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Sample records for cellular structure formation

  1. Effect of poisson ratio on cellular structure formation.

    PubMed

    Bischofs, I B; Schwarz, U S

    2005-08-05

    Mechanically active cells in soft media act as force dipoles. The resulting elastic interactions are long ranged and favor the formation of strings. We show analytically that due to screening, the effective interaction between strings decays exponentially, with a decay length determined only by geometry. Both for disordered and ordered arrangements of cells, we predict novel phase transitions from paraelastic to ferroelastic and antiferroelastic phases as a function of the Poisson ratio.

  2. Sulfolobus turreted icosahedral virus c92 protein responsible for the formation of pyramid-like cellular lysis structures.

    PubMed

    Snyder, Jamie C; Brumfield, Susan K; Peng, Nan; She, Qunxin; Young, Mark J

    2011-07-01

    Host cells infected by Sulfolobus turreted icosahedral virus (STIV) have been shown to produce unusual pyramid-like structures on the cell surface. These structures represent a virus-induced lysis mechanism that is present in Archaea and appears to be distinct from the holin/endolysin system described for DNA bacteriophages. This study investigated the STIV gene products required for pyramid formation in its host Sulfolobus solfataricus. Overexpression of STIV open reading frame (ORF) c92 in S. solfataricus alone is sufficient to produce the pyramid-like lysis structures in cells. Gene disruption of c92 within STIV demonstrates that c92 is an essential protein for virus replication. Immunolocalization of c92 shows that the protein is localized to the cellular membranes forming the pyramid-like structures.

  3. Cellular control over spicule formation in sea urchin embryos: A structural approach.

    PubMed

    Beniash, E; Addadi, L; Weiner, S

    1999-03-01

    The spicules of the sea urchin embryo form in intracellular membrane-delineated compartments. Each spicule is composed of a single crystal of calcite and amorphous calcium carbonate. The latter transforms with time into calcite by overgrowth of the preexisting crystal. Relationships between the membrane surrounding the spiculogenic compartment and the spicule mineral phase were studied in the transmission electron microscope (TEM) using freeze-fracture. In all the replicas observed the spicules were tightly surrounded by the membrane. Furthermore, a variety of structures that are related to the material exchange process across the membrane were observed. The spiculogenic cells were separated from other cell types of the embryo, frozen, and freeze-dried on the TEM grids. The contents of electron-dense granules in the spiculogenic cells were shown by electron diffraction to be composed of amorphous calcium carbonate. These observations are consistent with the notion that the amorphous calcium carbonate-containing granules contain the precursor mineral phase for spicule formation and that the membrane surrounding the forming spicule is involved both in transport of material and in controlling spicule mineralization.

  4. Formin’ cellular structures

    PubMed Central

    Bogdan, Sven; Schultz, Jörg; Grosshans, Jörg

    2014-01-01

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

  5. Phase separation and the formation of cellular bodies

    NASA Astrophysics Data System (ADS)

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

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

  6. Influence of Nutrient Availability and Quorum Sensing on the Formation of Metabolically Inactive Microcolonies Within Structurally Heterogeneous Bacterial Biofilms: An Individual-Based 3D Cellular Automata Model.

    PubMed

    Machineni, Lakshmi; Rajapantul, Anil; Nandamuri, Vandana; Pawar, Parag D

    2017-03-01

    The resistance of bacterial biofilms to antibiotic treatment has been attributed to the emergence of structurally heterogeneous microenvironments containing metabolically inactive cell populations. In this study, we use a three-dimensional individual-based cellular automata model to investigate the influence of nutrient availability and quorum sensing on microbial heterogeneity in growing biofilms. Mature biofilms exhibited at least three structurally distinct strata: a high-volume, homogeneous region sandwiched between two compact sections of high heterogeneity. Cell death occurred preferentially in layers in close proximity to the substratum, resulting in increased heterogeneity in this section of the biofilm; the thickness and heterogeneity of this lowermost layer increased with time, ultimately leading to sloughing. The model predicted the formation of metabolically dormant cellular microniches embedded within faster-growing cell clusters. Biofilms utilizing quorum sensing were more heterogeneous compared to their non-quorum sensing counterparts, and resisted sloughing, featuring a cell-devoid layer of EPS atop the substratum upon which the remainder of the biofilm developed. Overall, our study provides a computational framework to analyze metabolic diversity and heterogeneity of biofilm-associated microorganisms and may pave the way toward gaining further insights into the biophysical mechanisms of antibiotic resistance.

  7. Pressure-actuated cellular structures.

    PubMed

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

    2012-03-01

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

  8. Cellular disulfide bond formation in bioactive peptides and proteins.

    PubMed

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

    2015-01-14

    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.

  9. A cellular automata model of bone formation.

    PubMed

    Van Scoy, Gabrielle K; George, Estee L; Opoku Asantewaa, Flora; Kerns, Lucy; Saunders, Marnie M; Prieto-Langarica, Alicia

    2017-04-01

    Bone remodeling is an elegantly orchestrated process by which osteocytes, osteoblasts and osteoclasts function as a syncytium to maintain or modify bone. On the microscopic level, bone consists of cells that create, destroy and monitor the bone matrix. These cells interact in a coordinated manner to maintain a tightly regulated homeostasis. It is this regulation that is responsible for the observed increase in bone gain in the dominant arm of a tennis player and the observed increase in bone loss associated with spaceflight and osteoporosis. The manner in which these cells interact to bring about a change in bone quality and quantity has yet to be fully elucidated. But efforts to understand the multicellular complexity can ultimately lead to eradication of metabolic bone diseases such as osteoporosis and improved implant longevity. Experimentally validated mathematical models that simulate functional activity and offer eventual predictive capabilities offer tremendous potential in understanding multicellular bone remodeling. Here we undertake the initial challenge to develop a mathematical model of bone formation validated with in vitro data obtained from osteoblastic bone cells induced to mineralize and quantified at 26 days of culture. A cellular automata model was constructed to simulate the in vitro characterization. Permutation tests were performed to compare the distribution of the mineralization in the cultures and the distribution of the mineralization in the mathematical models. The results of the permutation test show the distribution of mineralization from the characterization and mathematical model come from the same probability distribution, therefore validating the cellular automata model.

  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. Cellular Regulation of Amyloid Formation in Aging and Disease

    PubMed Central

    Stroo, Esther; Koopman, Mandy; Nollen, Ellen A. A.; Mata-Cabana, Alejandro

    2017-01-01

    As the population is aging, the incidence of age-related neurodegenerative diseases, such as Alzheimer and Parkinson disease, is growing. The pathology of neurodegenerative diseases is characterized by the presence of protein aggregates of disease specific proteins in the brain of patients. Under certain conditions these disease proteins can undergo structural rearrangements resulting in misfolded proteins that can lead to the formation of aggregates with a fibrillar amyloid-like structure. Cells have different mechanisms to deal with this protein aggregation, where the molecular chaperone machinery constitutes the first line of defense against misfolded proteins. Proteins that cannot be refolded are subjected to degradation and compartmentalization processes. Amyloid formation has traditionally been described as responsible for the proteotoxicity associated with different neurodegenerative disorders. Several mechanisms have been suggested to explain such toxicity, including the sequestration of key proteins and the overload of the protein quality control system. Here, we review different aspects of the involvement of amyloid-forming proteins in disease, mechanisms of toxicity, structural features, and biological functions of amyloids, as well as the cellular mechanisms that modulate and regulate protein aggregation, including the presence of enhancers and suppressors of aggregation, and how aging impacts the functioning of these mechanisms, with special attention to the molecular chaperones. PMID:28261044

  12. Crack Propagation in Bamboo's Hierarchical Cellular Structure

    PubMed Central

    Habibi, Meisam K.; Lu, Yang

    2014-01-01

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

  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. Cosmic structure formation

    NASA Technical Reports Server (NTRS)

    Bertschinger, Edumund

    1994-01-01

    This article reviews the prevailing paradigm for how galaxies and larger structures formed in the universe: gravitational instability. Basic observational facts are summarized to motivate the standard cosmological framework underlying most detailed investigations of structure formation. The observed univers approaches spatial uniformity on scales larger than about 10(exp 26) cm. On these scales gravitational dynamics is almost linear and therefore relatively easy to relate to observations of large-scale structure. On smaller scales cosmic structure is complicated not only by nonlinear gravitational clustering but also by nonlinear nongravitational gas dynamical processes. The complexity of these phenomena makes galaxy formation one of the grand challenge problems of the physical sciences. No fully satisfactory theory can presently account in detail for the observed cosmic structure. However, as this article summarizes, significant progress has been made during the last few years.

  15. 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.

  16. 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

  17. Lightweight Cellular Metals with High Structural Efficiency

    DTIC Science & Technology

    2003-09-01

    10-2 10-1 0.01 0.1 Open-Cell Closed-Cell ERG Fraunhofer Alulight Alporas Cymat Relative Density, ρ* /ρ s Closed-Cell Open-Cell 10-4 10-3 10-2 10-1...0.01 0.1 Open-Cell Closed-Cell ERG Fraunhofer Alulight Alporas Cymat Relative Density, ρ* /ρ s Closed-Cell Open-Cell Stochastic Foams: Modulus and...Structures NATO ARW 22 Stiffness limited design at minimum weight Applications of Cellular Metals Cymat , Inc. Messiah College Beams (free area), columns

  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. Chiral hexagonal cellular sandwich structures: dynamic response

    NASA Astrophysics Data System (ADS)

    Spadoni, A.; Ruzzene, M.; Scarpa, F.

    2005-05-01

    Periodic cellular configurations with negative Poisson's ratio have attracted the attention of several researchers because of their superior dynamic characteristics. Among the geometries featuring a negative Poisson's ratio, the chiral topology possesses a geometric complexity that guarantees unique deformed configurations when excited at one of its natural frequencies. Specifically, localized deformations have been observed even at relatively low excitation frequencies. This is of particular importance as resonance can be exploited to minimize the power required for the appearance of localized deformations, thus giving practicality to the concept. The particular nature of these deformed configurations and the authority provided by the chiral geometry, suggest the application of the proposed structural configuration for the design of innovative lifting bodies, such as helicopter rotor blades or airplane wings. The dynamic characteristics of chiral structures are here investigated through a numerical model and experimental investigations. The numerical formulation uses dynamic shape functions to accurately describe the behavior of the considered structural assembly over a wide frequency range. The model is used to predict frequency response functions, and to investigate the occurrence of localized deformations. Experimental tests are also performed to demonstrate the accuracy of the model and to illustrate the peculiarities of the behavior of the considered chiral structures.

  20. 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

  1. The Cellular Biology of Flexor Tendon Adhesion Formation

    PubMed Central

    Wong, Jason K.F.; Lui, Yin H.; Kapacee, Zoher; Kadler, Karl E.; Ferguson, Mark W. J.; McGrouther, Duncan A.

    2009-01-01

    Intrasynovial flexor tendon injuries of the hand can frequently be complicated by tendon adhesions to the surrounding sheath, limiting finger function. We have developed a new tendon injury model in the mouse to investigate the three-dimensional cellular biology of intrasynovial flexor tendon healing and adhesion formation. We investigated the cell biology using markers for inflammation, proliferation, collagen synthesis, apoptosis, and vascularization/myofibroblasts. Quantitative immunohistochemical image analysis and three-dimensional reconstruction with cell mapping was performed on labeled serial sections. Flexor tendon adhesions were also assessed 21 days after wounding using transmission electron microscopy to examine the cell phenotypes in the wound. When the tendon has been immobilized, the mouse can form tendon adhesions in the flexor tendon sheath. The cell biology of tendon healing follows the classic wound healing response of inflammation, proliferation, synthesis, and apoptosis, but the greater activity occurs in the surrounding tissue. Cells that have multiple “fibripositors” and cells with cytoplasmic protrusions that contain multiple large and small diameter fibrils can be found in the wound during collagen synthesis. In conclusion, adhesion formation occurs due to scarring between two damaged surfaces. The mouse model for flexor tendon injury represents a new platform to study adhesion formation that is genetically tractable. PMID:19834058

  2. 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

  3. Detonation cellular structure and image proces

    NASA Astrophysics Data System (ADS)

    Shepherd, J. E.; Tieszen, S. R.

    Gaseous detonations universally exhibit an instability that is manifested as cellular patterns on witness plates (sooted foils) or open shutter photographs. The characteristic dimension or cell width lambda of the periodic cellular pattern has previously been shown to correlate with failure diameter, critical diffraction aperture dimension and direct initiation energy requirements. Due to the importance of predicting these parameters in assessing detonability hazards, a quantitative method for cell size mesurement is urgently needed. We discuss a technique based on digital image processing of sooted foil records and illustrate the results with data from experiments performed in the Heated Detonation Tube facility at Sandia. We demonstrate that image processing can be used to eliminate some of the uncertainty now present in cell size measurements. The possibility of quantifying cellular irregularity is also explored.

  4. 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

  5. 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.

  6. 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

  7. Cellular Shape Memory Alloy Structures: Experiments & Modeling (Part 1)

    DTIC Science & Technology

    2012-08-01

    AFOSR  Grant  #FA9550-­‐08-­‐1-­‐0313 Cellular  Shape  Memory   Alloy  Structures:   Experiments  &  Modeling J.  Shaw  (UM...2012 4. TITLE AND SUBTITLE Cellular Shape Memory Alloy Structures: Experiments & Modeling (Part 1) 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...dense,  0.37  g/cc) Combine benefits of light-weight cellular structures with Shape Memory Alloy (SMA) adaptive behavior CombinaKon •Amplified

  8. Influence of marihuana on cellular structures and biochemical activities.

    PubMed

    Tahir, S K; Zimmerman, A M

    1991-11-01

    Cannabinoids are known to affect a number of cellular systems and functions, but the basis for their action is unclear. In this paper we review the current evidence describing cannabinoid effects on various levels of cellular structure and activity and we present our current studies on the influence of delta-9-tetrahydrocannabinol, cannabidiol and cannabinol on one cellular system, the cytoskeleton. The organization of two cytoskeletal structures, microtubules and microfilaments, were examined and the mRNA levels of tubulin and actin, the major protein components of microtubules and microfilaments, respectively, were analysed.

  9. 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)

  10. Analysis of vibration of two-dimensional periodic cellular structures

    NASA Astrophysics Data System (ADS)

    Jeong, Sang Min (Joseph)

    The vibration of and wave propagation in periodic cellular structures are analyzed. Cellular structures exhibit a number of desirable multifunctional properties, which make them attractive in a variety of engineering applications. These include ultra-light structures, thermal and acoustic insulators, and impact amelioration systems, among others. Cellular structures with deterministic architecture can be considered as example of periodic structures. Periodic structures feature unique wave propagation characteristics, whereby elastic waves propagate only in specific frequency bands, known as "pass band", while they are attenuated in all other frequency bands, known as "stop bands". Such dynamic properties are here exploited to provide cellular structures with the capability of behaving as directional, pass-band mechanical filters, thus complementing their well documented multifunctional characteristics. This work presents a methodology for the analysis of the dynamic behavior of periodic cellular structures, which allows the evaluation of location and spectral width of propagation and attenuation regions in non-dimensional form. The filtering characteristics are tested and demonstrated for structures of various geometry and topology, including cylindrical grid-like structures, Kagome and tetrhedral truss core lattices. Experimental investigations is done on a 2-D lattice manufactured out of aluminum. The complete wave field of the specimen at various frequencies is measured using a Scanning Laser Doppler Vibrometer (SLDV). Experimental results show good agreement with the methodology and computational tools developed in this work. The results demonstrate how wave propagation characteristics are defined by cell geometry and configuration. Numerical and experimental results show the potential of periodic cellular structures as mechanical filters and/or isolators of vibrations.

  11. Lightweight Multifunctional Linear Cellular Alloy Ballistic Structures

    DTIC Science & Technology

    2006-04-26

    for densification. For this program, square cell LCA honeycomb with both maraging steel and super invar compositions were fabricated using SAI’s...provide high levels of energy absorption; 5 to 7 times that of that of conventional materials. Maraging steel honeycomb structure having a density of 2.1 g...cm3 and yield strength ~650 MPa, has been shown to absorb ~180 MJ/m3. Figure 2 shows stress train curves for maraging steel under quasistatic and

  12. Cellular structure of lean hydrogen flames in microgravity

    NASA Technical Reports Server (NTRS)

    Patnaik, G.; Kailasanath, K.

    1990-01-01

    Detailed, time-dependent, two-dimensional numerical simulations of premixed laminar flames have been used to study the initiation and subsequent development of cellular structures in lean hydrogen-air flames. The model includes detailed hydrogen-oxygen combustion with 24 elementary reactions of eight reactive species and a nitrogen diluent, molecular diffusion of all species, thermal conduction, viscosity, and convection. This model has been used to study the nonlinear evolution of cellular flame structure and shows that cell splitting, as observed in experiments, can be predicted numerically for sufficiently reactive mixtures. The structures that evolved also resembled the cellular structures observed in experiments. The present study shows that the 'cell-split limit' postulated from experimental observations is an intrinsic property of the mixture and that external factors such as heat losses are not necessary to cause this limit.

  13. Three-dimensional detonation cellular structures in rectangular ducts using an improved CESE scheme

    NASA Astrophysics Data System (ADS)

    Shen, Yang; Shen, Hua; Liu, Kai-Xin; Chen, Pu; Zhang, De-Liang

    2016-11-01

    The three-dimensional premixed H2-O2 detonation propagation in rectangular ducts is simulated using an in-house parallel detonation code based on the second-order space-time conservation element and solution element (CE/SE) scheme. The simulation reproduces three typical cellular structures by setting appropriate cross-sectional size and initial perturbation in square tubes. As the cross-sectional size decreases, critical cellular structures transforming the rectangular or diagonal mode into the spinning mode are obtained and discussed in the perspective of phase variation as well as decreasing of triple point lines. Furthermore, multiple cellular structures are observed through examples with typical aspect ratios. Utilizing the visualization of detailed three-dimensional structures, their formation mechanism is further analyzed. Project supported by the National Natural Science Foundation of China (Grant Nos. 10732010 and 10972010).

  14. Clot Formation in the Sipunculid Worm Themiste petricola: A Haemostatic and Immune Cellular Response

    PubMed Central

    Lombardo, Tomás; Blanco, Guillermo A.

    2012-01-01

    Clot formation in the sipunculid Themiste petricola, a coelomate nonsegmented marine worm without a circulatory system, is a cellular response that creates a haemostatic mass upon activation with sea water. The mass with sealing properties is brought about by homotypic aggregation of granular leukocytes present in the coelomic fluid that undergo a rapid process of fusion and cell death forming a homogenous clot or mass. The clot structure appears to be stabilized by abundant F-actin that creates a fibrous scaffold retaining cell-derived components. Since preservation of fluid within the coelom is vital for the worm, clotting contributes to rapidly seal the body wall and entrap pathogens upon injury, creating a matrix where wound healing can take place in a second stage. During formation of the clot, microbes or small particles are entrapped. Phagocytosis of self and non-self particles shed from the clot occurs at the clot neighbourhood, demonstrating that clotting is the initial phase of a well-orchestrated dual haemostatic and immune cellular response. PMID:22550489

  15. 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.

  16. 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.

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

    PubMed Central

    Reeves, Raymond

    2009-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Chen, Q.; Rice, A. F.

    2005-03-01

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

  19. 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.

  20. 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

  1. 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

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  4. Structure and formation of microplasmin.

    PubMed Central

    Wu, H L; Shi, G Y; Wohl, R C; Bender, M L

    1987-01-01

    The structure of human microplasmin, prepared from plasmin in alkaline solution, has been studied. Microplasmin consists of two polypeptide chains connected by disulfide bonds. One polypeptide is the B chain of plasmin consisting of 230 amino acids, and the other peptide is the COOH-terminal portion of the A chain of plasmin consisting of 31 amino acid residues. Microplasmin has a molecular weight of 28,635, calculated from its primary sequence. It is slightly more positively charged than plasminogen and is a more hydrophobic molecule. The proposed scheme for the formation of microplasmin involves autolysis at specific peptide bonds and scrambling of especially sensitive disulfide bonds in alkaline solution. PMID:2962191

  5. 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

  6. Development of tailored cellular structure as a novel catalyst integration platform for microreactors

    NASA Astrophysics Data System (ADS)

    Chen, Haibiao

    A silica cellular structure was synthesized as a novel means of enhancing the geometrical surface area of a silicon microreactor with cell diameter, cell interconnectivity, and skeleton density as critical and controllable structural features. Based on theoretical considerations of the pressure drop, mixing, and mechanical stability issues associated with microreactor applications, cell diameter of ˜10 mum, cell interconnectivity of ˜0.4, and fully dense skeleton were determined as synthesis targets. In this synthesis method, surface-selective infiltration, assembly, and partial sintering of polystyrene microspheres in the microchannel were used as mechanisms to create a sacrificial template which represented an inverse structure of the final cellular structure. The polymer template was infiltrated with a silica precursor, and the infiltrated structure was dried and calcined at 500°C to remove the polymer phase and subsequently sintered at 1100°C to form dense silica skeleton. With the use of ˜16 mum polystyrene microspheres, the average cell diameter of ˜12 mum was achieved in the final cellular structure. Cell interconnectivity was controlled to be ˜0.4 by sintering the polystyrene microspheres at 100°C for 180 seconds. Volume shrinkage and crack formation during drying of the infiltrated template structure were significant when the precursor contained small silica particles in the range of several manometers. The volume shrinkage and crack formation could be prevented during drying using the silica precursor containing larger silica particles in the range of ˜40 to 500 nm. However, instability in the cellular structure occurred during sintering due to the delayed volume shrinkage of the specimens prepared with the larger silica particles. Also, the larger particles were more difficult to infiltrate into the interstitial space of the polymer template. In comparison to free-standing cellular specimens prepared by a similar template method, the volume

  7. 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.

  8. A novel role for high-mobility group a proteins in cellular senescence and heterochromatin formation.

    PubMed

    Narita, Masashi; Narita, Masako; Krizhanovsky, Valery; Nuñez, Sabrina; Chicas, Agustin; Hearn, Stephen A; Myers, Michael P; Lowe, Scott W

    2006-08-11

    Cellular senescence is a stable state of proliferative arrest that provides a barrier to malignant transformation and contributes to the antitumor activity of certain chemotherapies. Senescent cells can accumulate senescence-associated heterochromatic foci (SAHFs), which may provide a chromatin buffer that prevents activation of proliferation-associated genes by mitogenic transcription factors. Surprisingly, we show that the High-Mobility Group A (HMGA) proteins, which can promote tumorigenesis, accumulate on the chromatin of senescent fibroblasts and are essential structural components of SAHFs. HMGA proteins cooperate with the p16(INK4a) tumor suppressor to promote SAHF formation and proliferative arrest and stabilize senescence by contributing to the repression of proliferation-associated genes. These antiproliferative activities are canceled by coexpression of the HDM2 and CDK4 oncogenes, which are often coamplified with HMGA2 in human cancers. Our results identify a component of the senescence machinery that contributes to heterochromatin formation and imply that HMGA proteins also act in tumor suppressor networks.

  9. Experimental approaches to identify cellular G-quadruplex structures and functions.

    PubMed

    Di Antonio, Marco; Rodriguez, Raphaël; Balasubramanian, Shankar

    2012-05-01

    Guanine-rich nucleic acids can fold into non-canonical DNA secondary structures called G-quadruplexes. The formation of these structures can interfere with the biology that is crucial to sustain cellular homeostases and metabolism via mechanisms that include transcription, translation, splicing, telomere maintenance and DNA recombination. Thus, due to their implication in several biological processes and possible role promoting genomic instability, G-quadruplex forming sequences have emerged as potential therapeutic targets. There has been a growing interest in the development of synthetic molecules and biomolecules for sensing G-quadruplex structures in cellular DNA. In this review, we summarise and discuss recent methods developed for cellular imaging of G-quadruplexes, and the application of experimental genomic approaches to detect G-quadruplexes throughout genomic DNA. In particular, we will discuss the use of engineered small molecules and natural proteins to enable pull-down, ChIP-Seq, ChIP-chip and fluorescence imaging of G-quadruplex structures in cellular DNA.

  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. The community structure of human cellular signaling network.

    PubMed

    Diao, Yuanbo; Li, Menglong; Feng, Zinan; Yin, Jiajian; Pan, Yi

    2007-08-21

    Living cell is highly responsive to specific chemicals in its environment, such as hormones and molecules in food or aromas. The reason is ascribed to the existence of widespread and diverse signal transduction pathways, between which crosstalks usually exist, thus constitute a complex signaling network. Evidently, knowledge of topology characteristic of this network could contribute a lot to the understanding of diverse cellular behaviors and life phenomena thus come into being. In this presentation, signal transduction data is extracted from KEGG to construct a cellular signaling network of Homo sapiens, which has 931 nodes and 6798 links in total. Computing the degree distribution, we find it is not a random network, but a scale-free network following a power-law of P(K) approximately K(-gamma), with gamma approximately equal to 2.2. Among three graph partition algorithms, the Guimera's simulated annealing method is chosen to study the details of topology structure and other properties of this cellular signaling network, as it shows the best performance. To reveal the underlying biological implications, further investigation is conducted on ad hoc community and sketch map of individual community is drawn accordingly. The involved experiment data can be found in the supplementary material.

  12. 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

  13. 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.

  14. 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.

  15. Cellular content of ubiquitin and formation of ubiquitin conjugates during chicken spermatogenesis.

    PubMed Central

    Agell, N; Mezquita, C

    1988-01-01

    Ubiquitin was purified from chicken testis and its content, biosynthesis and formation of conjugates was determined in germinal cells at successive stages of spermatogenesis. Free ubiquitin increased markedly during spermatogenesis, reaching its maximum level in early spermatids. High levels of ubiquitin were still present in late spermatids but were not detectable in mature spermatozoa. Biosynthesis of ubiquitin occurred in vitro in a fraction containing meiotic and pre-meiotic cells, and during spermiogenesis, in early and late spermatids. The cellular content of free ubiquitin increased after ATP depletion, especially in early spermatids. Lysates of chicken testis cells, particularly those obtained from spermatids, were able to form nuclear (24 and 27 kDa) and extranuclear (55-90 kDa) ubiquitin conjugates in vitro. The presence of increasing levels of ubiquitin and ubiquitin conjugates in chicken spermatids may suggest a possible involvement of this protein in the marked changes of protein turnover, chromatin structure and cell-cell interactions that spermatids undergo during spermiogenesis. Images Fig. 1. Fig. 2. Fig. 7. PMID:2839150

  16. 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.

  17. Characterization of cuttlebone for a biomimetic design of cellular structures

    NASA Astrophysics Data System (ADS)

    Cadman, Joseph; Zhou, Shiwei; Chen, Yuhang; Li, Wei; Appleyard, Richard; Li, Qing

    2010-03-01

    Cuttlebone is a natural material possessing the multifunctional properties of high porosity, high flexural stiffness and compressive strength, making it a fine example of design optimization of cellular structures created by nature. Examination of cuttlebone using scanning electron microscopy (SEM) reveals an approximately periodic microstructure, appropriate for computational characterization using direct homogenization techniques. In this paper, volume fractions and stiffness tensors were determined based on two different unit cell models that were extracted from two different cuttlefish samples. These characterized results were then used as the target values in an inverse homogenization procedure aiming to re-generate microstructures with the same properties as cuttlebone. Unit cells with similar topologies to the original cuttlebone unit cells were achieved, attaining the same volume fraction (i.e. bulk density) and the same (or very close) stiffness tensor. In addition, a range of alternate unit cell topologies were achieved also attaining the target properties, revealing the non-unique nature of this inverse homogenization problem.

  18. Natural photonic crystals: formation, structure, function

    NASA Astrophysics Data System (ADS)

    Bartl, Michael H.; Dahlby, Michael R.; Barrows, Frank P.; Richens, Zachary J.; Terooatea, Tommy; Jorgensen, Matthew R.

    2012-03-01

    The structure and properties of natural photonic crystals are discussed using the colored scales of the beetle Lamprocyphus augustus as an example. While the exact mechanism behind the formation of these biopolymeric photonic structures has yet to be fully explored, similarities of these structures to intracellular cubic membrane architectures are introduced. Some crucial parameters behind the formation of cubic membranes are discussed. Using these insights, intracellular cubic membrane structures are transformed into an extracellular environment.

