upon application of an electric field between a template and a substrate sandwiching an air gap and a polymer film, the polymer is pulled toward the template and further flows into the template cavities, resulting in a hierarchical structure with primary and secondary patterns determined by electrohydrodynamic instability and by the template features, respectively. In this work, the fabrication of a hierarchical structure by electrohydrodynamic structure formation is studied using numerical simulations and experimental tests. The proposed method is then employed for the one-step fabrication of a hierarchical structure exhibiting a gradual transition in the periodicity of the primary structure using a slant template and a flat polymer film, which presents an excellent performance on controllable wettability.

  17. Generation of Hierarchically Ordered Structures on a Polymer Film by Electrohydrodynamic Structure Formation.

    PubMed

    Tian, Hongmiao; Shao, Jinyou; Hu, Hong; Wang, Li; Ding, Yucheng

    2016-06-29

    The extensive applications of hierarchical structures in optoelectronics, micro/nanofluidics, energy conservation, etc., have led to the development of a variety of approaches for their fabrication, which can be categorized as bottom-up or top-down strategies. Current bottom-up and top-down strategies bear a complementary relationship to each other due to their processing characteristics, i.e., the advantages of one method correspond to the disadvantages of the other, and vice versa. Here we propose a novel method based on electrohydrodynamic structure formation, aimed at combining the main advantages of the two strategies. The method allows the fabrication of a hierarchically ordered structure with well-defined geometry and high mechanical durability on a polymer film, through a simple and low-cost process also suitable for mass-production. In this approach, upon application of an electric field between a template and a substrate sandwiching an air gap and a polymer film, the polymer is pulled toward the template and further flows into the template cavities, resulting in a hierarchical structure with primary and secondary patterns determined by electrohydrodynamic instability and by the template features, respectively. In this work, the fabrication of a hierarchical structure by electrohydrodynamic structure formation is studied using numerical simulations and experimental tests. The proposed method is then employed for the one-step fabrication of a hierarchical structure exhibiting a gradual transition in the periodicity of the primary structure using a slant template and a flat polymer film, which presents an excellent performance on controllable wettability. PMID:27268135

  18. Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison

    PubMed Central

    Wegel, Eva; Göhler, Antonia; Lagerholm, B. Christoffer; Wainman, Alan; Uphoff, Stephan; Kaufmann, Rainer; Dobbie, Ian M.

    2016-01-01

    Many biological questions require fluorescence microscopy with a resolution beyond the diffraction limit of light. Super-resolution methods such as Structured Illumination Microscopy (SIM), STimulated Emission Depletion (STED) microscopy and Single Molecule Localisation Microscopy (SMLM) enable an increase in image resolution beyond the classical diffraction-limit. Here, we compare the individual strengths and weaknesses of each technique by imaging a variety of different subcellular structures in fixed cells. We chose examples ranging from well separated vesicles to densely packed three dimensional filaments. We used quantitative and correlative analyses to assess the performance of SIM, STED and SMLM with the aim of establishing a rough guideline regarding the suitability for typical applications and to highlight pitfalls associated with the different techniques. PMID:27264341

  19. Application of biospeckles for assessment of structural and cellular changes in muscle tissue.

    PubMed

    Maksymenko, Oleksandr P; Muravsky, Leonid I; Berezyuk, Mykola I

    2015-09-01

    A modified spatial-temporal speckle correlation technique for operational assessment of structural changes in muscle tissues after slaughtering is considered. Coefficient of biological activity as a quantitative indicator of structural changes of biochemical processes in biological tissues is proposed. The experimental results have shown that this coefficient properly evaluates the biological activity of pig and chicken muscle tissue samples. Studying the degradation processes in muscle tissue during long-time storage in a refrigerator by measuring the spatial-temporal dynamics of biospeckle patterns is carried out. The reduction of the bioactivity level of refrigerated muscle tissue samples connected with the initiation of muscle fiber cracks and ruptures, reduction of sarcomeres, nuclei deformation, nuclear chromatin diminishing, and destruction of mitochondria is analyzed. PMID:26359810

  20. Application of biospeckles for assessment of structural and cellular changes in muscle tissue

    NASA Astrophysics Data System (ADS)

    Maksymenko, Oleksandr P.; Muravsky, Leonid I.; Berezyuk, Mykola I.

    2015-09-01

    A modified spatial-temporal speckle correlation technique for operational assessment of structural changes in muscle tissues after slaughtering is considered. Coefficient of biological activity as a quantitative indicator of structural changes of biochemical processes in biological tissues is proposed. The experimental results have shown that this coefficient properly evaluates the biological activity of pig and chicken muscle tissue samples. Studying the degradation processes in muscle tissue during long-time storage in a refrigerator by measuring the spatial-temporal dynamics of biospeckle patterns is carried out. The reduction of the bioactivity level of refrigerated muscle tissue samples connected with the initiation of muscle fiber cracks and ruptures, reduction of sarcomeres, nuclei deformation, nuclear chromatin diminishing, and destruction of mitochondria is analyzed.

  1. A new tubular graphene form of a tetrahedrally connected cellular structure.

    PubMed

    Bi, Hui; Chen, I-Wei; Lin, Tianquan; Huang, Fuqiang

    2015-10-21

    3D architectures constructed from a tubular graphene network can withstand repeated >95% compression cycling without damage. Aided by intertubular covalent bonding, this material takes full advantage of the graphene tube's unique attributes, including complete pre- and post-buckling elasticity, outstanding electrical conductivity, and extraordinary physicochemical stability. A highly connected tubular graphene will thus be the ultimate, structurally robust, ultrastrong, ultralight material. PMID:26305918

  2. Cellular and molecular mechanisms activating the cell death processes by chalcones: Critical structural effects.

    PubMed

    Champelovier, Pierre; Chauchet, Xavier; Hazane-Puch, Florence; Vergnaud, Sabrina; Garrel, Catherine; Laporte, François; Boutonnat, Jean; Boumendjel, Ahcène

    2013-12-01

    Chalcones are naturally occurring compounds with diverse pharmacological activities. Chalcones derive from the common structure: 1,3-diphenylpropenone. The present study aims to better understand the mechanistic pathways triggering chalcones anticancer effects and providing evidences that minor structural difference could lead to important difference in mechanistic effect. We selected two recently investigated chalcones (A and B) and investigated them on glioblastoma cell lines. It was found that chalcone A induced an apoptotic process (type I PCD), via the activation of caspase-3, -8 and -9. Chalcone A also increased CDK1/cyclin B ratios and decreased the mitochondrial transmembrane potential (ΔΨm). Chalcone B induced an autophagic cell death process (type II PCD), ROS-related but independent of both caspases and protein synthesis. Both chalcones increased Bax/Bcl2 ratios and decreased Ki67 and CD71 antigen expressions. The present investigation reveals that despite the close structure of chalcones A and B, significant differences in mechanism of effect were found.

  3. Cellular and molecular mechanisms activating the cell death processes by chalcones: Critical structural effects.

    PubMed

    Champelovier, Pierre; Chauchet, Xavier; Hazane-Puch, Florence; Vergnaud, Sabrina; Garrel, Catherine; Laporte, François; Boutonnat, Jean; Boumendjel, Ahcène

    2013-12-01

    Chalcones are naturally occurring compounds with diverse pharmacological activities. Chalcones derive from the common structure: 1,3-diphenylpropenone. The present study aims to better understand the mechanistic pathways triggering chalcones anticancer effects and providing evidences that minor structural difference could lead to important difference in mechanistic effect. We selected two recently investigated chalcones (A and B) and investigated them on glioblastoma cell lines. It was found that chalcone A induced an apoptotic process (type I PCD), via the activation of caspase-3, -8 and -9. Chalcone A also increased CDK1/cyclin B ratios and decreased the mitochondrial transmembrane potential (ΔΨm). Chalcone B induced an autophagic cell death process (type II PCD), ROS-related but independent of both caspases and protein synthesis. Both chalcones increased Bax/Bcl2 ratios and decreased Ki67 and CD71 antigen expressions. The present investigation reveals that despite the close structure of chalcones A and B, significant differences in mechanism of effect were found. PMID:24134853

  4. Increased power to weight ratio of piezoelectric energy harvesters through integration of cellular honeycomb structures

    NASA Astrophysics Data System (ADS)

    Chandrasekharan, N.; Thompson, L. L.

    2016-04-01

    The limitations posed by batteries have compelled the need to investigate energy harvesting methods to power small electronic devices that require very low operational power. Vibration based energy harvesting methods with piezoelectric transduction in particular has been shown to possess potential towards energy harvesters replacing batteries. Current piezoelectric energy harvesters exhibit considerably lower power to weight ratio or specific power when compared to batteries the harvesters seek to replace. To attain the goal of battery-less self-sustainable device operation the power to weight ratio gap between piezoelectric energy harvesters and batteries need to be bridged. In this paper the potential of integrating lightweight honeycomb structures with existing piezoelectric device configurations (bimorph) towards achieving higher specific power is investigated. It is shown in this study that at low excitation frequency ranges, replacing the solid continuous substrate of conventional bimorph with honeycomb structures of the same material results in a significant increase in power to weight ratio of the piezoelectric harvester. At higher driving frequency ranges it is shown that unlike the traditional piezoelectric bimorph with solid continuous substrate, the honeycomb substrate bimorph can preserve optimum global design parameters through manipulation of honeycomb unit cell parameters. Increased operating lifetime and design flexibility of the honeycomb core piezoelectric bimorph is demonstrated as unit cell parameters of the honeycomb structures can be manipulated to alter mass and stiffness properties of the substrate, resulting in unit cell parameter significantly influencing power generation.

  5. Bacillus anthracis TIR Domain-Containing Protein Localises to Cellular Microtubule Structures and Induces Autophagy

    PubMed Central

    Carlsson, Emil; Thwaite, Joanne E.; Jenner, Dominic C.; Spear, Abigail M.; Flick-Smith, Helen; Atkins, Helen S.; Ding, Jeak Ling

    2016-01-01

    Toll-like receptors (TLRs) recognise invading pathogens and mediate downstream immune signalling via Toll/IL-1 receptor (TIR) domains. TIR domain proteins (Tdps) have been identified in multiple pathogenic bacteria and have recently been implicated as negative regulators of host innate immune activation. A Tdp has been identified in Bacillus anthracis, the causative agent of anthrax. Here we present the first study of this protein, designated BaTdp. Recombinantly expressed and purified BaTdp TIR domain interacted with several human TIR domains, including that of the key TLR adaptor MyD88, although BaTdp expression in cultured HEK293 cells had no effect on TLR4- or TLR2- mediated immune activation. During expression in mammalian cells, BaTdp localised to microtubular networks and caused an increase in lipidated cytosolic microtubule-associated protein 1A/1B-light chain 3 (LC3), indicative of autophagosome formation. In vivo intra-nasal infection experiments in mice showed that a BaTdp knockout strain colonised host tissue faster with higher bacterial load within 4 days post-infection compared to the wild type B. anthracis. Taken together, these findings indicate that BaTdp does not play an immune suppressive role, but rather, its absence increases virulence. BaTdp present in wild type B. anthracis plausibly interact with the infected host cell, which undergoes autophagy in self-defence. PMID:27391310

  6. Bacillus anthracis TIR Domain-Containing Protein Localises to Cellular Microtubule Structures and Induces Autophagy.

    PubMed

    Carlsson, Emil; Thwaite, Joanne E; Jenner, Dominic C; Spear, Abigail M; Flick-Smith, Helen; Atkins, Helen S; Byrne, Bernadette; Ding, Jeak Ling

    2016-01-01

    Toll-like receptors (TLRs) recognise invading pathogens and mediate downstream immune signalling via Toll/IL-1 receptor (TIR) domains. TIR domain proteins (Tdps) have been identified in multiple pathogenic bacteria and have recently been implicated as negative regulators of host innate immune activation. A Tdp has been identified in Bacillus anthracis, the causative agent of anthrax. Here we present the first study of this protein, designated BaTdp. Recombinantly expressed and purified BaTdp TIR domain interacted with several human TIR domains, including that of the key TLR adaptor MyD88, although BaTdp expression in cultured HEK293 cells had no effect on TLR4- or TLR2- mediated immune activation. During expression in mammalian cells, BaTdp localised to microtubular networks and caused an increase in lipidated cytosolic microtubule-associated protein 1A/1B-light chain 3 (LC3), indicative of autophagosome formation. In vivo intra-nasal infection experiments in mice showed that a BaTdp knockout strain colonised host tissue faster with higher bacterial load within 4 days post-infection compared to the wild type B. anthracis. Taken together, these findings indicate that BaTdp does not play an immune suppressive role, but rather, its absence increases virulence. BaTdp present in wild type B. anthracis plausibly interact with the infected host cell, which undergoes autophagy in self-defence. PMID:27391310

  7. Crystal structures of complexes of NAD+-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    NASA Astrophysics Data System (ADS)

    Filippova, E. V.; Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-01

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD+). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD+-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 Å resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  8. Crystal structures of complexes of NAD{sup +}-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 with formate

    SciTech Connect

    Filippova, E. V. Polyakov, K. M.; Tikhonova, T. V.; Stekhanova, T. N.; Boiko, K. M.; Sadykhov, I. G.; Tishkov, V. I.; Popov, V. O.; Labru, N.

    2006-07-15

    Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI{sub 2} with the coupled reduction of nicotinamide adenine dinucleotide (NAD{sup +}). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD{sup +}-azide complex) of FDH have been established earlier. In the present study, the structures of FDH complexes with formate are solved at 2.19 and 2.28 A resolution by the molecular replacement method and refined to the R factors of 22.3 and 20.5%, respectively. Both crystal structures contain four protein molecules per asymmetric unit. These molecules form two dimers identical to the dimer of the apo form of FDH. Two possible formatebinding sites are found in the active site of the FDH structure. In the complexes the sulfur atom of residue Cys354 exists in the oxidized state.

  9. Investigation of mechanical properties for open cellular structure CoCrMo alloy fabricated by selective laser melting process

    NASA Astrophysics Data System (ADS)

    Azidin, A.; Taib, Z. A. M.; Harun, W. S. W.; Che Ghani, S. A.; Faisae, M. F.; Omar, M. A.; Ramli, H.

    2015-12-01

    Orthodontic implants have been a major focus through mechanical and biological performance in advance to fabricate shape of complex anatomical. Designing the part with a complex mechanism is one of the challenging process and addition to achieve the balance and desired mechanical performance brought to the right manufacture technique to fabricate. Metal additive manufacturing (MAM) is brought forward to the newest fabrication technology in this field. In this study, selective laser melting (SLM) process was utilized on a medical grade cobalt-chrome molybdenum (CoCrMo) alloy. The work has focused on mechanical properties of the CoCrMo open cellular structures samples with 60%, 70%, and 80% designed volume porosity that could potentially emulate the properties of human bone. It was observed that hardness values decreased as the soaking time increases except for bottom face. For compression test, 60% designed volume porosity demonstrated highest ultimate compressive strength compared to 70% and 80%.

  10. From thermodynamic cell models to partitioning cellular automata for diffusion in zeolites. I. Structure of the algorithm

    NASA Astrophysics Data System (ADS)

    Pazzona, Federico G.; Demontis, Pierfranco; Suffritti, Giuseppe B.

    2009-12-01

    In the study of adsorption of simple adsorbates in microporous materials like zeolites, thermodynamic models of small grand-canonical cells with very local interactions [e.g., see K. G. Ayappa, J. Chem. Phys. 111, 4736 (1999)] have been proven to be able to produce thermodynamic properties in very good agreement with the results of experiments and atomistic simulations. In this paper we present in details the structure and implementation of a thermodynamic partitioning cellular automaton (PCA) devised as a dynamical version of thermodynamic cell models and proposed as an easy environment to perform coarse-grained simulations of adsorption/diffusion of simple interacting molecules in microporous materials. Local evolution rules and memory effects are introduced to make our PCA able to complete the static picture provided by thermodynamic cell models with the simulation of transport properties.

  11. Structural and Cellular Characterization of Electrospun Recombinant Human Tropoelastin Biomaterials1

    PubMed Central

    McKenna, Kathryn A.; Gregory, Kenton W.; Sarao, Rebecca C.; Maslen, Cheryl L.; Glanville, Robert W.; Hinds, Monica T.

    2012-01-01

    An off-the-shelf vascular graft biomaterial for vascular bypass surgeries is an unmet clinical need. The vascular biomaterial must support cell growth, be non-thrombogenic, minimize intimal hyperplasia, match the structural properties of native vessels, and allow for regeneration of arterial tissue. Electrospun recombinant human tropoelastin (rTE) as a medial component of a vascular graft scaffold was investigated in this study by evaluating its structural properties, as well as its ability to support primary smooth muscle cell adhesion and growth. rTE solutions of 9, 15, and 20 wt% concentrations were electropun into sheets with average fiber diameters of 167 ± 32, 522 ± 67, and 735 ± 270 nm, and average pore sizes of 0.4 ± 0.1, 5.8 ± 4.3, and 4.9 ± 2.4 μm, respectively. Electrospun rTE fibers were cross-linked with disuccinimidyl suberate (DSS) to produce an insoluble fibrous polymeric recombinant tropoelastin (prTE) biomaterial. The smooth muscle cells attached via integrin binding. The proliferation of the smooth muscle cells on the electrospun prTE biomaterial was comparable to growth on prTE coated glass, glass alone and tissue culture plastic. Electrospun tropoelastin demonstrated the cell compatibility and design flexibility required of a graft biomaterial for vascular applications. PMID:21586601

  12. Haplotype Structure and Expression Divergence at the Drosophila Cellular Immune Gene eater

    PubMed Central

    Juneja, Punita; Lazzaro, Brian P.

    2010-01-01

    The protein Eater plays an important role in microbial recognition and defensive phagocytosis in Drosophila melanogaster. We sequenced multiple alleles of the eater gene from an African and a North American population of D. melanogaster and found signatures of a partial selective sweep in North America that is localized around the second intron. This pattern is consistent with local adaptation to novel selective pressures during range expansion out of Africa. The North American sample is divided into two predominant haplotype groups, and the putatively selected haplotype is associated with a significantly higher gene expression level, suggesting that gene regulation is a possible target of selection. The eater alleles contain from 22 to 40 repeat units that are characterized by the presence of a cysteine-rich NIM motif. NIM repeats in the structural stalk of the protein exhibit concerted evolution as a function of physical location in the repeat array. Several NIM repeats within eater have previously been implicated in binding to microbial ligands, a function which in principle might subject them to special evolutionary pressures. However, we find no evidence of elevated positive selection on these pathogen-interacting units. Our study presents an instance where gene expression rather than protein structure is thought to drive the adaptive evolution of a pathogen recognition molecule in the immune system. PMID:20444883

  13. The family of iron responsive RNA structures regulated by changes in cellular iron and oxygen.

    PubMed

    Leipuviene, R; Theil, E C

    2007-11-01

    The life of aerobes is dependent on iron and oxygen for efficient bioenergetics. Due to potential risks associated with iron/oxygen chemistry, iron acquisition, concentration, storage, utilization, and efflux are tightly regulated in the cell. A central role in regulating iron/oxygen chemistry in animals is played by mRNA translation or turnover via the iron responsive element (IRE)/iron regulatory protein (IRP) system. The IRE family is composed of three-dimensional RNA structures located in 3' or 5' untranslated regions of mRNA. To date, there are 11 different IRE mRNAs in the family, regulated through translation initiation or mRNA stability. Iron or oxidant stimuli induce a set of graded responses related to mRNA-specific IRE substructures, indicated by differential responses to iron in vivo and binding IRPs in vitro. Molecular effects of phosphorylation, iron and oxygen remain to be added to the structural information of the IRE-RNA and IRP repressor in the regulatory complex.

  14. Hydrophilic interaction liquid chromatography-tandem mass spectrometry quantitative method for the cellular analysis of varying structures of gemini surfactants designed as nanomaterial drug carriers.

    PubMed

    Donkuru, McDonald; Michel, Deborah; Awad, Hanan; Katselis, George; El-Aneed, Anas

    2016-05-13

    Diquaternary gemini surfactants have successfully been used to form lipid-based nanoparticles that are able to compact, protect, and deliver genetic materials into cells. However, what happens to the gemini surfactants after they have released their therapeutic cargo is unknown. Such knowledge is critical to assess the quality, safety, and efficacy of gemini surfactant nanoparticles. We have developed a simple and rapid liquid chromatography electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method for the quantitative determination of various structures of gemini surfactants in cells. Hydrophilic interaction liquid chromatography (HILIC) was employed allowing for a short simple isocratic run of only 4min. The lower limit of detection (LLOD) was 3ng/mL. The method was valid to 18 structures of gemini surfactants belonging to two different structural families. A full method validation was performed for two lead compounds according to USFDA guidelines. The HILIC-MS/MS method was compatible with the physicochemical properties of gemini surfactants that bear a permanent positive charge with both hydrophilic and hydrophobic elements within their molecular structure. In addition, an effective liquid-liquid extraction method (98% recovery) was employed surpassing previously used extraction methods. The analysis of nanoparticle-treated cells showed an initial rise in the analyte intracellular concentration followed by a maximum and a somewhat more gradual decrease of the intracellular concentration. The observed intracellular depletion of the gemini surfactants may be attributable to their bio-transformation into metabolites and exocytosis from the host cells. Obtained cellular data showed a pattern that grants additional investigations, evaluating metabolite formation and assessing the subcellular distribution of tested compounds.