  19. Cellular Model Simulations of Solidification Structures in Ternary Alloys

    NASA Astrophysics Data System (ADS)

    Alsoruji, Ghazi H.

    Solidification processes are an important part of many modem manufacturing processes. They can be found in different casting and welding processes. The solidification structure is very important for the quality of any product manufactured by such processes. This is so because the casting or weldment microstructure determines their mechanical properties. For welding processes, solidification theories can explain the evolution of the fusion zone microstructure and how this microstructure is influenced by the solidification parameters such as the temperature gradient and the solidification rate. In order to investigate the solidification parameters' effect on the microstructure, a numerical model based on Cellular Automaton combined with the finite difference method (CA-FD) is presented in this thesis. The simulation is conducted on a finite three dimensional control volume of the fusion zone. The model takes into account the solute-, curvature-, and kinetic undercooling. The temperatures are assumed to be distributed linearly within the control volume. The model predicts the morphology and density of the microstructure according to different values of the cooling rate and initial temperatures. It is demonstrated that the solidification structure has a columnar morphology at high temperature gradients and low cooling rates. The morphology changes to dendritic as the temperature gradient decreases and/or the cooling rate increases. It is also shown that an increase in the cooling rate results in the densification of the solidification structure. The results demonstrate that an increase in the initial substrate roughness can result in the increase in the density of the solidification structure. The simulation results show an agreement with the constitutional undercooling theory of solidification structures.

  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. Singlet oxygen oxidation of isolated and cellular DNA: product formation and mechanistic insights.

    PubMed

    Cadet, Jean; Ravanat, Jean-Luc; Martinez, Glaucia R; Medeiros, Marisa H G; Di Mascio, Paolo

    2006-01-01

    This survey focuses on recent aspects of the singlet oxygen oxidation of the guanine moiety of nucleosides, oligonucleotides, isolated and cellular DNA that has been shown to be the exclusive DNA target for this biologically relevant photogenerated oxidant. A large body of mechanistic data is now available from studies performed on nucleosides in both aprotic solvents and aqueous solutions. A common process to both reaction conditions is the formation of 8-oxo-7,8-dihydroguanine by reduction of 8-hydroperoxyguanine that arises from the rearrangement of initially formed endoperoxide across the 4,8-bond of the purine moiety. However, in organic solvent the hydroperoxide is converted as a major degradation pathway into a dioxirane that subsequently decomposes into a complex pattern of oxidation products. A different reaction that involved the formation of a highly reactive quinonoid intermediate consecutively to the loss of a water molecule from the 8-hydroperoxide has been shown to occur in aqueous solution. Subsequent addition of a water molecule at C5 leads to the generation of a spiroiminodihy-dantoin compound via a rearrangement that involves an acyl shift. However, in both isolated and cellular DNA the latter decomposition pathway is at the best a minor process, because only 8-oxo-7,8-dihydroguanine has been found to be generated. It is interesting to point out that singlet oxygen has been shown to contribute predominantly to the formation of 8-oxo-7,8-dihydroguanine in the DNA of bacterial and human cells upon exposure to UVA radiation. It may be added that the formation of secondary singlet-oxygen oxidation products of 8-oxo-7,8-dihydroguanine, including spiroiminodihydantoin and oxaluric acid that were characterized in nucleosides and oligonucleotide, respectively, have not yet been found in cellular DNA.

  2. Radiation-induced damage to cellular DNA: Chemical nature and mechanisms of lesion formation

    NASA Astrophysics Data System (ADS)

    Cadet, Jean; Wagner, J. Richard

    2016-11-01

    This mini-review focuses on the recent identification of several novel radiation-induced single and tandem modifications in cellular DNA. For this purpose accurate high-performance electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) was applied allowing their quantitative measurement and unambiguous characterization. Exposure of human cells to gamma rays led to the formation of several modified bases arising from the rearrangement of the pyrimidine ring of thymine, cytosine and 5-methylcytosine subsequent to initial addition of an hydroxyl radical (•OH) to the 5,6-ethylenic bond. In addition, 5-hydroxymethylcytosine, an novel epigenetic mark, and 5-formylcytosine, were found to be generated consecutively to •OH-mediated hydrogen abstraction from the methyl group of 5-methylcytosine. Relevant mechanistic information on one-oxidation reactions of cellular DNA was also gained from the detection of 5-hydroxycytosine and guanine-thymine intra-strand adducts whose formation is rationalized by the generation of related base radical cation. Attempts to search for the radiation-induced formation of purine 5‧,8-cyclo-2‧-deoxyribonucleosides were unsuccessful with the exception of trace amounts of (5‧S)-5‧,8-cyclo-2‧-deoxyadenosine.

  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. Tissue and cellular basis for impaired bone formation in aluminum-related osteomalacia in the pig.

    PubMed Central

    Sedman, A B; Alfrey, A C; Miller, N L; Goodman, W G

    1987-01-01

    Bone formation is impaired in aluminum-associated bone disease. Reductions in the number of osteoblasts or in the function of individual osteoblasts could account for this finding. Thus, quantitative bone histology and measurements of bone formation were done at three skeletal sites in piglets given aluminum (Al) parenterally, 1.5 mg/kg per d, for 8 wk (Al, n = 4) and in control animals (C, n = 4). Bone Al was 241 +/- 40 mg/kg per dry weight in Al and 1.6 +/- 0.9 in C, P less than 0.001. All Al-treated animals developed osteomalacia with increases in osteoid seam width, osteoid volume, and mineralization lag time at each skeletal site, P less than 0.05 vs. C for all values. Mineralized bone formation at the tissue level was lower in Al than in C, P less than 0.05 for each skeletal site, due to reductions in active bone forming surface. Bone formation at the cellular level was similar in each group, however, and total osteoid production by osteoblasts did not differ in C and Al. Aluminum impairs the formation of mineralized bone in vivo by decreasing the number of active osteoblasts, and this change can be distinguished from the effect of aluminum to inhibit, either directly or indirectly, the calcification of osteoid. PMID:3793934

  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. Directed self-assembly of large scaffold-free multi-cellular honeycomb structures.

    PubMed

    Tejavibulya, Nalin; Youssef, Jacquelyn; Bao, Brian; Ferruccio, Toni-Marie; Morgan, Jeffrey R

    2011-09-01

    A significant challenge to the field of biofabrication is the rapid construction of large three-dimensional (3D) living tissues and organs. Multi-cellular spheroids have been used as building blocks. In this paper, we create large multi-cellular honeycomb building blocks using directed self-assembly, whereby cell-to-cell adhesion, in the context of the shape and obstacles of a micro-mold, drives the formation of a 3D structure. Computer-aided design, rapid prototyping and replica molding were used to fabricate honeycomb-shaped micro-molds. Nonadhesive hydrogels cast from these micro-molds were equilibrated in the cell culture medium and seeded with two types of mammalian cells. The cells settled into the honeycomb recess were unable to attach to the nonadhesive hydrogel and so cell-to-cell adhesion drove the self-assembly of a large multi-cellular honeycomb within 24 h. Distinct morphological changes occurred to the honeycomb and its cells indicating the presence of significant cell-mediated tension. Unlike the spheroid, whose size is constrained by a critical diffusion distance needed to maintain cell viability, the overall size of the honeycomb is not limited. The rapid production of the honeycomb building unit, with its multiple rings of high-density cells and open lumen spaces, offers interesting new possibilities for biofabrication strategies.

  7. 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.

  8. Specific Human and Candida Cellular Interactions Lead to Controlled or Persistent Infection Outcomes during Granuloma-Like Formation

    PubMed Central

    Misme-Aucouturier, Barbara; Albassier, Marjorie

    2016-01-01

    ABSTRACT A delayed type of multicellular process could be crucial during chronic candidiasis in determining the course of infection. This reaction, consisting of organized immune cells surrounding the pathogen, initiates an inflammatory response to avoid fungal dissemination. The goal of the present study was to examine, at an in vitro cellular scale, Candida and human immune cell interaction dynamics during a long-term period. By challenging human peripheral blood immune cells from 10 healthy donors with 32 Candida albicans and non-albicans (C. glabrata, C. tropicalis, C. parapsilosis, C. dubliniensis, C. lusitaniae, C. krusei, and C. kefyr) clinical isolates, we showed that Candida spp. induced the formation of granuloma-like structures within 6 days after challenge, but their sizes and the respective fungal burdens differed according to the Candida species. These two parameters are positively correlated. Phenotypic characteristics, such as hypha formation and higher axenic growth rate, seem to contribute to yeast persistence within granuloma-like structures. We showed an interindividual variability of the human response against Candida spp. Higher proportions of neutrophils and elevated CD4+/CD8+ T cell ratios during the first days after challenge were correlated with early production of gamma interferon (IFN-γ) and associated with controlled infection. In contrast, the persistence of Candida could result from upregulation of proinflammatory cytokines such as interleukin-6 (IL-6), IFN-γ, and tumor necrosis factor alpha (TNF-α) and a poor anti-inflammatory negative feedback (IL-10). Importantly, regulatory subsets of NK cells and CD4lo CD8hi doubly positive (DP) lymphocytes at late stage infiltrate granuloma-like structures and could correlate with the IL-10 and TNF-α production. These data offer a base frame to explain cellular events that guide infection control or fungal persistence. PMID:27799331

  9. 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.

  10. Emergence of linguistic-like structures in one-dimensional cellular automata

    NASA Astrophysics Data System (ADS)

    Bertacchini, Francesca; Bilotta, Eleonora; Caldarola, Fabio; Pantano, Pietro; Bustamante, Leonardo Renteria

    2016-10-01

    In this paper we give a summary of some empirical investigations which show high analogies between Cellular Automata and linguistic structures. In particular we show as coupling regular domains of Cellular Automata we find complex emerging structures similar to combination of words, phonemes and morphemes in natural languages.

  11. 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

  12. Mapping brain structure and function: cellular resolution, global perspective.

    PubMed

    Zupanc, Günther K H

    2017-04-01

    A comprehensive understanding of the brain requires analysis, although from a global perspective, with cellular, and even subcellular, resolution. An important step towards this goal involves the establishment of three-dimensional high-resolution brain maps, incorporating brain-wide information about the cells and their connections, as well as the chemical architecture. The progress made in such anatomical brain mapping in recent years has been paralleled by the development of physiological techniques that enable investigators to generate global neural activity maps, also with cellular resolution, while simultaneously recording the organism's behavioral activity. Combination of the high-resolution anatomical and physiological maps, followed by theoretical systems analysis of the deduced network, will offer unprecedented opportunities for a better understanding of how the brain, as a whole, processes sensory information and generates behavior.

  13. 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.

  14. 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.

  15. 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

  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. 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

  18. "Parking-garage" structures in nuclear astrophysics and cellular biophysics

    NASA Astrophysics Data System (ADS)

    Berry, D. K.; Caplan, M. E.; Horowitz, C. J.; Huber, Greg; Schneider, A. S.

    2016-11-01

    A striking shape was recently observed for the endoplasmic reticulum, a cellular organelle consisting of stacked sheets connected by helical ramps [Terasaki et al., Cell 154, 285 (2013), 10.1016/j.cell.2013.06.031]. This shape is interesting both for its biological function, to synthesize proteins using an increased surface area for ribosome factories, and its geometric properties that may be insensitive to details of the microscopic interactions. In the present work, we find very similar shapes in our molecular dynamics simulations of the nuclear pasta phases of dense nuclear matter that are expected deep in the crust of neutron stars. There are dramatic differences between nuclear pasta and terrestrial cell biology. Nuclear pasta is 14 orders of magnitude denser than the aqueous environs of the cell nucleus and involves strong interactions between protons and neutrons, while cellular-scale biology is dominated by the entropy of water and complex assemblies of biomolecules. Nonetheless, the very similar geometry suggests both systems may have similar coarse-grained dynamics and that the shapes are indeed determined by geometrical considerations, independent of microscopic details. Many of our simulations self-assemble into flat sheets connected by helical ramps. These ramps may impact the thermal and electrical conductivities, viscosity, shear modulus, and breaking strain of neutron star crust. The interaction we use, with Coulomb frustration, may provide a simple model system that reproduces many biologically important shapes.

  19. Evolution of atomic structure during nanoparticle formation

    DOE PAGES

    Tyrsted, Christoffer; Lock, Nina; Jensen, Kirsten M. Ø.; ...

    2014-04-14

    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 structuremore » 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.« less

  20. Correlation between effects of 24 different cytochalasins on cellular structures and cellular events and those on actin in vitro

    PubMed Central

    Yahara, I; Harada, F; Sekita, S; Yoshihira, K; Natori, S

    1982-01-01

    To compare the effects of cytochalasins on the cellular level with those on the molecular level, 24 cytochalasins, 20 natural compounds and 4 derivatives, were used. The following effects were tested for each of 24 cytochalasins; (a) four high dose (2-20 muM) effects on the cellular level: rounding up of fibroblastic cells, contraction of actin cables, formation of hairy filaments containing actin, and inhibition of lymphocyte capping; (b) a low dose (0.2-2 muM) effect: inhibition of membrane ruffling; and (c) two in vitro effects: an inhibition of actin filament elongation (the high affinity effect [low dose effect] in vitro) and an effect on viscosity of actin filaments(the low affinity effect [high dose effect] in vitro). These results indicated that there are almost the same hierarchic orders of relative effectiveness of different cytochalasins between low and high dose effects and between cellular and molecular effects. From the data obtained with the 24 cytochalasins, we have calculated correlation coefficients of 0.87 and 0.79 between an effect in vivo, inhibition of capping, and an effect in vitro, inhibition of actin filament elongation, as well as between inhibition of capping and another effect in vitro, effect on viscosity of actin filaments, respectively. Furthermore, a correlation coefficient between the high affinity effect and the low affinity effect determined in vitro was calculated to be 0.90 from the data obtained in this study. The strong positive correlation among low and high dose effects in vivo and those in vitro suggests that most of the effects caused by a cytochalasin, irrespective of doses or affected phenomena, might be attributed to the interaction between the drug and the common target protein, actin. In the course of the immunofluorescence microscope study on cytochalasin-treated cells using actin antibody, we have found that aspochalasin D, a 10-isopropylcytochalasin, strongly induced the formation of rodlets containing actin in

  1. Mechanisms for Cellular NO Oxidation and Nitrite Formation in Lung Epithelial Cells

    PubMed Central

    Zhao, Xue-Jun; Wang, Ling; Shiva, Sruti; Tejero, Jesus; Wang, Jun; Frizzell, Sam; Gladwin, Mark T.

    2013-01-01

    either nitrite or cellular S-nitrosothiol (SNO) formation compared to scrambled siRNA control under basal conditions or cytokine stimulation. These data suggest that lung epithelial cells possess NO oxidase activity, which is enhanced in cell membrane associated proteins and not regulated by intracellular or secreted Cp, indicating that alternative NO oxidases determine hypoxic and normoxic nitrite formation from NO in human lung epithelial cells. PMID:23639566

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    PubMed Central

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

    2016-01-01

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

  10. Stochastic metallic-glass cellular structures exhibiting benchmark strength.

    PubMed

    Demetriou, Marios D; Veazey, Chris; Harmon, John S; Schramm, Joseph P; Johnson, William L

    2008-10-03

    By identifying the key characteristic "structural scales" that dictate the resistance of a porous metallic glass against buckling and fracture, stochastic highly porous metallic-glass structures are designed capable of yielding plastically and inheriting the high plastic yield strength of the amorphous metal. The strengths attainable by the present foams appear to equal or exceed those by highly engineered metal foams such as Ti-6Al-4V or ferrous-metal foams at comparable levels of porosity, placing the present metallic-glass foams among the strongest foams known to date.

  11. Continuum Theory of Dislocations: Cell Structure Formation

    NASA Astrophysics Data System (ADS)

    Limkumnerd, Surachate; Sethna, James P.

    2005-03-01

    Line-like topological defects inside metals are called dislocations. These dislocations in late stages of hardening form patterns called cell structures. We are developing a mesoscale theory for the formation of cell structures that systematically derives the order parameter fields and evolution laws from the conserved topological Burgers vector density or the Nye dislocation tensor. (In classical plasticity theories, describing scales large compared to these cells, one normally bypasses the complicated motions of the dislocations by supplying yield surface and plastic hardening function in order to determine the evolution of state variables.) Using Landau approach and a closure approximation, an evolution equation for the dislocation density tensor is obtained by employing simple symmetry arguments and the constraint that the elastic energy must decrease with time at fixed stress. The evolution laws lead to singularity formation at finite times, which we expect will be related to the formation of cell walls. Implementation of finite difference simulations using the upwind scheme and the results in one and higher dimensions will be discussed.

  12. Stochastic structure formation in random media

    NASA Astrophysics Data System (ADS)

    Klyatskin, V. I.

    2016-01-01

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

  13. 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.

  14. 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.

  15. Cellular and Molecular Changes Associated with Onion Skin Formation Suggest Involvement of Programmed Cell Death

    PubMed Central

    Galsurker, Ortal; Doron-Faigenboim, Adi; Teper-Bamnolker, Paula; Daus, Avinoam; Fridman, Yael; Lers, Amnon; Eshel, Dani

    2017-01-01

    Skin formation of onion (Allium cepa L.) bulb involves scale desiccation accompanied by scale senescence, resulting in cell death and tissue browning. Understanding the mechanism of skin formation is essential to improving onion skin and bulb qualities. Although onion skin plays a crucial role in postharvest onion storage and shelf life, its formation is poorly understood. We investigated the mode of cell death in the outermost scales that are destined to form the onion skin. Surprisingly, fluorescein diacetate staining and scanning electron microscopy indicated that the outer scale desiccates from the inside out. This striking observation suggests that cell death in the outer scales, during skin formation, is an internal and organized process that does not derive only from air desiccation. DNA fragmentation, a known hallmark of programmed cell death (PCD), was revealed in the outer scales and gradually decreased toward the inner scales of the bulb. Transmission electron microscopy further revealed PCD-related structural alterations in the outer scales which were absent from the inner scales. De novo transcriptome assembly for three different scales: 1st (outer), 5th (intermediate) and 8th (inner) fleshy scales identified 2,542 differentially expressed genes among them. GO enrichment for cluster analysis revealed increasing metabolic processes in the outer senescent scale related to defense response, PCD processes, carbohydrate metabolism and flavonoid biosynthesis, whereas increased metabolism and developmental growth processes were identified in the inner scales. High expression levels of PCD-related genes were identified in the outer scale compared to the inner ones, highlighting the involvement of PCD in outer-skin development. These findings suggest that a program to form the dry protective skin exists and functions only in the outer scales of onion. PMID:28119713

  16. Cellular and Molecular Changes Associated with Onion Skin Formation Suggest Involvement of Programmed Cell Death.

    PubMed

    Galsurker, Ortal; Doron-Faigenboim, Adi; Teper-Bamnolker, Paula; Daus, Avinoam; Fridman, Yael; Lers, Amnon; Eshel, Dani

    2016-01-01

    Skin formation of onion (Allium cepa L.) bulb involves scale desiccation accompanied by scale senescence, resulting in cell death and tissue browning. Understanding the mechanism of skin formation is essential to improving onion skin and bulb qualities. Although onion skin plays a crucial role in postharvest onion storage and shelf life, its formation is poorly understood. We investigated the mode of cell death in the outermost scales that are destined to form the onion skin. Surprisingly, fluorescein diacetate staining and scanning electron microscopy indicated that the outer scale desiccates from the inside out. This striking observation suggests that cell death in the outer scales, during skin formation, is an internal and organized process that does not derive only from air desiccation. DNA fragmentation, a known hallmark of programmed cell death (PCD), was revealed in the outer scales and gradually decreased toward the inner scales of the bulb. Transmission electron microscopy further revealed PCD-related structural alterations in the outer scales which were absent from the inner scales. De novo transcriptome assembly for three different scales: 1st (outer), 5th (intermediate) and 8th (inner) fleshy scales identified 2,542 differentially expressed genes among them. GO enrichment for cluster analysis revealed increasing metabolic processes in the outer senescent scale related to defense response, PCD processes, carbohydrate metabolism and flavonoid biosynthesis, whereas increased metabolism and developmental growth processes were identified in the inner scales. High expression levels of PCD-related genes were identified in the outer scale compared to the inner ones, highlighting the involvement of PCD in outer-skin development. These findings suggest that a program to form the dry protective skin exists and functions only in the outer scales of onion.

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

    PubMed

    Li, Jianchao; Lu, Qing; Zhang, Mingjie

    2016-08-01

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

  18. 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).

  19. STRUCTURE FORMATION IN THE SYMMETRON MODEL

    SciTech Connect

    Davis, Anne-Christine; Li Baojiu; Mota, David F.; Winther, Hans A.

    2012-03-20

    Scalar fields, strongly coupled to matter, can be present in nature and still be invisible to local experiments if they are subject to a screening mechanism. The symmetron is one such mechanism that relies on restoration of a spontaneously broken symmetry in regions of high density to shield the scalar fifth force. We have investigated structure formation in the symmetron model by using N-body simulations and find observable signatures in both the linear and nonlinear matter power spectrum and on the halo mass function. The mechanism for suppressing the scalar fifth force in high-density regions is also found to work very well.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Specificity of cellular expression of C. variopedatus polychaete innexin in the developing embryo: evolutionary aspects of innexins' heterogeneous gene structures.

    PubMed

    Potenza, Nicoletta; del Gaudio, Rosanna; Chiusano, Maria Luisa; Russo, Giuseppina Maria Rosaria; Geraci, Giuseppe

    2003-01-01

    Innexins are a family of membrane proteins involved in the formation of gap junctions in invertebrates. They have been found to participate in several aspects of cell differentiation and in embryonic patterning through the formation of specific intercellular communication channels. We present here data showing that the recently identified innexin of the marine worm Chaetopterus variopedatus is expressed only in particular cells of the early stage, demonstrating cell specificity of innexin expression also in polychaete annelids. Phylogenetic analysis of all known innexins results in a phylogenetic tree clearly distinguishing insect, nematode, and other invertebrate innexins. Comparative analysis of proteins and known related genes shows that the apparent similarity of protein composition, overall structural organization, and specificity of cellular expression, typical of innexins of all studied organisms, correspond to highly heterogeneous gene structures even for genes that are in close contiguity on the same chromosome. A possible evolutionary motive producing this situation is discussed.

  5. 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.

  6. Modulated structure formation in demixing paraffin blends

    NASA Astrophysics Data System (ADS)

    Gilbert, E. P.

    Small angle scattering (SANS and SAXS) and differential scanning calorimetry have been measured from C28:C36 normal paraffin mixtures of varying composition quenched from the melt. Satellite peaks are observed in the SAXS whose offset in Q, relative to Bragg diffraction peaks associated with the average structure, are composition dependent. The offset is close to the position of the most intense peak observed in SANS. Scattering from the quenched structures is consistent with a correlated displacement and substitutional disorder model yielding modulations that are incommensurate with the average lattice. DSC shows an additional endotherm in the mixtures that is not present in the pure components and is associated with this superstructure formation.

  7. Tribological behavior of Ti6Al4V cellular structures produced by Selective Laser Melting.

    PubMed

    Bartolomeu, F; Sampaio, M; Carvalho, O; Pinto, E; Alves, N; Gomes, J R; Silva, F S; Miranda, G

    2017-05-01

    Additive manufacturing (AM) technologies enable the fabrication of innovative structures with complex geometries not easily manufactured by traditional processes. Regarding metallic cellular structures with tailored/customized mechanical and wear performance aiming to biomedical applications, Selective Laser Melting (SLM) is a remarkable solution for their production. Focusing on prosthesis and implants, in addition to a suitable Young's modulus it is important to assess the friction response and wear resistance of these cellular structures in a natural environment. In this sense, five cellular Ti6Al4V structures with different open-cell sizes (100-500µm) were designed and produced by SLM. These structures were tribologicaly tested against alumina using a reciprocating sliding ball-on-plate tribometer. Samples were submerged in Phosphate Buffered Saline (PBS) fluid at 37°C, in order to mimic in some extent the human body environment. The results showed that friction and wear performance of Ti6Al4V cellular structures is influenced by the structure open-cell size. The higher wear resistance was obtained for structures with 100µm designed open-cell size due to the higher apparent area of contact to support tribological loading.

  8. 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

  9. 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.

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

    PubMed

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

    2014-10-03

    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.

  11. 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.

  12. 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

  13. Modulating cellular recombination potential through alterations in RecA structure and regulation.

    PubMed

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

    2010-12-01

    The wild-type Escherichia 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 sixfold. Autoinhibition by the RecA C-terminus can affect recombination frequency by factors up to fourfold. 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 E. 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.

  14. 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

  15. 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.

  16. Phosphatidylinositol 4-kinase IIβ negatively regulates invadopodia formation and suppresses an invasive cellular phenotype

    PubMed Central

    Alli-Balogun, Ganiyu Olabanji; Gewinner, Christina A.; Jacobs, Ruth; Kriston-Vizi, Janos; Waugh, Mark G.; Minogue, Shane

    2016-01-01

    The type II phosphatidylinositol 4-kinase (PI4KII) enzymes synthesize the lipid phosphatidylinositol 4-phosphate (PI(4)P), which has been detected at the Golgi complex and endosomal compartments and recruits clathrin adaptors. Despite common mechanistic similarities between the isoforms, the extent of their redundancy is unclear. We found that depletion of PI4KIIα and PI4KIIβ using small interfering RNA led to actin remodeling. Depletion of PI4KIIβ also induced the formation of invadopodia containing membrane type I matrix metalloproteinase (MT1-MMP). Depletion of PI4KII isoforms also differentially affected trans-Golgi network (TGN) pools of PI(4)P and post-TGN traffic. PI4KIIβ depletion caused increased MT1-MMP trafficking to invasive structures at the plasma membrane and was accompanied by reduced colocalization of MT1-MMP with membranes containing the endosomal markers Rab5 and Rab7 but increased localization with the exocytic Rab8. Depletion of PI4KIIβ was sufficient to confer an aggressive invasive phenotype on minimally invasive HeLa and MCF-7 cell lines. Mining oncogenomic databases revealed that loss of the PI4K2B allele and underexpression of PI4KIIβ mRNA are associated with human cancers. This finding supports the cell data and suggests that PI4KIIβ may be a clinically significant suppressor of invasion. We propose that PI4KIIβ synthesizes a pool of PI(4)P that maintains MT1-MMP traffic in the degradative pathway and suppresses the formation of invadopodia. PMID:27798239

  17. 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

  18. 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.

  19. 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

  20. Septin9 is involved in septin filament formation and cellular stability.

    PubMed

    Füchtbauer, Annette; Lassen, Louise B; Jensen, Astrid B; Howard, Jennifer; Quiroga, Adán de Salas; Warming, Søren; Sørensen, Annette B; Pedersen, Finn S; Füchtbauer, Ernst-Martin

    2011-08-01

    Septin9 (Sept9) is a member of the filament-forming septin family of structural proteins and is associated with a variety of cancers and with hereditary neuralgic amyotrophy. We have generated mice with constitutive and conditional Sept9 knockout alleles. Homozygous deletion of Sept9 results in embryonic lethality around day 10 of gestation whereas mice homozygous for the conditional allele develop normally. Here we report the consequences of homozygous loss of Sept9 in immortalized murine embryonic fibroblasts. Proliferation rate was not changed but cells without Sept9 had an altered morphology compared to normal cells, particularly under low serum stress. Abnormal, fragmented, and multiple nuclei were more frequent in cells without Sept9. Cell migration, as measured by gap-filling and filter-invasion assays, was impaired, but individual cells did not move less than wild-type cells. Sept9 knockout cells showed a reduced resistance to hypo-osmotic stress. Stress fiber and vinculin staining at focal adhesion points was less prominent. Long septin filaments stained for Sept7 disappeared. Instead, staining was found in short, often curved filaments and rings. Furthermore, Sept7 was no longer localized to the mitotic spindle. Together, these data reveal the importance of Sept9 for septin filament formation and general cell stability.

  1. Diagnosing delayed ettringite formation in concrete structures

    SciTech Connect

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

    2008-06-15

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

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

    PubMed

    Guan, Lirui; Disney, Matthew D

    2013-09-16

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

  3. Photothermal evaluation of the influence of nicotine, antitumor drugs, and radiation on cellular absorbing structures

    NASA Astrophysics Data System (ADS)

    Zharov, Vladimir P.; Galitovsky, Valentin; Chowdhury, Parimal; Chambers, Timothy

    2004-07-01

    This short review presents findings from a recent evaluation of the diagnostic capabilities of a new experimental design of the advanced photothermal (PT) imaging system; specifically, its performance in studying the impact of nicotine, a combination of antitumor drugs, and radiation on the absorbing structures of various cells. We used this imaging system to test our hypothesis that low doses of chemicals or drugs lead to changes in cell metabolism, that these changes are accompanied by the shrinking of cellular absorbing zones (e.g. organelles), and that these reactions cause increased local absorption. Conversely, high (toxic) doses may lead to swelling of organelles or release of chromophores into the intracellular space, causing decreased local absorption. In this study, we compared PT images and PT responses of the pancreatic exocrine tumor cell line AR42J resulting from exposure to various concentrations of nicotine versus those of control cells. We found that responses were almost proportional to the drug concentration in concentrations ranging from 1 nM-100 μM, reached saturation at a maximum of approximately 100 μM-1 mM, and then fell rapidly at concentrations ranging from 1-50 mM. We also examined the influence of antitumor drugs (vinblastine and paclitaxel) on KB3 carcinoma cells, with drug concentrations ranging from 10-10 nM to 10 nM. In this instance, exposure initially led to slight cell activation, which was then followed by decreased cellular PT response. Drug administration led to corresponding changes in the amplitude and spatial intracellular localization of PT responses, including bubble formation, as an indicator of local absorption level. Additionally, it was shown that, depending on cell type, x-ray radiation may produce effects similar to those resulting from exposure to drugs. Independent verification with a combined PT-fluorescence assay and conventional staining kits (trypan blue, Annexin V-propidium iodide [PI]) revealed that this

  4. 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.

  5. 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.

  6. Distinct BimBH3 (BimSAHB) stapled peptides for structural and cellular studies.

    PubMed

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

    2014-03-21

    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.

  7. Cellular requirements for the formation of EA rosettes by human monocytes.

    PubMed Central

    Passwell, J H; Schneeberger, E; Merler, E

    1978-01-01

    The binding of sensitized red cells to Fc receptors in human monocytes was studied by evaluating the effects of various pharmacological reagents and other treatments on EA rosette formation. Cytochalasin B and 2-deoxyglucose inhibited rosette formation in a dose-dependent manner. Sodium azide and incubation at 4 degrees also inhibited rosette formation, while at 37 degrees increased numbers of RBCs bound to the monocytes. The microtubular poisons, vinblastine and colchicine at high concentrations resulted in decreased adherence of monocytes and inhibition of rosette formation, while at low concentrations of colchicine, enhanced rosette formation was sometimes observed. Contrary to the effects on rosette formation, binding of [125I] IgG to monocyte monolayers was not altered by treatment of the monocytes with drugs. Magnesium ions were required to promote monocyte adherence, but both magnesium and calcium were needed for the best rosette formation. We conclude that the formation of EA rosettes is dependent not merely on binding of IgG to the Fc receptor but requires metabolically active monocytes, an intact cytostructure and suitable environmental conditions (temperature and cation concentration). Images Figure 3 PMID:738764

  8. 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.

  9. 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.

  10. 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.

  11. Formation of terahertz beams produced by artificial dielectric periodical structures

    NASA Astrophysics Data System (ADS)

    Khodzitsky, Mikhail K.; Vozianova, Anna V.; Gill, Viktoria V.; Chernyadiev, Alexander V.; Grebenchukov, Alexandr N.; Minin, Igor V.; Minin, Oleg V.

    2016-09-01

    This paper presents an investigation of terajets formation by dielectric periodic structure at terahertz frequencies in effective medium regime (photonic metamaterial). The dispersions of effective permittivity for three periodic structures formed by different types of plastics (ABS, PLA, Crystal) were analytically obtained for both regimes. Numerical simulation of this structure was performed by using COMSOL Multiphysics. The terajet formation was numerically shown.

  12. 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.

  13. 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.

  14. A Unique Tool for Cellular Structural Biology: In-cell NMR*

    PubMed Central

    Luchinat, Enrico; Banci, Lucia

    2016-01-01

    Conventional structural and chemical biology approaches are applied to macromolecules extrapolated from their native context. When this is done, important structural and functional features of macromolecules, which depend on their native network of interactions within the cell, may be lost. In-cell nuclear magnetic resonance is a branch of biomolecular NMR spectroscopy that allows macromolecules to be analyzed in living cells, at the atomic level. In-cell NMR can be applied to several cellular systems to obtain biologically relevant structural and functional information. Here we summarize the existing approaches and focus on the applications to protein folding, interactions, and post-translational modifications. PMID:26677229

  15. Roles of afadin in the formation of the cellular architecture of the mouse hippocampus and dentate gyrus.

    PubMed

    Miyata, Muneaki; Maruo, Tomohiko; Kaito, Aika; Wang, Shujie; Yamamoto, Hideaki; Fujiwara, Takeshi; Mizoguchi, Akira; Mandai, Kenji; Takai, Yoshimi

    2017-03-01

    The hippocampal formation with tightly packed neurons, mainly at the dentate gyrus, CA3, CA2, and CA1 regions, constitutes a one-way neural circuit, which is associated with learning and memory. We previously showed that the cell adhesion molecules nectins and its binding protein afadin play roles in the formation of the mossy fiber synapses which are formed between the mossy fibers of the dentate gyrus granule cells and the dendrites of the CA3 pyramidal cells. We showed here that in the afadin-deficient hippocampal formation, the dentate gyrus granules cells and the CA3, CA2, and CA1 pyramidal cells were abnormally located; the mossy fiber trajectory was abnormally elongated; the CA3 pyramidal cells were abnormally differentiated; and the densities of the presynaptic boutons on the mossy fibers and the apical dendrites of the CA3 pyramidal cells were decreased. These results indicate that afadin plays roles not only in the formation of the mossy fiber synapses but also in the formation of the cellular architecture of the hippocampus and the dentate gyrus.

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

    PubMed

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

    2013-03-01

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

  17. Linking Cellular and Mechanical Processes in Articular Cartilage Lesion Formation: A Mathematical Model

    PubMed Central

    Kapitanov, Georgi I.; Wang, Xiayi; Ayati, Bruce P.; Brouillette, Marc J.; Martin, James A.

    2016-01-01

    Post-traumatic osteoarthritis affects almost 20% of the adult US population. An injurious impact applies a significant amount of physical stress on articular cartilage and can initiate a cascade of biochemical reactions that can lead to the development of osteoarthritis. In our effort to understand the underlying biochemical mechanisms of this debilitating disease, we have constructed a multiscale mathematical model of the process with three components: cellular, chemical, and mechanical. The cellular component describes the different chondrocyte states according to the chemicals these cells release. The chemical component models the change in concentrations of those chemicals. The mechanical component contains a simulation of a blunt impact applied onto a cartilage explant and the resulting strains that initiate the biochemical processes. The scales are modeled through a system of partial-differential equations and solved numerically. The results of the model qualitatively capture the results of laboratory experiments of drop-tower impacts on cartilage explants. The model creates a framework for incorporating explicit mechanics, simulated by finite element analysis, into a theoretical biology framework. The effort is a step toward a complete virtual platform for modeling the development of post-traumatic osteoarthritis, which will be used to inform biomedical researchers on possible non-invasive strategies for mitigating the disease. PMID:27843894

  18. 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.

  19. Nonlinear structure formation in flat cosmological models

    NASA Technical Reports Server (NTRS)

    Martel, Hugo

    1995-01-01

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

  20. 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

  1. Piezoelectric cellular micro-structured PDMS material for micro-sensors and energy harvesting

    NASA Astrophysics Data System (ADS)

    Kachroudi, A.; Basrour, S.; Rufer, L.; Jomni, F.

    2015-12-01

    This paper reports a novel low-cost fabrication process of a charged cellular microstructured polydimethylsiloxane (PDMS) material referred as piezo-electret or ferro-electret for micro-sensors applications. The dielectric spectra reached on these structures exhibit a high piezoelectric longitudinal coefficient d33 of 350pC/N. A mechanical characterization method proves the reliability of this material for low-frequencies applications around 100Hz.

  2. 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.

  3. 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.

  4. 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

  5. Contributions of Channel Noise to Cellular Responses in the Hippocampal Formation

    NASA Astrophysics Data System (ADS)

    White, John A.

    1998-03-01

    Synchronized firing of nerve cells seems to be an important mechanism used in information processing by higher brain centers. Often, this synchronized activity is oscillatory: rates at which cells fire action potentials rise and fall sinusoidally. In the hippocampal region of the brain -- a part of the brain crucial for learning and memory -- a synchronized pattern of oscillatory activity called the theta rhythm seems crucial for memory-related functions. Some nerve cells of the hippocampal region are individual oscillators: their nonlinear properties make them electrically ``resonant'' at theta frequencies (4-12 Hz). It is presumed that these properties are important for theta-locked synchronization. We have used coordinate experimental and computational studies to study the cellular mechanisms underlying membrane-potential oscillations, with several conclusions. First, nonlinear oscillations and action potentials in these nerve cells are generated principally by four populations of ion channels: two that are selective for sodium and two that are selective for potassium. Second, the number of sodium channels contributing to theta-locked oscillations is small (< 10^4), making ``channel noise'' from the stochastic flicker between conductance states in sodium channels an important noise source in these cells. Third, simulations indicate that channel noise broadens the range of qualitative behaviors that these nerve cells can exhibit with DC stimulation. Fourth, the nonlinear dependence of channel noise on membrane potential may contribute to inter-spike interval statistics seen in experimental preparations. Fifth, channel noise is likely to increase the probability of response to weak periodic stimuli that roughly mimic stimulation patterns seen in live animals. The details of this effect depend critically on the mean lifetime of the open-channel state. Together, these results imply that the properties of single ion channels have important manifestations at the

  6. Protein kinase CK2: structure, regulation and role in cellular decisions of life and death.

    PubMed Central

    Litchfield, David W

    2003-01-01

    Protein kinase CK2 ('casein kinase II') has traditionally been classified as a messenger-independent protein serine/threonine kinase that is typically found in tetrameric complexes consisting of two catalytic (alpha and/or alpha') subunits and two regulatory beta subunits. Accumulated biochemical and genetic evidence indicates that CK2 has a vast array of candidate physiological targets and participates in a complex series of cellular functions, including the maintenance of cell viability. This review summarizes current knowledge of the structural and enzymic features of CK2, and discusses advances that challenge traditional views of this enzyme. For example, the recent demonstrations that individual CK2 subunits exist outside tetrameric complexes and that CK2 displays dual-specificity kinase activity raises new prospects for the precise elucidation of its regulation and cellular functions. This review also discusses a number of the mechanisms that contribute to the regulation of CK2 in cells, and will highlight emerging insights into the role of CK2 in cellular decisions of life and death. In this latter respect, recent evidence suggests that CK2 can exert an anti-apoptotic role by protecting regulatory proteins from caspase-mediated degradation. The mechanistic basis of the observation that CK2 is essential for viability may reside in part in this ability to protect cellular proteins from caspase action. Furthermore, this anti-apoptotic function of CK2 may contribute to its ability to participate in transformation and tumorigenesis. PMID:12396231

  7. The data-and-signals cellular automaton and its application to growing structures.

    PubMed

    Stauffer, André; Sipper, Moshe

    2004-01-01

    In a traditional cellular automaton (CA) a cell is implemented by a rule table defining its state at the next time step, given its present state and those of its neighbors. The cell thus deals only with states. We present a novel CA where the cell handles data and signals. The cell is designed as a digital system comprising a processing unit and a control unit. This allows the realization of various growing structures, including self-replicating loops and biomorphs. We also describe the hardware implementation of these structures within our electronic wall for bio-inspired applications, the BioWall.

  8. 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.

  9. 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

  10. Cell surface attachment structures contribute to biofilm formation and xylem colonization by Erwinia amylovora.

    PubMed

    Koczan, Jessica M; Lenneman, Bryan R; McGrath, Molly J; Sundin, George W

    2011-10-01

    Biofilm formation plays a critical role in the pathogenesis of Erwinia amylovora and the systemic invasion of plant hosts. The functional role of the exopolysaccharides amylovoran and levan in pathogenesis and biofilm formation has been evaluated. However, the role of biofilm formation, independent of exopolysaccharide production, in pathogenesis and movement within plants has not been studied previously. Evaluation of the role of attachment in E. amylovora biofilm formation and virulence was examined through the analysis of deletion mutants lacking genes encoding structures postulated to function in attachment to surfaces or in cellular aggregation. The genes and gene clusters studied were selected based on in silico analyses. Microscopic analyses and quantitative assays demonstrated that attachment structures such as fimbriae and pili are involved in the attachment of E. amylovora to surfaces and are necessary for the production of mature biofilms. A time course assay indicated that type I fimbriae function earlier in attachment, while type IV pilus structures appear to function later in attachment. Our results indicate that multiple attachment structures are needed for mature biofilm formation and full virulence and that biofilm formation facilitates entry and is necessary for the buildup of large populations of E. amylovora cells in xylem tissue.

  11. Structural classification of proteins using texture descriptors extracted from the cellular automata image.

    PubMed

    Kavianpour, Hamidreza; Vasighi, Mahdi

    2017-02-01

    Nowadays, having knowledge about cellular attributes of proteins has an important role in pharmacy, medical science and molecular biology. These attributes are closely correlated with the function and three-dimensional structure of proteins. Knowledge of protein structural class is used by various methods for better understanding the protein functionality and folding patterns. Computational methods and intelligence systems can have an important role in performing structural classification of proteins. Most of protein sequences are saved in databanks as characters and strings and a numerical representation is essential for applying machine learning methods. In this work, a binary representation of protein sequences is introduced based on reduced amino acids alphabets according to surrounding hydrophobicity index. Many important features which are hidden in these long binary sequences can be clearly displayed through their cellular automata images. The extracted features from these images are used to build a classification model by support vector machine. Comparing to previous studies on the several benchmark datasets, the promising classification rates obtained by tenfold cross-validation imply that the current approach can help in revealing some inherent features deeply hidden in protein sequences and improve the quality of predicting protein structural class.

  12. 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.

  13. 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.

  14. Comparison of structural, architectural and mechanical aspects of cellular and acellular bone in two teleost fish.

    PubMed

    Cohen, Liat; Dean, Mason; Shipov, Anna; Atkins, Ayelet; Monsonego-Ornan, Efrat; Shahar, Ron

    2012-06-01

    The histological diversity of the skeletal tissues of fishes is impressive compared with that of other vertebrate groups, yet our understanding of the functional consequences of this diversity is limited. In particular, although it has been known since the mid-1800s that a large number of fish species possess acellular bones, the mechanical advantages and consequences of this structural characteristic - and therefore the nature of the evolution of this feature - remain unclear. Although several studies have examined the material properties of fish bone, these have used a variety of techniques and there have been no direct contrasts of acellular and cellular bone. We report on a comparison of the structural and mechanical properties of the ribs and opercula between two freshwater fish - the common carp Cyprinus carpio (a fish with cellular bone) and the tilapia Oreochromis aureus (a fish with acellular bone). We used light microscopy to show that the bones in both fish species exhibit poor blood supply and possess discrete tissue zones, with visible layering suggesting differences in the underlying collagen architecture. We performed identical micromechanical testing protocols on samples of the two bone types to determine the mechanical properties of the bone material of opercula and ribs. Our data support the consensus of literature values, indicating that Young's moduli of cellular and acellular bones are in the same range, and lower than Young's moduli of the bones of mammals and birds. Despite these similarities in mechanical properties between the bone tissues of the fish species tested here, cellular bone had significantly lower mineral content than acellular bone; furthermore, the percentage ash content and bone mineral density values (derived from micro-CT scans) show that the bone of these fishes is less mineralized than amniote bone. Although we cannot generalize from our data to the numerous remaining teleost species, the results presented here suggest

  15. 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.

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

    PubMed

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

    2014-06-01

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

  17. Constraint-based Hybrid Cellular Automaton Topology Optimization for Advanced Lightweight Blast Resistant Structure Development

    DTIC Science & Technology

    2011-11-01

    2 1.3 Hybrid Cellular Automata (HCA...1. Hybrid cellular automata based topology optimization example (3, 4). .........................1 Figure 2. Topometry optimization (6...3 Figure 4. Hybrid cellular automata -based topology optimization flowchart (3, 4, 9

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

    PubMed

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

    2012-01-01

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

  19. 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.

  20. 6 ANEUPLOIDY TOLERANCE IN RHESUS MACAQUE PRE-IMPLANTATION EMBRYOS VIA MICRONUCLEI FORMATION, CELLULAR FRAGMENTATION, AND BLASTOMERE EXCLUSION.

    PubMed

    Daughtry, B L; Rosenkrantz, J L; Lazar, N; Redmayne, N; Nevonen, K A; Carbone, L; Chavez, S L

    2016-01-01

    A primary contributor to in vitro fertilization (IVF) failure is the presence of unbalanced chromosomes in pre-implantation embryos. Previous array-based and next-generation sequencing (NGS) studies determined that ~50 to 80% of human embryos are aneuploid at the cleavage stage. During early mitotic divisions, many human embryos also sequester mis-segregated chromosomes into micronuclei and concurrently undergo cellular fragmentation. We hypothesised that cellular fragmentation represents a response to mis-segregated chromosomes that are encapsulated into micronuclei. Here, we utilised the rhesus macaque pre-implantation embryo as a model to study human embryonic aneuploidy using a combination of Eeva(TM) time-lapse imaging for evaluating cell divisions, single-cell/-fragment DNA-Sequencing (DNA-Seq), and confocal microscopy of nuclear structures. Results from our time-lapse image analysis demonstrated that there are considerable differences in the timing of the first and third mitotic divisions between rhesus blastocysts and those that arrested before this stage in development (P<0.01; ANOVA). By examining the chromosome content of each blastomere from cleavage stage embryos via DNA-Seq, we determined that rhesus embryos have an aneuploidy frequency up to ~62% (N=26) with several embryos exhibiting chromosomal mosaicism between blastomeres (N=6). Certain blastomeres also exhibited reciprocal whole chromosomal gains or losses, indicating that these embryos had undergone mitotic non-disjunction early in development. In addition, findings of reciprocal sub-chromosomal deletions/duplications among blastomeres suggest that chromosomal breakage had occurred in some embryos as well. Embryo immunostaining for the nuclear envelope protein, LAMIN-B1, demonstrated that fragmented cleavage-stage rhesus embryos often contain micronuclei and that cellular fragments can enclose DNA. Our DNA-Seq analysis confirmed that cellular fragments might encapsulate whole and/or partial

  1. 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.

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

    PubMed

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

    2012-05-01

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

  3. 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

  4. Plate-impact loading of cellular structures formed by selective laser melting

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    Porous materials are of great interest because of improved energy absorption over their solid counterparts. Their properties, however, have been difficult to optimize. Additive manufacturing has emerged as a potential technique to closely define the structure and properties of porous components, i.e. density, strut width and pore size; however, the behaviour of these materials at very high impact energies remains largely unexplored. We describe an initial study of the dynamic compression response of lattice materials fabricated through additive manufacturing. Lattices consisting of an array of intersecting stainless steel rods were fabricated into discs using selective laser melting. The resulting discs were impacted against solid stainless steel targets at velocities ranging from 300 to 700 m s-1 using a gas gun. Continuum CTH simulations were performed to identify key features in the measured wave profiles, while 3D simulations, in which the individual cells were modelled, revealed details of microscale deformation during collapse of the lattice structure. The validated computer models have been used to provide an understanding of the deformation processes in the cellular samples. The study supports the optimization of cellular structures for application as energy absorbers.

  5. 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.

  6. Formation of tribological structures by laser ablation

    NASA Astrophysics Data System (ADS)

    Schilling, Niels; Paschke, Mike; Hendow, Sami T.; Klotzbach, Udo

    2012-03-01

    Many technical applications can benefit from the use of tribological structures in minimizing abrasive material wear and energy consumption without the integration of additional materials in a working assembly. Especially in lubricated friction systems, the tribological character can be significantly improved through the addition of oriented and repetitive microstructure. In this study, experimental tests are discussed for a small range of structure dimensions to verify the effect of optimizing the tribological contact performance. A nanosecond pulsed fiber laser is used to create various test structures with different sizes and form. The quality of the fabricated surface pattern, particularly form correctness, feathering and material modification effects of the ablated area is characterized and optimized. The influence of pulse duration, pulse energy and pulse delay using normal pulsing is presented and compared to various burst modes.

  7. 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.

  8. 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.

  9. The Wnt11 Signaling Pathway in Potential Cellular EMT and Osteochondral Differentiation Progression in Nephrolithiasis Formation.

    PubMed

    He, Deng; Lu, Yuchao; Hu, Henglong; Zhang, Jiaqiao; Qin, Baolong; Wang, Yufeng; Xing, Shuai; Xi, Qilin; Wang, Shaogang

    2015-07-17

    The molecular events leading to nephrolithiasis are extremely complex. Previous studies demonstrated that calcium and transforming growth factor-β1 (TGF-β1) may participate in the pathogenesis of stone formation, but the explicit mechanism has not been defined. Using a self-created genetic hypercalciuric stone-forming (GHS) rat model, we observed that the increased level of serous/uric TGF-β1 and elevated intracellular calcium in primary renal tubular epithelial cells (PRECs) was associated with nephrolithiasis progression in vivo. In the setting of high calcium plus high TGF-β1 in vitro, PRECs showed great potential epithelial to mesenchymal transition (EMT) progression and osteochondral differentiation properties, representing the multifarious increased mesenchymal and osteochondral phenotypes (Zeb1, Snail1, Col2A1, OPN, Sox9, Runx2) and decreased epithelial phenotypes (E-cadherin, CK19) bythe detection of mRNAs and corresponding proteins. Moreover, TGF-β-dependent Wnt11 knockdown and L-type Ca2+ channel blocker could greatly reverse EMT progression and osteochondral differentiation in PRECs. TGF-β1 alone could effectively promote EMT, but it had no effect on osteochondral differentiation in NRK cells (Rat kidney epithelial cell line). Stimulation with Ca2+ alone did not accelerate differentiation of NRK. Co-incubation of extracellular Ca2+ and TGF-β1 synergistically promotes EMT and osteochondral differentiation in NRK control cells. Our data supplied a novel view that the pathogenesis of calcium stone development may be associated with synergic effects of TGF-β1 and Ca2+, which promote EMT and osteochondral differentiation via Wnt11 and the L-type calcium channel.

  10. Modelling of the new formation structures in the near space.

    PubMed

    Kulikova, N V; Pivnenko, E A

    1992-01-01

    Complex numerical model of young meteor stream formation taking into account reactive deceleration of cometary nucleus and its form change in the process of stream formation is discussed. The model made it possible to predict the existence of fine and superfine structures for young meteor streams, the characteristics of which agree with the observational data on the Draconid and Leonid meteor showers.

  11. 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.

  12. Semiconductor structure and recess formation etch technique

    DOEpatents

    Lu, Bin; Sun, Min; Palacios, Tomas Apostol

    2017-02-14

    A semiconductor structure has a first layer that includes a first semiconductor material and a second layer that includes a second semiconductor material. The first semiconductor material is selectively etchable over the second semiconductor material using a first etching process. The first layer is disposed over the second layer. A recess is disposed at least in the first layer. Also described is a method of forming a semiconductor structure that includes a recess. The method includes etching a region in a first layer using a first etching process. The first layer includes a first semiconductor material. The first etching process stops at a second layer beneath the first layer. The second layer includes a second semiconductor material.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  14. Structure Formation in the Universe from Texture Induced Fluctuations

    NASA Astrophysics Data System (ADS)

    Durrer, Ruth; Zhou, Zhi-Hong

    1995-03-01

    We discuss structure formation with topological defects. First we present a partially new, local, and gauge invariant system of perturbation equations to treat microwave background and dark matter fluctuations induced by topological defects or any other type of seeds. We show that this system is well suited for numerical analysis of structure formation by applying it to the texture scenario. Our numerical results cover a larger dynamical range than previous investigations and are complementary to them since we use substantially different methods.

  15. 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.

  16. Cuttlebone-like V2O5 Nanofibre Scaffolds – Advances in Structuring Cellular Solids

    NASA Astrophysics Data System (ADS)

    Knöller, Andrea; Runčevski, Tomče; Dinnebier, Robert E.; Bill, Joachim; Burghard, Zaklina

    2017-02-01

    The synthesis of ceramic materials combining high porosity and permeability with good mechanical stability is challenging, as optimising the latter requires compromises regarding the first two properties. Nonetheless, significant progress can be made in this direction by taking advantage of the structural design principles evolved by nature. Natural cellular solids achieve good mechanical stability via a defined hierarchical organisation of the building blocks they are composed of. Here, we report the first synthetic, ceramic-based scaffold whose architecture closely mimics that of cuttlebone –a structural biomaterial whose porosity exceeds that of most other natural cellular solids, whilst preserving an excellent mechanical strength. The nanostructured, single-component scaffold, obtained by ice-templated assembly of V2O5 nanofibres, features a highly sophisticated and elaborate architecture of equally spaced lamellas, which are regularly connected by pillars as lamella support. It displays an unprecedented porosity of 99.8 %, complemented by an enhanced mechanical stability. This novel bioinspired, functional material not only displays mechanical characteristics similar to natural cuttlebone, but the multifunctionality of the V2O5 nanofibres also renders possible applications, including catalysts, sensors and electrodes for energy storage.

  17. Structure and Cellular Roles of the RMI Core Complex from the Bloom Syndrome Dissolvasome

    SciTech Connect

    Hoadley, Kelly A.; Xu, Dongyi; Xue, Yutong; Satyshur, Kenneth A.; Wang, Weidong; Keck, James L.

    2010-11-11

    BLM, the protein product of the gene mutated in Bloom syndrome, is one of five human RecQ helicases. It functions to separate double Holliday junction DNA without genetic exchange as a component of the dissolvasome, which also includes topoisomerase III{alpha} and the RMI (RecQ-mediated genome instability) subcomplex (RMI1 and RMI2). We describe the crystal structure of the RMI core complex, comprising RMI2 and the C-terminal OB domain of RMI1. The overall RMI core structure strongly resembles two-thirds of the trimerization core of the eukaryotic single-stranded DNA-binding protein, Replication Protein A. Immunoprecipitation experiments with RMI2 variants confirm key interactions that stabilize the RMI core interface. Disruption of this interface leads to a dramatic increase in cellular sister chromatid exchange events similar to that seen in BLM-deficient cells. The RMI core interface is therefore crucial for BLM dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins.

  18. Cuttlebone-like V2O5 Nanofibre Scaffolds – Advances in Structuring Cellular Solids

    PubMed Central

    Knöller, Andrea; Runčevski, Tomče; Dinnebier, Robert E.; Bill, Joachim; Burghard, Zaklina

    2017-01-01

    The synthesis of ceramic materials combining high porosity and permeability with good mechanical stability is challenging, as optimising the latter requires compromises regarding the first two properties. Nonetheless, significant progress can be made in this direction by taking advantage of the structural design principles evolved by nature. Natural cellular solids achieve good mechanical stability via a defined hierarchical organisation of the building blocks they are composed of. Here, we report the first synthetic, ceramic-based scaffold whose architecture closely mimics that of cuttlebone –a structural biomaterial whose porosity exceeds that of most other natural cellular solids, whilst preserving an excellent mechanical strength. The nanostructured, single-component scaffold, obtained by ice-templated assembly of V2O5 nanofibres, features a highly sophisticated and elaborate architecture of equally spaced lamellas, which are regularly connected by pillars as lamella support. It displays an unprecedented porosity of 99.8 %, complemented by an enhanced mechanical stability. This novel bioinspired, functional material not only displays mechanical characteristics similar to natural cuttlebone, but the multifunctionality of the V2O5 nanofibres also renders possible applications, including catalysts, sensors and electrodes for energy storage. PMID:28218301

  19. 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

  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.

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

    PubMed Central

    1989-01-01

    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

  2. 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.

  3. 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.