  15. Interplay between cellular activity and three-dimensional scaffold-cell constructs with different foam structure processed by electron beam melting.

    PubMed

    Nune, Krishna C; Misra, R Devesh K; Gaytan, Sara M; Murr, Lawrence E

    2015-05-01

    The cellular activity, biological response, and consequent integration of scaffold-cell construct in the physiological system are governed by the ability of cells to adhere, proliferate, and biomineralize. In this regard, we combine cellular biology and materials science and engineering to fundamentally elucidate the interplay between cellular activity and interconnected three-dimensional foamed architecture obtained by a novel process of electron beam melting and computational tools. Furthermore, the organization of key proteins, notably, actin, vinclulin, and fibronectin, involved in cellular activity and biological functions and relationship with the structure was explored. The interconnected foamed structure with ligaments was favorable to cellular activity that includes cell attachment, proliferation, and differentiation. The primary rationale for favorable modulation of cellular functions is that the foamed structure provided a channel for migration and communication between cells leading to highly mineralized extracellular matrix (ECM) by the differentiating osteoblasts. The filopodial interaction amongst cells on the ligaments was a governing factor in the secretion of ECM, with consequent influence on maturation and mineralization.

  16. Structure and Soot Formation Properties of Laminar Flames

    NASA Technical Reports Server (NTRS)

    El-Leathy, A. M.; Xu, F.; Faeth, G. M.

    2001-01-01

    Soot formation within hydrocarbon-fueled flames is an important unresolved problem of combustion science for several reasons: soot emissions are responsible for more deaths than any other combustion-generated pollutant, thermal loads due to continuum radiation from soot limit the durability of combustors, thermal radiation from soot is mainly responsible for the growth and spread of unwanted fires, carbon monoxide emissions associated with soot emissions are responsible for most fire deaths, and limited understanding of soot processes in flames is a major impediment to the development of computational combustion. Motivated by these observations, soot processes within laminar premixed and nonpremixed (diffusion) flames are being studied during this investigation. The study is limited to laminar flames due to their experimental and computational tractability, noting the relevance of these results to practical flames through laminar flamelet concepts. Nonbuoyant flames are emphasized because buoyancy affects soot processes in laminar diffusion flames whereas effects of buoyancy are small for most practical flames. This study involves both ground- and space-based experiments, however, the following discussion will be limited to ground-based experiments because no space-based experiments were carried out during the report period. The objective of this work was to complete measurements in both premixed and nonpremixed flames in order to gain a better understanding of the structure of the soot-containing region and processes of soot nucleation and surface growth in these environments, with the latter information to be used to develop reliable ways of predicting soot properties in practical flames. The present discussion is brief, more details about the portions of the investigation considered here can be found in refs. 8-13.

  17. Hikurangi Plateau: Crustal structure, rifted formation, and Gondwana subduction history

    NASA Astrophysics Data System (ADS)

    Davy, Bryan; Hoernle, Kaj; Werner, Reinhard

    2008-07-01

    Seismic reflection profiles across the Hikurangi Plateau Large Igneous Province and adjacent margins reveal the faulted volcanic basement and overlying Mesozoic-Cenozoic sedimentary units as well as the structure of the paleoconvergent Gondwana margin at the southern plateau limit. The Hikurangi Plateau crust can be traced 50-100 km southward beneath the Chatham Rise where subduction cessation timing and geometry are interpreted to be variable along the margin. A model fit of the Hikurangi Plateau back against the Manihiki Plateau aligns the Manihiki Scarp with the eastern margin of the Rekohu Embayment. Extensional and rotated block faults which formed during the breakup of the combined Manihiki-Hikurangi plateau are interpreted in seismic sections of the Hikurangi Plateau basement. Guyots and ridge-like seamounts which are widely scattered across the Hikurangi Plateau are interpreted to have formed at 99-89 Ma immediately following Hikurangi Plateau jamming of the Gondwana convergent margin at ˜100 Ma. Volcanism from this period cannot be separately resolved in the seismic reflection data from basement volcanism; hence seamount formation during Manihiki-Hikurangi Plateau emplacement and breakup (125-120 Ma) cannot be ruled out. Seismic reflection data and gravity modeling suggest the 20-Ma-old Hikurangi Plateau choked the Cretaceous Gondwana convergent margin within 5 Ma of entry. Subsequent uplift of the Chatham Rise and slab detachment has led to the deposition of a Mesozoic sedimentary unit that thins from ˜1 km thickness northward across the plateau. The contrast with the present Hikurangi Plateau subduction beneath North Island, New Zealand, suggests a possible buoyancy cutoff range for LIP subduction consistent with earlier modeling.

  18. Merger histories in warm dark matter structure formation scenarios

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Devriendt, Julien E. G.; Mahmood, Asim; Silk, Joseph

    2002-02-01

    Observations on galactic scales seem to be in contradiction with recent high-resolution N-body simulations. This so-called cold dark matter (CDM) crisis has been addressed in several ways, ranging from a change in fundamental physics by introducing self-interacting cold dark matter particles to a tuning of complex astrophysical processes such as global and/or local feedback. All these efforts attempt to soften density profiles and reduce the abundance of satellites in simulated galaxy haloes. In this paper, we explore a different approach that consists of filtering the dark matter power spectrum on small scales, thereby altering the formation history of low-mass objects. The physical motivation for damping these fluctuations lies in the possibility that the dark matter particles have a different nature, i.e. are warm (WDM) rather than cold. We show that this leads to some interesting new results in terms of the merger history and large-scale distribution of low-mass haloes, compared with the standard CDM scenario. However, WDM does not appear to be the ultimate solution, in the sense that it is not able to fully solve the CDM crisis, even though one of the main drawbacks, namely the abundance of satellites, can be remedied. Indeed, the cuspiness of the halo profiles still persists, at all redshifts, and for all haloes and sub-haloes that we investigated. Despite the persistence of the cuspiness problem of DM haloes, WDM seems to be still worth taking seriously, as it alleviates the problems of over-abundant sub-structures in galactic haloes and possibly the lack of angular momentum of simulated disc galaxies. WDM also lessens the need to invoke strong feedback to solve these problems, and may provide a natural explanation of the clustering properties and ages of dwarfs.

  19. Time lapse microscopy observation of cellular structural changes and image analysis of drug treated cancer cells to characterize the cellular heterogeneity.

    PubMed

    Vaiyapuri, Periasamy S; Ali, Alshatwi A; Mohammad, Akbarsha A; Kandhavelu, Jeyalakshmi; Kandhavelu, Meenakshisundaram

    2015-01-01

    The effect of Calotropis gigantea latex (CGLX) on human mammary carcinoma cells is not well established. We present the results of this drug activity at total population and single cell level. CGLX inhibited the growth of MCF7 cancer cells at lower IC50 concentration (17 µL/mL). Microscopy of IC50 drug treated cells at 24 hr confirming the appearance of morphological characteristics of apoptotic and necrotic cells, associated with 70% of DNA damage. FACS analysis confirmed that, 10 and 20% of the disruption of cellular mitochondrial nature by at 24 and 48 h, respectively. Microscopic image analysis of total population level proved that MMP changes were statistically significant with P values. The cell to cell variation was confirmed by functional heterogeneity analysis which proves that CGLX was able to induce the apoptosis without the contribution of mitochondria. We conclude that CGLX inhibits cell proliferation, survival, and heterogeneity of pathways in human mammary carcinoma cells.

  20. Primary structure and cellular localization of callinectin, an antimicrobial peptide from the blue crab.

    PubMed

    Noga, Edward J; Stone, Kathryn L; Wood, Abbey; Gordon, William L; Robinette, David

    2011-04-01

    We report the complete amino acid sequence of callinectin, a 32 amino acid, proline-, arginine-rich antimicrobial peptide (AMP) with four cysteines and having the sequence WNSNRRFRVGRPPVVGRPGCVCFRAPCPCSNY-amide. The primary structure of callinectin is highly similar to arasins, AMPs recently identified in the small spider crab (Hyas araneus). Callinectin exists in three isomers that vary in the functional group on the tryptophan (W) residue. The most prevalent isomer had a hydroxy-N-formylkynurenine group, while the other two isomers had either N-formylkynurenine or hydroxy-tryptophan. Using a sequence highly similar to native callinectin, we chemically synthesized a peptide which we called callinectin-like peptide (CLP). Via immuno-electron microscopy, affinity-purified rabbit antibodies raised to CLP successfully localized the site of callinectin in blue crab hemocytes to the large electron-dense granules that are found primarily in large granule hemocytes.

  1. Primary structure and cellular localization of callinectin, an antimicrobial peptide from the blue crab

    PubMed Central

    Noga, Edward J.; Stone, Kathryn L.; Wood, Abbey; Gordon, William L.; Robinette, David

    2011-01-01

    We report the complete amino acid sequence of callinectin, a 32 amino acid, proline-, arginine-rich AMP with four cysteines and having the sequence WNSNRRFRVGRPPVVGRPGCVCFRAPCPCSNY-amide. The primary structure of callinectin is highly similar to arasins, AMPs recently identified in the small spider crab (Hyas araneus). Callinectin exists in three isomers that vary in the functional group on the tryptophan (W) residue. The most prevalent isomer had a hydroxy-N-formylkynurenine group, while the other two isomers had either N-formylkynurenine or hydroxy-tryptophan. Using a sequence highly similar to native callinectin, we chemically synthesized a peptide which we called callinectin-like peptide (CLP). Via immunoelectron microscopy, affinity-purified rabbit antibodies raised to CLP successfully localized the site of callinectin in blue crab hemocytes to the large electron-dense granules that are found primarily in large granule hemocytes. PMID:21115038

  2. Cellular functions and X-ray structure of anthrolysin O, a cholesterol-dependent cytolysin secreted by Bacillus anthracis.

    PubMed

    Bourdeau, Raymond W; Malito, Enrico; Chenal, Alexandre; Bishop, Brian L; Musch, Mark W; Villereal, Mitch L; Chang, Eugene B; Mosser, Elise M; Rest, Richard F; Tang, Wei-Jen

    2009-05-22

    Anthrolysin O (ALO) is a pore-forming, cholesterol-dependent cytolysin (CDC) secreted by Bacillus anthracis, the etiologic agent for anthrax. Growing evidence suggests the involvement of ALO in anthrax pathogenesis. Here, we show that the apical application of ALO decreases the barrier function of human polarized epithelial cells as well as increases intracellular calcium and the internalization of the tight junction protein occludin. Using pharmacological agents, we also found that barrier function disruption requires increased intracellular calcium and protein degradation. We also report a crystal structure of the soluble state of ALO. Based on our analytical ultracentrifugation and light scattering studies, ALO exists as a monomer. Our ALO structure provides the molecular basis as to how ALO is locked in a monomeric state, in contrast to other CDCs that undergo antiparallel dimerization or higher order oligomerization in solution. ALO has four domains and is globally similar to perfringolysin O (PFO) and intermedilysin (ILY), yet the highly conserved undecapeptide region in domain 4 (D4) adopts a completely different conformation in all three CDCs. Consistent with the differences within D4 and at the D2-D4 interface, we found that ALO D4 plays a key role in affecting the barrier function of C2BBE cells, whereas PFO domain 4 cannot substitute for this role. Novel structural elements and unique cellular functions of ALO revealed by our studies provide new insight into the molecular basis for the diverse nature of the CDC family.

  3. Cellular Functions and X-ray Structure of Anthrolysin O, a Cholesterol-dependent Cytolysin Secreted by Bacillus anthracis

    SciTech Connect

    Bourdeau, Raymond W.; Malito, Enrico; Chenal, Alexandre; Bishop, Brian L.; Musch, Mark W.; Villereal, Mitch L.; Chang, Eugene B.; Mosser, Elise M.; Rest, Richard F.; Tang, Wei-Jen

    2009-06-02

    Anthrolysin O (ALO) is a pore-forming, cholesterol-dependent cytolysin (CDC) secreted by Bacillus anthracis, the etiologic agent for anthrax. Growing evidence suggests the involvement of ALO in anthrax pathogenesis. Here, we show that the apical application of ALO decreases the barrier function of human polarized epithelial cells as well as increases intracellular calcium and the internalization of the tight junction protein occludin. Using pharmacological agents, we also found that barrier function disruption requires increased intracellular calcium and protein degradation. We also report a crystal structure of the soluble state of ALO. Based on our analytical ultracentrifugation and light scattering studies, ALO exists as a monomer. Our ALO structure provides the molecular basis as to how ALO is locked in a monomeric state, in contrast to other CDCs that undergo antiparallel dimerization or higher order oligomerization in solution. ALO has four domains and is globally similar to perfringolysin O (PFO) and intermedilysin (ILY), yet the highly conserved undecapeptide region in domain 4 (D4) adopts a completely different conformation in all three CDCs. Consistent with the differences within D4 and at the D2-D4 interface, we found that ALO D4 plays a key role in affecting the barrier function of C2BBE cells, whereas PFO domain 4 cannot substitute for this role. Novel structural elements and unique cellular functions of ALO revealed by our studies provide new insight into the molecular basis for the diverse nature of the CDC family.

  4. Inhibition of Coxsackie B Virus Infection by Soluble Forms of Its Receptors: Binding Affinities, Altered Particle Formation, and Competition with Cellular Receptors

    PubMed Central

    Goodfellow, Ian G.; Evans, David J.; Blom, Anna M.; Kerrigan, Dave; Miners, J. Scott; Morgan, B. Paul; Spiller, O. Brad

    2005-01-01

    We previously reported that soluble decay-accelerating factor (DAF) and coxsackievirus-adenovirus receptor (CAR) blocked coxsackievirus B3 (CVB3) myocarditis in mice, but only soluble CAR blocked CVB3-mediated pancreatitis. Here, we report that the in vitro mechanisms of viral inhibition by these soluble receptors also differ. Soluble DAF inhibited virus infection through the formation of reversible complexes with CVB3, while binding of soluble CAR to CVB induced the formation of altered (A) particles with a resultant irreversible loss of infectivity. A-particle formation was characterized by loss of VP4 from the virions and required incubation of CVB3-CAR complexes at 37°C. Dimeric soluble DAF (DAF-Fc) was found to be 125-fold-more effective at inhibiting CVB3 than monomeric DAF, which corresponded to a 100-fold increase in binding affinity as determined by surface plasmon resonance analysis. Soluble CAR and soluble dimeric CAR (CAR-Fc) bound to CVB3 with 5,000- and 10,000-fold-higher affinities than the equivalent forms of DAF. While DAF-Fc was 125-fold-more effective at inhibiting virus than monomeric DAF, complement regulation by DAF-Fc was decreased 4 fold. Therefore, while the virus binding was a cooperative event, complement regulation was hindered by the molecular orientation of DAF-Fc, indicating that the regions responsible for complement regulation and virus binding do not completely overlap. Relative contributions of CVB binding affinity, receptor binding footprint on the virus capsid, and induction of capsid conformation alterations for the ability of cellular DAF and CAR to act as receptors are discussed. PMID:16140777

  5. Formation of human hepatocyte-like cells with different cellular phenotypes by human umbilical cord blood-derived cells in the human-rat chimeras

    SciTech Connect

    Sun, Yan; Xiao, Dong; Zhang, Ruo-Shuang; Cui, Guang-Hui; Wang, Xin-Hua; Chen, Xi-Gu . E-mail: xiguchen1516@yahoo.com.cn

    2007-06-15

    We took advantage of the proliferative and permissive environment of the developing pre-immune fetus to develop a noninjury human-rat xenograft small animal model, in which the in utero transplantation of low-density mononuclear cells (MNCs) from human umbilical cord blood (hUCB) into fetal rats at 9-11 days of gestation led to the formation of human hepatocyte-like cells (hHLCs) with different cellular phenotypes, as revealed by positive immunostaining for human-specific alpha-fetoprotein (AFP), cytokeratin 19 (CK19), cytokeratin 8 (CK8), cytokeratin 18 (CK18), and albumin (Alb), and with some animals exhibiting levels as high as 10.7% of donor-derived human cells in the recipient liver. More interestingly, donor-derived human cells stained positively for CD34 and CD45 in the liver of 2-month-old rat. Human hepatic differentiation appeared to partially follow the process of hepatic ontogeny, as evidenced by the expression of AFP gene at an early stage and albumin gene at a later stage. Human hepatocytes generated in this model retained functional properties of normal hepatocytes. In this xenogeneic system, the engrafted donor-derived human cells persisted in the recipient liver for at least 6 months after birth. Taken together, these findings suggest that the donor-derived human cells with different cellular phenotypes are found in the recipient liver and hHLCs hold biological activity. This humanized small animal model, which offers an in vivo environment more closely resembling the situations in human, provides an invaluable approach for in vivo investigating human stem cell behaviors, and further in vivo examining fundamental mechanisms controlling human stem cell fates in the future.

  6. Native aggregation as a cause of origin of temporary cellular structures needed for all forms of cellular activity, signaling and transformations

    PubMed Central

    2010-01-01

    According to the hypothesis explored in this paper, native aggregation is genetically controlled (programmed) reversible aggregation that occurs when interacting proteins form new temporary structures through highly specific interactions. It is assumed that Anfinsen's dogma may be extended to protein aggregation: composition and amino acid sequence determine not only the secondary and tertiary structure of single protein, but also the structure of protein aggregates (associates). Cell function is considered as a transition between two states (two states model), the resting state and state of activity (this applies to the cell as a whole and to its individual structures). In the resting state, the key proteins are found in the following inactive forms: natively unfolded and globular. When the cell is activated, secondary structures appear in natively unfolded proteins (including unfolded regions in other proteins), and globular proteins begin to melt and their secondary structures become available for interaction with the secondary structures of other proteins. These temporary secondary structures provide a means for highly specific interactions between proteins. As a result, native aggregation creates temporary structures necessary for cell activity. "One of the principal objects of theoretical research in any department of knowledge is to find the point of view from which the subject appears in its greatest simplicity." Josiah Willard Gibbs (1839-1903) PMID:20534114

  7. Fluoride-containing bioactive glasses: Glass design, structure, bioactivity, cellular interactions, and recent developments.

    PubMed

    Shah, Furqan A

    2016-01-01

    Bioactive glasses (BGs) are known to bond to both hard and soft tissues. Upon exposure to an aqueous environment, BG undergoes ion exchange, hydrolysis, selective dissolution and precipitation of an apatite layer on their surface, which elicits an interfacial biological response resulting in bioactive fixation, inhibiting further dissolution of the glass, and preventing complete resorption of the material. Fluorine is considered one of the most effective in-vivo bone anabolic factors. In low concentrations, fluoride ions (F(-)) increase bone mass and mineral density, improve the resistance of the apatite structure to acid attack, and have well documented antibacterial properties. F(-) ions may be incorporated into the glass in the form of calcium fluoride (CaF2) either by part-substitution of network modifier oxides, or by maintaining the ratios of the other constituents relatively constant. Fluoride-containing bioactive glasses (FBGs) enhance and control osteoblast proliferation, differentiation and mineralisation. And with their ability to release fluoride locally, FBGs make interesting candidates for various clinical applications, dentinal tubule occlusion in the treatment of dentin hypersensitivity. This paper reviews the chemistry of FBGs and the influence of F(-) incorporation on the thermal properties, bioactivity, and cytotoxicity; and novel glass compositions for improved mechanical properties, processing, and bioactive potential.

  8. Nanosilicon carbide/hydroxyapatite nanocomposites: structural, mechanical and in vitro cellular properties.

    PubMed

    Hesaraki, Saeed; Ebadzadeh, Touraj; Ahmadzadeh-Asl, Shaghayegh

    2010-07-01

    In this study, bioceramic nanocomposites were synthesized by sintering compacted bodies of hydroxyapatite (HA) mixed with 5 or 15 wt% nanosilicon carbide at 1,100 or 1,200 degrees C in a reducing atmosphere. Pure hydroxyapatite was also prepared for comparison. Phase compositions, structural and physical properties of the composites were studied using appropriate techniques. Some in vitro biological properties of the composites were also investigated by using newrat calvaria osteoblastic cells. X-ray diffraction analysis indicated that tricalcium phosphate (TCP) comprising negligible alpha-TCP and considerable beta-TCP were formed in composites during sintering meanwhile hydroxyapatite and silicon carbide (SiC) were also existed in the composition. Based on the results, that composite made of 5 wt% nanosilicon carbide exhibited higher bending strength, fracture toughness and bulk density than pure HA and composite with 15 wt% silicon carbide. The scanning electron microscopy coupled with energy dispersive X-ray analysis revealed that the addition of nanosilicon carbide suppressed the grain growth and yielded a feature of island-type clusters consisting of blistered calcium phosphate (HA and TCP) and SiC grains. Also, in this study, better proliferation rate and alkaline phosphatase activity were observed for the osteoblastic cells seeded on top of the composites compared to pure HA. Overall, the results indicated that the composite of 95 wt% hydroxyapatite and 5 wt% SiC exhibited better mechanical and biological properties than pure HA and further addition of SiC failed strength and toughness.