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

    PubMed

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

    2016-06-03

    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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  7. Proper Cellular Reorganization during Drosophila Spermatid Individualization Depends on Actin Structures Composed of Two Domains, Bundles and Meshwork, That Are Differentially Regulated and Have Different Functions

    PubMed Central

    Noguchi, Tatsuhiko; Lenartowska, Marta; Rogat, Aaron D.; Frank, Deborah J.

    2008-01-01

    During spermatid individualization in Drosophila, actin structures (cones) mediate cellular remodeling that separates the syncytial spermatids into individual cells. These actin cones are composed of two structural domains, a front meshwork and a rear region of parallel bundles. We show here that the two domains form separately in time, are regulated by different sets of actin-associated proteins, can be formed independently, and have different roles. Newly forming cones were composed only of bundles, whereas the meshwork formed later, coincident with the onset of cone movement. Polarized distributions of myosin VI, Arp2/3 complex, and the actin-bundling proteins, singed (fascin) and quail (villin), occurred when movement initiated. When the Arp2/3 complex was absent, meshwork formation was compromised, but surprisingly, the cones still moved. Despite the fact that the cones moved, membrane reorganization and cytoplasmic exclusion were abnormal and individualization failed. In contrast, when profilin, a regulator of actin assembly, was absent, bundle formation was greatly reduced. The meshwork still formed, but no movement occurred. Analysis of this actin structure's formation and participation in cellular reorganization provides insight into how the mechanisms used in cell motility are modified to mediate motile processes within specialized cells. PMID:18353976

  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. 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

  10. Connecting the density structure of molecular clouds with star formation

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    In the current paradigm of turbulence-regulated interstellar medium (ISM), star formation rates of entire galaxies are intricately linked to the density structure of the individual molecular clouds. This density structure is essentially encapsulated in the probability distribution function of volume densities (ρ-PDF), which directly affects the star formation rates predicted by analytic models. Contrasting its fundamental role, the ρ-PDF function has remained virtually unconstrained by observations. I describe in this contribution the recent progress in attaining observational constraints for the column density PDFs (N-PDFs) of molecular clouds that function as a proxy of the ρ-PDFs. Specifically, observational works point towards a universal correlation between the shape of the N-PDFs and star formation activity in molecular clouds. The correlation is in place from the scales of a parsec up to the scales of entire galaxies, making it a fundamental, global link between the ISM structure and star formation.

  11. Nonlinear structure formation in nonlocal gravity

    NASA Astrophysics Data System (ADS)

    Barreira, Alexandre; Li, Baojiu; Hellwing, Wojciech A.; Baugh, Carlton M.; Pascoli, Silvia

    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 ~ 1014 Msolar/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 gtrsim 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.

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

    PubMed

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

    2011-01-01

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

  13. 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

  14. 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.

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

    PubMed

    Henry, Jonathan T; Crosson, Sean

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Li, Suyi; Wang, K. W.

    2015-04-01

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

  17. Click chemistry for the conservation of cellular structures and fluorescent proteins: ClickOx.

    PubMed

    Löschberger, Anna; Niehörster, Thomas; Sauer, Markus

    2014-05-01

    Reactive oxygen species (ROS), including hydrogen peroxide, are known to cause structural damage not only in living, but also in fixed, cells. Copper-catalyzed azide-alkyne cycloaddition (click chemistry) is known to produce ROS. Therefore, fluorescence imaging of cellular structures, such as the actin cytoskeleton, remains challenging when combined with click chemistry protocols. In addition, the production of ROS substantially weakens the fluorescence signal of fluorescent proteins. This led us to develop ClickOx, which is a new click chemistry protocol for improved conservation of the actin structure and better conservation of the fluorescence signal of green fluorescent protein (GFP)-fusion proteins. Herein we demonstrate that efficient oxygen removal by addition of an enzymatic oxygen scavenger system (ClickOx) considerably reduces ROS-associated damage during labeling of nascent DNA with ATTO 488 azide by Cu(I)-catalyzed click chemistry. Standard confocal and super-resolution fluorescence images of phalloidin-labeled actin filaments and GFP/yellow fluorescent protein-labeled cells verify the conservation of the cytoskeleton microstructure and fluorescence intensity, respectively. Thus, ClickOx can be used advantageously for structure preservation in conventional and most notably in super-resolution microscopy methods.

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

    PubMed Central

    Henry, Jonathan T.; Crosson, Sean

    2012-01-01

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

  19. 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.

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

    PubMed Central

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

    2014-01-01

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

  1. Structural distortions in molecular-based quantum cellular automata: a minimal model based study.

    PubMed

    Bonilla, Alejandro Santana; Gutierrez, Rafael; Sandonas, Leonardo Medrano; Nozaki, Daijiro; Bramanti, Alessandro Paolo; Cuniberti, Gianaurelio

    2014-09-07

    Molecular-based quantum cellular automata (m-QCA), as an extension of quantum-dot QCAs, offer a novel alternative in which binary information can be encoded in the molecular charge configuration of a cell and propagated via nearest-neighbor Coulombic cell-cell interactions. Appropriate functionality of m-QCAs involves a complex relationship between quantum mechanical effects, such as electron transfer processes within the molecular building blocks, and electrostatic interactions between cells. The influence of structural distortions of single m-QCA are addressed in this paper within a minimal model using an diabatic-to-adiabatic transformation. We show that even small changes of the classical square geometry between driver and target cells, such as those induced by distance variations or shape distortions, can make cells respond to interactions in a far less symmetric fashion, modifying and potentially impairing the expected computational behavior of the m-QCA.

  2. 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).

  3. 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.

  4. 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.

  5. 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.

  6. Role of extra-cellular fatty acids in vancomycin induced biofilm formation by vancomycin resistant Staphylococcus aureus.

    PubMed

    Mirani, Zulfiqar Ali; Jamil, Nusrat

    2013-03-01

    In the present study a vancomycin resistant Staphylococcus aureus (S. aureus) (VRSA) (Labeled as CP2) was isolated from the blood of a post-operative cardiac patient is described. It harbors a plasmid which carry vanA gene and exhibited low-level vancomycin resistance (MIC 16μg/mL), was sensitive to teicoplanin. It has been observed that sub-lethal dose of vancomycin induced biofilm formation by CP2 on nylon and silicon indwelling. The results divulge new insights into associations between vancomycin induced biofilms and extra-cellular fatty acids. Gas chromatography coupled with mass spectrometry (GC-MS) revealed that biofilm matrix of CP2 contains a variety of saturated and un-saturated fatty acids, especially, diverse species of octadecanoic (C18:0) and octadecenoic acids (C18:1). A large difference in fatty acids composition was noticed in biofilms, isolated from hydrophobic and hydrophilic surfaces. CP2 produced thicker layer of biofilms on hydrophobic silicon and nylon surfaces which contains variety of saturated, un-saturated and cyclic fatty acids. Contrary to this on hydrophilic glass surfaces it produced thinner layer of biofilm which contains only straight chain saturated fatty acids. These fatty acid components seem to play a crucial role in cell-cell communication and in the establishment of biofilms, consequently, advantageous for pathogens to survive in hospital environment under enormous antibiotics pressure.

  7. Cellular response of osteoblasts to low modulus Ti-24Nb-4Zr-8Sn alloy mesh structure.

    PubMed

    Nune, K C; Misra, R D K; Li, S J; Hao, Y L; Yang, R

    2017-03-01

    Titanium alloys (Ti-6Al-4V and Ti-6Al-7Nb) are widely used for implants, which are characterized by high elastic modulus (∼110 GPa) with (α + β) structure and that may induce undesirable stress shielding effect and immune responses associated with the presence of toxic elements. In this regard, we have combined the attributes of a new alloy design and the concept of additive manufacturing to fabricate 3D scaffolds with an interconnected porous structure. The new alloy is a β-type Ti-24Nb-4Zr-8Sn (Ti2448) alloy with significantly reduced modulus. In the present study, we explore the biological response of electron beam melted low modulus Ti2448 alloy porous mesh structure through the elucidation of bioactivity and osteoblast functions. The cellular activity was explored in terms of cell-to-cell communication involving proliferation, spreading, synthesis of extracellular and intracellular proteins, differentiation, and mineralization. The formation of fine apatite-like crystals on the surface during immersion test in simulated body fluid confirmed the bioactivity of the scaffold surface, which provided the favorable osteogenic microenvironment for cell-material interaction. The combination of unique surface chemistry and interconnected porous architecture provided the desired pathway for supply of nutrients and oxygen to cells and a favorable osteogenic micro-environment for incorporation (on-growth and in-growth) of osteoblasts. The proliferation and differentiation of pre-osteoblasts and their ability to form a well mineralized bone-like extracellular matrix (ECM) by secreting bone markers (ALP, calcium, etc.) over the struts of the scaffold point toward the determining role of unique surface chemistry and 3D architecture of the Ti2448 alloy mesh structure in modulating osteoblasts functions. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 859-870, 2017.

  8. Cellular Organization of Normal Mouse Liver: A Histological, Quantitative Immunocytochemical, and Fine Structural Analysis

    PubMed Central

    Baratta, Janie L.; Ngo, Anthony; Lopez, Bryan; Kasabwalla, Natasha; Longmuir, Kenneth J.; Robertson, Richard T.

    2009-01-01

    The cellular organization of normal mouse liver was studied using light and electron microscopy and quantitative immunocytochemical techniques. The general histological organization of the mouse liver is similar to livers of other mammalian species, with a lobular organization based on the distributions of portal areas and central venules. The parenchymal hepatocytes were detected with immunocytochemical techniques to recognize albumin or biotin containing cells. The macrophage Kupffer cells were identified with F4-80 immunocytochemistry, Ito stellate cells were identified with GFAP immunocytochemistry, and endothelial cells were labeled with the CD-34 antibody. Kupffer cells were labeled with intravascularly administered fluorescently labeled latex microspheres of both large (0.5 μm) and small (0.03 μm) diameters, while endothelial cells were labeled only with small diameter microspheres. Neither hepatocytes nor Ito stellate cells were labeled by intravascularly administered latex microspheres. The principal fine structural features of hepatocytes and non-parenchymal cells of mouse liver are similar to those reported for rat. Counts of immunocytochemically labeled cells with stained nuclei indicated that hepatocytes constituted approximately 52% of all labeled cells, Kupffer cells about 18%, Ito cells about 8%, and endothelial cells about 22% of all labeled cells. Approximately 35% of the hepatocytes contained two nuclei; none of the Kupffer or Ito cells were double nucleated. The presence of canaliculi and a bile duct system appear similar to that reported for other mammalian species. The cellular organization of the mouse liver is quite similar to that of other mammalian species, confirming that the mouse presents a useful animal model for studies of liver structure and function. PMID:19255771

  9. 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.

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

    PubMed Central

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

    2015-01-01

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

  11. A review of reagents for fluorescence microscopy of cellular compartments and structures, Part III: reagents for actin, tubulin, cellular membranes, and whole cell and cytoplasm.

    PubMed

    Kilgore, Jason A; Dolman, Nick J; Davidson, Michael W

    2014-01-02

    Non-antibody commercial fluorescent reagents for imaging of cytoskeletal structures have been limited primarily to tubulin and actin, with the main factor in choice based mainly on whether cells are live or fixed and permeabilized. A wider range of options exist for cell membrane dyes, and the choice of reagent primarily depends on the preferred localization in the cell (i.e., all membranes or only the plasma membrane) and usage (i.e., whether the protocol involves fixation and permeabilization). For whole-cell or cytoplasmic imaging, the choice of reagent is determined mostly by the length of time that the cells need to be visualized (hours or days) and by fixation status. Presented here is a discussion on choosing commercially available reagents for these cellular structures, with an emphasis on use for microscopic imaging, with a featured reagent for each structure, a recommended protocol, troubleshooting guide, and example image.

  12. Structure Formation Mechanisms during Solid Ti with Molten Al Interaction

    NASA Astrophysics Data System (ADS)

    Gurevich, L.; Pronichev, D.; Trunov, M.

    2016-02-01

    The study discuses advantages and disadvantages of previously proposed mechanisms of the formation of structure between solid Ti and molten Al and presents a new mechanism based on the reviewed and experimental data. The previously proposed mechanisms were classified into three groups: mechanisms of precipitation, mechanisms of destruction and mechanisms of chemical interaction between intermetallics and melt. The reviewed mechanisms did not explain the formation of heterogeneous interlayer with globular aluminide particles and thin layers of pure Al, while the present study reveals variation in the solid Ti/molten Al reaction kinetics during various phases of laminated metal-intermetallic composite formation. The proposed mechanism considers formed during composite fabrication thin oxide interlayers between Ti and Al evolution and its impact on the intermetallic compound formation and explains the initial slow rate of intermetallic interlayer formation and its subsequent acceleration when the oxide foils are ruptured.

  13. An effective assay for high cellular resolution time-lapse imaging of sensory placode formation and morphogenesis

    PubMed Central

    2011-01-01

    Background The vertebrate peripheral nervous system contains sensory neurons that arise from ectodermal placodes. Placodal cells ingress to move inside the head to form sensory neurons of the cranial ganglia. To date, however, the process of placodal cell ingression and underlying cellular behavior are poorly understood as studies have relied upon static analyses on fixed tissues. Visualizing placodal cell behavior requires an ability to distinguish the surface ectoderm from the underlying mesenchyme. This necessitates high resolution imaging along the z-plane which is difficult to accomplish in whole embryos. To address this issue, we have developed an imaging system using cranial slices that allows direct visualization of placode formation. Results We demonstrate an effective imaging assay for capturing placode development at single cell resolution using chick embryonic tissue ex vivo. This provides the first time-lapse imaging of mitoses in the trigeminal placodal ectoderm, ingression, and intercellular contacts of placodal cells. Cell divisions with varied orientations were found in the placodal ectoderm all along the apical-basal axis. Placodal cells initially have short cytoplasmic processes during ingression as young neurons and mature over time to elaborate long axonal processes in the mesenchyme. Interestingly, the time-lapse imaging data reveal that these delaminating placodal neurons begin ingression early on from within the ectoderm, where they start to move and continue on to exit as individual or strings of neurons through common openings on the basal side of the epithelium. Furthermore, dynamic intercellular contacts are abundant among the delaminating placodal neurons, between these and the already delaminated cells, as well as among cells in the forming ganglion. Conclusions This new imaging assay provides a powerful method to analyze directly development of placode-derived sensory neurons and subsequent ganglia formation for the first time in

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

    PubMed Central

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

    2015-01-01

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

  16. 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.

  17. 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.

  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.

    2017-03-01

    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. [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.

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

    PubMed

    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

    2015-09-01

    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 (93)LEQEHNNLV(101) and (168)LLLHDSIQI(176) 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].

  1. 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

  2. Contribution of cotranslational folding to the rate of formation of native protein structure.

    PubMed Central

    Fedorov, A N; Baldwin, T O

    1995-01-01

    To compare the process of protein folding in the cell with refolding following denaturation in vitro, we have investigated and compared the kinetics of renaturation of a full-length protein upon dilution from concentrated urea with the rate of folding in the course of biosynthesis. Formation of enzymatically active bacterial luciferase, an alpha beta heterodimer, occurred 2 min after completion of beta-subunit synthesis in an Escherichia coli cell-free system. Renaturation of urea-denatured beta subunit, either in the presence of the cell-free protein synthesis system or in buffer solutions, proceeded more slowly. Cellular components present in the cell-free protein synthesis system slightly accelerated the rate of refolding of urea-unfolded beta subunit. The results indicate that the luciferase beta subunit begins the folding process cotranslationally and that cotranslational folding contributes to the rapid formation of the native structure in the cell. Images Fig. 1 PMID:7862665

  3. Formation and structure of amorphous carbon char from polymer materials

    NASA Astrophysics Data System (ADS)

    Lawson, John W.; Srivastava, Deepak

    2008-04-01

    Amorphous carbonaceous char produced from burning polymer solids has insulating properties that make it valuable in thermal protection and fire-retardant systems. A pyrolytic molecular dynamics simulation method is devised to study the transformation of the local microstructure from virgin polymer to a dense, disordered char. Release of polymer hydrogen is found to be critical to allow the system to collapse into a highly coordinated char structure. Mechanisms of the char formation process and the morphology of the resulting structures are elucidated.

  4. Deamidation accelerates amyloid formation and alters amylin fiber structure

    PubMed Central

    Dunkelberger, Emily B.; Buchanan, Lauren E.; Marek, Peter; Cao, Ping; Raleigh, Daniel P.; Zanni, Martin T.

    2012-01-01

    Deamidation of asparagine and glutamine is the most common non-enzymatic, post-translational modification. Deamidation can influence the structure, stability, folding, and aggregation of proteins and has been proposed to play a role in amyloid formation. However there are no structural studies of the consequences of deamidation on amyloid fibers, in large part because of the difficulty of studying these materials using conventional methods. Here we examine the effects of deamidation on the kinetics of amyloid formation by amylin, the causative agent of type 2 diabetes. We find that deamidation accelerates amyloid formation and the deamidated material is able to seed amyloid formation by unmodified amylin. Using site-specific isotope labeling and two-dimensional infrared (2D IR) spectroscopy, we show that fibers formed by samples that contain deamidated polypeptide contain reduced amounts of β-sheet. Deamidation leads to disruption of the N-terminal β-sheet between Ala-8 and Ala-13, but β-sheet is still retained near Leu-16. The C-terminal sheet is disrupted near Leu-27. Analysis of potential sites of deamidation together with structural models of amylin fibers reveals that deamidation in the N-terminal β-sheet region may be the cause for the disruption of the fiber structure at both the N- and C-terminal β-sheet. Thus, deamidation is a post-translational modification that creates fibers which have an altered structure, but can still act as a template for amylin aggregation. Deamidation is very difficult to detect with standard methods used to follow amyloid formation, but isotope labeled IR spectroscopy provides a means for monitoring sample degradation and investigating the structural consequences of deamidation. PMID:22734583

  5. Bifurcation of learning and structure formation in neuronal maps

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed Central

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

    2015-01-01

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

  7. Formation of first structures in a ΛCDM Universe

    NASA Astrophysics Data System (ADS)

    Villalón, C.; Domínguez Romero, M.

    We developed simulations of the formation and evolution of the first structures using an AMR, grid-based code: Enzo. Our simulations are aimed to follow the complex physics of the joint evolution of super massive black holes and galaxies in the reionization epoch.

  8. 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

  9. 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

  10. Formation of structure in small lead clusters under thermal effect

    NASA Astrophysics Data System (ADS)

    Baidyshev, V. S.; Gafner, Yu. Ya.

    2016-12-01

    The thermal effect on lead clusters with radii up to 5.5 nm has been investigated by the molecular dynamics method using a modified tight-binding potential TB-SMA. The melting of Pb nanoparticles of these sizes is strictly homogeneous, without the formation of a surface liquidlike layer. The primary fcc phase in the particles is retained upon heating in the overwhelming majority of model experiments. An analysis of the structure formation during crystallization has shown that structures with pentagonal symmetry are preferred for lead clusters in this case. It is noted that an increase in the nanoparticle size leads to the dominance of the dodecahedral structure over the icosahedral one.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Nanostructuring biosynthetic hydrogels for tissue engineering: a cellular and structural analysis.

    PubMed

    Frisman, Ilya; Seliktar, Dror; Bianco-Peled, Havazelet

    2012-01-01

    The nanostructuring of hydrogel scaffolds used in tissue engineering provides the ability to control cellular fate and tissue morphogenesis through cell-matrix interactions. Here we describe a method to provide nanostructure to a biosynthetic hydrogel scaffold made from crosslinked poly(ethylene glycol)-fibrinogen conjugates (PEG-fibrinogen), by modifying them with the block-copolymer Pluronic® F127. The copolymeric additive self-assembled into micelles at certain concentrations and temperatures, thereby creating nanostructures within the crosslinked hydrogel. Small-angle X-ray scattering (SAXS) and transmission electron microscopy at cryogenic temperature were used to detect Pluronic® F127 micelles embedded within the crosslinked PEG-fibrinogen hydrogels. The density and order of the micelles within the hydrogel matrix increased as the relative Pluronic® F127 concentration was raised. The transient stability of the micelles within the hydrogel network was analyzed using time-dependent swelling and Pluronic® F127 release measurements. These characterizations revealed that most of the Pluronic® F127 molecules diffuse out of the hydrogels after 4 days in aqueous buffer and SAXS analysis confirmed a significant change in the structure and interactions of the micelles during this time. Cell culture experiments evaluating the three-dimensional fibroblast morphology within the matrix indicated a strong correlation between cell spreading and the hydrogel's characteristic mesh size. The present research thereby provides a more quantitative understanding of how structural features in an encapsulating hydrogel environment can affect cell morphogenesis towards tissue regeneration.

  16. Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model

    PubMed Central

    Benítez, Mariana; Espinosa-Soto, Carlos; Padilla-Longoria, Pablo; Alvarez-Buylla, Elena R

    2008-01-01

    Background Dynamical models are instrumental for exploring the way information required to generate robust developmental patterns arises from complex interactions among genetic and non-genetic factors. We address this fundamental issue of developmental biology studying the leaf and root epidermis of Arabidopsis. We propose an experimentally-grounded model of gene regulatory networks (GRNs) that are coupled by protein diffusion and comprise a meta-GRN implemented on cellularised domains. Results Steady states of the meta-GRN model correspond to gene expression profiles typical of hair and non-hair epidermal cells. The simulations also render spatial patterns that match the cellular arrangements observed in root and leaf epidermis. As in actual plants, such patterns are robust in the face of diverse perturbations. We validated the model by checking that it also reproduced the patterns of reported mutants. The meta-GRN model shows that interlinked sub-networks contribute redundantly to the formation of robust hair patterns and permits to advance novel and testable predictions regarding the effect of cell shape, signalling pathways and additional gene interactions affecting spatial cell-patterning. Conclusion The spatial meta-GRN model integrates available experimental data and contributes to further understanding of the Arabidopsis epidermal system. It also provides a systems biology framework to explore the interplay among sub-networks of a GRN, cell-to-cell communication, cell shape and domain traits, which could help understanding of general aspects of patterning processes. For instance, our model suggests that the information needed for cell fate determination emerges from dynamic processes that depend upon molecular components inside and outside differentiating cells, suggesting that the classical distinction of lineage versus positional cell differentiation may be instrumental but rather artificial. It also suggests that interlinkage of nonlinear and redundant

  17. Structure formation with scalar field dark matter: the field approach

    SciTech Connect

    Magaña, Juan; Sánchez-Salcedo, F.J.; Matos, Tonatiuh; Suárez, Abril E-mail: tmatos@fis.cinvestav.mx E-mail: jsanchez@astro.unam.mx

    2012-10-01

    We study the formation of structure in the Universe assuming that dark matter can be described by a scalar field Φ-tilde with a potential V(Φ) = −m{sup 2}Φ-tilde {sup 2}/2+λΦ-tilde {sup 4}/4. We derive the evolution equations of the scalar field in the linear regime of perturbations. We investigate the symmetry breaking and possibly a phase transition of this scalar field in the early Universe. At low temperatures, the scalar perturbations have an oscillating growing mode and therefore, this kind of dark matter could lead to the formation of gravitational structures. In order to study the nonlinear regime, we use the spherical collapse model and show that, in the quadratic potential limit, this kind of dark matter can form virialized structures. The main difference with the traditional Cold Dark Matter paradigm is that the formation of structure in the scalar field model can occur at earlier times. Thus, if the dark matter behaves as a scalar field, large galaxies are expected to be formed already at high redshifts.

  18. 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.

  19. Structure of electrorheological fluids: a dielectric study of chain formation.

    PubMed

    Horváth, B; Szalai, I

    2012-12-01

    A dielectric measurement method has been proposed to apply to the study of the microstructure of electrorheological (ER) fluids. To test our measurement method the dielectric permittivity increment caused by pair and chain formation was measured in dilute Brownian ER fluids composed of silicone oil and nanosized silica particles. The critical values of the electric field required to induce structure formation were experimentally determined from the electric field dependence of the measured permittivity increment. From the electric field induced time evolution of the relative permittivity of ER fluids, the characteristic times of the pair and chain formation were calculated. Our experimental results for the time constants are in good agreement with the corresponding theoretical data obtained from the Eyring theory.

  20. 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.

  1. Black Hole Mergers as Probes of Structure Formation

    NASA Technical Reports Server (NTRS)

    Alicea-Munoz, Emily

    2008-01-01

    Observations of gravitational waves from massive black hole (MBH) mergers can provide us with important clues about the era of structure formation in the early universe. Previous research in this field has been limited to calculating merger rates of MBHs using different models where many assumptions are made about the specific values of physical parameters of the mergers, resulting in merger rate estimates that span 5 to 6 orders of magnitude. We develop a semi-analytical, phenomenological model that includes plausible combinations of several physical parameters involved in the mergers. which we then turn around to determine how well LISA observations will be able to enhance our understanding of the universe during the critical z approximately equal to 5-30 structure formation era. We do this by generating synthetic LISA observable data (masses, redshifts, merger rates), which are then analyzed using a Markov Chain Monte Carlo (MCMC) method. This allows us to constrain the physical parameters of the mergers.

  2. Strain phase separation: Formation of ferroelastic domain structures

    NASA Astrophysics Data System (ADS)

    Xue, Fei; Li, Yongjun; Gu, Yijia; Zhang, Jinxing; Chen, Long-Qing

    2016-12-01

    Phase decomposition is a well-known process leading to the formation of two-phase mixtures. Here we show that a strain imposed on a ferroelastic crystal promotes the formation of mixed phases and domains, i.e., strain phase separation with local strains determined by a common tangent construction on the free energy versus strain curves. It is demonstrated that a domain structure can be understood using the concepts of domain/phase rule, lever rule, and coherent and incoherent strain phase separation, in a complete analogy to phase decomposition. The proposed strain phase separation model is validated using phase-field simulations and experimental observations of PbTi O3 and BiFe O3 thin films as examples. The proposed model provides a simple tool to guide and design domain structures of ferroelastic systems.

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

    PubMed

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

    2015-08-03

    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.

  4. 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.

  5. 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.

  6. Formation and structure of amorphous carbon char from polymer materials

    NASA Astrophysics Data System (ADS)

    Lawson, John; Srivastava, Deepak

    2008-03-01

    Amorphous carbonaceous char produced from burning polymer solids has insulating properties that makes it valuable for aerospace thermal protection systems as well as for fire retardants. A pyrolytic molecular dynamics simulation method is devised to study the transformation of the local microstructure from virgin polymer to a dense, disordered char. Release of polymer hydrogen is found to be critical to allow the system to collapse into a highly coordinated structure. Mechanisms of the char formation process and the morphology of the resulting structure are elucidated.

  7. Al-Ti-Zr master alloys: Structure formation

    NASA Astrophysics Data System (ADS)

    Popova, E. A.; Shubin, A. B.; Kotenkov, P. V.; Pastukhov, E. A.; Bodrova, L. E.; Fedorova, O. M.

    2012-05-01

    The effects of the composition of ternary Al-Ti-Zr master alloys, the overheating of their melts with respect to liquidus, and exposure to low-frequency vibrations on the structure formation in them are studied. It is shown that complex aluminide Al3(Zr x Ti1 - x ) with a metastable L12-type cubic lattice coinciding with the structure type of α Al primarily precipitates during the crystallization of Al-Ti-Zr melts under certain conditions. This fact makes such master alloys promising for modifying aluminum alloys.

  8. Asymmetry-driven structure formation in pair plasmas

    SciTech Connect

    Mahajan, S. M.; Shatashvili, N. L.; Berezhiani, V. I.

    2009-12-15

    The nonlinear propagation of electromagnetic waves in pair plasmas, in which the electrostatic potential plays a very important but subdominant role of a 'binding glue' is investigated. Several mechanisms for structure formation are investigated, in particular, the 'asymmetry' in the initial temperatures of the constituent species. It is shown that the temperature asymmetry leads to a (localizing) nonlinearity that is qualitatively different from the ones originating in ambient mass or density difference. The temperature-asymmetry-driven focusing-defocusing nonlinearity supports stable localized wave structures in 1-3 dimensions, which, for certain parameters, may have flat-top shapes.

  9. Cellular parameters for track structure modelling of radiation hazard in space

    NASA Astrophysics Data System (ADS)

    Hollmark, M.; Lind, B.; Gudowska, I.; Waligorski, M.