  9. Fluoride-containing bioactive glasses: Glass design, structure, bioactivity, cellular interactions, and recent developments.

    PubMed

    Shah, Furqan A

    2016-01-01

    Bioactive glasses (BGs) are known to bond to both hard and soft tissues. Upon exposure to an aqueous environment, BG undergoes ion exchange, hydrolysis, selective dissolution and precipitation of an apatite layer on their surface, which elicits an interfacial biological response resulting in bioactive fixation, inhibiting further dissolution of the glass, and preventing complete resorption of the material. Fluorine is considered one of the most effective in-vivo bone anabolic factors. In low concentrations, fluoride ions (F(-)) increase bone mass and mineral density, improve the resistance of the apatite structure to acid attack, and have well documented antibacterial properties. F(-) ions may be incorporated into the glass in the form of calcium fluoride (CaF2) either by part-substitution of network modifier oxides, or by maintaining the ratios of the other constituents relatively constant. Fluoride-containing bioactive glasses (FBGs) enhance and control osteoblast proliferation, differentiation and mineralisation. And with their ability to release fluoride locally, FBGs make interesting candidates for various clinical applications, dentinal tubule occlusion in the treatment of dentin hypersensitivity. This paper reviews the chemistry of FBGs and the influence of F(-) incorporation on the thermal properties, bioactivity, and cytotoxicity; and novel glass compositions for improved mechanical properties, processing, and bioactive potential. PMID:26478431

  10. Structure of cellular ESCRT-III spirals and their relationship to HIV budding

    PubMed Central

    Cashikar, Anil G; Shim, Soomin; Roth, Robyn; Maldazys, Michael R; Heuser, John E; Hanson, Phyllis I

    2014-01-01

    The ESCRT machinery along with the AAA+ ATPase Vps4 drive membrane scission for trafficking into multivesicular bodies in the endocytic pathway and for the topologically related processes of viral budding and cytokinesis, but how they accomplish this remains unclear. Using deep-etch electron microscopy, we find that endogenous ESCRT-III filaments stabilized by depleting cells of Vps4 create uniform membrane-deforming conical spirals which are assemblies of specific ESCRT-III heteropolymers. To explore functional roles for ESCRT-III filaments, we examine HIV-1 Gag-mediated budding of virus-like particles and find that depleting Vps4 traps ESCRT-III filaments around nascent Gag assemblies. Interpolating between the observed structures suggests a new role for Vps4 in separating ESCRT-III from Gag or other cargo to allow centripetal growth of a neck constricting ESCRT-III spiral. DOI: http://dx.doi.org/10.7554/eLife.02184.001 PMID:24878737

  11. Shape memory thermal lag and superelastic rate sensitivity of SMA cellular structures

    NASA Astrophysics Data System (ADS)

    Watkins, Ryan T.; Shaw, John A.; Grummon, David S.

    2013-04-01

    An experimental characterization is presented of the thermo-mechanical response of honeycombs and corrugations made of a NiTi shape memory alloy (SMA). Of particular interest are the shape memory cycle, the superelastic response, the shape memory thermal lag and the superelastic rate sensitivity. A series of in-plane compression experiments are presented on fabricated honeycombs and their responses are compared to typical monolithic SMAs, such as NiTi wire. Given local material strain limits, NiTi honeycombs exhibit an order of magnitude increase in recoverable deformation, both in the shape memory effect and superelastic effect. This comes at the cost of a reduced load carrying capacity by two orders of magnitude and a reduced (homogenized) compressive stiffness by four orders of magnitude. Due to their sparse structure and enhanced heat transfer characteristics, SMA honeycombs exhibit less superelastic rate sensitivity by two orders of magnitude while having similar thermal lag to SMA wire. The implications of these scaling results are discussed, including possible new regimes of application of SMAs for reusable energy absorption devices and high stroke actuators.

  12. Experimental study on detonation parameters and cellular structures of fuel cloud

    NASA Astrophysics Data System (ADS)

    Xie, Li-Feng; Li, Bin; Zhang, Yu-Lei

    2012-04-01

    In this paper, detonation parameters of fuel cloud, such as propylene oxide (PO), isopropyl nitrate (IPN), hexane, 90# oil and decane were measured in a self-designed and constructed vertical shock tube. Results show that the detonation pressure and velocity of PO increase to a peak value and then decrease smoothly with increasing equivalence ratio. Several nitrate sensitizers were added into PO to make fuel mixtures, and test results indicated that the additives can efficiently enhance detonation velocity and pressure of fuel cloud and one type of additive n-propyl nitrate (NPN) played the best in the improvement. The critical initiation energy that directly initiated detonation of all the test liquid fuel clouds showed a U-shape curve relationship with equivalence ratios. The optimum concentration lies on the rich-fuel side ( ϕ > 1). The critical initiation energy is closely related to molecular structure and volatility of fuels. IPN and PO have similar critical values while that of alkanes are larger. Detonation cell sizes of PO were respectively investigated at 25°C, 35°C and 50°C with smoked foil technique. The cell width shows a U-shape curve relationship with equivalence ratios at all temperatures. The minimal cell width also lies on the rich-fuel side ( ϕ > 1). The cell width of PO vapor is slightly larger than that of PO cloud. Therefore, the detonation reaction of PO at normal temperature is controlled by gas phase reaction.

  13. Topics in cosmology: Structure formation, dark energy and recombination

    NASA Astrophysics Data System (ADS)

    Alizadeh, Esfandiar

    The field of theoretical cosmology consists of numerous, inter-related branches, whose ambitious goal is to uncover the history of the universe from its beginning to its future. Achieving this, no doubt, requires a deep understanding of many areas of physics. In this thesis I touch upon a few of these areas in which I worked during my PhD studies. Chapter (2) describes our work in finding the accretion and merger history of dark matter halos. Dark matter halos are the collapsed dark matter structures in the late time evolution of the universe, whose existence is vital for the formation of galaxies in the Universe as they act as the potential wells where normal matter (collectively called Baryons) can accumulate, cool, and form stars. It is then no surprise that the properties of galaxies depends on the properties of the dark matter halo in which it resides, including its merger history, i.e. the number of times it merged with other halos. Even though these merger rates can be calculated theoretically for infinitesimal time steps, in order to find the merger history over an extended period of time one had to use either Monte-Carlo simulations to build up the total rates of merging and accreting from the infinitesimal rates or use N-body simulations. In chapter (2) we show how we used random walk formalism to write down an analytical (integral) equation for the merger history of halos. We have solved this equation numerically and find very good agreement with Monte-Carlo simulations. This work can be used in theories of galaxy formation and evolution. We then switch from the overdense regions of the Universe, halos, to the underdense ones, voids. These structures have not attracted as much attention from cosmologists as their overdense counterparts in probing the cosmological models. We show here that the shapes of voids as a probe can be of use for future surveys to pin down the equation of state of the dark energy, i.e. the ratio of its pressure to its energy

  14. Flexible Virtual Structure Consideration in Dynamic Modeling of Mobile Robots Formation

    NASA Astrophysics Data System (ADS)

    El Kamel, A. Essghaier; Beji, L.; Lerbet, J.; Abichou, A.

    2009-03-01

    In cooperative mobile robotics, we look for formation keeping and maintenance of a geometric configuration during movement. As a solution to these problems, the concept of a virtual structure is considered. Based on this idea, we have developed an efficient flexible virtual structure, describing the dynamic model of n vehicles in formation and where the whole formation is kept dependant. Notes that, for 2D and 3D space navigation, only a rigid virtual structure was proposed in the literature. Further, the problem was limited to a kinematic behavior of the structure. Hence, the flexible virtual structure in dynamic modeling of mobile robots formation presented in this paper, gives more capabilities to the formation to avoid obstacles in hostile environment while keeping formation and avoiding inter-agent collision.

  15. Ancient cellular structures and modern humans: change of survival strategies before prolonged low solar activity period

    NASA Astrophysics Data System (ADS)

    Ragulskaya, Mariya; Rudenchik, Evgeniy; Gromozova, Elena; Voychuk, Sergei; Kachur, Tatiana

    The study of biotropic effects of modern space weather carries the information about the rhythms and features of adaptation of early biological systems to the outer space influence. The influence of cosmic rays, ultraviolet waves and geomagnetic field on early life has its signs in modern biosphere processes. These phenomena could be experimentally studied on present-day biological objects. Particularly inorganic polyphosphates, so-called "fossil molecules", attracts special attention as the most ancient molecules which arose in inanimate nature and have been accompanying biological objects at all stages of evolution. Polyphosphates-containing graves of yeast's cells of Saccharomyces cerevisiae strain Y-517, , from the Ukrainian Collection of Microorganisms was studied by daily measurements during 2000-2013 years. The IZMIRAN daily data base of physiological parameters dynamics during 2000-2013 years were analyzed simultaneously (25 people). The analysis showed significant simultaneous changes of the statistical parameters of the studied biological systems in 2004 -2006. The similarity of simultaneous changes of adaptation strategies of human organism and the cell structures of Saccharomyces cerevisiae during the 23-24 cycles of solar activity are discussed. This phenomenon could be due to a replacement of bio-effective parameters of space weather during the change from 23rd to 24th solar activity cycle and nonstandard geophysical peculiarities of the 24th solar activity cycle. It could be suggested that the observed similarity arose as the optimization of evolution selection of the living systems in expectation of probable prolonged period of low solar activity (4-6 cycles of solar activity).

  16. Cellular immunostimulation by CpG-sequence-coated DNA origami structures.

    PubMed

    Schüller, Verena J; Heidegger, Simon; Sandholzer, Nadja; Nickels, Philipp C; Suhartha, Nina A; Endres, Stefan; Bourquin, Carole; Liedl, Tim

    2011-12-27

    To investigate the potential of DNA origami constructs as programmable and noncytotoxic immunostimulants, we tested the immune responses induced by hollow 30-helix DNA origami tubes covered with up to 62 cytosine-phosphate-guanine (CpG) sequences in freshly isolated spleen cells. Unmethylated CpG sequences that are highly specific for bacterial DNA are recognized by a specialized receptor of the innate immune system localized in the endosome, the Toll-like receptor 9 (TLR9). When incubated with oligonucleotides containing CpGs, immune cells are stimulated through TLR9 to produce and secrete cytokine mediators such as interleukin-6 (IL-6) and interleukin-12p70 (IL-12p70), a process associated with the initiation of an immune response. In our studies, the DNA origami tube built from an 8634 nt long variant of the commonly used single-stranded DNA origami scaffold M13mp18 and 227 staple oligonucleotides decorated with 62 CpG-containing oligonucleotides triggered a strong immune response, characterized by cytokine production and immune cell activation, which was entirely dependent on TLR9 stimulation. Such decorated origami tubes also triggered higher immunostimulation than equal amounts of CpG oligonucleotides associated with a standard carrier system such as Lipofectamine. In the absence of CpG oligonucleotides, cytokine production induced by the origami tubes was low and was not related to TLR9 recognition. Fluorescent microscopy revealed localization of CpG-containing DNA origami structures in the endosome. The DNA constructs showed in contrast to Lipofectamine no detectable toxicity and did not affect the viability of splenocytes. We thus demonstrate that DNA origami constructs represent a delivery system for CpG oligonucleotides that is both efficient and nontoxic. PMID:22092186

  17. c-Myc and AMPK Control Cellular Energy Levels by Cooperatively Regulating Mitochondrial Structure and Function

    PubMed Central

    Edmunds, Lia R.; Sharma, Lokendra; Wang, Huabo; Kang, Audry; d’Souza, Sonia; Lu, Jie; McLaughlin, Michael; Dolezal, James M.; Gao, Xiaoli; Weintraub, Susan T.; Ding, Ying; Zeng, Xuemei; Yates, Nathan; Prochownik, Edward V.

    2015-01-01

    The c-Myc (Myc) oncoprotein and AMP-activated protein kinase (AMPK) regulate glycolysis and oxidative phosphorylation (Oxphos) although often for different purposes. Because Myc over-expression depletes ATP with the resultant activation of AMPK, we explored the potential co-dependency of and cross-talk between these proteins by comparing the consequences of acute Myc induction in ampk+/+ (WT) and ampk-/- (KO) murine embryo fibroblasts (MEFs). KO MEFs showed a higher basal rate of glycolysis than WT MEFs and an appropriate increase in response to activation of a Myc-estrogen receptor (MycER) fusion protein. However, KO MEFs had a diminished ability to increase Oxphos, mitochondrial mass and reactive oxygen species in response to MycER activation. Other differences between WT and KO MEFs, either in the basal state or following MycER induction, included abnormalities in electron transport chain function, levels of TCA cycle-related oxidoreductases and cytoplasmic and mitochondrial redox states. Transcriptional profiling of pathways pertinent to glycolysis, Oxphos and mitochondrial structure and function also uncovered significant differences between WT and KO MEFs and their response to MycER activation. Finally, an unbiased mass-spectrometry (MS)-based survey capable of quantifying ~40% of all mitochondrial proteins, showed about 15% of them to be AMPK- and/or Myc-dependent in their steady state. Significant differences in the activities of the rate-limiting enzymes pyruvate kinase and pyruvate dehydrogenase, which dictate pyruvate and acetyl coenzyme A abundance, were also differentially responsive to Myc and AMPK and could account for some of the differences in basal metabolite levels that were also detected by MS. Thus, Myc and AMPK are highly co-dependent and appear to engage in significant cross-talk across numerous pathways which support metabolic and ATP-generating functions. PMID:26230505

  18. Formation of regular structures in the process of phase separation.

    PubMed

    Krekhov, Alexei

    2009-03-01

    Phase separation under directional quenching has been studied in a Cahn-Hilliard model. In distinct contrast to the disordered patterns which develop under a homogeneous quench, periodic stripe patterns are generated behind the quench front. Their wavelength is uniquely defined by the velocity of the quench interface in a wide range. Numerical simulations match perfectly analytical results obtained in the limit of small and large velocities of the quench interface. Additional periodic modulation of the quench interface may lead to cellular patterns. The quenching protocols analyzed are expected to be an effective tool in technological applications to design nanostructured materials. PMID:19392008

  19. Star Formation Histories of Dwarf Galaxies: Keys to Galaxy Formation and Dark Matter Structure

    NASA Astrophysics Data System (ADS)

    Boylan-Kolchin, Michael

    2014-10-01

    We propose to perform a suite of hydrodynamical simulations in order to understand the connection between dwarf galaxy star formation histories, stellar content, and central dark matter densities. This will leverage one of HST's unique and enduring scientific contributions, deep and uniform photometry of nearby dwarf galaxies that enables reconstructions of their ancient {z 6-10} star formation histories, to shed light on some of the main problems in galaxy formation and cosmology.Analysis of HST observations has definitively shown that dwarfs exhibit a surprising variety of star formation histories: some dwarfs host nearly purely ancient populations, while others have formed 90% of their stars after redshift 1. This diversity is unexpected in current theoretical models, which predict primarily old stellar populations in low-mass objects. The topic of star formation histories of dwarfs has also received significant attention recently in the context of possible small-scale problems of the LCDM model: if episodic bursts of star formation inject energy into dwarfs' dark matter halos, it may provide a natural explanation of the observed low densities of dwarf galaxies within LCDM.Our simulations will adopt physically-motivated, explicit feedback prescriptions that are fixed by our knowledge of stellar evolution. We will choose halos having diverse mass assembly histories within a narrow range of mass and compare their star formation histories to HST observations of nearby isolated dwarf galaxies, thereby testing fundamental aspects of galaxy formation modeling and dark matter astrophysics. Data from our simulations will be publicly released via a dedicated website.

  20. Modeling and Simulation of the Impact Response of Filled and Unfilled Linear Cellular Alloys for Structural Energetic Material Applications

    NASA Astrophysics Data System (ADS)

    Jakus, Adam; Fredenburg, Anthony; Thadhani, Naresh

    2008-04-01

    We are investigating the mechanics of impact-induced stress transfer between a linear cellular alloy (LCA) and a reactive filler to determine the effect of cell geometry on deformation and fragmentation. LCAs are honeycomb structures made of maraging steel, and provide structural integrity for the reactive filler such as a powder mixture of Ta+Fe2O3. 3-D computations are used to determine stress and strain distributions in both filled and unfilled LCAs during impact. The strength and failure models used for maraging steel and the response of Ta+Fe2O3 are validated through experiment. The failure response of three different geometries: 9-cell, pie, and reinforced pie, are compared with the response of a hollow cylinder, for impact velocities of 100, 200, and 300 m/s. Unfilled, the cylindrical geometry provides the least resistance to deformation and fragmentation, while the reinforced pie LCA provides the most resistance. Understanding of the mechanics of deformation and failure is used to determine the most effective geometry for stress transfer to the filler.

  1. Sequences, structural models, and cellular localization of the actin- related proteins Arp2 and Arp3 from Acanthamoeba

    PubMed Central

    1995-01-01

    We cloned and sequenced the two actin-related proteins (Arps) present in the profilin-binding complex of Acanthamoeba (Machesky, L. M., S. J. Atkinson, C. Ampe, J. Vandekerckhove, and T. D. Pollard. 1994, J. Cell Biol. 127:107-115). The sequence of Arp2 is more similar to other Arp2s than to actin, while the sequence of Arp3 is more similar to other Arp3s than to actin. Phylogenetic analysis of all known Arps demonstrates that most group into three major families, which are likely to be shared across all eukaryotic phyla. Together with conventional actins, the Arps form a larger family distinct from structurally related ATPases such as Hsp70's and sugar kinases. Atomic models of the Arps based on their sequences and the structure of actin provide some clues about function. Both Arps have atoms appropriately placed to bind ATP and divalent cation. Arp2, but not Arp3, has a conserved profilin-binding site. Neither Arp has the residues required to copolymerize with actin, but an Arp heterodimer present in the profilin-binding complex might serve as a pointed end nucleus for actin polymerization. Both Acanthamoeba Arps are soluble in cell homogenates, and both are concentrated in the cortex of Acanthamoeba. The cellular concentrations are 1.9 microM Arp2 and 5.1 microM Arp3, substoichiometric to actin (200 microM) but comparable to many actin- binding proteins. PMID:7593166

  2. Chirality as a physical aspect of structure formation in biological macromolecular systems

    NASA Astrophysics Data System (ADS)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  3. Ultra-sensitive detection of tumorigenic cellular impurities in human cell-processed therapeutic products by digital analysis of soft agar colony formation.

    PubMed

    Kusakawa, Shinji; Yasuda, Satoshi; Kuroda, Takuya; Kawamata, Shin; Sato, Yoji

    2015-01-01

    Contamination with tumorigenic cellular impurities is one of the most pressing concerns for human cell-processed therapeutic products (hCTPs). The soft agar colony formation (SACF) assay, which is a well-known in vitro assay for the detection of malignant transformed cells, is applicable for the quality assessment of hCTPs. Here we established an image-based screening system for the SACF assay using a high-content cell analyzer termed the digital SACF assay. Dual fluorescence staining of formed colonies and the dissolution of soft agar led to accurate detection of transformed cells with the imaging cytometer. Partitioning a cell sample into multiple wells of culture plates enabled digital readout of the presence of colonies and elevated the sensitivity for their detection. In practice, the digital SACF assay detected impurity levels as low as 0.00001% of the hCTPs, i.e. only one HeLa cell contained in 10,000,000 human mesenchymal stem cells, within 30 days. The digital SACF assay saves time, is more sensitive than in vivo tumorigenicity tests, and would be useful for the quality control of hCTPs in the manufacturing process. PMID:26644244

  4. Cellular prion protein: A co-receptor mediating neuronal cofilin-actin rod formation induced by β-amyloid and proinflammatory cytokines

    PubMed Central

    Walsh, Keifer P; Kuhn, Thomas B; Bamburg, James R

    2014-01-01

    Increasing evidence suggests that proteins exhibiting “prion-like” behavior cause distinct neurodegenerative diseases, including inherited, sporadic and acquired types. The conversion of cellular prion protein (PrPC) to its infectious protease resistant counterpart (PrPRes) is the essential feature of prion diseases. However, PrPC also performs important functions in transmembrane signaling, especially in neurodegenerative processes. Beta-amyloid (Aβ) synaptotoxicity and cognitive dysfunction in mouse models of Alzheimer disease are mediated by a PrPC-dependent pathway. Here we review how this pathway converges with proinflammatory cytokine signaling to activate membrane NADPH oxidase (NOX) and generate reactive oxygen species (ROS) leading to dynamic remodeling of the actin cytoskeleton. The NOX signaling pathway may also be integrated with those of other transmembrane receptors clustered in PrPC-enriched membrane domains. Such a signal convergence along the PrPC-NOX axis could explain the relevance of PrPC in a broad spectrum of neurodegenerative disorders, including neuroinflammatory-mediated alterations in synaptic function following traumatic brain injury. PrPC overexpression alone activates NOX and generates a local increase in ROS that initiates cofilin activation and formation of cofilin-saturated actin bundles (rods). Rods sequester cofilin from synaptic regions where it is required for plasticity associated with learning and memory. Rods can also interrupt vesicular transport by occluding the neurite within which they form. Through either or both mechanisms, rods may directly mediate the synaptic dysfunction that accompanies various neurodegenerative disorders. PMID:25426519

  5. Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs.