    Based on irradiation with 45 MeV/u N and B ions and with Co-60 gamma rays, track structure cellular parameters have been fitted for V 79-379A Chinese hamster lung fibroblasts and for human melanoma cells (AA wtp53). These sets of parameters will be used to develop a calculation of radiation hazard in deep space, based on the system for evaluating, summing and reporting occupational exposures proposed in 1967 by subcommittee of the NCRP, but never issued as an NCRP report. The key concepts of this system were: i) expression of the risk from all radiation exposures relative to that from a whole-body exposure to Co-60 radiation; ii) relating the risk from any exposure to that of the standard (Co-60) radiation through an "effectiveness factor" (ef), a product of sub-factors representing radiation quality, body region irradiated, and depth of penetration of radiation; the product of absorbed dose by ef being termed the "exposure record unit" (eru); iii) development of ef values and a cumulative eru record for external and internal emitters. Application of this concept should provide a better description of the Gy -equivalent presently in use by NASA for evaluating risk in deep space than the equivalent dose, following ICRP-60 recommendations. Dose and charged particle fluence levels encountered in space, particularly after Solar Particle Events, require that deterministic rather than stochastic effects be considered. Also, synergistic effects due to simultaneous multiple charged particle transfers, may have to be considered. Thus, models applicable in radiotherapy, where the Gy -equivalent is also applied, in conjunction with transport calculations performed using, e.g. the ADAM and EVA phantoms, along the concepts of the 1967 NCRP system, may be more appropriate for evaluating the radiation hazard from external fields with a large flux and a major high-LET component.

  10. Structure formation of surfactant membranes under shear flow

    NASA Astrophysics Data System (ADS)

    Shiba, Hayato; Noguchi, Hiroshi; Gompper, Gerhard

    2013-07-01

    Shear-flow-induced structure formation in surfactant-water mixtures is investigated numerically using a meshless-membrane model in combination with a particle-based hydrodynamics simulation approach for the solvent. At low shear rates, uni-lamellar vesicles and planar lamellae structures are formed at small and large membrane volume fractions, respectively. At high shear rates, lamellar states exhibit an undulation instability, leading to rolled or cylindrical membrane shapes oriented in the flow direction. The spatial symmetry and structure factor of this rolled state agree with those of intermediate states during lamellar-to-onion transition measured by time-resolved scatting experiments. Structural evolution in time exhibits a moderate dependence on the initial condition.

  11. Crystal structure representations for machine learning models of formation energies

    SciTech Connect

    Faber, Felix; Lindmaa, Alexander; von Lilienfeld, O. Anatole; Armiento, Rickard

    2015-04-20

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

  12. Large-scale structure formation with global topological defects

    NASA Astrophysics Data System (ADS)

    Durrer, Ruth; Zhou, Zhi-Hong

    1996-05-01

    We investigate cosmological structure formation seeded by topological defects which may form during a phase transition in the early Universe. First, we derive a partially new, local, and gauge-invariant system of perturbation equations to treat microwave background and dark matter fluctuations induced by topological defects or any other type of seeds. We then show that this system is well suited for numerical analysis of structure formation by applying it to seeds induced by fluctuations of a global scalar field. Our numerical results cover a larger dynamical range than those covered by previous investigations and are complementary to them since we use substantially different methods. The resulting microwave background fluctuations are compatible with older simulations. We also obtain a scale-invariant spectrum of fluctuations although with somewhat higher amplitude. On the other hand, our dark matter results yield a smaller bias parameter compatible with b~2 on scales of 20h-1 Mpc in contrast with previous work which yielded larger bias factors. Our conclusions are thus more positive. According to the aspects analyzed in this work, global topological defect-induced fluctuations yield viable scenarios of structure formation and do better than standard CDM on large scales.

  13. 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.

  14. 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.

  15. The structure of reionization in hierarchical galaxy formation models

    NASA Astrophysics Data System (ADS)

    Kim, Han-Seek; Wyithe, J. Stuart B.; Raskutti, Sudhir; Lacey, C. G.; Helly, J. C.

    2013-01-01

    Understanding the epoch of reionization and the properties of the first galaxies represents an important goal for modern cosmology. The structure of reionization and hence the observed power spectrum of redshifted 21-cm fluctuations are known to be sensitive to the astrophysical properties of the galaxies that drove reionization. Thus, detailed measurements of the 21-cm power spectrum and its evolution could lead to measurements of the properties of early galaxies that are otherwise inaccessible. In this paper, we make predictions for the ionized structure during reionization and the 21-cm power spectrum based on detailed models of galaxy formation. We combine the semi-analytic galform model implemented within the Millennium-II dark matter simulation, with a semi-numerical scheme to describe the resulting ionization structure. Semi-analytic models based on the Millennium-II Simulation follow the properties of galaxies within haloes of mass greater than ˜1.4 × 108 M⊙ at z > 6, corresponding to the faint sources thought to dominate reionization. Using these models we show that the details of supernovae (SNe) and radiative feedback affect the structure and distribution of ionized regions, and hence the slope and amplitude of the 21-cm power spectrum. These results indicate that forthcoming measurements of the 21-cm power spectrum could be used to uncover details of early galaxy formation. We find that the strength of SN feedback is the dominant effect governing the evolution of structure during reionization. In particular, we show SN feedback to be more important than radiative feedback, the presence of which we find does not influence either the total stellar mass or overall ionizing photon budget. Thus, if SN feedback is effective at suppressing star formation in high-redshift galaxies, we find that photoionization feedback does not lead to self-regulation of the reionization process as has been thought.

  16. 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.

  17. Anisotropic cellular network formation in engineered muscle tissue through the self-organization of neurons and endothelial cells.

    PubMed

    Takahashi, Hironobu; Shimizu, Tatsuya; Nakayama, Masamichi; Yamato, Masayuki; Okano, Teruo

    2015-02-18

    Tissue anisotropy directed by cell sheets: Aligned myoblasts can be harvested as an anisotropic cell sheet using a micropatterned thermoresponsive substrate. Neurons and endothelial cells sandwiched between multiple anisotropic cell sheets self-organize oriented cellular networks in the tissue construct. This simple tissue engineering technique is useful for the creation of biomimetic microstructures in complex tissue, required for future advances in regenerative medicine.

  18. Regulating temporospatial dynamics of morphogen for structure formation of the lacrimal gland by chitosan biomaterials.

    PubMed

    Hsiao, Ya-Chuan; Yang, Tsung-Lin

    2017-01-01

    The lacrimal gland is an important organ responsible for regulating tear synthesis and secretion. The major work of lacrimal gland (LG) is to lubricate the ocular surface and maintain the health of eyes. Functional deterioration of the lacrimal gland happens because of aging, diseases, or therapeutic complications, but without effective treatments till now. The LG originates from the epithelium of ocular surface and develops by branching morphogenesis. To regenerate functional LGs, it is required to explore the way of recapitulating and facilitating the organ to establish the intricate and ramified structure. In this study, we proposed an approach using chitosan biomaterials to create a biomimetic environment beneficial to the branching structure formation of developing LG. The morphogenetic effect of chitosan was specific and optimized to promote LG branching. With chitosan, increase in temporal expression and local concentration of endogenous HGF-related molecules creates an environment around the emerging tip of LG epithelia. By efficiently enhancing downstream signaling of HGF pathways, the cellular activities and behaviors were activated to contribute to LG branching morphogenesis. The morphogenetic effect of chitosan was abolished by either ligand or receptor deprivation, or inhibition of downstream signaling transduction. Our results elucidated the underlying mechanism accounting for chitosan morphogenetic effects on LG, and also proposed promising approaches with chitosan to assist tissue structure formation of the LG.

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

    PubMed

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

    2013-09-03

    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.

  20. 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

  1. Electric field structures in thin films: formation and properties.

    PubMed

    Cassidy, Andrew; Plekan, Oksana; Balog, Richard; Dunger, Jack; Field, David; Jones, Nykola C

    2014-08-21

    A newly discovered class of molecular materials, so-called "spontelectrics", display spontaneous electric fields. Here we show that the novel properties of spontelectrics can be used to create composite spontelectrics, illustrating how electric fields in solid films may be structured on the nanoscale by combining layers of different spontelectric materials. This is demonstrated using the spontelectric materials nitrous oxide, toluene, isoprene, isopentane, and CF2Cl2. These yield a variety of tailored electric field structures, with individual layers harboring fields between 10(7) and 10(8) V/m. Fields may be of the same sign or of opposite sign, the latter enabling the creation of nanoscale potential wells. The formation of fields is followed using an established electron beam technique, employing the ASTRID synchrotron storage ring. The influence of temperature on heterolayer structures, displaying new Curie effects, and the nature of the interfacial region between different spontelectrics are also discussed.

  2. 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.

  3. 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.

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

    NASA Astrophysics Data System (ADS)

    Gowda, Prarthana; Ramamurty, Upadrasta; Misra, Abha

    2014-03-01

    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.

  5. DNA-Protein Cross-links: Formation, Structural Identities, and Biological Outcomes

    PubMed Central

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

    2015-01-01

    CONSPECTUS Non-covalent 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

  6. Structures and energetics for O2 formation in photosystem II.

    PubMed

    Siegbahn, Per E M

    2009-12-21

    Water oxidation, forming O(2) from water and sunlight, is a fundamental process for life on earth. In nature, the enzyme photosystem II (PSII) catalyzes this reaction. The oxygen evolving complex (OEC), the complex within PSII that catalyzes the actual formation of the O-O bond, contains four manganese atoms and one calcium atom connected by oxo bonds. Seven amino acid side chains in the structure, mostly carboxylates, are ligated to the metal atoms. In the study of many enzyme mechanisms, theoretical modeling using density functional theory has served as an indispensable tool. This Account summarizes theoretical research to elucidate the mechanism for water oxidation in photosynthesis, including the most recent findings. The development of successively larger models, ranging from 50 atoms in the active site up to the present model size of 170 atoms, has revealed the mechanism of O(2) formation with increasing detail. The X-ray crystal structures of PSII have provided a framework for optimizing the theoretical models. By constraint of the backbone atoms to be at the same positions as those in the X-ray structures, the theoretical structures are in good agreement with both the measured electron density and extended X-ray absorption fine structure (EXAFS) interpretations. By following the structural and energetic changes in those structures through the different steps in the catalytic process, we have modeled the oxidation of the catalytic complex, the binding of the two substrate water molecules, and the subsequent deprotonations of those substrate molecules. In these models, the OEC forms a basin into which the water molecules naturally fit. These findings demonstrate that the binding of the second water molecule causes a reconstruction, results that are consistent with earlier EXAFS measurements. Most importantly, this Account describes a low-barrier mechanism for formation of the O-O bond, involving an oxygen radical that reacts with a mu-oxo ligand of the OEC

  7. Formation of the structure and properties of β-type titanium alloy upon thermomechanical treatment

    NASA Astrophysics Data System (ADS)

    Shaboldo, O. P.; Vitorskii, Ya. M.; Sagaradze, V. V.; Pecherkina, N. L.; Skotnikova, M. A.

    2017-01-01

    The rapid quenching of β-type titanium alloy from 800°C and cold deformation by drawing (ɛ = 24%) leads to the formation of a cellular-banded structure with a cell size of 200 × 400 nm and high density of dislocations ( 5 × 1014 m-2). During subsequent aging at 450°C, the decomposition of the β-phase occurs with a heterogeneous precipitation (at dislocations) of plates of the α phase with a thickness of 10-30 nm and length of 50-100 nm. The small size and high density of α crystals (5 × 1021 m-3) provide a substantial increase in the strength characteristics of the alloy.

  8. 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.

  9. 71-Kilodalton Heat Shock Cognate Protein Acts as a Cellular Receptor for Syncytium Formation Induced by Human T-Cell Lymphotropic Virus Type 1

    PubMed Central

    Sagara, Yasuko; Ishida, Chuzo; Inoue, Yukiko; Shiraki, Hiroshi; Maeda, Yoshiaki

    1998-01-01

    We previously reported that the region corresponding to amino acids 197 to 216 of the gp46 surface glycoprotein (gp46-197) served as a binding domain for the interaction between gp46 and trypsin-sensitive membrane components of the target cell, leading to syncytium formation induced by human T-cell lymphotropic virus type 1 (HTLV-1)-bearing cells. Our new evidence shows that the 71-kDa heat shock cognate protein (HSC70) acts as a cellular receptor for syncytium formation. Using affinity chromatography with the peptide gp46-197, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, we isolated three components (bands A, B, and C) from MOLT-4 cell lysate which exhibited specific interactions with gp46 and inhibitory activities for syncytium formation induced by HTLV-1-bearing cells. Band A and B components were identified as HSC70 and β-actin, respectively, through amino acid sequencing by tandem mass spectrometry and immunostaining with specific monoclonal antibodies. Band C is likely to be a nonprotein component, because full activity for syncytium formation was seen after extensive trypsin digestion. Anti-HSC70 monoclonal antibody clearly blocked syncytium formation in a coculture of HTLV-1-bearing cells and indicator cells, whereas no inhibition was seen with anti-β-actin monoclonal antibody. Furthermore, flow cytometric analysis indicated that anti-HSC70 antibody reacted with MOLT-4 cells. Thus, we propose that HSC70 expressed on the target cell surface acts as a cellular acceptor to gp46 exposed on the HTLV-1-infected cell for syncytium formation, thereby leading to cell-to-cell transmission of HTLV-1. PMID:9420256

  10. 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,…

  11. Gap formation following climatic events in spatially structured plant communities

    PubMed Central

    Liao, Jinbao; De Boeck, Hans J.; Li, Zhenqing; Nijs, Ivan

    2015-01-01

    Gaps play a crucial role in maintaining species diversity, yet how community structure and composition influence gap formation is still poorly understood. We apply a spatially structured community model to predict how species diversity and intraspecific aggregation shape gap patterns emerging after climatic events, based on species-specific mortality responses. In multispecies communities, average gap size and gap-size diversity increased rapidly with increasing mean mortality once a mortality threshold was exceeded, greatly promoting gap recolonization opportunity. This result was observed at all levels of species richness. Increasing interspecific difference likewise enhanced these metrics, which may promote not only diversity maintenance but also community invasibility, since more diverse niches for both local and exotic species are provided. The richness effects on gap size and gap-size diversity were positive, but only expressed when species were sufficiently different. Surprisingly, while intraspecific clumping strongly promoted gap-size diversity, it hardly influenced average gap size. Species evenness generally reduced gap metrics induced by climatic events, so the typical assumption of maximum evenness in many experiments and models may underestimate community diversity and invasibility. Overall, understanding the factors driving gap formation in spatially structured assemblages can help predict community secondary succession after climatic events. PMID:26114803

  12. Formation of the Galactic Stellar Halo. I. Structure and Kinematics

    NASA Astrophysics Data System (ADS)

    Bekki, Kenji; Chiba, Masashi

    2001-09-01

    We perform numerical simulations for the formation of the Galactic stellar halo, based on the currently favored cold dark matter theory of galaxy formation. Our numerical models, taking into account both dynamical and chemical evolution processes in a consistent manner, are aimed at explaining the observed structure and kinematics of the stellar halo in the context of hierarchical galaxy formation. The main results of the present simulations are summarized as follows: (1) Basic physical processes involved in the formation of the stellar halo, composed of metal-deficient stars with [Fe/H]<=-1.0, are described by both dissipative and dissipationless merging of subgalactic clumps and their resultant tidal disruption in the course of gravitational contraction of the Galaxy at high redshift (z>1). (2) The simulated halo has a density profile similar to the observed power-law form of ρ(r)~r-3.5 and also has a metallicity distribution similar to the observations. The halo shows virtually no radial gradient for stellar ages and only a small gradient for metallicities. (3) The dual nature of the halo, i.e., its inner flattened and outer spherical density distribution, is reproduced, at least qualitatively, by the present model. The outer spherical halo is formed via essentially dissipationless merging of small subgalactic clumps, whereas the inner flattened one is formed via three different mechanisms, i.e., dissipative merging between larger, more massive clumps, adiabatic contraction due to the growing Galactic disk, and gaseous accretion onto the equatorial plane. (4) For the simulated metal-poor stars with [Fe/H]<=-1.0, there is no strong correlation between metal abundances and orbital eccentricities, in good agreement with the recent observations. Moreover, the observed fraction of the low-eccentricity stars is reproduced correctly for [Fe/H]<=-1.6 and approximately for the intermediate-abundance range of -1.6<[Fe/H]<=-1.0. (5) The mean rotational velocity of the

  13. Different insight into amphiphilic PEG-PLA copolymers: influence of macromolecular architecture on the micelle formation and cellular uptake.

    PubMed

    Garofalo, Cinzia; Capuano, Giovanna; Sottile, Rosa; Tallerico, Rossana; Adami, Renata; Reverchon, Ernesto; Carbone, Ennio; Izzo, Lorella; Pappalardo, Daniela

    2014-01-13

    One constrain in the use of micellar carriers as drug delivery systems (DDSs) is their low stability in aqueous solution. In this study "tree-shaped" copolymers of general formula mPEG-(PLA)n (n = 1, 2 or 4; mPEG = poly(ethylene glycol) monomethylether 2K or 5K Da; PLA = atactic or isotactic poly(lactide)) were synthesized to evaluate the architecture and chemical composition effect on the micelles formation and stability. Copolymers with mPEG/PLA ratio of about 1:1 wt/wt were obtained using a "core-first" synthetic route. Dynamic Light Scattering (DLS), Field Emission Scanning Electron Microscopy (FESEM), and Zeta Potential measurements showed that mPEG2K-(PD,LLA)2 copolymer, characterized by mPEG chain of 2000 Da and two blocks of atactic PLA, was able to form monodisperse and stable micelles. To analyze the interaction among micelles and tumor cells, FITC conjugated mPEG-(PLA)n were synthesized. The derived micelles were tested on two, histological different, tumor cell lines: HEK293t and HeLa cells. Fluorescence Activated Cells Sorter (FACS) analysis showed that the FITC conjugated mPEG2K-(PD,LLA)2 copolymer stain tumor cells with high efficiency. Our data demonstrate that both PEG size and PLA structure control the biological interaction between the micelles and biological systems. Moreover, using confocal microscopy analysis, the staining of tumor cells obtained after incubation with mPEG2K-(PD,LLA)2 was shown to be localized inside the tumor cells. Indeed, the mPEG2K-(PD,LLA)2 paclitaxel-loaded micelles mediate a potent antitumor cytotoxicity effect.

  14. 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

  15. Cosmological structure formation in Decaying Dark Matter models

    SciTech Connect

    Cheng, Dalong; Chu, M.-C.; Tang, Jiayu E-mail: mcchu@phy.cuhk.edu.hk

    2015-07-01

    The standard cold dark matter (CDM) model predicts too many and too dense small structures. We consider an alternative model that the dark matter undergoes two-body decays with cosmological lifetime τ into only one type of massive daughters with non-relativistic recoil velocity V{sub k}. This decaying dark matter model (DDM) can suppress the structure formation below its free-streaming scale at time scale comparable to τ. Comparing with warm dark matter (WDM), DDM can better reduce the small structures while being consistent with high redshfit observations. We study the cosmological structure formation in DDM by performing self-consistent N-body simulations and point out that cosmological simulations are necessary to understand the DDM structures especially on non-linear scales. We propose empirical fitting functions for the DDM suppression of the mass function and the concentration-mass relation, which depend on the decay parameters lifetime τ, recoil velocity V{sub k} and redshift. The fitting functions lead to accurate reconstruction of the the non-linear power transfer function of DDM to CDM in the framework of halo model. Using these results, we set constraints on the DDM parameter space by demanding that DDM does not induce larger suppression than the Lyman-α constrained WDM models. We further generalize and constrain the DDM models to initial conditions with non-trivial mother fractions and show that the halo model predictions are still valid after considering a global decayed fraction. Finally, we point out that the DDM is unlikely to resolve the disagreement on cluster numbers between the Planck primary CMB prediction and the Sunyaev-Zeldovich (SZ) effect number count for τ ∼ H{sub 0}{sup −1}.

  16. 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.

  17. 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

  18. Formation and evolution of structure in loop cosmology.

    PubMed

    Bojowald, Martin; Kagan, Mikhail; Singh, Parampreet; Hernández, Hector H; Skirzewski, Aureliano

    2007-01-19

    Inhomogeneous cosmological perturbation equations are derived in loop quantum gravity, taking into account corrections, in particular, in gravitational parts. This provides a framework for calculating the evolution of modes in structure formation scenarios related to inflationary or bouncing models. Applications here are corrections to the Newton potential and to the evolution of large scale modes which imply nonconservation of curvature perturbations possibly noticeable in a running spectral index. These effects are sensitive to quantization procedures and test the characteristic behavior of correction terms derived from quantum gravity.

  19. Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding

    SciTech Connect

    Vaezeslami, Soheila; Jia, Xiaofei; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H.

    2008-12-01

    A water network stabilizes the structure of cellular retionic acid binding protein II. The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the α2 helix at its entrance. This chain of interactions acts as a ‘pillar’ that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the α2 helix adopting an altered conformation compared with wild-type CRABPII.

  20. Formation of three-dimensional Parylene C structures via thermoforming

    NASA Astrophysics Data System (ADS)

    Kim, B. J.; Chen, B.; Gupta, M.; Meng, E.

    2014-06-01

    The thermoplastic nature of Parylene C is leveraged to enable the formation of three-dimensional structures using a thermal forming (thermoforming) technique. Thermoforming involves the heating of Parylene films above its glass transition temperature while they are physically confined in the final desired conformation. Micro and macro scale three-dimensional structures composed of Parylene thin films were developed using the thermoforming process, and the resulting chemical and mechanical changes to the films were characterized. No large changes to the surface and bulk chemistries of the polymer were observed following the thermoforming process conducted in vacuum. Heat treated structures exhibited increased stiffness by a maximum of 37% depending on the treatment temperature, due to an increase in crystallinity of the Parylene polymer. This study revealed important property changes resulting from the process, namely (1) the development of high strains in thermoformed areas of small radii of curvature (30-90 µm) and (2) ˜1.5% bulk material shrinkage in thermoformed multilayered Parylene-Parylene and Parylene-metal-Parylene films. Thermoforming is a simple process whereby three-dimensional structures can be achieved from Parylene C-based thin film structures with tunable mechanical properties as a function of treatment temperature.

  1. CG hypomethylation in Lsh-/- mouse embryonic fibroblasts is associated with de novo H3K4me1 formation and altered cellular plasticity.

    PubMed

    Yu, Weishi; Briones, Victorino; Lister, Ryan; McIntosh, Carl; Han, Yixing; Lee, Eunice Y; Ren, Jianke; Terashima, Minoru; Leighty, Robert M; Ecker, Joseph R; Muegge, Kathrin

    2014-04-22

    DNA methylation patterns are established in early embryogenesis and are critical for cellular differentiation. To investigate the role of CG methylation in potential enhancer formation, we assessed H3K4me1 modification in murine embryonic fibroblasts (MEFs) derived from the DNA methylation mutant Lsh(-/-) mice. We report here de novo formation of putative enhancer elements at CG hypomethylated sites that can be dynamically altered. We found a subset of differentially enriched H3K4me1 regions clustered at neuronal lineage genes and overlapping with known cis-regulatory elements present in brain tissue. Reprogramming of Lsh(-/-) MEFs into induced pluripotent stem (iPS) cells leads to increased neuronal lineage gene expression of premarked genes and enhanced differentiation potential of Lsh(-/-) iPS cells toward the neuronal lineage pathway compared with WT iPS cells in vitro and in vivo. The state of CG hypomethylation and H3K4me1 enrichment is partially maintained in Lsh(-/-) iPS cells. The acquisition of H3K27ac and activity of subcloned fragments in an enhancer reporter assay indicate functional activity of several of de novo H3K4me1-marked sequences. Our results suggest a functional link of H3K4me1 enrichment at CG hypomethylated sites, enhancer formation, and cellular plasticity.

  2. Towards a computational modeling of structure formation in colloidal drying

    NASA Astrophysics Data System (ADS)

    Wagner, Alexander

    2014-03-01

    We present lattice Boltzmann models at different scales for the simulation of colloidal drying in the presence of polymers and structure formation in resulting phase-separation fronts. When a drop of colloid polymer mixture is exposed to an environment in which the solvent in which these particles are suspended evaporates an accumulation of non-volotile material at the rim of the drop is observed (coffee ring effect). When the solvent concentration is reduced bejond a certain threshold, the colloid polymer mixture undergoes phase separation. The structures formed by this phase-separation is observed to depend on the processing conditions. In this presentation we will briefly present the experimental observations and our numerical approach to address the observed phenomena.

  3. 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.

  4. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds.

    PubMed

    Chen, B; Greenside, P; Paik, H; Sirota, M; Hadley, D; Butte, A J

    2015-10-01

    A central premise in systems pharmacology is that structurally similar compounds have similar cellular responses; however, this principle often does not hold. One of the most widely used measures of cellular response is gene expression. By integrating gene expression data from Library of Integrated Network-based Cellular Signatures (LINCS) with chemical structure and bioactivity data from PubChem, we performed a large-scale correlation analysis of chemical structures and gene expression profiles of over 11,000 compounds taking into account confounding factors such as biological conditions (e.g., cell line, dose) and bioactivities. We found that structurally similar compounds do indeed yield similar gene expression profiles. There is an ∼20% chance that two structurally similar compounds (Tanimoto Coefficient ≥ 0.85) share significantly similar gene expression profiles. Regardless of structural similarity, two compounds tend to share similar gene expression profiles in a cell line when they are administrated at a higher dose or when the cell line is sensitive to both compounds.

  5. Banded Electron Structure Formation in the Inner Magnetosphere

    NASA Technical Reports Server (NTRS)

    Liemohn, M. W.; Khazanov, G. V.

    1997-01-01

    Banded electron structures in energy-time spectrograms have been observed in the inner magnetosphere concurrent with a sudden relaxation of geomagnetic activity. In this study, the formation of these banded structures is considered with a global, bounce-averaged model of electron transport, and it is concluded that this structure is a natural occurrence when plasma sheet electrons are captured on closed drift paths near the Earth. These bands do not appear unless there is capture of plasma sheet electrons; convection along open drift paths making open pass around the Earth do not have time to develop this feature. The separation of high-energy bands from the injection population due to the preferential advection of the gradient-curvature drift creates spikes in the energy distribution, which overlap to form a series of bands in the energy spectrograms. The lowest band is the bulk of the injected population in the sub-key energy range. Using the Kp history for an observed banded structure event, a cloud of plasma sheet electrons is captured and the development of their distribution function is examined and discussed.

  6. Identification of long-lived proteins reveals exceptional stability of essential cellular structures

    PubMed Central

    Park, Sung Kyu; Harris, Michael S.; Ingolia, Nicholas T.; Yates, John R.; Hetzer, Martin W.

    2013-01-01

    Intracellular proteins with long lifespans have recently been linked to age-dependent defects, ranging from decreased fertility to the functional decline of neurons. Why long-lived proteins exist in metabolically active cellular environments and how they are maintained over time remains poorly understood. Here we provide a system-wide identification of proteins with exceptional lifespans in the rat brain. These proteins are inefficiently replenished despite being translated robustly throughout adulthood. Using nucleoporins as a paradigm for long-term protein persistence, we found that nuclear pore complexes (NPCs) are maintained over a cell’s life through slow but finite exchange of even its most stable subcomplexes. This maintenance is limited, however, as some nucleoporin levels decrease during aging, providing a rationale for the previously observed age-dependent deterioration of NPC function. Our identification of a long-lived proteome reveals cellular components that are at increased risk for damage accumulation, linking long-term protein persistence to the cellular aging process. PMID:23993091

  7. 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.

  8. 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

  9. 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)

  10. Interpreting the developmental dance of the megakaryocyte: a review of the cellular and molecular processes mediating platelet formation.

    PubMed

    Machlus, Kellie R; Thon, Jonathan N; Italiano, Joseph E

    2014-04-01

    Platelets are essential for haemostasis, and thrombocytopenia (platelet counts <150 × 10(9) /l) is a major clinical problem encountered across a number of conditions, including immune thrombocytopenic purpura, myelodysplastic syndromes, chemotherapy, aplastic anaemia, human immunodeficiency virus infection, complications during pregnancy and delivery, and surgery. Circulating blood platelets are specialized cells that function to prevent bleeding and minimize blood vessel injury. Platelets circulate in their quiescent form, and upon stimulation, activate to release their granule contents and spread on the affected tissue to create a physical barrier that prevents blood loss. The current model of platelet formation states that large progenitor cells in the bone marrow, called megakaryocytes, release platelets by extending long, branching processes, designated proplatelets, into sinusoidal blood vessels. This review will focus on different factors that impact megakaryocyte development, proplatelet formation and platelet release. It will highlight recent studies on thrombopoeitin-dependent megakaryocyte maturation, endomitosis and granule formation, cytoskeletal contributions to proplatelet formation, the role of apoptosis, and terminal platelet formation and release.