    PubMed

    Brown, Jessica A; Valenstein, Max L; Yario, Therese A; Tycowski, Kazimierz T; Steitz, Joan A

    2012-11-20

    Stability of the long noncoding-polyadenylated nuclear (PAN) RNA from Kaposi's sarcoma-associated herpesvirus is conferred by an expression and nuclear retention element (ENE). The ENE protects PAN RNA from a rapid deadenylation-dependent decay pathway via formation of a triple helix between the U-rich internal loop of the ENE and the 3'-poly(A) tail. Because viruses borrow molecular mechanisms from their hosts, we searched highly abundant human long-noncoding RNAs and identified putative ENE-like structures in metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) RNAs. Unlike the PAN ENE, the U-rich internal loops of both predicted cellular ENEs are interrupted by G and C nucleotides and reside upstream of genomically encoded A-rich tracts. We confirmed the ability of MALAT1 and MENβ sequences containing the predicted ENE and A-rich tract to increase the levels of an intronless β-globin reporter RNA. UV thermal denaturation profiles at different pH values support formation of a triple-helical structure composed of multiple U•A-U base triples and a single C•G-C base triple. Additional analyses of the MALAT1 ENE revealed that robust stabilization activity requires an intact triple helix, strong stems at the duplex-triplex junctions, a G-C base pair flanking the triplex to mediate potential A-minor interactions, and the 3'-terminal A of the A-rich tract to form a blunt-ended triplex lacking unpaired nucleotides at the duplex-triplex junction. These examples of triple-helical, ENE-like structures in cellular noncoding RNAs, are unique.

  6. Dissipative structure formation in lipid/lipopolymer monolayers.

    PubMed

    Seitz, Peter C; Reif, Michael; Yoshikawa, Kenichi; Jordan, Rainer; Tanaka, Motomu

    2011-03-17

    We study the formation of dissipative microstructures in monomolecular films of surfactant mixtures, which occur near the three-phase contact line during Langmuir-Blodgett transfer onto a solid substrate. Continuous stripes parallel to the transfer direction are generated over several centimeters, indicating the phase separation of phospholipids and lipids with polymer head groups (lipopolymers). The systematic variation of transfer conditions revealed that transfer speed and subphase viscosity determine the stripe-to-stripe distance from several micrometers to submicrometers. To account for the physical mechanism of such pattern formation, we characterize the local film thickness and the membrane composition in the vicinity of the three-phase contact line using imaging ellipsometry and fluorescence microscopy. At relatively slow rates of substrate lifting, the power law exponent that we found between the interstripe distance and the transfer speed suggests that the stripe formation is due to spinodal decomposition, which can be accounted under the framework of the Cahn-Hilliard equation, whereas at relatively high rates, the distance is found to be proportional to the substrate speed, suggesting a dominant effect of the shear force on the stripe formation.

  7. Competition and Diversity among Radio Formats: Legal and Structural Issues.

    ERIC Educational Resources Information Center

    Glasser, Theodore L.

    That competition in broadcasting may not bring about sufficiently heterogeneous programing has long been the subject of debate among policymakers, and nowhere has that debate been more acrimonious than in its application to the diversification of radio formats. While the Federal Communications Commission (FCC) prefers to leave questions of…

  8. Dissipative structure formation in lipid/lipopolymer monolayers.

    PubMed

    Seitz, Peter C; Reif, Michael; Yoshikawa, Kenichi; Jordan, Rainer; Tanaka, Motomu

    2011-03-17

    We study the formation of dissipative microstructures in monomolecular films of surfactant mixtures, which occur near the three-phase contact line during Langmuir-Blodgett transfer onto a solid substrate. Continuous stripes parallel to the transfer direction are generated over several centimeters, indicating the phase separation of phospholipids and lipids with polymer head groups (lipopolymers). The systematic variation of transfer conditions revealed that transfer speed and subphase viscosity determine the stripe-to-stripe distance from several micrometers to submicrometers. To account for the physical mechanism of such pattern formation, we characterize the local film thickness and the membrane composition in the vicinity of the three-phase contact line using imaging ellipsometry and fluorescence microscopy. At relatively slow rates of substrate lifting, the power law exponent that we found between the interstripe distance and the transfer speed suggests that the stripe formation is due to spinodal decomposition, which can be accounted under the framework of the Cahn-Hilliard equation, whereas at relatively high rates, the distance is found to be proportional to the substrate speed, suggesting a dominant effect of the shear force on the stripe formation. PMID:21338143

  9. Formation, structure, and orientation of gold silicide on gold surfaces

    NASA Technical Reports Server (NTRS)

    Green, A. K.; Bauer, E.

    1976-01-01

    The formation of gold silicide on Au films evaporated onto Si(111) surfaces is studied by Auger electron spectroscopy (AES) and low-energy electron diffraction (LEED). Surface condition, film thickness, deposition temperature, annealing temperature, and heating rate during annealing are varied. Several oriented crystalline silicide layers are observed.

  10. Structure-guided Mutational Analysis of Gene Regulation by the Bacillus subtilis pbuE Adenine-responsive Riboswitch in a Cellular Context*

    PubMed Central

    Marcano-Velázquez, Joan G.; Batey, Robert T.

    2015-01-01

    Riboswitches are a broadly distributed form of RNA-based gene regulation in Bacteria and, more rarely, Archaea and Eukarya. Most often found in the 5′-leader sequence of bacterial mRNAs, they are generally composed of two functional domains: a receptor (aptamer) domain that binds an effector molecule and a regulatory domain (or expression platform) that instructs the expression machinery. One of the most studied riboswitches is the Bacillus subtilis adenine-responsive pbuE riboswitch, which regulates gene expression at the transcriptional level, up-regulating expression in response to increased intracellular effector concentrations. In this work, we analyzed sequence and structural elements that contribute to efficient ligand-dependent regulatory activity in a co-transcriptional and cellular context. Unexpectedly, we found that the P1 helix, which acts as the antitermination element of the switch in this RNA, supported ligand-dependent activation of a reporter gene over a broad spectrum of lengths from 3 to 10 bp. This same trend was also observed using a minimal in vitro single-turnover transcription assay, revealing that this behavior is intrinsic to the RNA sequence. We also found that the sequences at the distal tip of the terminator not directly involved in alternative secondary structure formation are highly important for efficient regulation. These data strongly support a model in which the switch is highly localized to the P1 helix adjacent to the ligand-binding pocket that likely presents a local kinetic block to invasion of the aptamer by the terminator. PMID:25550163

  11. Contributions of EspA Filaments and Curli Fimbriae in Cellular Adherence and Biofilm Formation of Enterohemorrhagic Escherichia coli O157:H7.

    PubMed

    Sharma, Vijay K; Kudva, Indira T; Bearson, Bradley L; Stasko, Judith A

    2016-01-01

    In Escherichia coli O157:H7 (O157), the filamentous structure of the type III secretion system is produced from the polymerization of the EspA protein. EspA filaments are essential for O157 adherence to epithelial cells. In previous studies, we demonstrated that O157 hha deletion mutants showed increased adherence to HEp-2 cells and produced abundant biofilms. Transcriptional analysis revealed increased expression of espA as well as the csgA gene, which encodes curli fimbriae that are essential for biofilm formation. In the present study, we constructed hha espA, hha csgA, and hha csgA espA deletion mutants to determine the relative importance of EspA and CsgA in O157 adherence to HEp-2 cells and biofilm formation. In vitro adherence assays, conducted at 37°C in a tissue culture medium containing 0.1% glucose, showed that HEp-2 cell adherence required EspA because hha espA and hha csgA espA mutants adhered to HEp-2 cells at higher levels only when complemented with an espA-expressing plasmid. Biofilm assays performed at 28°C in a medium lacking glucose showed dependency of biofilm formation on CsgA; however EspA was not produced under these conditions. Despite production of detectable levels of EspA at 37°C in media supplemented with 0.1% glucose, the biofilm formation occurred independent of EspA. These results indicate dependency of O157 adherence to epithelial cells on EspA filaments, while CsgA promoted biofilm formation under conditions mimicking those found in the environment (low temperature with nutrient limitations) and in the digestive tract of an host animal (higher temperature and low levels of glucose).

  12. Contributions of EspA Filaments and Curli Fimbriae in Cellular Adherence and Biofilm Formation of Enterohemorrhagic Escherichia coli O157:H7

    PubMed Central

    Sharma, Vijay K.; Kudva, Indira T.; Bearson, Bradley L.; Stasko, Judith A.

    2016-01-01

    In Escherichia coli O157:H7 (O157), the filamentous structure of the type III secretion system is produced from the polymerization of the EspA protein. EspA filaments are essential for O157 adherence to epithelial cells. In previous studies, we demonstrated that O157 hha deletion mutants showed increased adherence to HEp-2 cells and produced abundant biofilms. Transcriptional analysis revealed increased expression of espA as well as the csgA gene, which encodes curli fimbriae that are essential for biofilm formation. In the present study, we constructed hha espA, hha csgA, and hha csgA espA deletion mutants to determine the relative importance of EspA and CsgA in O157 adherence to HEp-2 cells and biofilm formation. In vitro adherence assays, conducted at 37°C in a tissue culture medium containing 0.1% glucose, showed that HEp-2 cell adherence required EspA because hha espA and hha csgA espA mutants adhered to HEp-2 cells at higher levels only when complemented with an espA-expressing plasmid. Biofilm assays performed at 28°C in a medium lacking glucose showed dependency of biofilm formation on CsgA; however EspA was not produced under these conditions. Despite production of detectable levels of EspA at 37°C in media supplemented with 0.1% glucose, the biofilm formation occurred independent of EspA. These results indicate dependency of O157 adherence to epithelial cells on EspA filaments, while CsgA promoted biofilm formation under conditions mimicking those found in the environment (low temperature with nutrient limitations) and in the digestive tract of an host animal (higher temperature and low levels of glucose). PMID:26900701

  13. Formation of copper porous structures under near-equilibrium chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Kornyushchenko, A. S.; Natalich, V. V.; Perekrestov, V. I.

    2016-05-01

    The mechanism of copper structure formation under near-equilibrium conditions in a chemically-active medium-condensate system has been investigated. The desired conditions have been implemented using CVD system. Copper chloride CuCl2 was used as a source material, and mixture of hydrogen with nitrogen served as a working gas. The influence of the evaporation temperature, condensation temperature and state of the growth surface on the porous structures formation has been investigated. It has been established, that the structure formation mechanism is determined by layer-by-layer or normal crystal growth, nucleation and growth of whiskers, and also by partial intergrowth of structural elements.

  14. Structure of modified ε-polylysine micelles and their application in improving cellular antioxidant activity of curcuminoids

    PubMed Central

    Yu, Hailong; Li, Ji; Shi, Ke; Huang, Qingrong

    2011-01-01

    The micelle structure of octenyl succinic anhydride modified ε-polylysine (M-EPL), an anti-microbial surfactant prepared from natural peptide ε-polylysine in aqueous solution has been studied using synchrotron small-angle X-ray scattering (SAXS). Our results revealed that M-EPLs formed spherical micelles with individual size of 24–26 Å in aqueous solution which could further aggregate to form a larger dimension with averaged radius of 268–308 Å. Furthermore, M-EPL micelle was able to encapsulate curcuminoids, a group of poorly-soluble bioactive compounds from turmeric with poor oral bioavailability, and improve their water solubility. Three loading methods, including solvent evaporation, dialysis, and high-speed homogenization were compared. The results indicated that the dialysis method generated the highest loading capacity and curcuminoids water solubility. The micelle encapsulation was confirmed as there were no free curcuminoid crystals detected in the differential scanning calorimetry analysis. It was also demonstrated that M-EPL encapsulation stabilized curcuminoids against hydrolysis at pH 7.4 and the encapsulated curcuminoids showed elevated cellular antioxidant activity compared with free curcuminoids. This work suggested that M-EPL could be used as new biopolymer micelles for delivering poorly soluble drugs/phytochemicals and improving their bioactivities. PMID:21894323

  15. Structure of modified [epsilon]-polylysine micelles and their application in improving cellular antioxidant activity of curcuminoids

    SciTech Connect

    Yu, Hailong; Li, Ji; Shi, Ke; Huang, Qingrong

    2015-10-15

    The micelle structure of octenyl succinic anhydride modified {var_epsilon}-polylysine (M-EPL), an anti-microbial surfactant prepared from natural peptide {var_epsilon}-polylysine in aqueous solution has been studied using synchrotron small-angle X-ray scattering (SAXS). Our results revealed that M-EPLs formed spherical micelles with individual size of 24-26 {angstrom} in aqueous solution which could further aggregate to form a larger dimension with averaged radius of 268-308 {angstrom}. Furthermore, M-EPL micelle was able to encapsulate curcuminoids, a group of poorly-soluble bioactive compounds from turmeric with poor oral bioavailability, and improve their water solubility. Three loading methods, including solvent evaporation, dialysis, and high-speed homogenization were compared. The results indicated that the dialysis method generated the highest loading capacity and curcuminoids water solubility. The micelle encapsulation was confirmed as there were no free curcuminoid crystals detected in the differential scanning calorimetry analysis. It was also demonstrated that M-EPL encapsulation stabilized curcuminoids against hydrolysis at pH 7.4 and the encapsulated curcuminoids showed elevated cellular antioxidant activity compared with free curcuminoids. This work suggested that M-EPL could be used as new biopolymer micelles for delivering poorly soluble drugs/phytochemicals and improving their bioactivities.

  16. Laser-induced structure formation on stretched polymer foils

    SciTech Connect

    Bityurin, Nikita; Arnold, Nikita; Baeuerle, Dieter; Arenholz, Enno

    2007-04-15

    Noncoherent structures that develop during UV laser ablation of stretched semicrystalline polymer foils are a very general phenomenon. A thermodynamic model based on stress relaxation within the modified layer of the polymer surface describes the main features of the observed phenomena, and, in particular, the dependence of the period of structures on laser wavelength, fluence, and number of laser pulses.

  17. BOOK REVIEW: Transport and Structural Formation in Plasmas

    NASA Astrophysics Data System (ADS)

    Thyagaraja, A.

    1999-06-01

    The book under review is one of a series of monographs on plasma physics published by the Institute of Physics under the editorship of Peter Stott and Hans Wilhelmsson. It is nicely produced and is aimed at research workers and advanced students of both laboratory (i.e. tokamak plasmas) and astrophysical plasma physics. The authors are prolific contributors to the subject of plasma turbulence and transport with a well-defined message: ``The authors' view is that the plasma structure, fluctuations and turbulent transport are continually regulating each other and, in addition, that the structural formation and structural transition of plasmas are typical of the physics of far from equilibrium systems. The book presents and explains why the plasma inhomogeneity is the ordering parameter governing transport and how self-sustained fluctuations can be driven through subcritical excitation even beyond linear instability''. This point of view is expounded in 24 chapters, including topics such as transport phenomena in toroidal plasmas (Chapters 2-4), low frequency modes and instabilities of confined systems (Chapters 5-7), renormalization (Chapter 8), self-sustained turbulence due to the current diffusive mode and resistive effects (Chapters 9-11), subcritical turbulence and numerical simulations (Chapters 12-14), scale invariance arguments (Chapter 15), electric field effects (Chapters 17-21) and self-organized dynamics (Chapter 22). The material is essentially drawn from the authors' many and varied original contributions to the plasma turbulence and transport literature. Whatever view one might have about the merits of this work, there is little doubt in this reviewer's mind that it is indeed thought-provoking and presents a worthy intellectual challenge to plasma theorists and experimentalists alike. The authors take a consistent stance and discuss the issues from their own standpoint. They observe that the plasmas one encounters in practice (for definiteness, the

  18. Interconnection of Salt-induced Hydrophobic Compaction and Secondary Structure Formation Depends on Solution Conditions

    PubMed Central

    Haldar, Shubhasis; Chattopadhyay, Krishnananda

    2012-01-01

    What happens in the early stage of protein folding remains an interesting unsolved problem. Rapid kinetics measurements with cytochrome c using submillisecond continuous flow mixing devices suggest simultaneous formation of a compact collapsed state and secondary structure. These data seem to indicate that collapse formation is guided by specific short and long range interactions (heteropolymer collapse). A contrasting interpretation also has been proposed, which suggests that the collapse formation is rapid, nonspecific, and a trivial solvent related compaction, which could as well be observed by a homopolymer (homopolymer collapse). We address this controversy using fluorescence correlation spectroscopy (FCS), which enables us to monitor the salt-induced compaction accompanying collapse formation and the associated time constant directly at single molecule resolution. In addition, we follow the formation of secondary structure using far UV CD. The data presented here suggest that both these models (homopolymer and heteropolymer) could be applicable depending on the solution conditions. For example, the formation of secondary structure and compact state is not simultaneous in aqueous buffer. In aqueous buffer, formation of the compact state occurs through a two-state co-operative transition following heteropolymer formalism, whereas secondary structure formation takes place gradually. In contrast, in the presence of urea, a compaction of the protein radius occurs gradually over an extended range of salt concentration following homopolymer formalism. The salt-induced compaction and the formation of secondary structure take place simultaneously in the presence of urea. PMID:22303014

  19. An exploratory study of high school students' conceptions of atomic and cellular structure and the relationship between atoms and cells

    NASA Astrophysics Data System (ADS)

    Roland, Elizabeth Anne Edwards

    . Many limitations related to this study suggest that results should not be generalized beyond the targeted population. KEYWORDS: Interdisciplinary, Non-scientific Conceptions, Atomic Structure, Cellular Structure, High School Science Education

  20. Formation of Surface Corrosion-Resistant Nanocrystalline Structures on Steel.

    PubMed

    Nykyforchyn, Hryhoriy; Kyryliv, Volodymyr; Maksymiv, Olha; Slobodyan, Zvenomyra; Tsyrulnyk, Oleksandr

    2016-12-01

    Engineering materials with nanocrystalline structure could be exploited under simultaneous action of mechanical loading and corrosion environments; therefore, their corrosion resistance is important. Surface nanocrystalline structure was generated on middle carbon steels by severe plastic deformation using the method of mechanical pulse friction treatment. This treatment additionally includes high temperature phase transformation and alloying. Using a complex of the corrosive, electrochemical and physical investigations, it was established that nanocrystalline structures can be characterized by lower or increased corrosion resistance in comparison with the reference material. It is caused by the action of two confronting factors: arising energy level and anticorrosive alloying of the surface layer.

  1. Formation of Surface Corrosion-Resistant Nanocrystalline Structures on Steel.

    PubMed

    Nykyforchyn, Hryhoriy; Kyryliv, Volodymyr; Maksymiv, Olha; Slobodyan, Zvenomyra; Tsyrulnyk, Oleksandr

    2016-12-01

    Engineering materials with nanocrystalline structure could be exploited under simultaneous action of mechanical loading and corrosion environments; therefore, their corrosion resistance is important. Surface nanocrystalline structure was generated on middle carbon steels by severe plastic deformation using the method of mechanical pulse friction treatment. This treatment additionally includes high temperature phase transformation and alloying. Using a complex of the corrosive, electrochemical and physical investigations, it was established that nanocrystalline structures can be characterized by lower or increased corrosion resistance in comparison with the reference material. It is caused by the action of two confronting factors: arising energy level and anticorrosive alloying of the surface layer. PMID:26831689

  2. Formation of Surface Corrosion-Resistant Nanocrystalline Structures on Steel

    NASA Astrophysics Data System (ADS)

    Nykyforchyn, Hryhoriy; Kyryliv, Volodymyr; Maksymiv, Olha; Slobodyan, Zvenomyra; Tsyrulnyk, Oleksandr

    2016-02-01

    Engineering materials with nanocrystalline structure could be exploited under simultaneous action of mechanical loading and corrosion environments; therefore, their corrosion resistance is important. Surface nanocrystalline structure was generated on middle carbon steels by severe plastic deformation using the method of mechanical pulse friction treatment. This treatment additionally includes high temperature phase transformation and alloying. Using a complex of the corrosive, electrochemical and physical investigations, it was established that nanocrystalline structures can be characterized by lower or increased corrosion resistance in comparison with the reference material. It is caused by the action of two confronting factors: arising energy level and anticorrosive alloying of the surface layer.

  3. Energy minimization for self-organized structure formation and actuation

    NASA Astrophysics Data System (ADS)

    Kofod, Guggi; Wirges, Werner; Paajanen, Mika; Bauer, Siegfried

    2007-02-01

    An approach for creating complex structures with embedded actuation in planar manufacturing steps is presented. Self-organization and energy minimization are central to this approach, illustrated with a model based on minimization of the hyperelastic free energy strain function of a stretched elastomer and the bending elastic energy of a plastic frame. A tulip-shaped gripper structure illustrates the technological potential of the approach. Advantages are simplicity of manufacture, complexity of final structures, and the ease with which any electroactive material can be exploited as means of actuation.

  4. FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.

    PubMed

    Bose, Tungadri; Dutta, Anirban; Mh, Mohammed; Gandhi, Hemang; Mande, Sharmila S

    2015-09-01

    Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

  5. STRUCTURE AND FORMATION OF ELLIPTICAL AND SPHEROIDAL GALAXIES

    SciTech Connect

    Kormendy, John; Fisher, David B.; Cornell, Mark E.; Bender, Ralf E-mail: dbfisher@astro.as.utexas.edu E-mail: bender@usm.uni-muenchen.de

    2009-05-15

    New surface photometry of all known elliptical galaxies in the Virgo cluster is combined with published data to derive composite profiles of brightness, ellipticity, position angle, isophote shape, and color over large radius ranges. These provide enough leverage to show that Sersic log I {proportional_to} r {sup 1/n} functions fit the brightness profiles I(r) of nearly all ellipticals remarkably well over large dynamic ranges. Therefore, we can confidently identify departures from these profiles that are diagnostic of galaxy formation. Two kinds of departures are seen at small radii. All 10 of our ellipticals with total absolute magnitudes M{sub VT} {<=} -21.66 have cuspy cores-'missing light'-at small radii. Cores are well known and naturally scoured by binary black holes (BHs) formed in dissipationless ('dry') mergers. All 17 ellipticals with -21.54 {<=} M{sub VT} {<=} -15.53 do not have cores. We find a new distinct component in these galaxies: all coreless ellipticals in our sample have extra light at the center above the inward extrapolation of the outer Sersic profile. In large ellipticals, the excess light is spatially resolved and resembles the central components predicted in numerical simulations of mergers of galaxies that contain gas. In the simulations, the gas dissipates, falls toward the center, undergoes a starburst, and builds a compact stellar component that, as in our observations, is distinct from the Sersic-function main body of the elliptical. But ellipticals with extra light also contain supermassive BHs. We suggest that the starburst has swamped core scouring by binary BHs. That is, we interpret extra light components as a signature of formation in dissipative ('wet') mergers. Besides extra light, we find three new aspects to the ('E-E') dichotomy into two types of elliptical galaxies. Core galaxies are known to be slowly rotating, to have relatively anisotropic velocity distributions, and to have boxy isophotes. We show that they have

  6. Block-copolymer-induced structure formation in microemulsions

    SciTech Connect

    Hilfiker, R.; Eicke, H.F.; Steeb, C.; Hofmeier, U. )

    1991-02-07

    Transient electric birefringence measurements were performed on water/AOT (sodium bis(2-ethylhexyl) sulfosuccinate)/isooctane microemulsions with various amounts of block-copoly(oxyethylene/isoprene/oxyethylene) added. The authors could show that addition of the copolymer leads to a formation of nanodroplet (ND)-copolymer-aggregates. The contributions of NDs and aggregates to the induced birefringence could easily be separated because the NDs exhibited a negative and the aggregates a positive induced birefringence and because the time scales corresponding to the two processes were different.

  7. Note on structure formation from cosmic string wakes

    SciTech Connect

    Duplessis, Francis; Brandenberger, Robert E-mail: rhb@physics.mcgill.ca

    2013-04-01

    The search for cosmic strings has been of renewed interest with the advent of precision cosmology. In this note we give a quantitative description of the nonlinear matter density fluctuations that can form from a scaling network of cosmic string wakes. Specifically, we compute the distribution of dark matter halos. These halos would possess strong correlations in position space that should have survived until today. We also discuss the challenges involved in their detection due to their small size and the complex dynamics of their formation.

  8. Learning the 3-D structure of objects from 2-D views depends on shape, not format

    PubMed Central

    Tian, Moqian; Yamins, Daniel; Grill-Spector, Kalanit

    2016-01-01

    Humans can learn to recognize new objects just from observing example views. However, it is unknown what structural information enables this learning. To address this question, we manipulated the amount of structural information given to subjects during unsupervised learning by varying the format of the trained views. We then tested how format affected participants' ability to discriminate similar objects across views that were rotated 90° apart. We found that, after training, participants' performance increased and generalized to new views in the same format. Surprisingly, the improvement was similar across line drawings, shape from shading, and shape from shading + stereo even though the latter two formats provide richer depth information compared to line drawings. In contrast, participants' improvement was significantly lower when training used silhouettes, suggesting that silhouettes do not have enough information to generate a robust 3-D structure. To test whether the learned object representations were format-specific or format-invariant, we examined if learning novel objects from example views transfers across formats. We found that learning objects from example line drawings transferred to shape from shading and vice versa. These results have important implications for theories of object recognition because they suggest that (a) learning the 3-D structure of objects does not require rich structural cues during training as long as shape information of internal and external features is provided and (b) learning generates shape-based object representations independent of the training format. PMID:27153196

  9. Formation and structural characteristics of thermosensitive multiblock copolymer vesicles.

    PubMed

    Ma, Shiying; Xiao, Mengying; Wang, Rong

    2013-12-23

    The spontaneous vesicle formation of ABABA-type amphiphilic multiblock copolymers bearing thermosensitive hydrophilic A-block in a selective solvent is studied using dissipative particle dynamics (DPD) approach. The formation process of vesicle through nucleation and growth pathway is observed by varying the temperature. The simulation results show that spherical micelle takes shape at high temperature. As temperature decreases, vesicles with small aqueous cavity appear and the cavity expands as well as the membrane thickness decreases with the temperature further decreasing. This finding is in agreement with the experimental observation. Furthermore, by continuously varying the temperature and the length of the hydrophobic block, a phase diagram is constructed, which can indicate the thermodynamically stable region for vesicles. The morphological phase diagram shows that vesicles can form in a larger parameter scope. The relationship between the hydrophilic and hydrophobic block length versus the aqueous cavity size and vesicle size are revealed. Simulation results demonstrate that the copolymers with shorter hydrophobic blocks length or the higher hydrophilicity are more likely to form vesicles with larger aqueous cavity size and vesicle size as well as thinner wall thickness. However, the increase in A-block length results to form vesicles with smaller aqueous cavity size and larger vesicle size. PMID:24304193

  10. Processes of ordered structure formation in polypeptide thin film solutions.

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G.

    2010-06-17

    An experimental study is presented on the hierarchical assembly of {alpha}-helical block copolymers polystyrene-poly({gamma}-benzyl-L-glutamate) into anisotropic ordered structures. We transformed thin solid films into solutions through exposure to solvent vapor and studied the nucleation and growth of ordered three-dimensional structures in such solutions, with emphasis on the dependence of these processes on supersaturation with respect to the solubility limit. Interestingly, polymer solubility could be significantly influenced via variation of humidity in the surrounding gas phase. It is concluded that the interfacial tension between the ordered structures and the solution increased with humidity. The same effect was observed for other protic non-solvents in the surrounding gas phase and is attributed to a complexation of poly({gamma}-benzyl-L-glutamate) by protic non-solvent molecules (via hydrogen-bonding interactions). This change of polymer solubility was demonstrated to be reversible by addition or removal of small amounts of protic non-solvent in the surrounding gas phase. At a constant polymer concentration, ordered ellipsoidal structures could be dissolved by removing water or methanol present in the solution. Such structures formed once again when water or methanol was reintroduced via the vapor phase.

  11. Formation of micro/nano structures out of soap bubbles

    NASA Astrophysics Data System (ADS)

    Bai, Xiao-Dan; Liu, Jing

    2007-07-01

    We proposed to synthesize, etch and construct micro/nano structures through manipulating the large-scale bubbles composed of specific chemical compounds. The core of the method lies in the chemical reaction occurred at the interfaces between two or more soap bubbles. A unique virtue of the bubble is that it can have a rather large diameter however an extremely small membrane thickness, whose smallest size could reach nano scale. Therefore, the chemical reaction and synthesis occurred in the common interface of such contacting bubbles would lead to products with very small size. Several typical micro structures were fabricated to demonstrate the feasibility of the new method. Being flexible, easily controllable and environment friendly, the present concept may open a straightforward low-cost way for making micro/nano structures.

  12. Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

    PubMed Central

    Braun, Hans-Georg; Meyer, Evelyn

    2013-01-01

    The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm) result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

  13. How chemistry influences cloud structure, star formation, and the IMF

    NASA Astrophysics Data System (ADS)

    Hocuk, S.; Cazaux, S.; Spaans, M.; Caselli, P.

    2016-03-01

    In the earliest phases of star-forming clouds, stable molecular species, such as CO, are important coolants in the gas phase. Depletion of these molecules on dust surfaces affects the thermal balance of molecular clouds and with that their whole evolution. For the first time, we study the effect of grain surface chemistry (GSC) on star formation and its impact on the initial mass function (IMF). We follow a contracting translucent cloud in which we treat the gas-grain chemical interplay in detail, including the process of freeze-out. We perform 3D hydrodynamical simulations under three different conditions, a pure gas-phase model, a freeze-out model, and a complete chemistry model. The models display different thermal evolution during cloud collapse as also indicated in Hocuk, Cazaux & Spaans, but to a lesser degree because of a different dust temperature treatment, which is more accurate for cloud cores. The equation of state (EOS) of the gas becomes softer with CO freeze-out and the results show that at the onset of star formation, the cloud retains its evolution history such that the number of formed stars differ (by 7 per cent) between the three models. While the stellar mass distribution results in a different IMF when we consider pure freeze-out, with the complete treatment of the GSC, the divergence from a pure gas-phase model is minimal. We find that the impact of freeze-out is balanced by the non-thermal processes; chemical and photodesorption. We also find an average filament width of 0.12 pc (±0.03 pc), and speculate that this may be a result from the changes in the EOS caused by the gas-dust thermal coupling. We conclude that GSC plays a big role in the chemical composition of molecular clouds and that surface processes are needed to accurately interpret observations, however, that GSC does not have a significant impact as far as star formation and the IMF is concerned.

  14. Formation of the internal structure of solids under severe load.

    PubMed

    Metlov, Leonid S

    2010-05-01

    An alternative form of kinetic equations, involving the internal and free energies symmetrically, has been derived in the framework of the theory of vacancies. Dynamical nature of irreversible phenomena during formation and motion of defects (dislocations) has been analyzed by a computer experiment. Results of this simulation are then extended into a thermodynamic identity, involving the law of conservation of energy at interaction with an environment (the first law of thermodynamics) and the law of energy transformation in the internal degrees of freedom (relaxation). This identity is compared to the analogous Jarzynski identity. The approach is illustrated by simulation of processes during severe plastic deformation; the Rybin kinetic equation for this case has been derived.

  15. Turbulence and Vorticity in Galaxy Clusters Generated by Structure Formation

    NASA Astrophysics Data System (ADS)

    Vazza, F.; Jones, T. W.; Brüggen, M.; Brunetti, G.; Gheller, C.; Porter, D.; Ryu, D.

    2016-09-01

    Turbulence is a key ingredient for the evolution of the intracluster medium, whose properties can be predicted with high resolution numerical simulations. We present initial results on the generation of solenoidal and compressive turbulence in the intracluster medium during the formation of a small-size cluster using highly resolved, non-radiative cosmological simulations, with a refined monitoring in time. In this first of a series of papers, we closely look at one simulated cluster whose formation was distinguished by a merger around z ˜ 0.3. We separate laminar gas motions, turbulence and shocks with dedicated filtering strategies and distinguish the solenoidal and compressive components of the gas flows using Hodge-Helmholtz decomposition. Solenoidal turbulence dominates the dissipation of turbulent motions (˜95%) in the central cluster volume at all epochs. The dissipation via compressive modes is found to be more important (˜30% of the total) only at large radii (≥0.5~rvir) and close to merger events. We show that enstrophy (vorticity squared) is good proxy of solenoidal turbulence. All terms ruling the evolution of enstrophy (i.e. baroclinic, compressive, stretching and advective terms) are found to be significant, but in amounts that vary with time and location. Two important trends for the growth of enstrophy in our simulation are identified: first, enstrophy is continuously accreted into the cluster from the outside, and most of that accreted enstrophy is generated near the outer accretion shocks by baroclinic and compressive processes. Second, in the cluster interior vortex stretching is dominant, although the other terms also contribute substantially.

  16. Microstructure of polycrystalline PBTTT films: domain mapping and structure formation.

    PubMed

    Schuettfort, Torben; Watts, Benjamin; Thomsen, Lars; Lee, Mijung; Sirringhaus, Henning; McNeill, Christopher R

    2012-02-28

    We utilize near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and scanning transmission X-ray microscopy (STXM) to study the microstructure and domain structure of polycrystalline films of the semiconducting polymer poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). Total electron yield NEXAFS spectroscopy is used to examine the surface structure of the first 1-2 molecular layers, while bulk-sensitive STXM is used to produce maps of domain orientation and order sampled through the entire film thickness. We study different phases of PBTTT including as-cast, terraced and nanoribbon morphologies produced via spin-coating as well as aligned films of as-cast and nanoribbon morphologies produced by zone-casting. For the terraced morphology, domains are observed that are larger than the size of the terraced surface features, and the calculated degree of order is reduced compared to the nanoribbon morphology. For zone-cast films, we find that, although little optical anisotropy is observed in the bulk of as-cast films, a high degree of surface structural anisotropy is observed with NEXAFS spectroscopy, similar to what is observed in annealed nanoribbon films. This observation indicates that the aligned surface structure in unannealed zone-cast films templates the bulk ordering of the aligned nanoribbon phase. STXM domain mapping of aligned nanoribbon films reveals elongated, micrometer-wide domains with each domain misoriented with respect to its neighbor by up to 45°, but with broad domain boundaries. Within each nanoribbon domain, a high degree of X-ray dichroism is observed, indicating correlated ordering throughout the bulk of the film.

  17. Structural Insights into Clostridium perfringens Delta Toxin Pore Formation

    PubMed Central

    Huyet, Jessica; Naylor, Claire E.; Savva, Christos G.; Gibert, Maryse; Popoff, Michel R.; Basak, Ajit K.

    2013-01-01

    Clostridium perfringens Delta toxin is one of the three hemolysin-like proteins produced by C. perfringens type C and possibly type B strains. One of the others, NetB, has been shown to be the major cause of Avian Nectrotic Enteritis, which following the reduction in use of antibiotics as growth promoters, has become an emerging disease of industrial poultry. Delta toxin itself is cytotoxic to the wide range of human and animal macrophages and platelets that present GM2 ganglioside on their membranes. It has sequence similarity with Staphylococcus aureus β-pore forming toxins and is expected to heptamerize and form pores in the lipid bilayer of host cell membranes. Nevertheless, its exact mode of action remains undetermined. Here we report the 2.4 Å crystal structure of monomeric Delta toxin. The superposition of this structure with the structure of the phospholipid-bound F component of S. aureus leucocidin (LukF) revealed that the glycerol molecules bound to Delta toxin and the phospholipids in LukF are accommodated in the same hydrophobic clefts, corresponding to where the toxin is expected to latch onto the membrane, though the binding sites show significant differences. From structure-based sequence alignment with the known structure of staphylococcal α-hemolysin, a model of the Delta toxin pore form has been built. Using electron microscopy, we have validated our model and characterized the Delta toxin pore on liposomes. These results highlight both similarities and differences in the mechanism of Delta toxin (and by extension NetB) cytotoxicity from that of the staphylococcal pore-forming toxins. PMID:23805259

  18. Unconstrained Structure Formation in Coarse-Grained Protein Simulations

    NASA Astrophysics Data System (ADS)

    Bereau, Tristan

    The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid

  19. Structure formation in a nonlocally modified gravity model

    SciTech Connect

    Park, Sohyun; Dodelson, Scott

    2013-01-01

    We study a nonlocally modified gravity model proposed by Deser and Woodard which gives an explanation for current cosmic acceleration. By deriving and solving the equations governing the evolution of the structure in the Universe, we show that this model predicts a pattern of growth that differs from standard general relativity (+dark energy) at the 10-30% level. These differences will be easily probed by the next generation of galaxy surveys, so the model should be tested shortly.

  20. Vortex ring structure at late stages of formation

    SciTech Connect

    Fabris, D.; Liepmann, D.

    1997-09-01

    High resolution DPIV measurements are made of a vortex ring formed by a piston/cylinder mechanism (Reynolds number 3700 and 7500). A complex ring structure is identified. The stopping condition of the piston leads to vortical fluid collecting near the forward stagnation point of the ring. In addition, the roll-up of the core produces a vorticity distribution that departs from a simple Gaussian profile. {copyright} {ital 1997 American Institute of Physics.}

  1. Investigation of hierarchical structure formation in ceramics with invar effect

    NASA Astrophysics Data System (ADS)

    Dedova, Elena S.; Shadrin, Vladimir S.; Shutilova, Ekaterina S.; Kulkov, Sergei N.

    2015-10-01

    The structure, phase composition and thermal properties of (Al2O3-20 wt % ZrO2)-ZrW2O8 ceramic composites obtained using nanosized, finely dispersed and coarse-grained initial powders were investigated. On the polished surface of composites homogeneously distributed white particles were observed. The chemical composition of the particles was determined. The phase composition of the composites was represented with corundum, monoclinic ZrO2 and two modifications of ZrW2O8 (tetragonal and cubic) regardless of initial powders morphology. Crystal structure parameters of the material obtained were determined. Linear thermal expansion coefficient values of the composites were determined and compared with those calculated using the mixture rule. The experimental data correlated well with the calculated values of CTE for Al2O3-20 wt % ZrO2 ceramics. The difference in thermal expansion values for composites obtained using initial components with different morphology may be attributed to phase transformations, features of hierarchical structures, internal stresses due to thermal expansion mismatch, which contribute significantly to thermal expansion of the ceramic composites.

  2. Dynamically-induced structures formation in congested magma

    NASA Astrophysics Data System (ADS)

    Petford, N.

    2008-12-01

    Crystal fabrics preserved in igneous rocks offer a glimpse into the magma emplacement process. Detailed field mapping, in combination with AMS studies, seem to provide the best available data for unravelling intrusion architecture on the decimetre scale. However, a full and proper understanding of the fluid dynamics of congested fluid-particle mixtures during shear remains elusive. This is a shame as without recourse to such fundamental understanding, the interpretation of structural field data in the context of magma flow remains problematic. One way to gain insight into the process is to treat flowing magma as a dynamic material with a rheology similar to sheared, congested slurries. The fancy that dense magma equates to a high temperature slurry is an attractive one, and opens up a way to examine the emplacement process that does not rely exclusively on equilibrium thermodynamics as a final explanation of commonly observed igneous structures. Instead, using examples from mafic rocks where cooling has been rapid, the idea is put forward that in high Peclet number suspensions (where particle diffusion is negligible), shearing and non- Newtonian behaviour imparts a rich diversity of structures including layering, grading and flow segregation. Key to understanding the rheology, hence flow dynamics of congested magma, is the particle microstructure, a still poorly known essence of suspension flows. Where magma transport is continental in scale and long lived (e.g. Large Igneous Provinces), rotation of the earth may in theory endow a small but potentially measurable imprint on the preserved flow fabric.

  3. Imaging of fine structures of cellular organelles in hydrated biological cells by a soft x-ray microscope combined with a fluorescence microscope

    NASA Astrophysics Data System (ADS)

    Kado, Masataka; Kishimoto, Maki; Tamotsu, Satoshi; Yasuda, Keiko; Aoyama, Masato; Shinohara, Kunio

    2013-09-01

    We have proposed and developed a new hybrid microscopy system using a soft x-ray microscope and a fluorescence microscope imaging the same biological cells at the nearly same time. Combining the powerful advantages such as high spatial resolution of the soft x-ray microscope and the accurate organelle identification of the fluorescence microscope, we can observe fine structures of the cellular organelles in live hydrated biological cells in situ. Staining the cells with several fluorescent dyes such as Mito-tracker, Phalloidin, and DAPI, the soft x-ray images of the cells have been directly compared with the fluorescent images and the cellular organelles such as mitochondria, actin filaments, and chromosomes in the soft x-ray images have been clearly identified. Since the soft x-ray microscope has higher spatial resolution than that of the fluorescence microscope, not only shape of the cellular organelles but also the fine structures of the cellular organelles of the live biological cells have been clearly observed for the first time.