  11. Epithelial Cell Transforming 2 and Aurora Kinase B Modulate Formation of Stress Granule-Containing Transcripts from Diverse Cellular Pathways in Astrocytoma Cells.

    PubMed

    Weeks, Adrienne; Agnihotri, Sameer; Lymer, Jennifer; Chalil, Alan; Diaz, Roberto; Isik, Semra; Smith, Christian; Rutka, James T

    2016-06-01

    Stress granules are small RNA-protein granules that modify the translational landscape during cellular stress to promote survival. The RhoGTPase RhoA is implicated in the formation of RNA stress granules. Our data demonstrate that the cytokinetic proteins epithelial cell transforming 2 and Aurora kinase B (AurkB) are localized to stress granules in human astrocytoma cells. AurkB and its downstream target histone-3 are phosphorylated during arsenite-induced stress. Chemical (AZD1152-HQPA) and siRNA inhibition of AurkB results in fewer and smaller stress granules when analyzed using high-throughput fluorescent-based cellomics assays. RNA immunoprecipitation with the known stress granule aggregates TIAR and G3BP1 was performed on astrocytoma cells, and subsequent analysis revealed that astrocytoma stress granules harbor unique mRNAs for various cellular pathways, including cellular migration, metabolism, translation, and transcriptional regulation. Human astrocytoma cell stress granules contain mRNAs that are known to be involved in glioma signaling and the mammalian target of rapamycin pathway. These data provide evidence that RNA stress granules are a novel form of epigenetic regulation in astrocytoma cells, which may be targetable by chemical inhibitors and enhance astrocytoma susceptibility to conventional therapy, such as radiation and chemotherapy.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26594372

  13. 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.

  14. 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.

  15. Structural basis of complement membrane attack complex formation

    PubMed Central

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

    2016-01-01

    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. PMID:26841837

  16. Structural basis of complement membrane attack complex formation.

    PubMed

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

    2016-02-04

    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.

  17. Laser induced formation of micro-rough structures

    NASA Astrophysics Data System (ADS)

    Singh, Rajiv K.; Fitz-Gerald, James M.

    1997-01-01

    Laser induced micro-rough structures (LIMS) are a by-product of laser ablation process and are created during multiple pulse irradiation on the surface of the material. Although LIMS have been found to be deleterious for the thin film deposition process, these surfaces have wide variety of applications in synthesis of adherent coatings in thermal expansion mismatched systems. Earlier models, based on interference effects of the laser beam, to explain the evolution of LIMS, are not consistent with the experimental results. Experiments were conducted on a wide variety of materials (e.g. SiC, alumina, YBaCuO superconductor, etc.) to understand the mechanisms for generation of the micro-rough structures. A novel model was developed to explain the characteristics of LIMS such as (i) feature orientation (ii) evolution of surface structures as a function of pulses, (iii) formation of LIMS within a energy window near ablation threshold and (iv) periodicity which is independent of the laser wavelength and incident angle.

  18. Finite element modelling of the actual structure of cellular materials determined by X-ray tomography

    SciTech Connect

    Youssef, S. . E-mail: souhail.youssef@insa-lyon.fr; Maire, E.; Gaertner, R.

    2005-02-01

    The initial microstructure and local deformation mechanisms of a polyurethane foam during a compression test are investigated by means of X-ray microtomography. A methodology to mesh the actual solid volume is described. The polymer material behaviour is assumed to be elastoplastic. A predictive finite element modelling of the mechanical behaviour of cellular materials is then implemented. The validation of the modelling procedure is performed in relation to the macroscopic mechanical response as well as to the local deformation mechanisms observed during the experiments.

  19. Erbium-formate frameworks templated by diammonium cations: syntheses, structures, structural transition and magnetic properties.

    PubMed

    Li, Mengyuan; Liu, Bin; Wang, Bingwu; Wang, Zheming; Gao, Song; Kurmoo, Mohamedally

    2011-06-14

    Two structurally different Er-formate frameworks, one NaCl-like [dmenH(2)][Er(HCOO)(4)](2) (1) and the other pillared-layer type [tmenH(2)][Er(HCOO)(4)](2) (2), were obtained when templated by the corresponding protonated N,N'-dimethylethylenediamine (dmenH(2)) and N,N,N',N'-tetramethyl- ethylenediamine (tmenH(2)). The shape and size of the template cations dictate the different coordination geometries of erbium and consequently the framework topologies, though erbium adopts eight coordination in the two compounds. In the NaCl-like structure of 1, erbium is coordinated by eight anti-anti bridging formates in a square antiprism, while in the pillared-layer structure of 2, it is coordinated by six anti-anti bridging formates and one chelating formate in a pentagonal bipyramid. 2 exhibits a structural phase transition around -70 °C which is related to the disorder-order transition of the template cation. Both compounds behave as paramagnets between 2 and 300 K. However, they display field-dependent ac-susceptibilities with complicated field-induced magnetic relaxation processes, and the major slow ones probably results from spin-lattice relaxation.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Redshift and structure formation in a spatially flat inhomogeneous universe

    NASA Astrophysics Data System (ADS)

    Moffat, J. W.; Tatarski, D. C.

    1992-05-01

    We study a spherically symmetric Tolman-Bondi cosmological model with globally flat spatial sections t=const. We consider the model valid for the description of the Universe after matter starts to dominate. The redshift and cosmological observations in the model are examined and a simple scenario of the changes in the structure formation when compared to the standard flat Friedmann-Robertson-Walker universe is proposed. This scenario is based on the fact that in our model different parts of the Universe spend unequal periods of time in the matter-dominated era. The correction to the cold-dark-matter spatial two-point correlation function is derived. Specific cases are examined corresponding to observationally based distributions of the density. We show that this not only leads to no contradictions, but significantly improves the fit of theoretically predicted correlation functions to observations.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Membrane plasmalogen composition and cellular cholesterol regulation: a structure activity study

    PubMed Central

    2010-01-01

    Background Disrupted cholesterol regulation leading to increased circulating and membrane cholesterol levels is implicated in many age-related chronic diseases such as cardiovascular disease (CVD), Alzheimer's disease (AD), and cancer. In vitro and ex vivo cellular plasmalogen deficiency models have been shown to exhibit impaired intra- and extra-cellular processing of cholesterol. Furthermore, depleted brain plasmalogens have been implicated in AD and serum plasmalogen deficiencies have been linked to AD, CVD, and cancer. Results Using plasmalogen deficient (NRel-4) and plasmalogen sufficient (HEK293) cells we investigated the effect of species-dependent plasmalogen restoration/augmentation on membrane cholesterol processing. The results of these studies indicate that the esterification of cholesterol is dependent upon the amount of polyunsaturated fatty acid (PUFA)-containing ethanolamine plasmalogen (PlsEtn) present in the membrane. We further elucidate that the concentration-dependent increase in esterified cholesterol observed with PUFA-PlsEtn was due to a concentration-dependent increase in sterol-O-acyltransferase-1 (SOAT1) levels, an observation not reproduced by 3-hydroxy-3-methyl-glutaryl-CoA (HMG-CoA) reductase inhibition. Conclusion The present study describes a novel mechanism of cholesterol regulation that is consistent with clinical and epidemiological studies of cholesterol, aging and disease. Specifically, the present study describes how selective membrane PUFA-PlsEtn enhancement can be achieved using 1-alkyl-2-PUFA glycerols and through this action reduce levels of total and free cholesterol in cells. PMID:20546600

  10. Constraints on vacuum energy from structure formation and Nucleosynthesis

    NASA Astrophysics Data System (ADS)

    Adams, Fred C.; Alexander, Stephon; Grohs, Evan; Mersini-Houghton, Laura

    2017-03-01

    This paper derives an upper limit on the density ρΛ of dark energy based on the requirement that cosmological structure forms before being frozen out by the eventual acceleration of the universe. By allowing for variations in both the cosmological parameters and the strength of gravity, the resulting constraint is a generalization of previous limits. The specific parameters under consideration include the amplitude Q of the primordial density fluctuations, the Planck mass Mpl, the baryon-to-photon ratio η, and the density ratio ΩM/Ωb. In addition to structure formation, we use considerations from stellar structure and Big Bang Nucleosynthesis (BBN) to constrain these quantities. The resulting upper limit on the dimensionless density of dark energy becomes ρΛ/Mpl4 < 10‑90, which is ~30 orders of magnitude larger than the value in our universe ρΛ/Mpl4 ~ 10‑120. This new limit is much less restrictive than previous constraints because additional parameters are allowed to vary. With these generalizations, a much wider range of universes can develop cosmic structure and support observers. To constrain the constituent parameters, new BBN calculations are carried out in the regime where η and G = Mpl‑2 are much larger than in our universe. If the BBN epoch were to process all of the protons into heavier elements, no hydrogen would be left behind to make water, and the universe would not be viable. However, our results show that some hydrogen is always left over, even under conditions of extremely large η and G, so that a wide range of alternate universes are potentially habitable.

  11. An invasive podosome-like structure promotes fusion pore formation during myoblast fusion

    PubMed Central

    Sens, Kristin L.; Zhang, Shiliang; Jin, Peng; Duan, Rui; Zhang, Guofeng; Luo, Fengbao; Parachini, Lauren

    2010-01-01

    Recent studies in Drosophila have implicated actin cytoskeletal remodeling in myoblast fusion, but the cellular mechanisms underlying this process remain poorly understood. Here we show that actin polymerization occurs in an asymmetric and cell type–specific manner between a muscle founder cell and a fusion-competent myoblast (FCM). In the FCM, a dense F-actin–enriched focus forms at the site of fusion, whereas a thin sheath of F-actin is induced along the apposing founder cell membrane. The FCM-specific actin focus invades the apposing founder cell with multiple finger-like protrusions, leading to the formation of a single-channel macro fusion pore between the two muscle cells. Two actin nucleation–promoting factors of the Arp2/3 complex, WASP and Scar, are required for the formation of the F-actin foci, whereas WASP but not Scar promotes efficient foci invasion. Our studies uncover a novel invasive podosome-like structure (PLS) in a developing tissue and reveal a previously unrecognized function of PLSs in facilitating cell membrane juxtaposition and fusion. PMID:21098115

  12. Differential expression and cellular localization of ERKs during organogenic nodule formation from internodes of Humulus lupulus var. Nugget.

    PubMed

    Sousa Silva, Marta; Margarida Fortes, Ana; Sanchéz Testillanob, Pilar; Risueño, Maria del Carmen; Salom'e Pais, Maria

    2004-08-01

    The expression and subcellular localization of extracellular signal-regulated kinase 1 or 2 (ERK1/2) homologues (HLERK1/2) during the process of organogenic nodule formation in Humulus lupulus var. Nugget was studied using antibodies specific for ERK1 and ERK2, and for phosphorylated mitogen-activated protein kinases (MAPKs). The increase in HLERK levels, detected by Western blotting 12 hours after wounding suggests their involvement in response to the wounding treatment applied for morphogenesis induction. In dividing cambial cells, occurring in between 4 and 7 days after morphogenesis induction, as well as in dividing prenodular cells (15 days after induction) HLERK1 and/or 2 were localized in the nucleus. However, as soon as nodular cells start proliferating to form shoot meristems, HLERK1 and 2 were detected in the cytoplasm and not in the nucleus. The data reported account for a differential expression and activation of HLERK1 and HLERK2 throughout the process of nodule formation and plantlet regeneration. HLERK1 appears to be expressed in the stages of nodule formation and plantlet regeneration, playing a possible role in controlling cell proliferation and differentiation. HLERK2 may be induced as a response to reactive oxygen species (ROS) generated by wounding of internodes as its expression is reduced in liquid medium with less oxygen availability compared to solid medium. However, addition of a ROS inhibitor to the liquid medium does not result in a further decrease in the HLERK2 level.

  13. Numerical analysis on mechanical behaviors of hierarchical cellular structures with negative Poisson’s ratio

    NASA Astrophysics Data System (ADS)

    Li, Dong; Yin, Jianhua; Dong, Liang; Lakes, Roderic S.

    2017-02-01

    Two-dimensional hierarchical re-entrant honeycomb structures were designed and the mechanical behaviors of the structures were studied using a finite element method. Hierarchical re-entrant structure of order n (n ≥ 1) was constructed by replacing each vertex of a lower order (n - 1) hierarchical re-entrant structure with a smaller re-entrant hexagon with identical strut aspect ratio. The Poisson’s ratio and energy absorption capacity of re-entrant structures of different hierarchical orders were studied under different compression velocities. The results showed that the Poisson’s ratio of the first and second order hierarchical structures can reach -1.36 and -1.33 with appropriate aspect ratio, 13.8% and 12.1% lower than that of the zeroth order hierarchical structure. The energy absorption capacity of the three models increased with an increasing compression velocity; the second order hierarchical structure exhibited the highest rate of increase in energy absorption capacity with an increasing compression velocity. The plateau stresses of the first and second order hierarchical structures were slightly lower than that of the zeroth order hierarchical structure; however the second order hierarchical structure exhibited the highest energy absorption capacity at high compression velocity (60 m s-1).

  14. Diversification of the AlpB Outer Membrane Protein of Helicobacter pylori Affects Biofilm Formation and Cellular Adhesion

    PubMed Central

    Osaki, Takako; Fukutomi, Toshiyuki; Hanawa, Tomoko; Kurata, Satoshi; Zaman, Cynthia; Hojo, Fuhito; Kamiya, Shigeru

    2016-01-01

    ABSTRACT Helicobacter pylori is one of the most common causes of bacterial infection in humans, and it forms biofilms on human gastric mucosal epithelium as well as on in vitro abiotic surfaces. Bacterial biofilm is critical not only for environmental survival but also for successful infection. We previously demonstrated that strain TK1402, which was isolated from a Japanese patient with duodenal and gastric ulcers, has high biofilm-forming ability in vitro relative to other strains. In addition, we showed that outer membrane vesicles (OMV) play an important role in biofilm formation. The aim of this study was to analyze which protein(s) in the OMV contributes to biofilm formation in TK1402. We obtained a spontaneous mutant strain derived from TK1402 lacking biofilm-forming ability. The protein profiles of the OMV were compared between this mutant strain and the wild type, and it was found that AlpB, an outer membrane protein in the OMV of the mutant strain, was markedly decreased compared to that of the wild type. Restoration of TK1402 alpB to the mutant strain fully recovered the ability to form biofilm. However, restoration with alpB from other strains demonstrated incomplete recovery of biofilm-forming ability. We therefore inferred that the variable region of AlpB (amino acid positions 121 to 146) was involved in TK1402 biofilm formation. In addition, diversification of the AlpB sequence was shown to affect the ability to adhere to AGS cells. These results demonstrate a new insight into the molecular mechanisms of host colonization by H. pylori. IMPORTANCE Bacterial biofilm is critical not only for environmental survival but also for successful infection. The mechanism of Helicobacter pylori adherence to host cells mediated by cell surface adhesins has been the focus of many studies, but little is known regarding factors involved in H. pylori biofilm formation. Our study demonstrated that AlpB plays an important role in biofilm formation and that this property

  15. Diversification of the AlpB Outer Membrane Protein of Helicobacter pylori Affects Biofilm Formation and Cellular Adhesion.

    PubMed

    Yonezawa, Hideo; Osaki, Takako; Fukutomi, Toshiyuki; Hanawa, Tomoko; Kurata, Satoshi; Zaman, Cynthia; Hojo, Fuhito; Kamiya, Shigeru

    2017-03-15

    Helicobacter pylori is one of the most common causes of bacterial infection in humans, and it forms biofilms on human gastric mucosal epithelium as well as on in vitro abiotic surfaces. Bacterial biofilm is critical not only for environmental survival but also for successful infection. We previously demonstrated that strain TK1402, which was isolated from a Japanese patient with duodenal and gastric ulcers, has high biofilm-forming ability in vitro relative to other strains. In addition, we showed that outer membrane vesicles (OMV) play an important role in biofilm formation. The aim of this study was to analyze which protein(s) in the OMV contributes to biofilm formation in TK1402. We obtained a spontaneous mutant strain derived from TK1402 lacking biofilm-forming ability. The protein profiles of the OMV were compared between this mutant strain and the wild type, and it was found that AlpB, an outer membrane protein in the OMV of the mutant strain, was markedly decreased compared to that of the wild type. Restoration of TK1402 alpB to the mutant strain fully recovered the ability to form biofilm. However, restoration with alpB from other strains demonstrated incomplete recovery of biofilm-forming ability. We therefore inferred that the variable region of AlpB (amino acid positions 121 to 146) was involved in TK1402 biofilm formation. In addition, diversification of the AlpB sequence was shown to affect the ability to adhere to AGS cells. These results demonstrate a new insight into the molecular mechanisms of host colonization by H. pyloriIMPORTANCE Bacterial biofilm is critical not only for environmental survival but also for successful infection. The mechanism of Helicobacter pylori adherence to host cells mediated by cell surface adhesins has been the focus of many studies, but little is known regarding factors involved in H. pylori biofilm formation. Our study demonstrated that AlpB plays an important role in biofilm formation and that this property depends

  16. 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.

  17. Jupiter’s Formation and Its Primordial Internal Structure

    NASA Astrophysics Data System (ADS)

    Lozovsky, Michael; Helled, Ravit; Rosenberg, Eric D.; Bodenheimer, Peter

    2017-02-01

    The composition of Jupiter and the primordial distribution of the heavy elements are determined by its formation history. As a result, in order to constrain the primordial internal structure of Jupiter, the growth of the core and the deposition and settling of accreted planetesimals must be followed in detail. In this paper we determine the distribution of the heavy elements in proto-Jupiter and determine the mass and composition of the core. We find that while the outer envelope of proto-Jupiter is typically convective and has a homogeneous composition, the innermost regions have compositional gradients. In addition, the existence of heavy elements in the envelope leads to much higher internal temperatures (several times 104 K) than in the case of a hydrogen–helium envelope. The derived core mass depends on the actual definition of the core: if the core is defined as the region in which the heavy-element mass fraction is above some limit (say, 0.5), then it can be much more massive (∼15 {M}\\oplus ) and more extended (10% of the planet’s radius) than in the case where the core is just the region with 100% heavy elements. In the former case Jupiter’s core also consists of hydrogen and helium. Our results should be taken into account when constructing internal structure models of Jupiter and when interpreting the upcoming data from the Juno (NASA) mission.

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

    PubMed Central

    2016-01-01

    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. PMID:26936244

  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. 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.

  1. High-resolution simulations of structure formation in the universe

    NASA Astrophysics Data System (ADS)

    Kravtsov, Andrey V.

    During the last decade, there has been ever increasing interest in the problem of galaxy formation in a cosmological context. Detailed studies of this phenomenon require three-dimensional numerical simulations of very high dynamic range. We have developed the Adaptive Refinement Tree (ART) numerical algorithm for high- resolution dissipationless and gasdynamical cosmological simulations. The algorithm follows particle trajectories and solves the equations of gasdynamics on both a cubic, uniform grid covering the entire computational volume and on finer meshes, introduced recursively in a fully adaptive manner in regions of interest. The refinement meshes are generated to effectively match an arbitrary geometry of the interesting regions, a property particularly important for cosmological simulations. In this thesis, I present a description of the method and its implementation, tests of the numerical code, and two applications which effectively demonstrate the high- resolution capabilities of the code. The first study concerns the abundances of galactic satellites in hierarchical models of structure formation. We find that the theoretical models predict much larger numbers of satellites around Milky Way-type galaxies than are actually observed. We then discuss several possible explanations for the differences in predicted and observed velocity functions, including the identification of some satellites with High-Velocity Clouds observed in the Local Group, and the existence of dark satellites which failed to accrete gas and form stars, due either to the expulsion of gas in the supernovae-driven winds or to gas heating by the intergalactic ionizing background. The second study concerns the problem of the galaxy clustering bias, the difference between the galaxy distribution and the overall distribution of matter, and its evolution with time. We use several statistics to study the bias evolution and find that in general, the bias is nonlinear and time- and scale

  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.

  3. Numerical Simulation of Solidification Structure of ESR Ingot Using Cellular Automaton Method

    NASA Astrophysics Data System (ADS)

    Wang, Xiaohua; Li, Ying

    2015-04-01

    The electroslag remelting (ESR) process is a widely used secondary remelting process for the production of high-value-added alloys and steels. The grain structure of ESR ingot has a great effect on the final properties of products. A multiscale mathematical model combining the macroscopic heat transport with the mesoscopic nucleation and grain growth was developed to predict the grain structure evolution of solidification ingot during the ESR process. A moving cell frame, which dynamically defines the calculation domain for grain structure simulation, was proposed to save the computation resources and time. The thermophysical properties of steel related to the solidification of rotor steel 30Cr1Mo1V were adopted in present model and the nucleation parameters, which were suitable for the ESR process, were determined using the trial and error method in numerical simulation. The multiscale mathematical model was validated by the comparison between predicted and experimentally observed grain structure, and the results showed that the model was capable of simulating the grain structure evolution during the ESR process. Finally, the preliminary investigation on the effect of industrial process parameters on the grain structure was carried out and the results showed that increasing melting rate caused finer columnar grain structure and changed the growth direction of columnar grain structure from the axial-radial growth into the radial growth at very high melting rate. Meanwhile, increasing the molten slag temperature made the columnar grain structure finer and reduced the thickness of the refined equiaxed grain layer both at the surface and bottom of the ESR ingot.

  4. 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.

  5. Identification of large-scale cellular structures on the Sun based on the SDO and PSPT data

    NASA Astrophysics Data System (ADS)

    Efremov, V. I.; Parfinenko, L. D.; Solov'ev, A. A.

    2015-03-01

    Three independent sets of data: (i) series of filtergrams obtained in line CaII K (393.416 nm) with the ground-based telescope Precision Solar Photometric Telescope (PSPT) of Mauna Loa Solar Observatory; (ii) series of filtergrams of Atmospheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO) in λ160 nm and (iii) series of magnetograms of Helioseismic and Magnetic Imager (HMI) of SDO have been processed to reveal reliably the existence of spatial cellular structures on the solar photosphere at scale about of 300 arcsec. This scale is intermediate between supergranules and giant cells (˜30,000 and ˜300,000 km across, respectively). To identify the different spatial structures the tens of two-dimensional power spectra ( 2DFFT) have been averaged. For one-dimensional photometric cross sections of frames, the Fourier power spectra ( FFT) and wavelet transforms (Morlet 5-th order) have been calculated.

  6. Cellular fine structures and histochemical reactions in the tissue of a cypress twig preserved in Baltic amber

    PubMed Central

    Koller, Barbara; Schmitt, Jürgen M.; Tischendorf, Gilbert

    2005-01-01

    A twig of a cypress plant preserved for ca. 45Myr in Baltic amber was analysed by light and electron microscopy. Cross-sections of the whole plant showed an almost intact tissue of the entire stem and leaves, revealing, to our knowledge, the oldest and most highly preserved tissue from an amber inclusion reported so far. The preparations are based on a new technique of internal imbedding, whereby the hollow spaces within the inclusion are filled with synthetic resin which stabilizes the cellular structures during the sectioning procedure. Cytological stains applied to the sections reacted with cell walls and nuclei. A strong green auto-fluorescence of the cuticle and the resin canals in the leaves was observed. Transmission electron micrographs revealed highly preserved fine structures of cell walls, membranes and organelles. The results were compared with taxonomically related recent Glyptostrobus and Juniperus plants. PMID:15695201

  7. 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.

  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. 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

  10. Formation of surface nanodroplets facing a structured microchannel wall.

    PubMed

    Yu, Haitao; Maheshwari, Shantanu; Zhu, Jiuyang; Lohse, Detlef; Zhang, Xuehua

    2017-04-11

    Surface nanodroplets are important units for lab-on-a-chip devices, compartmentalised catalytic reactions, high-resolution near-field imaging, and many others. Solvent exchange is a simple solution-based bottom-up approach for producing surface nanodroplets by displacing a good solvent of the droplet liquid by a poor one in a narrow channel in the laminar regime. The droplet size is controlled by the solution composition and the flow conditions during the solvent exchange. In this paper, we investigated the effects of local microfluidic structures on the formation of surface nanodroplets. The microstructures consist of a microgap with a well-defined geometry, embedded on the opposite microchannel wall, facing the substrate where nucleation takes place. For a given channel height, the dimensionless control parameters were the Peclet number of the flow, the ratio between the gap height and the channel height, and the aspect ratio between the gap length and the channel height. We found and explained three prominent features in the surface nanodroplet distribution at the surface opposite to the microgap: (i) enhanced volume of the droplets; (ii) asymmetry as compared to the location of the gap in the spatial droplet distribution with increasing Pe; (iii) reduced exponent of the effective scaling law of the droplet size with Pe. The droplet size also varied with the aspect and height ratios of the microgap at a given Pe value. Our simulations of the profile of oversaturation in the channel reveal that the droplet size distribution may be attributed to the local flow patterns induced by the gap. Finally, in a tapered microchannel, a gradient of surface nanodroplet size was obtained. Our work shows the potential for controlling nanodroplet size and spatial organization on a homogeneous surface in a bottom-up approach by simple microfluidic structures.

  11. Cosmic structure formation: From first stars to large-scale filamentary structure

    NASA Astrophysics Data System (ADS)

    Cai, Zheng

    Theory of cosmic structure formation outlines how stars, galaxies, clusters of galaxies, and large-scale structures formed out of primordial density fluctuations. It presents us a picture of cosmic mass assembly, and places strong constraints on cosmological model. Both observations and theories suggest that structures formation follows a "bottom up" process, in which small, low-mass component form first, and gradually develop into larger, more massive systems. This dissertation focuses on three crucial stages of cosmic structure formation: first generation stars, quasar host galaxies and the large-scale galaxy overdensities. In Chapter 1, I present an overview of structure formation, acquainting readers with a general picture from first object in the Universe to large-scale structures at later epochs. In Chapter 2 and Chapter 3, I derive strong constraints to the star formation rates (SFRs) of very massive Population III (Pop III) stars in two high redshift galaxies at z = 7. By probing the He II emission lines for both galaxies, I conclude that the contributions of very massive Pop III stars to total the SFRs are less than 3%. In Chapter 4, I move to more massive systems, quasar host galaxies at z ˜ 3. Using damped Lyman alpha absorption systems as natural coronagraphs, I report that rest-frame far-UV emission of quasar host galaxy correlates strongly with quasar luminosity. This result suggests a co-evolution of supermassive black holes and their host galaxies. In Chapter 5, I develop a novel method for searching the most massive protoclusters at z = 2--3, by utilizing intergalactic Lyman alpha absorption. My investigations suggest that large intergalactic Lyman alpha absorption systems effectively trace the most overdense regions at large scale of ˜15 h -1 Mpc. In Chapter 6, I present our imaging observations of an extreme galaxy overdensity (protocluster) BOSS1441+4000, which is discovered using the techniques developed in Chapter 5. Furthermore, I report an

  12. 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.

  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. Dynamic phase separation: from coarsening to turbulence via structure formation.

    PubMed

    Golovin, A A; Pismen, L M

    2004-09-01

    We investigate some new two-dimensional evolution models belonging to the class of convective Cahn-Hilliard models: (i) a local model with a scalar order parameter, (ii) a nonlocal model with a scalar order parameter, and (iii) a model with a vector order parameter. These models are applicable to phase-separating system where concentration gradients cause hydrodynamic motion due to buoyancy or Marangoni effect. The numerical study of the models shows transition from coarsening, typical of Cahn-Hilliard systems, to spatiotemporally irregular behavior (turbulence), typical of the Kuramoto-Sivashinsky equation, which is obtained in the limit of very strong driving. The transition occurs not in a straightforward way, but through the formation of spatial patterns that emerge for intermediate values of the driving intensity. As in driven one-dimensional models studied before, the mere presence of the driving force, however small, breaks the symmetry between the two separating phases, as well as increases the coarsening rate. With increasing driving, coarsening stops. The dynamics is generally irregular at strong driving, but exhibits specific structural features.