  4. Structural ensembles of the north belt of Venus deformations and possible mechanisms of their formation

    NASA Technical Reports Server (NTRS)

    Markov, M. S.

    1986-01-01

    The author discusses structural formations in the northern deformation belt of Venus, studied according to the data of the radar pictures obtained with the Venera 15 and 16 probes. He shows that it consists of regions of compression with submeridional orientation, regions of displacement, extending in the sublatitudinal direction and individual slightly deformed blocks. He puts forward the hypothesis that the formation of these structures is related with horizontal movements in the mantle in the sublatitudinal direction.

  5. Foreign body impact event damage formation in composite structures

    NASA Technical Reports Server (NTRS)

    Bucinell, Ronald B.

    1994-01-01

    This report discusses a methodology that can be used to assess the effect of foreign body impacts on composite structural integrity. The described effort focuses on modeling the effect of a central impact on a 5 3/4 inch filament wound test article. The discussion will commence with details of the material modeling that was used to establish the input properties for the analytical model. This discussion is followed by an overview of the impact assessment methodology. The progress on this effort to date is reviewed along with a discussion of tasks that have yet to be completed.

  6. Disentangling effects of nuclear structure in heavy element formation.

    PubMed

    Hinde, D J; Thomas, R G; du Rietz, R; Diaz-Torres, A; Dasgupta, M; Brown, M L; Evers, M; Gasques, L R; Rafiei, R; Rodriguez, M D

    2008-05-23

    Forming the same heavy compound nucleus with different isotopes of the projectile and target elements allows nuclear structure effects in the entrance channel (resulting in static deformation) and in the dinuclear system to be disentangled. Using three isotopes of Ti and W, forming 232Cm, with measurement spanning the capture barrier energies, alignment of the heavy prolate deformed nucleus is shown to be the main reason for the broadening of the mass distribution of the quasifission fragments as the beam energy is reduced. The complex, consistently evolving mass-angle correlations that are observed carry more information than the integrated mass or angular distributions, and should severely test models of quasifission.

  7. Disentangling Effects of Nuclear Structure in Heavy Element Formation

    SciTech Connect

    Hinde, D. J.; Thomas, R. G.; Rietz, R. du; Diaz-Torres, A.; Dasgupta, M.; Brown, M. L.; Evers, M.; Gasques, L. R.; Rafiei, R.; Rodriguez, M. D.

    2008-05-23

    Forming the same heavy compound nucleus with different isotopes of the projectile and target elements allows nuclear structure effects in the entrance channel (resulting in static deformation) and in the dinuclear system to be disentangled. Using three isotopes of Ti and W, forming {sup 232}Cm, with measurement spanning the capture barrier energies, alignment of the heavy prolate deformed nucleus is shown to be the main reason for the broadening of the mass distribution of the quasifission fragments as the beam energy is reduced. The complex, consistently evolving mass-angle correlations that are observed carry more information than the integrated mass or angular distributions, and should severely test models of quasifission.

  8. Simulations of the formation of large-scale structure

    NASA Astrophysics Data System (ADS)

    White, S. D. M.

    Numerical studies related to the simulation of structure growth are examined. The linear development of fluctuations in the early universe is studied. The research of Aarseth, Gott, and Turner (1979) based on N-body integrators that obtained particle accelerations by direct summation of the forces due to other objects is discussed. Consideration is given to the 'pancake theory' of Zel'dovich (1970) for the evolution from adiabatic initial fluctuation, the neutrino-dominated universe models of White, Frenk, and Davis (1983), and the simulations of Davis et al. (1985).

  9. Modelling the structural controls of primary kaolinite formation

    NASA Astrophysics Data System (ADS)

    Tierney, R. L.; Glass, H. J.

    2016-09-01

    An abundance of kaolinite was formed within the St. Austell outcrop of the Cornubian batholith in Cornwall, southwest England, by the hydrous dissolution of feldspar crystals. The permeability of Cornish granites is low and alteration acts pervasively from discontinuity features, with montmorillonite recognised as an intermediate assemblage in partially kaolinised material. Structural features allowed fluids to channel through the impermeable granite and pervade deep into the rock. Areas of high structural control are hypothesised to link well with areas of advanced alteration. As kaolinisation results in a loss of competence, we present a method of utilising discontinuity orientations from nearby unaltered granites alongside the local tectonic history to calculate strain rates and delineate a discrete fracture network. Simulation of the discrete fracture network is demonstrated through a case study at Higher Moor, where kaolinite is actively extracted from a pit. Reconciliation of fracture connectivity and permeability against measured subsurface data show that higher values of modelled properties match with advanced kaolinisation observed in the field. This suggests that the technique may be applicable across various industries and disciplines.

  10. Dynamics of structure formation in crystallizable block copolymers

    SciTech Connect

    Rangarajan, P.; Register, R.A.; Adamson, D.H.

    1995-12-31

    Isothermal crystallization of polyolefin diblock copolymers from homogeneous and weakly segregated melts has been tracked using simultaneous, synchrotron-based small and wide-angle x-ray scattering (SAXS and WAXS). The polymers are prepared by hydrogenating polydiene diblocks, and contain crystallizable polyethylene ({open_quotes}E{close_quotes}; hydrogenated high 1,4-polybutadiene) blocks and a variety of amorphous polyolefin blocks. All polymers exhibit a well-ordered lamellar morphology at room temperature, as evidenced by 2-3 clear SAXS reflections, even for compositions containing as little as 12% E. In polymers crystallizing from homogeneous melts, the WAXS reflections from the E crystallites grow in parallel with the 3-4 SAXS reflections, so microphase separation is driven by crystallization. These structures, which are reminiscent of strong segregation (as indicated by the multiple SAXS reflections), are obtained by cooling only 20{degrees}C below the melting point. For a polymer having a weakly segregated melt, crystallization eradicates the melt morphology, but larger domain spacings were observed for higher crystallization temperatures, unlike the path-independent values obtained on crystallization from single-phase melts, suggesting that melt segregation hinders the development of the equilibrium crystallization-driven structure.

  11. Minimal continuum theories of structure formation in dense active fluids

    NASA Astrophysics Data System (ADS)

    Dunkel, Jörn; Heidenreich, Sebastian; Bär, Markus; Goldstein, Raymond E.

    2013-04-01

    Self-sustained dynamical phases of living matter can exhibit remarkable similarities over a wide range of scales, from mesoscopic vortex structures in microbial suspensions and motility assays of biopolymers to turbulent large-scale instabilities in flocks of birds or schools of fish. Here, we argue that, in many cases, the phenomenology of such active states can be efficiently described in terms of fourth- and higher-order partial differential equations. Structural transitions in these models can be interpreted as Landau-type kinematic transitions in Fourier (wavenumber) space, suggesting that microscopically different biological systems can share universal long-wavelength features. This general idea is illustrated through numerical simulations for two classes of continuum models for incompressible active fluids: a Swift-Hohenberg-type scalar field theory, and a minimal vector model that extends the classical Toner-Tu theory and appears to be a promising candidate for the quantitative description of dense bacterial suspensions. We discuss how microscopic symmetry-breaking mechanisms can enter macroscopic continuum descriptions of collective microbial motion near surfaces, and conclude by outlining future applications.

  12. Two-cell detonation: losses effects on cellular structure and propagation in rich H2-NO2/N2O4-Ar mixtures

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    Detonation experiments in H2-NO2/N2O4-Ar mixtures (Equivalence ratio 1.2 and initial pressure lower than 0.1 MPa) confined in a tube of internal diameter 52 mm reveal two propagation regimes depending on initial pressure: (1) a quasi-CJ regime is observed along with a double cellular structure at high pressures; (2) at lower pressures, a low velocity detonation regime is observed with a single structure. Transition between this two regimes happens when the spinning detonation of the larger cell vanishes. Each detonation regime is characterized by velocity and pressure measurements and cellular structure records. Coherence between all experimental data for each experiment leads in assumption that losses are responsible for the transition between one regime to another. In a second part, we study such behaviour for a two-step mixture through numerical simulations using a global two-step chemical kinetics and a simple losses model. Numerical simulations qualitatively agree with experiments. Both detonation regimes with their own cellular structures are reproduced.

  13. Formation of 2D nanoparticles with block structure in simultaneous electric explosion of conductors

    SciTech Connect

    Kryzhevich, Dmitrij S. E-mail: kost@ispms.ru; Zolnikov, Konstantin P. E-mail: kost@ispms.ru; Abdrashitov, Andrei V.; Lerner, Marat I.; Psakhie, Sergey G.

    2014-11-14

    A molecular dynamics simulation of nanoparticle formation in simultaneous electric explosion of conductors is performed. Interatomic interaction is described using potentials calculated in the framework of the embedded atom method. High-rate heating results in failure of the conductors with the formation of nanoparticles. The influence of the heating rate, temperature distribution over the specimen cross-section and the distance between simultaneously exploded conductors on the structure of formed nanoparticles is studied. The calculation results show that the electric explosion of conductors allows the formation of nanoparticles with block structure.

  14. Distributed attitude synchronization of formation flying via consensus-based virtual structure

    NASA Astrophysics Data System (ADS)

    Cong, Bing-Long; Liu, Xiang-Dong; Chen, Zhen

    2011-06-01

    This paper presents a general framework for synchronized multiple spacecraft rotations via consensus-based virtual structure. In this framework, attitude control systems for formation spacecrafts and virtual structure are designed separately. Both parametric uncertainty and external disturbance are taken into account. A time-varying sliding mode control (TVSMC) algorithm is designed to improve the robustness of the actual attitude control system. As for the virtual attitude control system, a behavioral consensus algorithm is presented to accomplish the attitude maneuver of the entire formation and guarantee a consistent attitude among the local virtual structure counterparts during the attitude maneuver. A multiple virtual sub-structures (MVSSs) system is introduced to enhance current virtual structure scheme when large amounts of spacecrafts are involved in the formation. The attitude of spacecraft is represented by modified Rodrigues parameter (MRP) for its non-redundancy. Finally, a numerical simulation with three synchronization situations is employed to illustrate the effectiveness of the proposed strategy.

  15. An Emerging Method for Rapid Characterization of Feed Structures and Feed Component Matrix at a Cellular Level and Relation to Feed Quality and Nutritive Value

    SciTech Connect

    Yu,P.

    2006-01-01

    Feed quality, feed characteristics, nutrient utilization and digestive behavior are closely related to: (i) total feed composition, (ii) feed intrinsic structures, and (iii) biological component matrix (such as protein to starch matrix, protein to carbohydrate matrix). Conventional 'wet' chemical analysis can determine total chemical composition, but fails to detect the feed intrinsic structures and biological component matrix due to destruction of feed samples during the processing for chemical analysis and the 'wet' chemical analysis cannot link structural information to chemical information within intact feed tissue. Recently, advanced synchrotron-based Fourier transform infrared (FTIR) microspectroscopy has been developed as a non-destructive and non-invasive structural-chemical analytical technique. This technique can link chemical information to structural information of biological samples within intact tissue within cellular dimensions. It can provide four kinds of information simultaneously: tissue composition, tissue structure, tissue chemistry and tissue environment. However, this novel technique has been found mainly for medical science research, extremely rare for feed science and nutrition research. The objective of this review article was to illustrate synchrotron-based FTIR microspectroscopy as a novel research tool for rapid characterization of feed structures at a cellular level and for detection of chemical features and molecular chemical make-up of feed biological component matrix and nutrient interaction. The emphasis of this article was to show that feed structural-chemical features at a cellular level are closely related to feed characteristics, feed quality and nutritive value in animals. The synchrotron-based technology will provide us with a greater understanding of the plant-animal interface.

  16. The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation

    PubMed Central

    Schulte, Tim; Mikaelsson, Cecilia; Beaussart, Audrey; Kikhney, Alexey; Deshmukh, Maya; Wolniak, Sebastian; Pathak, Anuj; Ebel, Christine; Löfling, Jonas; Fogolari, Federico; Henriques-Normark, Birgitta; Dufrêne, Yves F.; Svergun, Dmitri; Nygren, Per-Åke; Achour, Adnane

    2016-01-01

    The major human pathogen Streptococcus pneumoniae is a leading cause of disease and death worldwide. Pneumococcal biofilm formation within the nasopharynx leads to long-term colonization and persistence within the host. We have previously demonstrated that the capsular surface-associated pneumococcal serine rich repeat protein (PsrP), key factor for biofilm formation, binds to keratin-10 (KRT10) through its microbial surface component recognizing adhesive matrix molecule (MSCRAMM)-related globular binding region domain (BR187–385). Here, we show that BR187–385 also binds to DNA, as demonstrated by electrophoretic mobility shift assays and size exclusion chromatography. Further, heterologous expression of BR187–378 or the longer BR120–378 construct on the surface of a Gram-positive model host bacterium resulted in the formation of cellular aggregates that was significantly enhanced in the presence of DNA. Crystal structure analyses revealed the formation of BR187–385 homo-dimers via an intermolecular β-sheet, resulting in a positively charged concave surface, shaped to accommodate the acidic helical DNA structure. Furthermore, small angle X-ray scattering and circular dichroism studies indicate that the aggregate-enhancing N-terminal region of BR120–166 adopts an extended, non-globular structure. Altogether, our results suggest that PsrP adheres to extracellular DNA in the biofilm matrix and thus promotes pneumococcal biofilm formation. PMID:27582320

  17. The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.

    PubMed

    Schulte, Tim; Mikaelsson, Cecilia; Beaussart, Audrey; Kikhney, Alexey; Deshmukh, Maya; Wolniak, Sebastian; Pathak, Anuj; Ebel, Christine; Löfling, Jonas; Fogolari, Federico; Henriques-Normark, Birgitta; Dufrêne, Yves F; Svergun, Dmitri; Nygren, Per-Åke; Achour, Adnane

    2016-01-01

    The major human pathogen Streptococcus pneumoniae is a leading cause of disease and death worldwide. Pneumococcal biofilm formation within the nasopharynx leads to long-term colonization and persistence within the host. We have previously demonstrated that the capsular surface-associated pneumococcal serine rich repeat protein (PsrP), key factor for biofilm formation, binds to keratin-10 (KRT10) through its microbial surface component recognizing adhesive matrix molecule (MSCRAMM)-related globular binding region domain (BR187-385). Here, we show that BR187-385 also binds to DNA, as demonstrated by electrophoretic mobility shift assays and size exclusion chromatography. Further, heterologous expression of BR187-378 or the longer BR120-378 construct on the surface of a Gram-positive model host bacterium resulted in the formation of cellular aggregates that was significantly enhanced in the presence of DNA. Crystal structure analyses revealed the formation of BR187-385 homo-dimers via an intermolecular β-sheet, resulting in a positively charged concave surface, shaped to accommodate the acidic helical DNA structure. Furthermore, small angle X-ray scattering and circular dichroism studies indicate that the aggregate-enhancing N-terminal region of BR120-166 adopts an extended, non-globular structure. Altogether, our results suggest that PsrP adheres to extracellular DNA in the biofilm matrix and thus promotes pneumococcal biofilm formation. PMID:27582320

  18. Structural characterization of a karstified limestone formation using GPR

    NASA Astrophysics Data System (ADS)

    Rousset, D.; Sénéchal, G.; Gaffet, S.

    2009-12-01

    The Laboratoire Souterrain à Bas Bruit (LSBB) at Rustrel - Pays d'Apt, France, is an Inter-disciplinary Underground Science and Technology Laboratory buried in a karstified limestone formation. A multidisciplinary program focused on water circulation monitoring is presently performed inside the tunnels. This program comprises the investigation of faults, fractures, karstification and stratigraphy ofthe limestone massif using GPR. We present the main results obtained from these data. The tunnel has been dug in lower cretaceous limestone which is characterized by a low clay content, high electrical resistivity which results in generally very low attenuation of electro-magnetic waves. 90% of the tunnels floor are made of concrete whereas other are made of bare limestone. This experimental site offers a unique opportunity of perfoming measurements within an unweathered limestone massif. The whole 3km long tunnel has been investigated using single offset shielded 250 MHz antennas in May 2009. Processing includes : DC and very low frequency removal, amplitude compensation preserving lateral variations, migration and time to depth conversion. When necessary predictive deconvolution has been applied to remove ringing effects. These data sets are characterized by good signal to noise ratio and a signal penetration down to 18 meters. These data allow us to accurately map the stratigraphy of the surrounding rocks across the concrete walls of the tunnel. Some 20 m deep vertical wells have been drilled inside the tunnel through observed reflectors. This is a strong validation of the GPR images. The estimated resolution is centimetric to decimetric and matches the required geologic accuracy. The GPR data set allows to extend previous geological results in depth, particularly in the concrete coated parts of the tunnel where conventional geological surveying is impossible. Thanks to the processing which preserves lateral amplitude variations, GPR sections exhibit prominent

  19. Identification of formation of initial native structure in onconase from an unfolded state.

    PubMed

    Gahl, Robert F; Oswald, Robert E; Scheraga, Harold A

    2012-01-10

    In the oxidative folding of onconase, the stabilization of intermediates early in the folding process gives rise to efficient formation of its biologically active form. To identify the residues responsible for the initial formation of structured intermediates, the transition from an ensemble of unstructured three-disulfide species, 3S(U), to a single structured three-disulfide intermediate species, des-[30-75] or 3S(F), at pH 8.0 and 25 °C was examined. This transition was first monitored by far-UV circular dichroism spectroscopy at pH 8.0 and 25 °C, showing that it occurs with the formation of secondary structure, presumably because of native interactions. The time dependence of formation of nativelike structure was then followed by nuclear magnetic resonance spectroscopy after we had arrested the transition at different times by lowering the pH to 3 and then acquiring (1)H-(15)N heteronuclear single-quantum coherence spectra at pH 3 and 16 °C to identify amide hydrogens that become part of nativelike structure. H/D exchange was utilized to reduce the intensity of resonances from backbone amide hydrogens not involved in structure, without allowing exchange of backbone amide hydrogens involved in initial structure. Six hydrogen-bonding residues, namely, Tyr38, Lys49, Ser82, Cys90, Glu91, and Ala94, were identified as being involved in the earliest detectable nativelike structure before complete formation of des-[30-75] and are further stabilized later in the formation of this intermediate through S-S/SH interchange. By observing the stabilization of the structures of these residues by their neighboring residues, we have identified the initial, nativelike structural elements formed in this transition, providing details of the initial events in the oxidative folding of onconase. PMID:22142378

  20. Angiopoietin 2 stimulates migration and tube-like structure formation of murine brain capillary endothelial cells through c-Fes and c-Fyn.

    PubMed

    Mochizuki, Yasushi; Nakamura, Takao; Kanetake, Hiroshi; Kanda, Shigeru

    2002-01-01

    The angiopoietin (Ang)/Tie2 system is exclusively involved in vasculogenesis and angiogenesis. Ang2 is known to inhibit Ang1-mediated phosphorylation of Tie2 as well as cellular responses during embryonic development. Recent studies have demonstrated that Ang2 has angiogenic activities in adult tissues and cultured endothelial cells. In the present study, we examined the downstream signaling pathways involved in Ang2-mediated cellular responses by murine brain capillary cell line, IBE cells. Tie2 was tyrosine phoshorylated by Ang2. Ang2 showed no effect on proliferation, but stimulated chemotaxis and tube-like structure formation. Phosphoinositide 3-kinase (PI 3-kinase) was activated by Ang2 through c-Fes and was involved in chemotaxis toward Ang2. Ang2 also activated c-Fyn in IBE cells. Cells expressing kinase-inactive c-Fyn attenuated Ang2-induced tube formation, suggesting that c-Fyn was responsible for Ang-2-mediated tube formation. Collecting these data, Ang2 activates c-Fes and c-Fyn, leading to migration and tube formation by murine capillary endothelial cells.

  1. Structure formation constraints on Sommerfeld-enhanced dark matter annihilation

    SciTech Connect

    Armendariz-Picon, Cristian; Neelakanta, Jayanth T. E-mail: jtneelak@syr.edu

    2012-12-01

    We study the growth of cosmic structure in a ΛCDM universe under the assumption that dark matter self-annihilates with an averaged cross section times relative velocity that grows with the scale factor, an increase known as Sommerfeld-enhancement. Such an evolution is expected in models in which a light force carrier in the dark sector enhances the annihilation cross section of dark matter particles, and has been invoked, for instance, to explain anomalies in cosmic ray spectra reported in the past. In order to make our results as general as possible, we assume that dark matter annihilates into a relativistic species that only interacts gravitationally with the standard model. This assumption also allows us to test whether the additional relativistic species mildly favored by cosmic-microwave background data could originate from dark matter annihilation. We do not find evidence for Sommerfeld-enhanced dark matter annihilation and derive the corresponding upper limits on the annihilation cross-section.