  15. Cosmology and Structure Formation with Scalar Field Dark Matter

    NASA Astrophysics Data System (ADS)

    Rindler-Daller, Tanja; Li, Bohua; Shapiro, Paul R.

    2013-04-01

    The exploration of the nature of the cosmological dark matter is an ongoing hot topic in modern cosmology and particle physics. Suggested candidates include ultra-light particles which are described by a real or complex scalar field. Previous literature has revealed the richness of this candidate in terms of its power to explain astrophysical and cosmological observations, from the background cosmological evolution to galactic rotation curves. However, a lot of research remains to be done to find out which parts of the parameter space of this kind of dark matter is able to explain observations on all scales consistently. In this talk, we will present our current and ongoing work on the study of complex scalar field dark matter (SFDM). We find that this SFDM underwent three distinctive states in the early Universe, a scalar-field dominated, a radiation-dominated and a matter-dominated phase. The timing and longevity of each phase places important first constraints on the parameters of the model. For this SFDM model, we revisit classical problems of structure formation theory, like the tophat collapse, the problem of virial shocks, and the cosmological infall problem for an isolated halo, in order to find viable model parameters which match the constraints from cosmology.

  16. Cosmological constraints on the radiation released during structure formation

    NASA Astrophysics Data System (ADS)

    Camarena, David; Marra, Valerio

    2016-11-01

    During the process of structure formation in the universe matter is converted into radiation through a variety of processes such as light from stars, infrared radiation from cosmic dust, and gravitational waves from binary black holes/neutron stars and supernova explosions. The production of this astrophysical radiation background (ARB) could affect the expansion rate of the universe and the growth of perturbations. Here, we aim at understanding to which level one can constraint the ARB using future cosmological observations. We model the energy transfer from matter to radiation through an effective interaction between matter and astrophysical radiation. Using future supernova data from large synoptic survey telescope and growth-rate data from Euclid we find that the ARB density parameter is constrained, at the 95% confidence level, to be Ω_{ar_0}<0.008. Estimates of the energy density produced by well-known astrophysical processes give roughly Ω_{ar_0}˜ 10^{-5}. Therefore, we conclude that cosmological observations will only be able to constrain exotic or not-well understood sources of radiation.

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

    SciTech Connect

    Führer, Florian; Rigopoulos, Gerasimos E-mail: gerasimos.rigopoulos@ncl.ac.uk

    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.

  18. 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.

  19. A comparison between track-structure, condensed-history Monte Carlo simulations and MIRD cellular S-values.

    PubMed

    Tajik-Mansoury, M A; Rajabi, H; Mozdarani, H

    2017-03-07

    The S-value is a standard measure in cellular dosimetry. S-values are calculated by applying analytical methods or by Monte Carlo simulation. In Monte Carlo simulation, particles are either tracked individually event-by-event or close events are condensed and processed collectively in different steps. Both of these methods have been employed for estimation of cellular S-values, but there is no consistency between the published results. In the present paper, we used the Geant4-DNA track-structure physics model as the reference to estimate the cellular S-values. We compared the results with the corresponding values obtained from the following three condensed-history physics models of Geant4: Penelope, Livermore and standard. The geometry and source were exactly the same in all the simulations. We utilized mono-energetic electrons with an initial kinetic energy in the range 1-700 keV as the source of radiation. We also compared our results with the MIRD S-values. We first drew an overall comparison between different data series and then compared the dependence of results on the energy of particles and the size of scoring compartments. The overall comparison indicated a very good linear correlation (R (2)  >  91%) and small bias (3%) between the results of the track-structure model and the condensed-history physics model. The bias between MIRD and the results of Monte Carlo track-structure simulation was considerable (-8%). However, the point-by-point comparison revealed differences of up to 28% between the condensed-history and the track-structure MC codes for self-absorption S-values in the 10-50 keV energy range. For the cross-absorption S-values, the difference was up to 34%. In this energy range, the difference between the MIRD S-values and the Geant4-DNA results was up to 68%. Our findings suggest that the consistency/inconsistency of the results obtained with different MC simulations depends on the size of the scoring volumes, the energy of the

  20. A comparison between track-structure, condensed-history Monte Carlo simulations and MIRD cellular S-values

    NASA Astrophysics Data System (ADS)

    Tajik-Mansoury, M. A.; Rajabi, H.; Mazdarani, H.

    2017-03-01

    The S-value is a standard measure in cellular dosimetry. S-values are calculated by applying analytical methods or by Monte Carlo simulation. In Monte Carlo simulation, particles are either tracked individually event-by-event or close events are condensed and processed collectively in different steps. Both of these methods have been employed for estimation of cellular S-values, but there is no consistency between the published results. In the present paper, we used the Geant4-DNA track-structure physics model as the reference to estimate the cellular S-values. We compared the results with the corresponding values obtained from the following three condensed-history physics models of Geant4: Penelope, Livermore and standard. The geometry and source were exactly the same in all the simulations. We utilized mono-energetic electrons with an initial kinetic energy in the range 1–700 keV as the source of radiation. We also compared our results with the MIRD S-values. We first drew an overall comparison between different data series and then compared the dependence of results on the energy of particles and the size of scoring compartments. The overall comparison indicated a very good linear correlation (R 2  >  91%) and small bias (3%) between the results of the track-structure model and the condensed-history physics model. The bias between MIRD and the results of Monte Carlo track-structure simulation was considerable (‑8%). However, the point-by-point comparison revealed differences of up to 28% between the condensed-history and the track-structure MC codes for self-absorption S-values in the 10–50 keV energy range. For the cross-absorption S-values, the difference was up to 34%. In this energy range, the difference between the MIRD S-values and the Geant4-DNA results was up to 68%. Our findings suggest that the consistency/inconsistency of the results obtained with different MC simulations depends on the size of the scoring volumes, the energy of the

  1. Mussel-inspired bioceramics with self-assembled Ca-P/polydopamine composite nanolayer: preparation, formation mechanism, improved cellular bioactivity and osteogenic differentiation of bone marrow stromal cells.

    PubMed

    Wu, Chengtie; Han, Pingping; Liu, Xiaoguo; Xu, Mengchi; Tian, Tian; Chang, Jiang; Xiao, Yin

    2014-01-01

    The nanostructured surface of biomaterials plays an important role in improving their in vitro cellular bioactivity as well as stimulating in vivo tissue regeneration. Inspired by the mussel's adhesive versatility, which is thought to be due to the plaque-substrate interface being rich in 3,4-dihydroxy-l-phenylalamine (DOPA) and lysine amino acids, in this study we developed a self-assembly method to prepare a uniform calcium phosphate (Ca-P)/polydopamine composite nanolayer on the surface of β-tricalcium phosphate (β-TCP) bioceramics by soaking β-TCP bioceramics in Tris-dopamine solution. It was found that the addition of dopamine, reaction temperature and reaction time are three key factors inducing the formation of a uniform Ca-P/polydopamine composite nanolayer. The formation mechanism of a Ca-P/polydopamine composite nanolayer involved two important steps: (i) the addition of dopamine to Tris-HCl solution decreases the pH value and accelerates Ca and P ionic dissolution from the crystal boundaries of β-TCP ceramics; (ii) dopamine is polymerized to form self-assembled polydopamine film and, at the same time, nanosized Ca-P particles are mineralized with the assistance of polydopamine, in which the formation of polydopamine occurs simultaneously with Ca-P mineralization (formation of nanosized microparticles composed of calcium phosphate-based materials), and finally a self-assembled Ca-P/polydopamine composite nanolayer forms on the surface of the β-TCP ceramics. Furthermore, the formed self-assembled Ca-P/polydopamine composite nanolayer significantly enhances the surface roughness and hydrophilicity of β-TCP ceramics, and stimulates the attachment, proliferation, alkaline phosphate (ALP) activity and bone-related gene expression (ALP, OCN, COL1 and Runx2) of human bone marrow stromal cells. Our results suggest that the preparation of self-assembled Ca-P/polydopamine composite nanolayers is a viable method to modify the surface of biomaterials by

  2. 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

  3. Digital Morphing Wing: Active Wing Shaping Concept Using Composite Lattice-Based Cellular Structures.

    PubMed

    Jenett, Benjamin; Calisch, Sam; Cellucci, Daniel; Cramer, Nick; Gershenfeld, Neil; Swei, Sean; Cheung, Kenneth C

    2017-03-01

    We describe an approach for the discrete and reversible assembly of tunable and actively deformable structures using modular building block parts for robotic applications. The primary technical challenge addressed by this work is the use of this method to design and fabricate low density, highly compliant robotic structures with spatially tuned stiffness. This approach offers a number of potential advantages over more conventional methods for constructing compliant robots. The discrete assembly reduces manufacturing complexity, as relatively simple parts can be batch-produced and joined to make complex structures. Global mechanical properties can be tuned based on sub-part ordering and geometry, because local stiffness and density can be independently set to a wide range of values and varied spatially. The structure's intrinsic modularity can significantly simplify analysis and simulation. Simple analytical models for the behavior of each building block type can be calibrated with empirical testing and synthesized into a highly accurate and computationally efficient model of the full compliant system. As a case study, we describe a modular and reversibly assembled wing that performs continuous span-wise twist deformation. It exhibits high performance aerodynamic characteristics, is lightweight and simple to fabricate and repair. The wing is constructed from discrete lattice elements, wherein the geometric and mechanical attributes of the building blocks determine the global mechanical properties of the wing. We describe the mechanical design and structural performance of the digital morphing wing, including their relationship to wind tunnel tests that suggest the ability to increase roll efficiency compared to a conventional rigid aileron system. We focus here on describing the approach to design, modeling, and construction as a generalizable approach for robotics that require very lightweight, tunable, and actively deformable structures.

  4. Digital Morphing Wing: Active Wing Shaping Concept Using Composite Lattice-Based Cellular Structures

    PubMed Central

    Jenett, Benjamin; Calisch, Sam; Cellucci, Daniel; Cramer, Nick; Gershenfeld, Neil; Swei, Sean

    2017-01-01

    Abstract We describe an approach for the discrete and reversible assembly of tunable and actively deformable structures using modular building block parts for robotic applications. The primary technical challenge addressed by this work is the use of this method to design and fabricate low density, highly compliant robotic structures with spatially tuned stiffness. This approach offers a number of potential advantages over more conventional methods for constructing compliant robots. The discrete assembly reduces manufacturing complexity, as relatively simple parts can be batch-produced and joined to make complex structures. Global mechanical properties can be tuned based on sub-part ordering and geometry, because local stiffness and density can be independently set to a wide range of values and varied spatially. The structure's intrinsic modularity can significantly simplify analysis and simulation. Simple analytical models for the behavior of each building block type can be calibrated with empirical testing and synthesized into a highly accurate and computationally efficient model of the full compliant system. As a case study, we describe a modular and reversibly assembled wing that performs continuous span-wise twist deformation. It exhibits high performance aerodynamic characteristics, is lightweight and simple to fabricate and repair. The wing is constructed from discrete lattice elements, wherein the geometric and mechanical attributes of the building blocks determine the global mechanical properties of the wing. We describe the mechanical design and structural performance of the digital morphing wing, including their relationship to wind tunnel tests that suggest the ability to increase roll efficiency compared to a conventional rigid aileron system. We focus here on describing the approach to design, modeling, and construction as a generalizable approach for robotics that require very lightweight, tunable, and actively deformable structures. PMID:28289574

  5. Foam and cluster structure formation by latex particles at the air/water interface

    NASA Astrophysics Data System (ADS)

    Ruiz-Garcia, Jaime; Gámez-Corrales, Rogelio; Ivlev, Boris I.

    1997-02-01

    We report the formation of two-dimensional foam and cluster structures by spherical polystyrene particles trapped at the air/water interface. The colloidal foam is a transient structure that evolves to the formation of clusters, but clusters can also be formed after deposition of the sample. We also observed the formation of small aggregates, whose formation along with the cluster stabilization can be explained in terms of a balance between electrostatic repulsive and van der Waals attractive interactions.

  6. 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.

  7. Innovative design of composite structures: Use of curvilinear fiber format to improve structural efficiency

    NASA Technical Reports Server (NTRS)

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

    1987-01-01

    To increase the effectiveness and efficiency of fiber-reinforced materials, the use of fibers in a curvilinear rather than the traditional straightline format is explored. The capacity of a laminated square plate with a central circular hole loaded in tension is investigated. The orientation of the fibers is chosen so that the fibers in a particular layer are aligned with the principle stress directions in that layer. Finite elements and an iteration scheme are used to find the fiber orientation. A noninteracting maximum strain criterion is used to predict load capacity. The load capacities of several plates with different curvilinear fibers format are compared with the capacities of more conventional straightline format designs. It is found that the most practical curvilinear design sandwiches a group of fibers in a curvilinear format between a pair of +/-45 degree layers. This design has a 60% greater load capacity than a conventional quasi-isotropic design with the same number of layers. The +/-45 degree layers are necessary to prevent matrix cracking in the curvilinear layers due to stresses perpendicular to the fibers in those layers. Greater efficiencies are achievable with composite structures than now realized.

  8. Outer membrane protein A (OmpA): a new player in shigella flexneri protrusion formation and inter-cellular spreading.

    PubMed

    Ambrosi, Cecilia; Pompili, Monica; Scribano, Daniela; Zagaglia, Carlo; Ripa, Sandro; Nicoletti, Mauro

    2012-01-01

    Outer membrane protein A (OmpA) is a multifaceted predominant outer membrane protein of Escherichia coli and other Enterobacteriaceae whose role in the pathogenesis of various bacterial infections has recently been recognized. Here, the role of OmpA on the virulence of Shigella flexneri has been investigated. An ompA mutant of wild-type S. flexneri 5a strain M90T was constructed (strain HND92) and it was shown to be severely impaired in cell-to-cell spreading since it failed to plaque on HeLa cell monolayers. The lack of OmpA significantly reduced the levels of IcsA while the levels of cell associated and released IcsP-cleaved 95 kDa amino-terminal portion of the mature protein were similar. Nevertheless, the ompA mutant displayed IcsA exposed across the entire bacterial surface. Surprisingly, the ompA mutant produced proper F-actin comet tails, indicating that the aberrant IcsA exposition at bacterial lateral surface did not affect proper activation of actin-nucleating proteins, suggesting that the absence of OmpA likely unmasks mature or cell associated IcsA at bacterial lateral surface. Moreover, the ompA mutant was able to invade and to multiply within HeLa cell monolayers, although internalized bacteria were found to be entrapped within the host cell cytoplasm. We found that the ompA mutant produced significantly less protrusions than the wild-type strain, indicating that this defect could be responsible of its inability to plaque. Although we could not definitely rule out that the ompA mutation might exert pleiotropic effects on other S. flexneri genes, complementation of the ompA mutation with a recombinant plasmid carrying the S. flexneri ompA gene clearly indicated that a functional OmpA protein is required and sufficient for proper IcsA exposition, plaque and protrusion formation. Moreover, an independent ompA mutant was generated. Since we found that both mutants displayed identical virulence profile, these results further supported the findings

  9. Cellular expression and crystal structure of the murine cytomegalovirus major histocompatibility complex class I-like glycoprotein, m153.

    PubMed

    Mans, Janet; Natarajan, Kannan; Balbo, Andrea; Schuck, Peter; Eikel, Daniel; Hess, Sonja; Robinson, Howard; Simic, Hrvoje; Jonjic, Stipan; Tiemessen, Caroline T; Margulies, David H

    2007-11-30

    Mouse cytomegalovirus (MCMV), a beta-herpesvirus that establishes latent and persistent infections in mice, is a valuable model for studying complex virus-host interactions. MCMV encodes the m145 family of putative immunoevasins with predicted major histocompatibility complex, class I (MHC-I) structure. Functions attributed to some family members include down-regulation of host MHC-I (m152) and NKG2D ligands (m145, m152, and m155) and interaction with inhibitory or activating NK receptors (m157). We present the cellular, biochemical, and structural characterization of m153, which is a heavily glycosylated homodimer, that does not require beta2m or peptide and is expressed at the surface of MCMV-infected cells. Its 2.4-A crystal structure confirms that this compact molecule preserves an MHC-I-like fold and reveals a novel mode of dimerization, confirmed by site-directed mutagenesis, and a distinctive disulfide-stabilized extended N terminus. The structure provides a useful framework for comparative analysis of the divergent members of the m145 family.

  10. 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.

  11. Halothane-induced alterations in cellular structure and proliferation of A549 cells.

    PubMed

    Stephanova, E; Topouzova-Hristova, T; Hazarosova, R; Moskova, V

    2008-12-01

    Genotoxicity, cytotoxicity or teratogenicity are among the well-known detrimental effects of the volatile anaesthetics. The aim of the present work was to study the structural changes, proliferative activity and the possibility of alveolar A549 cells to recover after in vitro exposure to halothane at 1.5 and 2.1mM concentrations. Our data indicated significant reduction of viability, suppression of mitotic activity more than 60%, and that these alterations were accompanied by disturbances of nuclear and nucleolar structures. The most prominent negative effect was the destruction of the lamellar bodies, the main storage organelles of pulmonary surfactant, substantial for the lung physiology. In conclusion, halothane applied at clinically relevant concentrations exerts genotoxic and cytotoxic effect on the alveolar cells in vitro, most likely as a consequence of stress-induced apoptosis, thus modulating the respiratory function.

  12. 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.

  13. 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.

  14. Unwinding the differences of the mammalian PERIOD clock proteins from crystal structure to cellular function.

    PubMed

    Kucera, Nicole; Schmalen, Ira; Hennig, Sven; Öllinger, Rupert; Strauss, Holger M; Grudziecki, Astrid; Wieczorek, Caroline; Kramer, Achim; Wolf, Eva

    2012-02-28

    The three PERIOD homologues mPER1, mPER2, and mPER3 constitute central components of the mammalian circadian clock. They contain two PAS (PER-ARNT-SIM) domains (PAS-A and PAS-B), which mediate homo- and heterodimeric mPER-mPER interactions as well as interactions with transcription factors and kinases. Here we present crystal structures of PAS domain fragments of mPER1 and mPER3 and compare them with the previously reported mPER2 structure. The structures reveal homodimers, which are mediated by interactions of the PAS-B β-sheet surface including a highly conserved tryptophan (Trp448(mPER1), Trp419(mPER2), Trp359(mPER3)). mPER1 homodimers are additionally stabilized by interactions between the PAS-A domains and mPER3 homodimers by an N-terminal region including a predicted helix-loop-helix motive. We have verified the existence of these homodimer interfaces in solution and inside cells using analytical gel filtration and luciferase complementation assays and quantified their contributions to homodimer stability by analytical ultracentrifugation. We also show by fluorescence recovery after photobleaching analyses that destabilization of the PAS-B/tryptophan dimer interface leads to a faster mobility of mPER2 containing complexes in human U2OS cells. Our study reveals structural and quantitative differences between the homodimeric interactions of the three mouse PERIOD homologues, which are likely to contribute to their distinct clock functions.

  15. Impact of Network Structure and Cellular Response on Spike Time Correlations

    PubMed Central

    Trousdale, James; Hu, Yu; Shea-Brown, Eric; Josić, Krešimir

    2012-01-01

    Novel experimental techniques reveal the simultaneous activity of larger and larger numbers of neurons. As a result there is increasing interest in the structure of cooperative – or correlated – activity in neural populations, and in the possible impact of such correlations on the neural code. A fundamental theoretical challenge is to understand how the architecture of network connectivity along with the dynamical properties of single cells shape the magnitude and timescale of correlations. We provide a general approach to this problem by extending prior techniques based on linear response theory. We consider networks of general integrate-and-fire cells with arbitrary architecture, and provide explicit expressions for the approximate cross-correlation between constituent cells. These correlations depend strongly on the operating point (input mean and variance) of the neurons, even when connectivity is fixed. Moreover, the approximations admit an expansion in powers of the matrices that describe the network architecture. This expansion can be readily interpreted in terms of paths between different cells. We apply our results to large excitatory-inhibitory networks, and demonstrate first how precise balance – or lack thereof – between the strengths and timescales of excitatory and inhibitory synapses is reflected in the overall correlation structure of the network. We then derive explicit expressions for the average correlation structure in randomly connected networks. These expressions help to identify the important factors that shape coordinated neural activity in such networks. PMID:22457608

  16. Associations of Unilateral Whisker and Olfactory Signals Induce Synapse Formation and Memory Cell Recruitment in Bilateral Barrel Cortices: Cellular Mechanism for Unilateral Training Toward Bilateral Memory

    PubMed Central

    Gao, Zilong; Chen, Lei; Fan, Ruicheng; Lu, Wei; Wang, Dangui; Cui, Shan; Huang, Li; Zhao, Shidi; Guan, Sudong; Zhu, Yan; Wang, Jin-Hui

    2016-01-01

    Somatosensory signals and operative skills learned by unilateral limbs can be retrieved bilaterally. In terms of cellular mechanism underlying this unilateral learning toward bilateral memory, we hypothesized that associative memory cells in bilateral cortices and synapse innervations between them were produced. In the examination of this hypothesis, we have observed that paired unilateral whisker and odor stimulations led to odorant-induced whisker motions in bilateral sides, which were attenuated by inhibiting the activity of barrel cortices. In the mice that showed bilateral cross-modal responses, the neurons in both sides of barrel cortices became to encode this new odor signal alongside the innate whisker signal. Axon projections and synapse formations from the barrel cortex, which was co-activated with the piriform cortex, toward its contralateral barrel cortex (CBC) were upregulated. Glutamatergic synaptic transmission in bilateral barrel cortices was upregulated and GABAergic synaptic transmission was downregulated. The associative activations of the sensory cortices facilitate new axon projection, glutamatergic synapse formation and GABAergic synapse downregulation, which drive the neurons to be recruited as associative memory cells in the bilateral cortices. Our data reveal the productions of associative memory cells and synapse innervations in bilateral sensory cortices for unilateral training toward bilateral memory. PMID:28018178

  17. Sub-micrometer axial resolution OCT for in-vivo imaging of the cellular structure of healthy and keratoconic human corneas

    PubMed Central

    Bizheva, Kostadinka; Tan, Bingyao; MacLelan, Benjamin; Kralj, Olivera; Hajialamdari, Mojtaba; Hileeto, Denise; Sorbara, Luigina

    2017-01-01

    Corneal degenerative conditions such as keratoconus (KC) cause progressive damage to the anterior corneal tissue and eventually severely compromise visual acuity. The ability to visualize corneal tissue damage in-vivo at cellular or sub-cellular level at different stages of development of KC and other corneal diseases, can aid the early diagnostics as well as the development of more effective treatment approaches for various corneal pathologies, including keratoconus. Here, we present the optical design of an optical coherence tomography system that can achieve 0.95 µm axial resolution in biological tissue and provide test results for the system’s spatial resolution and sensitivity. Corneal images acquired in-vivo with this system from healthy and keratoconic human subjects reveal the cellular and sub-cellular structure of the corneal epithelium, as well as the normal and abnormal structure of the Bowman’s membrane and the anterior corneal stroma. PMID:28270986

  18. Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding

    SciTech Connect

    Vaezeslami, Soheila; Jia, Xiaofei; Vasileiou, Chrysoula; Borhan, Babak; Geiger, James H.

    2009-09-02

    The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the {alpha} 2 helix at its entrance. This chain of interactions acts as a 'pillar' that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the {alpha}2 helix adopting an altered conformation compared with wild-type CRABPII.

  19. 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

  20. 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%.

  1. 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.

  2. Cellular Structural Changes in Candida albicans Caused by the Hydroalcoholic Extract from Sapindus saponaria L.

    PubMed

    Shinobu-Mesquita, Cristiane S; Bonfim-Mendonça, Patricia S; Moreira, Amanda L; Ferreira, Izabel C P; Donatti, Lucelia; Fiorini, Adriana; Svidzinski, Terezinha I E

    2015-05-22

    Vulvovaginal candidiasis (VVC) is a disease caused by the abnormal growth of yeast-like fungi in the mucosa of the female genital tract. Candida albicans is the principal etiological agent involved in VVC, but reports have shown an increase in the prevalence of Candida non-C. albicans (CNCA) cases, which complicates VVC treatment because CNCA does not respond well to antifungal therapy. Our group has reported the in vitro antifungal activity of extracts from Sapindus saponaria L. The present study used scanning electron microscopy and transmission electron microscopy to further evaluate the antifungal activity of hydroalcoholic extract from S. saponaria (HE) against yeast obtained from VVC and structural changes induced by HE. We observed the antifungal activity of HE against 125 vaginal yeasts that belonged to four different species of the Candida genus and S. cerevisae. The results suggest that saponins that are present in HE act on the cell wall or membrane of yeast at the first moments after contact, causing damage to these structures and cell lysis.

  3. 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

  4. 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.

  5. Structural determinants for the formation of sulfhemeprotein complexes

    PubMed Central

    Román-Morales, Elddie; Pietri, Ruth; Ramos-Santana, Brenda; Vinogradov, Serge N.; Lewis-Ballester, Ariel; López-Garriga, Juan

    2010-01-01

    Several hemoglobins were explored by UV-Vis and resonance Raman spectroscopy to define sulfheme complex formation. Evaluation of these proteins upon the reaction with H2O2 or O2 in the presence of H2S suggest: (a) the formation of the sulfheme derivate requires a HisE7 residue in the heme distal site with an adequate orientation to form an active ternary complex; (b) that the ternary complex intermediate involves the HisE7, the peroxo or ferryl species, and the H2S molecule. This moiety precedes and triggers the sulfheme formation. PMID:20732304

  6. Enhancement of energy absorption in a closed-cell aluminum by the modification of cellular structures

    SciTech Connect

    Miyoshi, T.; Itoh, M.; Mukai, T.; Kanahashi, H.; Kohzu, H.; Tanabe, S.; Higashi, K.

    1999-10-22

    Recently, there is a high interest in using light-weight metallic foams (e.g., Al and Mg) for automotive, railway and aerospace applications where weight reduction and improvement in comfort are needed. Metallic foams also have a potential for absorbing impact energy during the crashing of a vehicle either against another vehicle or a pedestrian. In this study, enhancement of absorption energy in a closed-cell structure has been performed by an increase in the aspect ratio of cell-wall thickness against the cell-edge length with the reduction of cell size. The absorbed energy in a modified foam is estimated comparing with that in a conventional ALPORAS with the same relative density.

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

    PubMed

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

    2014-05-30

    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.

  8. The effect of a negative Poisson’s ratio on thermal stresses in cellular metallic structures

    NASA Astrophysics Data System (ADS)

    Adler, L.; Warmuth, F.; Lodes, M. A.; Osmanlic, F.; Körner, C.

    2016-11-01

    To investigate the influence of auxetic behavior on thermally induced stresses, finite element analysis simulations of the displacement and stress fields in locally heated three dimensional auxetic and cubic structures are compared. The simulations were carried out in Comsol for a cubic as well as a chiral array of 30 mm length in each spatial dimension (3 × 3 × 3 unit cells). The center cells of these arrays were heated for 20 s. For two boundary conditions (free and clamped), deformation mechanisms are analyzed. It is found, that the auxetic behavior can effectively reduce thermal stresses by internal node rotation and strut bending, especially for constrained (clamped) boundary conditions. A stress reduction of a factor of 3.3 in comparisons to a simple cubic cell array could be evaluated.

  9. 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.

  10. 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.

  11. Design, Synthesis, Biochemical Studies, Cellular Characterization, and Structure-Based Computational Studies of Small Molecules Targeting the Urokinase Receptor

    PubMed Central

    Wang, Fang; Knabe, W. Eric; Li, Liwei; Jo, Inha; Mani, Timmy; Roehm, Hartmut; Oh, Kyungsoo; Li, Jing; Khanna, May; Meroueh, Samy O.