  2. Modulation of crystal formation by bone phosphoproteins: structural specificity of the osteopontin-mediated inhibition of hydroxyapatite formation.

    PubMed

    Hunter, G K; Kyle, C L; Goldberg, H A

    1994-06-15

    Osteopontin is a phosphorylated sialoprotein containing a conserved sequence of contiguous aspartic acid residues. This protein is expressed at high levels in mineralized tissues and has previously been shown to inhibit the in vitro formation of hydroxyapatite (HA). In the present study, protein modification and model compound studies have been used to identify the structural features of osteopontin that are responsible for its crystal-modulating properties. Using metastable calcium phosphate solutions buffered by autotitration, osteopontin caused half-maximal inhibition of HA formation at a concentration (IC50) of 0.06 microgram/ml. The hen egg yolk phosphoprotein phosvitin was a much weaker inhibitor, while dextran sulphate had no effect. The synthetic polypeptide poly(aspartic acid) was almost as effective an inhibitor of HA formation as osteopontin (IC50 0.11 microgram/ml), whereas poly(glutamic acid) was more than a thousand times less potent (IC50 155 micrograms/ml). In a steady-state agarose gel system, much higher polypeptide concentrations were required for inhibition of HA formation, but a similar relative order of inhibitory effectiveness was observed. Treatment of osteopontin with alkaline phosphatase removed 84% of the covalently bound phosphate and reduced its HA-inhibiting activity by more than 40-fold. Treatment with glycine ethyl ester in the presence of carbodi-imide modified 86% of the carboxylate groups in osteopontin and reduced its inhibitory activity by 6-fold. These findings indicate that osteopontin is a potent inhibitor of HA formation. This activity requires phosphate and carboxylate groups, possibly including the conserved sequence of contiguous aspartic acid residues. Osteopontin may act as an inhibitor of phase separation in physiological fluids of high supersaturation.

  3. Formation and finite element analysis of tethered bilayer lipid structures.

    PubMed

    Kwak, Kwang Joo; Valincius, Gintaras; Liao, Wei-Ching; Hu, Xin; Wen, Xuejin; Lee, Andrew; Yu, Bo; Vanderah, David J; Lu, Wu; Lee, L James

    2010-12-01

    Rapid solvent exchange of an ethanolic solution of diphytanoyl phosphatidylcholine (DPhyPC) in the presence of a mixed self-assembled monolayer (SAM) [thiolipid/β-mercaptoethanol (βME) (3/7 mol/mol) on Au] shows a transition from densely packed tethered bilayer lipid membranes [(dp)tBLMs], to loosely packed tethered bilayer lipid membranes [(lp)tBLMs], and tethered bilayer liposome nanoparticles (tBLNs) with decreasing DPhyPC concentration. The tethered lipidic constructs in the aqueous medium were analyzed by atomic force microscopy (AFM) and electrochemical impedance spectroscopy (EIS). Finite element analysis (FEA) was applied to interpret spectral EIS features without referring to equivalent circuit modeling. Using structural data obtained earlier from neutron reflectometry and dielectric constants of lipid bilayers, we reproduced experimentally observed features of the electrochemical impedance (EI) spectra of complex surface constructs involving small pinhole defects, large membrane-free patches, and bound liposomes. We demonstrated by FEA that highly insulating (dp)tBLMs with low-defect density exhibit EI spectra in the shape of a perfect semicircle with or without low-frequency upward "tails" in the Cole-Cole representation. Such EI spectra were observed at DPhyPC concentrations of >5 × 10(-3) mol L(-1). While AFM was not able to visualize very small lateral defects in such films, EI spectra unambiguously signaled their presence by increased low frequency "tails". Using FEA we demonstrate that films with large diameter visible defects (>25 nm by AFM) produce EI spectral features consisting of two semicircles of comparable size. Such films were typically obtained at DPhyPC concentrations of <5 × 10(-3) mol L(-1). At DPhyPC concentrations of <1.0 × 10(-3) mol L(-1) the planar bilayer structures were replaced by ellipsoidal liposomes with diameters ranging from 50 to 500 nm as observed in AFM images. Despite the distinct surface morphology change, the EI

  4. Formation and finite element analysis of tethered bilayer lipid structures.

    PubMed

    Kwak, Kwang Joo; Valincius, Gintaras; Liao, Wei-Ching; Hu, Xin; Wen, Xuejin; Lee, Andrew; Yu, Bo; Vanderah, David J; Lu, Wu; Lee, L James

    2010-12-01

    Rapid solvent exchange of an ethanolic solution of diphytanoyl phosphatidylcholine (DPhyPC) in the presence of a mixed self-assembled monolayer (SAM) [thiolipid/β-mercaptoethanol (βME) (3/7 mol/mol) on Au] shows a transition from densely packed tethered bilayer lipid membranes [(dp)tBLMs], to loosely packed tethered bilayer lipid membranes [(lp)tBLMs], and tethered bilayer liposome nanoparticles (tBLNs) with decreasing DPhyPC concentration. The tethered lipidic constructs in the aqueous medium were analyzed by atomic force microscopy (AFM) and electrochemical impedance spectroscopy (EIS). Finite element analysis (FEA) was applied to interpret spectral EIS features without referring to equivalent circuit modeling. Using structural data obtained earlier from neutron reflectometry and dielectric constants of lipid bilayers, we reproduced experimentally observed features of the electrochemical impedance (EI) spectra of complex surface constructs involving small pinhole defects, large membrane-free patches, and bound liposomes. We demonstrated by FEA that highly insulating (dp)tBLMs with low-defect density exhibit EI spectra in the shape of a perfect semicircle with or without low-frequency upward "tails" in the Cole-Cole representation. Such EI spectra were observed at DPhyPC concentrations of >5 × 10(-3) mol L(-1). While AFM was not able to visualize very small lateral defects in such films, EI spectra unambiguously signaled their presence by increased low frequency "tails". Using FEA we demonstrate that films with large diameter visible defects (>25 nm by AFM) produce EI spectral features consisting of two semicircles of comparable size. Such films were typically obtained at DPhyPC concentrations of <5 × 10(-3) mol L(-1). At DPhyPC concentrations of <1.0 × 10(-3) mol L(-1) the planar bilayer structures were replaced by ellipsoidal liposomes with diameters ranging from 50 to 500 nm as observed in AFM images. Despite the distinct surface morphology change, the EI

  5. Biological pattern formation: from basic mechanisms to complex structures

    NASA Astrophysics Data System (ADS)

    Koch, A. J.; Meinhardt, H.

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns? Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of Drosophila and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  6. Nonlinear structure formation in the cubic Galileon gravity model

    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

    2013-10-01

    We model the linear and nonlinear growth of large scale structure in the Cubic Galileon gravity model, by running a suite of N-body cosmological simulations using the ECOSMOG code. Our simulations include the Vainshtein screening effect, which reconciles the Cubic Galileon model with local tests of gravity. In the linear regime, the amplitude of the matter power spectrum increases by ∼ 20% with respect to the standard ΛCDM model today. The modified expansion rate accounts for ∼ 15% of this enhancement, while the fifth force is responsible for only ∼ 5%. This is because the effective unscreened gravitational strength deviates from standard gravity only at late times, even though it can be twice as large today. In the nonlinear regime (k∼>0.1h Mpc{sup −1}), the fifth force leads to only a modest increase (∼<8%) in the clustering power on all scales due to the very efficient operation of the Vainshtein mechanism. Such a strong effect is typically not seen in other models with the same screening mechanism. The screening also results in the fifth force increasing the number density of halos by less than 10%, on all mass scales. Our results show that the screening does not ruin the validity of linear theory on large scales which anticipates very strong constraints from galaxy clustering data. We also show that, whilst the model gives an excellent match to CMB data on small angular scales (l∼>50), the predicted integrated Sachs-Wolfe effect is in tension with Planck/WMAP results.

  7. Biological pattern formation: from basic mechanisms to complex structures

    SciTech Connect

    Koch, A.J.; Meinhardt, H. )

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  8. Structural parameters modulating the cellular uptake of disulfide-rich cyclic cell-penetrating peptides: MCoTI-II and SFTI-1.

    PubMed

    D'Souza, Charlotte; Henriques, Sónia Troeira; Wang, Conan K; Craik, David J

    2014-12-17

    Peptides are emerging as a new class of therapeutics due to their high potency and specificity for a range of targets, including the inhibition of protein-protein interactions. Disulfide-rich cyclic peptides, in particular, have attracted much attention in drug design due to their ultra-stable structure. Moreover, some of them have been shown to internalize into cells, which makes them potential scaffolds to deliver pharmaceutically bioactive sequences to intracellular targets. Here we examined the effects of structural modifications on the cell-penetrating properties of two disulfide-rich cyclic cell-penetrating peptides, Momordica cochinchinensis trypsin inhibitor II (MCoTI-II) and sunflower trypsin inhibitor-1 (SFTI-1). We found that the cellular uptake of MCoTI-II can be improved by increasing the overall positive charge of the native sequence. On the other hand, mutations to SFTI-1 did not significantly influence its cellular uptake, suggesting a non-specific endocytosis-dependent mechanism of cellular uptake. This study provides an understanding of the structural features affecting the internalization of MCoTI-II and SFTI-1, and hence provides a guide for the development of these disulfide-rich cyclic scaffolds into potential drug leads. PMID:24985034

  9. A numerical investigation into the influence of the properties of cobalt chrome cellular structures on the load transfer to the periprosthetic femur following total hip arthroplasty.

    PubMed

    Hazlehurst, Kevin Brian; Wang, Chang Jiang; Stanford, Mark

    2014-04-01

    Stress shielding of the periprosthetic femur following total hip arthroplasty is a problem that can promote the premature loosening of femoral stems. In order to reduce the need for revision surgery it is thought that more flexible implant designs need to be considered. In this work, the mechanical properties of laser melted square pore cobalt chrome molybdenum cellular structures have been incorporated into the design of a traditional monoblock femoral stem. The influence of incorporating the properties of cellular structures on the load transfer to the periprosthetic femur was investigated using a three dimensional finite element model. Eleven different stiffness configurations were investigated by using fully porous and functionally graded approaches. This investigation confirms that the periprosthetic stress values depend on the stiffness configuration of the stem. The numerical results showed that stress shielding is reduced in the periprosthetic Gruen zones when the mechanical properties of cobalt chrome molybdenum cellular structures are used. This work identifies that monoblock femoral stems manufactured using a laser melting process, which are designed for reduced stiffness, have the potential to contribute towards reducing stress shielding.

  10. Structural parameters modulating the cellular uptake of disulfide-rich cyclic cell-penetrating peptides: MCoTI-II and SFTI-1.

    PubMed

    D'Souza, Charlotte; Henriques, Sónia Troeira; Wang, Conan K; Craik, David J

    2014-12-17

    Peptides are emerging as a new class of therapeutics due to their high potency and specificity for a range of targets, including the inhibition of protein-protein interactions. Disulfide-rich cyclic peptides, in particular, have attracted much attention in drug design due to their ultra-stable structure. Moreover, some of them have been shown to internalize into cells, which makes them potential scaffolds to deliver pharmaceutically bioactive sequences to intracellular targets. Here we examined the effects of structural modifications on the cell-penetrating properties of two disulfide-rich cyclic cell-penetrating peptides, Momordica cochinchinensis trypsin inhibitor II (MCoTI-II) and sunflower trypsin inhibitor-1 (SFTI-1). We found that the cellular uptake of MCoTI-II can be improved by increasing the overall positive charge of the native sequence. On the other hand, mutations to SFTI-1 did not significantly influence its cellular uptake, suggesting a non-specific endocytosis-dependent mechanism of cellular uptake. This study provides an understanding of the structural features affecting the internalization of MCoTI-II and SFTI-1, and hence provides a guide for the development of these disulfide-rich cyclic scaffolds into potential drug leads.

  11. Formation and evolution of tweed structures on high-purity aluminum polycrystalline foils under cyclic tension

    NASA Astrophysics Data System (ADS)

    Kuznetsov, P. V.; Vlasov, I. V.; Sklyarova, E. A.; Smekalina, T. V.

    2015-10-01

    Peculiarities of formation and evolution of tweed structures on the surface of high-purity aluminum polycrystalline foils under cyclic tension were studied using an atom force microscope and a white light interferometer. Tweed structures of micron and submicron sizes were found on the foils at different number of cycles. In the range of 42,000 < N < 95,000 cycles destruction of tweed patterns is observed, which leads to their disappearance from the surface of the foils. Formation of tweed structures of various scales is discussed in terms of the Grinfeld instability.

  12. Formation and evolution of tweed structures on high-purity aluminum polycrystalline foils under cyclic tension

    SciTech Connect

    Kuznetsov, P. V.; Vlasov, I. V.; Sklyarova, E. A.; Smekalina, T. V.

    2015-10-27

    Peculiarities of formation and evolution of tweed structures on the surface of high-purity aluminum polycrystalline foils under cyclic tension were studied using an atom force microscope and a white light interferometer. Tweed structures of micron and submicron sizes were found on the foils at different number of cycles. In the range of 42,000 < N < 95,000 cycles destruction of tweed patterns is observed, which leads to their disappearance from the surface of the foils. Formation of tweed structures of various scales is discussed in terms of the Grinfeld instability.

  13. Structure of the catalytic domain of the human mitochondrial Lon protease: proposed relation of oligomer formation and activity.

    PubMed

    García-Nafría, Javier; Ondrovicová, Gabriela; Blagova, Elena; Levdikov, Vladimir M; Bauer, Jacob A; Suzuki, Carolyn K; Kutejová, Eva; Wilkinson, Anthony J; Wilson, Keith S

    2010-05-01

    ATP-dependent proteases are crucial for cellular homeostasis. By degrading short-lived regulatory proteins, they play an important role in the control of many cellular pathways and, through the degradation of abnormally misfolded proteins, protect the cell from a buildup of aggregates. Disruption or disregulation of mammalian mitochondrial Lon protease leads to severe changes in the cell, linked with carcinogenesis, apoptosis, and necrosis. Here we present the structure of the proteolytic domain of human mitochondrial Lon at 2 A resolution. The fold resembles those of the three previously determined Lon proteolytic domains from Escherichia coli, Methanococcus jannaschii, and Archaeoglobus fulgidus. There are six protomers in the asymmetric unit, four arranged as two dimers. The intersubunit interactions within the two dimers are similar to those between adjacent subunits of the hexameric ring of E. coli Lon, suggesting that the human Lon proteolytic domain also forms hexamers. The active site contains a 3(10) helix attached to the N-terminal end of alpha-helix 2, which leads to the insertion of Asp852 into the active site, as seen in M. jannaschii. Structural considerations make it likely that this conformation is proteolytically inactive. When comparing the intersubunit interactions of human with those of E. coli Lon taken with biochemical data leads us to propose a mechanism relating the formation of Lon oligomers with a conformational shift in the active site region coupled to a movement of a loop in the oligomer interface, converting the proteolytically inactive form seen here to the active one in the E. coli hexamer.

  14. Structure of the catalytic domain of the human mitochondrial Lon protease: Proposed relation of oligomer formation and activity

    PubMed Central

    García-Nafría, Javier; Ondrovičová, Gabriela; Blagova, Elena; Levdikov, Vladimir M; Bauer, Jacob A; Suzuki, Carolyn K; Kutejová, Eva; Wilkinson, Anthony J; Wilson, Keith S

    2010-01-01

    ATP-dependent proteases are crucial for cellular homeostasis. By degrading short-lived regulatory proteins, they play an important role in the control of many cellular pathways and, through the degradation of abnormally misfolded proteins, protect the cell from a buildup of aggregates. Disruption or disregulation of mammalian mitochondrial Lon protease leads to severe changes in the cell, linked with carcinogenesis, apoptosis, and necrosis. Here we present the structure of the proteolytic domain of human mitochondrial Lon at 2 Å resolution. The fold resembles those of the three previously determined Lon proteolytic domains from Escherichia coli, Methanococcus jannaschii, and Archaeoglobus fulgidus. There are six protomers in the asymmetric unit, four arranged as two dimers. The intersubunit interactions within the two dimers are similar to those between adjacent subunits of the hexameric ring of E. coli Lon, suggesting that the human Lon proteolytic domain also forms hexamers. The active site contains a 310 helix attached to the N-terminal end of α-helix 2, which leads to the insertion of Asp852 into the active site, as seen in M. jannaschii. Structural considerations make it likely that this conformation is proteolytically inactive. When comparing the intersubunit interactions of human with those of E. coli Lon taken with biochemical data leads us to propose a mechanism relating the formation of Lon oligomers with a conformational shift in the active site region coupled to a movement of a loop in the oligomer interface, converting the proteolytically inactive form seen here to the active one in the E. coli hexamer. PMID:20222013

  15. Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism.

    PubMed

    Tong, Chunfa; Shen, Lianying; Lv, Yafei; Wang, Zhong; Wang, Xiaoling; Feng, Sisi; Li, Xin; Sui, Yihan; Pang, Xiaoming; Wu, Rongling

    2014-01-01

    Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation.

  16. Solution NMR structure of CsgE: Structural insights into a chaperone and regulator protein important for functional amyloid formation.

    PubMed

    Shu, Qin; Krezel, Andrzej M; Cusumano, Zachary T; Pinkner, Jerome S; Klein, Roger; Hultgren, Scott J; Frieden, Carl

    2016-06-28

    Curli, consisting primarily of major structural subunit CsgA, are functional amyloids produced on the surface of Escherichia coli, as well as many other enteric bacteria, and are involved in cell colonization and biofilm formation. CsgE is a periplasmic accessory protein that plays a crucial role in curli biogenesis. CsgE binds to both CsgA and the nonameric pore protein CsgG. The CsgG-CsgE complex is the curli secretion channel and is essential for the formation of the curli fibril in vivo. To better understand the role of CsgE in curli formation, we have determined the solution NMR structure of a double mutant of CsgE (W48A/F79A) that appears to be similar to the wild-type (WT) protein in overall structure and function but does not form mixed oligomers at NMR concentrations similar to the WT. The well-converged structure of this mutant has a core scaffold composed of a layer of two α-helices and a layer of three-stranded antiparallel β-sheet with flexible N and C termini. The structure of CsgE fits well into the cryoelectron microscopy density map of the CsgG-CsgE complex. We highlight a striking feature of the electrostatic potential surface in CsgE structure and present an assembly model of the CsgG-CsgE complex. We suggest a structural mechanism of the interaction between CsgE and CsgA. Understanding curli formation can provide the information necessary to develop treatments and therapeutic agents for biofilm-related infections and may benefit the prevention and treatment of amyloid diseases. CsgE could establish a paradigm for the regulation of amyloidogenesis because of its unique role in curli formation. PMID:27298344

  17. FORMATION OF A PROPELLER STRUCTURE BY A MOONLET IN A DENSE PLANETARY RING

    SciTech Connect

    Michikoshi, Shugo; Kokubo, Eiichiro E-mail: kokubo@th.nao.ac.jp

    2011-05-10

    The Cassini spacecraft discovered a propeller-shaped structure in Saturn's A. This propeller structure is thought to be formed by gravitational scattering of ring particles by an unseen embedded moonlet. Self-gravity wakes are prevalent in dense rings due to gravitational instability. Strong gravitational wakes affect the propeller structure. Here, we derive the condition for the formation of a propeller structure by a moonlet embedded in a dense ring with gravitational wakes. We find that a propeller structure is formed when the wavelength of the gravitational wakes is smaller than the Hill radius of the moonlet. We confirm this formation condition by performing numerical simulations. This condition is consistent with observations of propeller structures in Saturn's A.

  18. Innovative design of composite structures: The use of curvilinear fiber format in structural design of composites

    NASA Technical Reports Server (NTRS)

    Charette, R. F.; Hyer, M. W.

    1990-01-01

    The influence is investigated of a curvilinear fiber format on load carrying capacity of a layered fiber reinforced plate with a centrally located hole. A curvilinear fiber format is descriptive of layers in a laminate having fibers which are aligned with the principal stress directions in those layers. Laminates of five curvilinear fiber format designs and four straightline fiber format designs are considered. A quasi-isotropic laminate having a straightline fiber format is used to define a baseline design for comparison with the other laminate designs. Four different plate geometries are considered and differentiated by two values of hole diameter/plate width equal to 1/6 and 1/3, and two values of plate length/plate width equal to 2 and 1. With the plates under uniaxial tensile loading on two opposing edges, alignment of fibers in the curvilinear layers with the principal stress directions is determined analytically by an iteration procedure. In-plane tensile load capacity is computed for all of the laminate designs using a finite element analysis method. A maximum strain failure criterion and the Tsai-Wu failure criterion are applied to determine failure loads and failure modes. Resistance to buckling of the laminate designs to uniaxial compressive loading is analyzed using the commercial code Engineering Analysis Language. Results indicate that the curvilinear fiber format laminates have higher in-plane tensile load capacity and comparable buckling resistance relative to the straightline fiber format laminates.

  19. Calcium and ascorbic acid affect cellular structure and water mobility in apple tissue during osmotic dehydration in sucrose solutions.

    PubMed

    Mauro, Maria A; Dellarosa, Nicolò; Tylewicz, Urszula; Tappi, Silvia; Laghi, Luca; Rocculi, Pietro; Rosa, Marco Dalla

    2016-03-15

    The effects of the addition of calcium lactate and ascorbic acid to sucrose osmotic solutions on cell viability and microstructure of apple tissue were studied. In addition, water distribution and mobility modification of the different cellular compartments were observed. Fluorescence microscopy, light microscopy and time domain nuclear magnetic resonance (TD-NMR) were respectively used to evaluate cell viability and microstructural changes during osmotic dehydration. Tissues treated in a sucrose-calcium lactate-ascorbic acid solution did not show viability. Calcium lactate had some effects on cell walls and membranes. Sucrose solution visibly preserved the protoplast viability and slightly influenced the water distribution within the apple tissue, as highlighted by TD-NMR, which showed higher proton intensity in the vacuoles and lower intensity in cytoplasm-free spaces compared to other treatments. The presence of ascorbic acid enhanced calcium impregnation, which was associated with permeability changes of the cellular wall and membranes. PMID:26575708

  20. The evolution of galaxies at constant number density: a less biased view of star formation, quenching, and structural formation

    NASA Astrophysics Data System (ADS)

    Ownsworth, Jamie R.; Conselice, Christopher J.; Mundy, Carl J.; Mortlock, Alice; Hartley, William G.; Duncan, Kenneth; Almaini, Omar

    2016-09-01

    Due to significant galaxy contamination and impurity in stellar mass selected samples (up to 95 per cent from z = 0-3), we examine the star formation history, quenching time-scales, and structural evolution of galaxies using a constant number density selection with data from the United Kingdom Infra-Red Deep Sky Survey Ultra-Deep Survey field. Using this methodology, we investigate the evolution of galaxies at a variety of number densities from z = 0-3. We find that samples chosen at number densities ranging from 3 × 10-4 to 10-5 galaxies Mpc-3 (corresponding to z ˜ 0.5 stellar masses of M* = 1010.95-11.6 M0) have a star-forming blue fraction of ˜50 per cent at z ˜ 2.5, which evolves to a nearly 100 per cent quenched red and dead population by z ˜ 1. We also see evidence for number density downsizing, such that the galaxies selected at the lowest densities (highest masses) become a homogeneous red population before those at higher number densities. Examining the evolution of the colours for these systems furthermore shows that the formation redshift of galaxies selected at these number densities is zform > 3. The structural evolution through size and Sérsic index fits reveal that while there remains evolution in terms of galaxies becoming larger and more concentrated in stellar mass at lower redshifts, the magnitude of the change is significantly smaller than for a mass-selected sample. We also find that changes in size and structure continues at z < 1, and is coupled strongly to passivity evolution. We conclude that galaxy structure is driving the quenching of galaxies, such that galaxies become concentrated before they become passive.

  1. Polyalanine and Abeta Aggregation Kinetics: Probing Intermediate Oligomer Formation and Structure Using Computer Simulations

    NASA Astrophysics Data System (ADS)

    Phelps, Erin Melissa

    2011-12-01

    The aggregation of proteins into stable, well-ordered structures known as amyloid fibrils has been associated with many neurodegenerative diseases. Amyloid fibrils are long straight, and un-branched structures containing several proto-filaments, each of which exhibits "cross beta structure," -- ribbon-like layers of large beta sheets whose strands run perpendicular to the fibril axis. It has been suggested in the literature that the pathway to fibril formation has the following steps: unfolded monomers associate into transient unstable oligomers, the oligomers undergo a rearrangement into the cross-beta structure and form into proto-filaments, these proto-filaments then associate and grow into fully formed fibrils. Recent experimental studies have determined that the unstable intermediate structures are toxic to cells and that their presence may play a key role in the pathogenesis of the amyloid diseases. Many efforts have been made to determine the structure of intermediate oligomer aggregates that form during the fibrillization process. The goal of this work is to provide details about the structure and formation kinetics of the unstable oligomers that appear in the fibril formation pathway. The specific aims of this work are to determine the steps in the fibril formation pathway and how the kinetics of fibrillization changes with variations in temperature and concentration. The method used is the application of discontinuous molecular dynamics to large systems of peptides represented with an intermediate resolution model, PRIME, that was previously developed in our group. Three different peptide sequences are simulated: polyalanine (KA14K), Abeta17-40, and Abeta17-42; the latter two are truncated sequences of the Alzheimer's peptide. We simulate the spontaneous assembly of these peptide chains from a random initial configuration of random coils. We investigate aggregation kinetics and oligomer formation of a system of 192 polyalanine (KA14K) chains over a

  2. Neotectonic stage in the formation of the Khokhlovskoe uranium deposit, eastern Transural region: Structural, hydrochemical, mineralogical, and geochemical formation conditions

    NASA Astrophysics Data System (ADS)

    Vinokurov, S. F.; Prokof'ev, V. Yu.; Malkovsky, V. I.; Dymkov, Yu. M.; Chugaev, A. V.; Nesterova, M. V.

    2013-11-01

    The structural, hydrochemical, mineralogical, and geochemical features of the Khokhlovskoe uranium deposit related to neotectonic processes are considered. The structural feature is expressed in neotectonic dislocations in the form of overall intense fragmentation of host rocks and widespread low-amplitude strike-slip faulting. The hydrochemical specificity is determined by the appearance of thermal carbonated formation water in ore-bearing aquifers. This water is similar in chemical and gas composition to hydrothermal solutions in fluid inclusions and mineral waters abundant in this district. The mineralogical and geochemical features comprise the occurrence of newly formed ferroan carbonates and late iron hydroxides in altered (bleached) pelitic rocks; the formation of silicic opal segregations in ore-bearing sand and sandstone; late sulfides, arsenides, and selenides of iron and other metals; and multiphase gel-pitchblende enriched in Zr especially typical of high-grade uranium ore. The age of high-grade ore determined by a precision uranium-ionium method coincides with the time when thermal carbonated water appeared in the host rocks. This time was estimated from a mathematical model of heat transfer and regional dynamics of underground water. This coincidence clearly indicates that the aforementioned processes are related to the late Quaternary neotectonic reactivation of the eastern Transural region.

  3. Revised age and structural interpretations of Nuka Formation at Nuka Ridge, northwestern Alaska

    USGS Publications Warehouse

    Tailleur, I.L.; Mamet, B.L.; Dutro, J.T.

    1973-01-01

    New collections of foraminifers and macrofossils from Nuka Ridge, the type area of the enigmatic Nuka Formation, demonstrate that the type Nuka Formation is not a continuous stratigraphic sequence as originally described. Paleontologic evidence indicates the presence of a structurally repeated sequence at Nuka Ridge consisting of Upper Mississippian (Meramec and younger) strata overlain by Permian beds which, in turn, are succeeded by Triassic(?) and Cretaceous rocks. Mississippian calcareous mudstone and limestone units are correlated with the Lisburne Group; microcline-bearing arkose units with Mississippian and Permian macrofossils and microfossils represent the Nuka Formation; units of chert are inferred to be of Permian and Triassic age; and wacke at the top of the sequence resembles unnamed wacke assigned to the Cretaceous elsewhere. These new data and their interpretations indicate that the type section of the Nuka Formation is inadequate. The standard for the Nuka Formation is therefore referred to a newly measured section of the middle arkosic unit of the old section.

  4. Formation of chain structures in systems of charged grains interacting via isotropic pair potentials

    SciTech Connect

    Vaulina, O. S.; Lisina, I. I.; Koss, K. G.

    2013-05-15

    Conditions for the formation of chain structures of charged grains confined in the gravitational field by external electric fields are studied analytically and numerically. The relationships between the parameters of the pair interaction potential, the number of grains, and the electric field gradient in the trap are found. A criterion for the violation of stable equilibrium in a quasi-one-dimensional chain of grains and the formation of a new configuration in the system is proposed.

  5. Formation of large-scale structure from cosmic strings and massive neutrinos

    NASA Technical Reports Server (NTRS)

    Scherrer, Robert J.; Melott, Adrian L.; Bertschinger, Edmund

    1989-01-01

    Numerical simulations of large-scale structure formation from cosmic strings and massive neutrinos are described. The linear power spectrum in this model resembles the cold-dark-matter power spectrum. Galaxy formation begins early, and the final distribution consists of isolated density peaks embedded in a smooth background, leading to a natural bias in the distribution of luminous matter. The distribution of clustered matter has a filamentary appearance with large voids.

  6. Oligomerization reactions of deoxyribonucleotides on montmorillonite clay - The effect of mononucleotide structure on phosphodiester bond formation

    NASA Technical Reports Server (NTRS)

    Ferris, James P.; KAMALUDDIN

    1989-01-01

    The formation of oligomers from deoxynucleotides, catalyzed by Na(+)-montmorillonite, was investigated with special attention given to the effect of the monomer structure on the phosphodiester bond formation. It was found that adenine deoxynucleotides bind more strongly to montmorillonite than do the corresponding ribonucleotides and thymidine nucleotides. Tetramers of 2-prime-dpA were detected in the reaction of 2-prime-d-5-prime-AMP with a water-soluble carbodiimide EDAC in the presence of Na(+)-montmorillonite, illustrating the possible role of minerals in the formation of biopolymers on the primitive earth.

  7. Origins of cellular geometry

    PubMed Central

    2011-01-01

    Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in developmental biology can also be asked of cells, but in most cases we do not know the answers. How much of cellular organization is dictated by global cell polarity cues as opposed to local interactions between cellular components? Does cellular structure persist across cell generations? What is the relationship between cell geometry and tissue organization? What ensures that intracellular structures are scaled to the overall size of the cell? Cell biology is only now beginning to come to grips with these questions. PMID:21880160

  8. Architected Cellular Materials

    NASA Astrophysics Data System (ADS)

    Schaedler, Tobias A.; Carter, William B.

    2016-07-01

    Additive manufacturing enables fabrication of materials with intricate cellular architecture, whereby progress in 3D printing techniques is increasing the possible configurations of voids and solids ad infinitum. Examples are microlattices with graded porosity and truss structures optimized for specific loading conditions. The cellular architecture determines the mechanical properties and density of these materials and can influence a wide range of other properties, e.g., acoustic, thermal, and biological properties. By combining optimized cellular architectures with high-performance metals and ceramics, several lightweight materials that exhibit strength and stiffness previously unachievable at low densities were recently demonstrated. This review introduces the field of architected materials; summarizes the most common fabrication methods, with an emphasis on additive manufacturing; and discusses recent progress in the development of architected materials. The review also discusses important applications, including lightweight structures, energy absorption, metamaterials, thermal management, and bioscaffolds.

  9. Structural Complexities Influencing Biostratigraphic Interpretations of the Permian Nansen Formation type-section, Ellesmere Island, Canada

    NASA Astrophysics Data System (ADS)

    Hill, M.; Guest, B.

    2011-12-01

    The Carboniferous to Permian aged Nansen Formation is a cyclic carbonate shelf deposit and potential hydrocarbon reservoir. This formation is the thickest, most widespread carbonate sequence in the Sverdrup Basin. Deformed during the Eurekan Orogeny, the Nansen Fm. is topographically prominent and responsible for the rugged topography on Axel Heiburg and Ellesmere Island. The type-section for the Nansen Fm. is located on the north side of Hare Fiord, along Girty Creek. At this location there is an estimated stratigraphic thickness of 2 km. Due to easier access most of the stratigraphic work has been completed on nearby glacially exposed sections that traverse parallel to Girty Creek along glacial margins. Extensive biostratigraphy was completed on a glacier section to the west, however, in a glacier section to the east of Girty Creek, structural complexities appear to be repeating sections of the formation. Here, the Nansen formation is bounded by two regional reverse faults. This has produced duplex structures, with clearly exposed stacked horses, footwall synclines, and truncations. By projecting the structures observed along the eastern glacier section to the western glacier section that was used for biostratigraphic studies, it is clear that these structures would affect biostratigraphic interpretations. It was previously noted by biostratigraphers that thrust faults appear to be repeating sections of the Nansen formation. However by correlating all observed faults with the biostratigraphy, we can determine the extent to which the faulting has affected the interpretations, and whether all faults or stratigraphic repetitions are accounted for.

  10. Introducing a more realistic model for opinion formation considering instability in social structure

    NASA Astrophysics Data System (ADS)

    Salehi, Sajjad; Taghiyareh, Fattaneh

    2016-06-01

    Opinion formation is a process through which interactions of individuals and dynamism of their opinions in effect of neighbors are modeled. In this paper, in an effort to model the opinion formation more realistically, we have introduced a model that considers the role of network structure in opinion dynamics. In this model, each individual changes his opinion in a way so as to decrease its difference with the opinion of trusted neighbors while he intensifies his dissention with the untrusted ones. Considering trust/distrust relations as a signed network, we have defined a structural indicator which shows the degree of instability in social structure and is calculated based on the structural balance theory. It is also applied as feedback to the opinion formation process affecting its dynamics. Our simulation results show formation of a set of clusters containing individuals holding opinions having similar values. Also, the opinion value of each individual is far from the ones of distrusted neighbors. Since this model considers distrust and instability of relations in society, it can offer a more realistic model of opinion formation.

  11. CO mapping of the Orion molecular cloud: The influence of star formation on cloud structure

    NASA Technical Reports Server (NTRS)

    Schloerb, F. P.; Snell, R. L.; Goldsmith, P. F.; Morgan, J. A.

    1986-01-01

    Regions of massive star formation have long been believed to have a profound influence on the structure of their surrounding molecular clouds. The ways in which massive star formation has altered the structure and kinematics of the Orion Molecular Cloud are discussed. The data to be discussed consists of a large scale map of the CO J=1-0 emission from approximately 3 square degrees of OMC-1. During 1985, the Five College Radio Astronomy Observatory 14M antenna was used to map a 2 deg x 1 deg region centered on alpha(1950) = 5(h)33(m)00(s) delta(1950) = -5 deg 30 min. The region mapped in 1985 covers the well known HII regions M42, M43, and NGC1977, and the CO map contains abundant evidence of the interaction between these regions and the molecular cloud. Indeed, the global structure of the cloud appears to have been strongly influenced by the continuous formation of massive stars within the cloud. Individual instances of some of these features are discussed. There appear to be two classes of features which are indicative of this interaction: CO bright rims and CO holes. During 1986, we have undertaken further mapping of OMC-1 to the south of the region covered by the 1985 map. This portion of the cloud contains significant regions of star formation, but O star formation has not occured and large HII regions have not developed to alter the appearance of the cloud. A detailed map of this region is thus an opportunity to view the structure of the molecular cloud before it has been altered by massive star formation. Preliminary analysis of data obtained in this region suggests that the structure and kinematics of the southern portion of the Orion cloud are indeed dramatically different from those of the region previously mapped. Comparison of the two regions thus supports models of the development of structure in molecular clouds through interaction with the HII regions formed within them.

  12. Biomimetic superelastic graphene-based cellular monoliths.

    PubMed

    Qiu, Ling; Liu, Jeffery Z; Chang, Shery L Y; Wu, Yanzhe; Li, Dan

    2012-01-01

    Many applications proposed for graphene require multiple sheets be assembled into a monolithic structure. The ability to maintain structural integrity upon large deformation is essential to ensure a macroscopic material which functions reliably. However, it has remained a great challenge to achieve high elasticity in three-dimensional graphene networks. Here we report that the marriage of graphene chemistry with ice physics can lead to the formation of ultralight and superelastic graphene-based cellular monoliths. Mimicking the hierarchical structure of natural cork, the resulting materials can sustain their structural integrity under a load of >50,000 times their own weight and can rapidly recover from >80% compression. The unique biomimetic hierarchical structure also provides this new class of elastomers with exceptionally high energy absorption capability and good electrical conductivity. The successful synthesis of such fascinating materials paves the way to explore the application of graphene in a self-supporting, structurally adaptive and 3D macroscopic form. PMID:23212370

  13. Effects of sub-lethal high-pressure homogenization treatment on the outermost cellular structures and the volatile-molecule profiles of two strains of probiotic lactobacilli

    PubMed Central

    Tabanelli, Giulia; Vernocchi, Pamela; Patrignani, Francesca; Del Chierico, Federica; Putignani, Lorenza; Vinderola, Gabriel; Reinheimer, Jorge A.; Gardini, Fausto; Lanciotti, Rosalba

    2015-01-01

    Applying sub-lethal levels of high-pressure homogenization (HPH) to lactic acid bacteria has been proposed as a method of enhancing some of their functional properties. Because the principal targets of HPH are the cell-surface structures, the aim of this study was to examine the effect of sub-lethal HPH treatment on the outermost cellular structures and the proteomic profiles of two known probiotic bacterial strains. Moreover, the effect of HPH treatment on the metabolism of probiotic cells within a dairy product during its refrigerated storage was investigated using SPME-GC-MS. Transmission electron microscopy was used to examine the microstructural changes in the outermost cellular structures due to HPH treatment. These alterations may be involved in the changes in some of the technological and functional properties of the strains that were observed after pressure treatment. Moreover, the proteomic profiles of the probiotic strains treated with HPH and incubated at 37°C for various periods showed different peptide patterns compared with those of the untreated cells. In addition, there were differences in the peaks that were observed in the low-mass spectral region (2000–3000 Da) of the spectral profiles of the control and treated samples. Due to pressure treatment, the volatile-molecule profiles of buttermilk inoculated with treated or control cells and stored at 4°C for 30 days exhibited overall changes in the aroma profile and in the production of molecules that improved its sensory profile, although the two different species imparted specific fingerprints to the product. The results of this study will contribute to understanding the changes that occur in the outermost cellular structures and the metabolism of LAB in response to HPH treatment. The findings of this investigation may contribute to elucidating the relationships between these changes and the alterations of the technological and functional properties of LAB induced by pressure treatment. PMID

  14. Effects of sub-lethal high-pressure homogenization treatment on the outermost cellular structures and the volatile-molecule profiles of two strains of probiotic lactobacilli.

    PubMed

    Tabanelli, Giulia; Vernocchi, Pamela; Patrignani, Francesca; Del Chierico, Federica; Putignani, Lorenza; Vinderola, Gabriel; Reinheimer, Jorge A; Gardini, Fausto; Lanciotti, Rosalba

    2015-01-01

    Applying sub-lethal levels of high-pressure homogenization (HPH) to lactic acid bacteria has been proposed as a method of enhancing some of their functional properties. Because the principal targets of HPH are the cell-surface structures, the aim of this study was to examine the effect of sub-lethal HPH treatment on the outermost cellular structures and the proteomic profiles of two known probiotic bacterial strains. Moreover, the effect of HPH treatment on the metabolism of probiotic cells within a dairy product during its refrigerated storage was investigated using SPME-GC-MS. Transmission electron microscopy was used to examine the microstructural changes in the outermost cellular structures due to HPH treatment. These alterations may be involved in the changes in some of the technological and functional properties of the strains that were observed after pressure treatment. Moreover, the proteomic profiles of the probiotic strains treated with HPH and incubated at 37°C for various periods showed different peptide patterns compared with those of the untreated cells. In addition, there were differences in the peaks that were observed in the low-mass spectral region (2000-3000 Da) of the spectral profiles of the control and treated samples. Due to pressure treatment, the volatile-molecule profiles of buttermilk inoculated with treated or control cells and stored at 4°C for 30 days exhibited overall changes in the aroma profile and in the production of molecules that improved its sensory profile, although the two different species imparted specific fingerprints to the product. The results of this study will contribute to understanding the changes that occur in the outermost cellular structures and the metabolism of LAB in response to HPH treatment. The findings of this investigation may contribute to elucidating the relationships between these changes and the alterations of the technological and functional properties of LAB induced by pressure treatment. PMID

  15. Structural Mapping of the Tunnunik Impact Structure, NWT, Canada: Insights in to Central Uplift Formation

    NASA Astrophysics Data System (ADS)

    Osinski, G. R.; Francis, R.; Hansen, J.; Marion, C. L.; Pickersgill, A. E.; Tornabene, L. L.

    2013-08-01

    We report on structural mapping of t