    2012-01-01

    The urokinase receptor (uPAR) serves as a docking site to the serine protease urokinase-type plasminogen activator (uPA) to promote extracellular matrix (ECM) degradation and tumor invasion and metastasis. Previously, we had reported a small molecule inhibitor of the uPAR•uPA interaction that emerged from structure-based virtual screening. Here, we measure the affinity of a large number of derivatives from commercial sources. Synthesis of additional compounds was carried out to probe the role of various groups on the parent compound. Extensive structure-based computational studies suggested a binding mode for these compounds that led to a structure-activity relationship study. Cellular studies in non-small cell lung cancer (NSCLC) cell lines that include A549, H460 and H1299 showed that compounds blocked invasion, migration and adhesion. The effects on invasion of active compounds were consistent with their inhibition of uPA and MMP proteolytic activity. These compounds showed weak cytotoxicity consistent with the confined role of uPAR to metastasis. PMID:22771232

  12. 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.

  13. The Bok globule BHR 160: structure and star formation

    NASA Astrophysics Data System (ADS)

    Haikala, L. K.; Reipurth, B.

    2017-01-01

    Context. BHR 160 is a virtually unstudied cometary globule within the Sco OB4 association in Scorpius at a distance of 1600 pc. It is part of a system of cometary clouds which face the luminous O star HD 155806. BHR 160 is special because it has an intense bright rim. Aims: We attempt to derive physical parameters for BHR 160 and to understand its structure and the origin of its peculiar bright rim. Methods: BHR 160 was mapped in the , and C18O(2-1) and (1-0) and CS (3-2) and (2-1) lines. These data, augmented with stellar photometry derived from the ESO VVV survey, were used to derive the mass and distribution of molecular material in BHR 160 and its surroundings. Archival mid-infrared data from the WISE satellite was used to find IR excess stars in the globule and its neighbourhood. Results: An elongated 1' by 0.´6 core lies adjacent to the globule bright rim. emission covers the whole globule, but the , C18Oand CS emission is more concentrated to the core. The line profiles indicate the presence of outflowing material near the core, but the spatial resolution of the mm data is not sufficient for a detailed spatial analysis. The BHR 160 mass estimated from the C18Omapping is100 ± 50 M⊙ (d/1.6 kpc)2 where d is the distance to the globule. Approximately 70% of the mass lies in the dense core. The total mass of molecular gas in the direction of BHR 160 is 210 ± 80 (d/1.6 kpc)2 M⊙ when estimated from the more extended VVV near-infrared photometry. We argue that the bright rim of BHR 160 is produced by a close-by early B-type star, HD 319648, that was likely recently born in the globule. This star is likely to have triggered the formation of a source, IRS 1, that is embedded within the core of the globule and detected only in Ks and by WISE and IRAS. Based on observations made with ESO Telescopes at the La Silla or Paranal Observatories.Reduced molecular line spectra (The SEST spectra as FITS files) are only available at the CDS via anonymous ftp to http

  14. The Relation Between Item Format and the Structure of the Eysenck Personality Inventory

    ERIC Educational Resources Information Center

    Velicer, Wayne F.; Stevenson, John F.

    1978-01-01

    A Likert seven-choice response format for personality inventories allows finer distinctions by subjects than the traditional two-choice format. The Eysenck Personality Inventory was employed in the present study to test the hypothesis that use of the expanded format would result in a clearer and more accurate indication of test structure.…

  15. 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.

  16. 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

  17. 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.

  18. Contrast-enhanced digital holographic imaging of cellular structures by manipulating the intracellular refractive index

    NASA Astrophysics Data System (ADS)

    Rommel, Christina E.; Dierker, Christian; Schmidt, Lisa; Przibilla, Sabine; von Bally, Gert; Kemper, Björn; Schnekenburger, Jürgen

    2010-07-01

    The understanding of biological reactions and evaluation of the significance for living cells strongly depends on the ability to visualize and quantify these processes. Digital holographic microscopy (DHM) enables quantitative phase contrast imaging for high resolution and minimal invasive live cell analysis without the need of labeling or complex sample preparation. However, due to the rather homogeneous intracellular refractive index, the phase contrast of subcellular structures is limited and often low. We analyze the impact of the specific manipulation of the intracellular refractive index by microinjection on the DHM phase contrast. Glycerol is chosen as osmolyte, which combines high solubility in aqueous solutions and biological compatibility. We show that the intracellular injection of glycerol causes a contrast enhancement that can be explained by a decrease of the cytosolic refractive index due to a water influx. The underlying principle is proven by experiments inducing cell shrinkage and with fixated cells. The integrity of the cell membrane is considered as a prerequisite and allows a reversible cell swelling and shrinking within a certain limit. The presented approach to control the intracellular phase contrast demonstrated for the example of DHM opens prospects for applications with other quantitative phase contrast imaging methods.

  19. 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.

  20. 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).

  1. Cellular and subcellular localization of CXCL12 and CXCR4 in rat nociceptive structures: physiological relevance.

    PubMed

    Reaux-Le Goazigo, Annabelle; Rivat, Cyril; Kitabgi, Patrick; Pohl, Michel; Melik Parsadaniantz, Stéphane

    2012-09-01

    Initial studies implicated the chemokine CXC motif ligand 12 (CXCL12) and its cognate CXC motif receptor 4 (CXCR4) in pain modulation. However, there has been no description of the distribution, transport and axonal sorting of CXCL12 and CXCR4 in rat nociceptive structures, and their direct participation in nociception modulation has not been demonstrated. Here, we report that acute intrathecal administration of CXCL12 induced mechanical hypersensitivity in naive rats. This effect was prevented by a CXCR4-neutralizing antibody. To determine the morphological basis of this behavioural response, we used light and electron microscopic immunohistochemistry to map CXCL12- and CXCR4-immunoreactive elements in dorsal root ganglia, lumbar spinal cord, sciatic nerve and skin. Light microscopy analysis revealed CXCL12 and CXCR4 immunoreactivity in calcitonin gene related peptide-containing peptidergic primary sensory neurons, which were both conveyed to central and peripheral sensory nerve terminals. Electron microscopy clearly demonstrated CXCL12 and CXCR4 immunoreactivity in primary sensory nerve terminals in the dorsal horn; both were sorted into small clear vesicles and large dense-core vesicles. This suggests that CXCL12 and CXCR4 are trafficked from nerve cell bodies to the dorsal horn. Double immunogold labelling for CXCL12 and calcitonin gene related peptide revealed partial vesicular colocalization in axonal terminals. We report, for the first time, that CXCR4 receptors are mainly located on the neuronal plasma membrane, where they are present at pre-synaptic and post-synaptic sites of central terminals. Receptor inactivation experiments, behavioural studies and morphological analyses provide strong evidence that the CXCL12/CXCR4 system is involved in modulation of nociceptive signalling.

  2. The Megavirus Chilensis Cu,Zn-Superoxide Dismutase: the First Viral Structure of a Typical Cellular Copper Chaperone-Independent Hyperstable Dimeric Enzyme

    PubMed Central

    Lartigue, Audrey; Burlat, Bénédicte; Coutard, Bruno; Chaspoul, Florence; Claverie, Jean-Michel

    2014-01-01

    ABSTRACT Giant viruses able to replicate in Acanthamoeba castellanii penetrate their host through phagocytosis. After capsid opening, a fusion between the internal membranes of the virion and the phagocytic vacuole triggers the transfer in the cytoplasm of the viral DNA together with the DNA repair enzymes and the transcription machinery present in the particles. In addition, the proteome analysis of purified mimivirus virions revealed the presence of many enzymes meant to resist oxidative stress and conserved in the Mimiviridae. Megavirus chilensis encodes a predicted copper, zinc superoxide dismutase (Cu,Zn-SOD), an enzyme known to detoxify reactive oxygen species released in the course of host defense reactions. While it was thought that the metal ions are required for the formation of the active-site lid and dimer stabilization, megavirus chilensis SOD forms a very stable metal-free dimer. We used electron paramagnetic resonance (EPR) analysis and activity measurements to show that the supplementation of the bacterial culture with copper and zinc during the recombinant expression of Mg277 is sufficient to restore a fully active holoenzyme. These results demonstrate that the viral enzyme's activation is independent of a chaperone both for disulfide bridge formation and for copper incorporation and suggest that its assembly may not be as regulated as that of its cellular counterparts. A SOD protein is encoded by a variety of DNA viruses but is absent from mimivirus. As in poxviruses, the enzyme might be dispensable when the virus infects Acanthamoeba cells but may allow megavirus chilensis to infect a broad range of eukaryotic hosts. IMPORTANCE Mimiviridae are giant viruses encoding more than 1,000 proteins. The virion particles are loaded with proteins used by the virus to resist the vacuole's oxidative stress. The megavirus chilensis virion contains a predicted copper, zinc superoxide dismutase (Cu,Zn-SOD). The corresponding gene is present in some megavirus

  3. The Rab GTPase Rab8 as a shared regulator of ciliogenesis and immune synapse assembly: From a conserved pathway to diverse cellular structures

    PubMed Central

    Patrussi, Laura; Baldari, Cosima T.

    2016-01-01

    ABSTRACT Rab GTPases, which form the largest branch of the Ras GTPase superfamily, regulate almost every step of vesicle-mediated trafficking. Among them, Rab8 is an essential participant in primary cilium formation. In a report recently published in the Journal of Cell Science, Finetti and colleagues identify Rab8 as a novel player in vesicular traffic in the non-ciliated T lymphocytes, which contributes to the assembly of the specialized signaling platform known as the immune synapse. By interacting with the v-SNARE VAMP-3, Rab8 is indeed responsible for the final docking/fusion step in T cell receptor (TCR) recycling to the immune synapse. A second important take-home message which comes to light from this work is that VAMP-3 also interacts with Rab8 at the base of the cilium in NIH-3T3 cells, where it regulates ciliary growth and targeting of Smoothened at the plasma membrane. Hence the data presented in this report, in addition to identifying Rab8 as a novel player in vesicular traffic to the immune synapse, reveal how both ciliated and non-ciliated cells take advantage of a conserved pathway to build highly specific cellular structures. PMID:26587735

  4. Memory formation: from network structure to neural dynamics.

    PubMed

    Feldt, Sarah; Wang, Jane X; Hetrick, Vaughn L; Berke, Joshua D; Zochowski, Michal

    2010-05-13

    Understanding the neural correlates of brain function is an extremely challenging task, since any cognitive process is distributed over a complex and evolving network of neurons that comprise the brain. In order to quantify observed changes in neuronal dynamics during hippocampal memory formation, we present metrics designed to detect directional interactions and the formation of functional neuronal ensembles. We apply these metrics to both experimental and model-derived data in an attempt to link anatomical network changes with observed changes in neuronal dynamics during hippocampal memory formation processes. We show that the developed model provides a consistent explanation of the anatomical network modifications that underlie the activity changes observed in the experimental data.

  5. 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.

  6. Fine structure of the spectra of the Kondo lattice model: Two-site cellular dynamical mean-field theory study

    NASA Astrophysics Data System (ADS)

    Osolin, Žiga; Žitko, Rok

    2017-01-01

    We study the antiferromagnetic and paramagnetic Kondo insulator phases of the Kondo lattice model on the cubic lattice at half filling using the cellular dynamical mean-field theory (CDMFT) with the numerical renormalization group (NRG) as the impurity solver, focusing on the fine details of the spectral function and self-energy. We find that the nonlocal correlations increase the gap in both the antiferromagnetic and Kondo insulator phases and shrink the extent of the antiferromagnetic phase in the phase diagram but do not alter any properties qualitatively. The agreement between the numerical CDMFT results and those within a simple hybridization picture, which adequately describes the overall band structure of the system but neglects all effects on the inelastic-scattering processes, is similar to that of the single-site DMFT results; there are deviations that are responsible for the additional fine structure, in particular for the asymmetric spectral resonances or dips that become more pronounced in the strong-coupling regime close to the antiferromagnet-paramagnetic quantum phase transition. These features appear broader in the CDMFT mostly due to numerical artifacts linked to more aggressive state truncation required in the NRG.

  7. 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.

  8. Proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation.

    PubMed

    Vaysse, Pierre-Joseph; Prat, Laure; Mangenot, Sophie; Cruveiller, Stéphane; Goulas, Philippe; Grimaud, Régis

    2009-12-01

    Many hydrocarbon-degrading bacteria form biofilms at the hydrocarbon-water interface to overcome the weak accessibility of these poorly water-soluble substrates. In order to gain insight into the cellular functions involved, we undertook a proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm developing at the hexadecane-water interface. Biofilm formation on hexadecane led to a global change in cell physiology involving modulation of the expression of 576 out of 1144 detected proteins when compared with planktonic cells growing on acetate. Biofilm cells overproduced a protein encoded by MARHY0478 that contains a conserved domain belonging to the family of the outer membrane transporters of hydrophobic compounds. Homologs of MARHY0478 were exclusively found in marine bacteria degrading alkanes or possessing alkane degradation genes, and hence presumably constitute a family of alkane transporters specific to marine bacteria. Interestingly, we also found that sessile cells growing on hexadecane overexpressed type VI secretion system components. This secretion system has been identified as a key factor in virulence and in symbiotic interaction with host organisms. This observation is the first experimental evidence of the contribution of a type VI secretion system to environmental adaptation, and raises the intriguing question about the role of this secretion machine in alkane assimilation.

  9. Common links in the structure and cellular localization of Rhizobium chitolipooligosaccharides and general Rhizobium membrane phospholipid and glycolipid components.

    PubMed

    Cedergren, R A; Lee, J; Ross, K L; Hollingsworth, R I

    1995-04-04

    Several common links between the structural chemistry of the chitolipooligosaccharides of Rhizobium and the general rhizobial membrane lipid and lipopolysaccharide chemistry of these bacteria have been uncovered. Aspects of common chemistry include sulfation, methylation, and the position and extent of fatty acyl chain unsaturation. We find that bacteria which are known to synthesize sulfated chitolipooligosaccharides (such as Rhizobium meliloti strains and the broad-host-range Rhizobium species strain NGR234) also have sulfated lipopolysaccharides. Their common origins of sulfation have been demonstrated by using mutants which are known to be impaired in sulfating their chitolipooligosaccharides. In such cases, there is a corresponding diminution or complete lack of sulfation of the lipopolysaccharides. The structural diversity of the fatty acids observed in the chitolipooligosaccharides is also observed in the other membrane lipids. For instance, the doubly unsaturated fatty acids which are known to be predominant components of R. meliloti chitolipooligosaccharides were also found in the usual phospholipids and glycolipids. Also, the known functionalization of the chitolipooligosaccharides of R. sp. NGR234 by O- and N-methylation was also reflected in the lipopolysaccharide of this organism. The common structural features of chitolipooligosaccharides and membrane components are consistent with a substantial degree of biosynthetic overlap and a large degree of cellular, spatial overlap between these molecules. The latter aspect is clearly demonstrated here since we show that the chitolipooligosaccharides are, in fact, normal membrane components of Rhizobium. This increases the importance of understanding the role of the bacterial cell surface chemistry in the Rhizobium/legume symbiosis and developing a comprehensive understanding of the highly integrated membrane lipid and glycolipid chemistry of Rhizobium.

  10. 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

  11. 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.

  12. FORMATION AND STRUCTURE OF THE SPORE OF BACILLUS COAGULANS

    PubMed Central

    Ohye, D. F.; Murrell, W. G.

    1962-01-01

    Spore formation in Bacillus coagulans has been studied by electron microscopy using an epoxy resin (Araldite) embedding technique. The developmental stages from the origin of the initial spore septum to the mature spore were investigated. The two forespore membranes developed from the double layer of cytoplasmic membrane. The cortex was progressively deposited between these two membranes. The inner membrane finally became the spore protoplasmic membrane, and the outer membrane part of the inner spore coat or the outer spore coat itself. In the mature spore the completed integuments around the spore protoplasm consisted of the cortex, a laminated inner coat, and a dense outer coat. No exosporium was observed. The method of formation of the cortex and the spore coats is discussed. PMID:14481435

  13. 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

  14. Formation of periodic structures on glass with laser irradiation

    NASA Astrophysics Data System (ADS)

    Peng, Ying Zi; An, Cheng Wu; Wu, Dong Jiang; Hong, Ming Hui; Lu, Yong Feng; Chong, Tow Chong

    2003-07-01

    Regular and tidy periodic structures hae been directly induced on glasses using a CW CO2 laser beam with linear polarization. It is experimentally shown that precise periodic structures with the period of several microns can be formed by means of well-set laser parameters. The orientation of the periodic structures formed is the same as that of the laser polarization no matter what the scanning direction is. The occurrence of periodic structures is very sensitive to laser power level and scanning velocity. To obtain appropriate periodic patterns, a combined condition of laser energy and scanning velocity must be satisfied. The period, width and height of the structures are dependent on processing parameters. An interesting phenomenon is that the period decreases with increasing scanning velocity. Permanent relieves with periods, widths and heights varied with the laser parameters are also studied.

  15. Network Formation: Neighborhood Structures, Establishment Costs, and Distributed Learning

    DTIC Science & Technology

    2012-09-19

    element equal to 1; and (iii) λ ≥ 0 is a parameter used to model possible perturbations in the decision making process, also called mutations [33...vol. 106, no. 2, pp. 265–295, 2002. [19] N. Olaizola and F. Valenciano, “One-way flow network formation under constraints,” University of the Basque ...57–84, 1993. [34] L. Breiman, Probability. Philadelphia: SIAM, 1992. [35] M. Kandori, G. Mailath, and R. Rob, “Learning, mutation , and long-run

  16. Granuloma formation by muramyl dipeptide associated with branched fatty acids, a structure probably essential for tubercle formation by Mycobacterium tuberculosis.

    PubMed Central

    Emori, K; Nagao, S; Shigematsu, N; Kotani, S; Tsujimoto, M; Shiba, T; Kusumoto, S; Tanaka, A

    1985-01-01

    Muramyl dipeptide, which does not induce epithelioid granuloma when injected alone dissolved in phosphate-buffered saline, could induce extensive granulomas in guinea pigs when chemically conjugated with branched, but not linear, fatty acids. Peptidoglycan fragments of Staphylococcus epidermidis could evoke epithelioid granulomas when incorporated in a water-in-oil emulsion. These findings suggest the importance of a lipid bound to muramyl dipeptide for granuloma formation. In view of the fact that mycobacteria uniquely contain large amounts of branched fatty acids, it was proposed that the complex of muramyl dipeptide and branched fatty acids, mostly mycolic acids, is a structure in tubercle bacilli responsible for tubercle formation. Images PMID:3924828

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Formation of core-shell structure in high entropy alloy coating by laser cladding

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Wu, Wanfei; He, Yizhu; Li, Mingxi; Guo, Sheng

    2016-02-01

    The formation of core-shell structure is an interesting phenomenon occurring during the solidification process, due to the liquid phase separation. The formation of core-shell structure in high-entropy alloys, a new class of advanced metallic materials, has not been reported previously, and thus constitutes an intriguing scientific question. Here, we firstly report the formation of core-shell structure in one laser cladded high-entropy alloy, where we show the nanosized-Y2O3 powder addition, serves as the catalyst for the liquid phase separation.

  4. The Spatial Distribution of Star Formation in Galaxies: Observing the Emergence of Galactic Structure

    NASA Astrophysics Data System (ADS)

    Nelson, Erica June

    A high resolution measurement of the distribution of star formation within galaxies is key to understanding the emergence of galactic structure. The aim of this thesis is to understand how the structure of galaxies is built by developing a new method to spatially resolve their star formation. Using Ha maps for 2676 galaxies, this thesis shows where star formation is distributed in galaxies during the epoch 0.7 < z < 1.5 when a third of the total star formation in the history of the universe occurred. Across the star formation rate - stellar mass plane (the "main sequence"), star formation is `spatially coherent': in galaxies with higher than average star formation rates, Ha is enhanced throughout the disk; similarly, in galaxies with low star formation rates Ha is depressed throughout the disk. This places constraints both on the mechanisms for enhancing and quenching star formation as well as on how the structure of galaxies is built. The disk scale length of star formation in galaxies is larger than that of the stars, a direct demonstration that the disks of galaxies grow inside-out. While most star formation in most galaxies occurs in disks, not all of it does. With the first spatially resolved measurement of the Balmer decrement at z > 1, it can be seen that galaxies with M* > 1010M ⊙ have significant dust attenuation toward their centers. This means that we are witnessing the build-up of the dense stellar cores of massive galaxies through dust-obscured in-situ star formation. The most massive galaxies are thought to have formed their dense stellar cores at even earlier cosmic epochs. This thesis presents the first confirmed example of a massive galaxy core in the process of formation at z = 2.3. It has one of the highest velocity dispersions ever measured for a normal star forming galaxy and also appears to be building through very dense, dust-enshrouded star formation.

  5. 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.

  6. Campylobacter jejuni CsrA complements an Escherichia coli csrA mutation for the regulation of biofilm formation, motility and cellular morphology but not glycogen accumulation

    PubMed Central

    2012-01-01

    Background Although Campylobacter jejuni is consistently ranked as one of the leading causes of bacterial diarrhea worldwide, the mechanisms by which C. jejuni causes disease and how they are regulated have yet to be clearly defined. The global regulator, CsrA, has been well characterized in several bacterial genera and is known to regulate a number of independent pathways via a post transcriptional mechanism, but remains relatively uncharacterized in the genus Campylobacter. Previously, we reported data illustrating the requirement for CsrA in several virulence related phenotypes of C. jejuni strain 81–176, indicating that the Csr pathway is important for Campylobacter pathogenesis. Results We compared the Escherichia coli and C. jejuni orthologs of CsrA and characterized the ability of the C. jejuni CsrA protein to functionally complement an E. coli csrA mutant. Phylogenetic comparison of E. coli CsrA to orthologs from several pathogenic bacteria demonstrated variability in C. jejuni CsrA relative to the known RNA binding domains of E. coli CsrA and in several amino acids reported to be involved in E. coli CsrA-mediated gene regulation. When expressed in an E. coli csrA mutant, C. jejuni CsrA succeeded in recovering defects in motility, biofilm formation, and cellular morphology; however, it failed to return excess glycogen accumulation to wild type levels. Conclusions These findings suggest that C. jejuni CsrA is capable of efficiently binding some E. coli CsrA binding sites, but not others, and provide insight into the biochemistry of C. jejuni CsrA. PMID:23051923

  7. Formation of titanium carbide coating with micro-porous structure

    NASA Astrophysics Data System (ADS)

    Luo, Yong; Ge, Shirong; Jin, Zhongmin; Fisher, John

    2010-03-01

    Micro-porous titanium carbide coating was successfully synthesized in a vacuum gas carburizing furnace by using a sequential diffusion technology. The composition and structure of the as-synthesized TiC were examined by X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and glow discharge mass spectrometry (GDMS), and scanning electron microscopy (SEM). All of the XRD, XPS and GDMS analysis results indicate that carbon atoms effectively diffused into the titanium alloys and formed a uniform acicular TiC coating with micro-porous structure.

  8. Structural Definition of an Antibody-Dependent Cellular Cytotoxicity Response Implicated in Reduced Risk for HIV-1 Infection

    PubMed Central

    Acharya, Priyamvada; Tolbert, William D.; Gohain, Neelakshi; Wu, Xueji; Yu, Lei; Liu, Tongyun; Huang, Wensheng; Huang, Chih-chin; Kwon, Young Do; Louder, Robert K.; Luongo, Timothy S.; McLellan, Jason S.; Pancera, Marie; Yang, Yongping; Zhang, Baoshan; Flinko, Robin; Foulke, James S.; Sajadi, Mohammad M.; Kamin-Lewis, Roberta; Robinson, James E.; Martin, Loïc; Kwong, Peter D.; Guan, Yongjun; DeVico, Anthony L.; Lewis, George K.

    2014-01-01

    ABSTRACT The RV144 vaccine trial implicated epitopes in the C1 region of gp120 (A32-like epitopes) as targets of potentially protective antibody-dependent cellular cytotoxicity (ADCC) responses. A32-like epitopes are highly immunogenic, as infected or vaccinated individuals frequently produce antibodies specific for these determinants. Antibody titers, as measured by enzyme-linked immunosorbent assay (ELISA) against these epitopes, however, do not consistently correlate with protection. Here, we report crystal structures of CD4-stabilized gp120 cores complexed with the Fab fragments of two nonneutralizing, A32-like monoclonal antibodies (MAbs), N5-i5 and 2.2c, that compete for antigen binding and have similar antigen-binding affinities yet exhibit a 75-fold difference in ADCC potency. We find that these MAbs recognize overlapping epitopes formed by mobile layers 1 and 2 of the gp120 inner domain, including the C1 and C2 regions, but bind gp120 at different angles via juxtaposed VH and VL contact surfaces. A comparison of structural and immunological data further showed that antibody orientation on bound antigen and the capacity to form multivalent antigen-antibody complexes on target cells were key determinants of ADCC potency, with the latter process having the greater impact. These studies provide atomic-level definition of A32-like epitopes implicated as targets of protective antibodies in RV144. Moreover, these studies establish that epitope structure and mode of antibody binding can dramatically affect the potency of Fc-mediated effector function against HIV-1. These results provide key insights for understanding, refining, and improving the outcome of HIV vaccine trials, in which relevant immune responses are facilitated by A32-like elicited responses. IMPORTANCE HIV-1 Env is a primary target for antibodies elicited during infection. Although a small number of infected individuals elicit broadly neutralizing antibodies, the bulk of the humoral response

  9. 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.

  10. Cellular polyethylene-naphthalate ferroelectrets: Foaming in supercritical carbon dioxide, structural and electrical preparation, and resulting piezoelectricity

    NASA Astrophysics Data System (ADS)

    Fang, P.; Wegener, M.; Wirges, W.; Gerhard, R.; Zirkel, L.

    2007-05-01

    Polymer foams with electrically charged cellular voids, the so-called ferroelectrets, are soft piezoelectric transducer materials. Several polymers such as polyethylene terephthalate or cyclo-olefin copolymers are under investigation with respect to their suitability as ferroelectrets. Here, the authors report an additional ferroelectret polymer, cellular polyethylene-naphthalate (PEN), which was prepared from commercial uniform polymer films by means of foaming in supercritical carbon dioxide, inflation, biaxial stretching, electrical charging, and metallization. Piezoelectric d33 coefficients of up to 140pC/N demonstrate the suitability of such cellular PEN films for transducer applications. Their piezoelectricity is partially stable at elevated temperatures as high as 100°C.

  11. 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.

    2017-01-01

    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 per cent) in the central cluster volume at all epochs. The dissipation via compressive modes is found to be more important (˜30 per cent of the total) only at large radii (≥0.5rvir) 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. Secondly, in the cluster interior vortex, stretching is dominant, although the other terms also contribute substantially.

  12. Structural Insights into Clostridium perfringens Delta Toxin Pore Formation.

    PubMed

    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.

  13. Micromechanics of Amorphous Metal/Polymer Hybrid Structures with 3D Cellular Architectures: Size Effects, Buckling Behavior, and Energy Absorption Capability.

    PubMed

    Mieszala, Maxime; Hasegawa, Madoka; Guillonneau, Gaylord; Bauer, Jens; Raghavan, Rejin; Frantz, Cédric; Kraft, Oliver; Mischler, Stefano; Michler, Johann; Philippe, Laetitia

    2017-02-01

    By designing advantageous cellular geometries and combining the material size effects at the nanometer scale, lightweight hybrid microarchitectured materials with tailored structural properties are achieved. Prior studies reported the mechanical properties of high strength cellular ceramic composites, obtained by atomic layer deposition. However, few studies have examined the properties of similar structures with metal coatings. To determine the mechanical performance of polymer cellular structures reinforced with a metal coating, 3D laser lithography and electroless deposition of an amorphous layer of nickel-boron (NiB) is used for the first time to produce metal/polymer hybrid structures. In this work, the mechanical response of microarchitectured structures is investigated with an emphasis on the effects of the architecture and the amorphous NiB thickness on their deformation mechanisms and energy absorption capability. Microcompression experiments show an enhancement of the mechanical properties with the NiB thickness, suggesting that the deformation mechanism and the buckling behavior are controlled by the brittle-to-ductile transition in the NiB layer. In addition, the energy absorption properties demonstrate the possibility of tuning the energy absorption efficiency with adequate designs. These findings suggest that microarchitectured metal/polymer hybrid structures are effective in producing materials with unique property combinations.

  14. 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

  15. Formation of limit-periodic structures by quadrupole particles confined to a triangular lattice

    NASA Astrophysics Data System (ADS)

    Rutkowski, David M.; Marcoux, Catherine; Socolar, Joshua E. S.; Hall, Carol K.

    2017-01-01

    We have performed Monte Carlo (MC) simulations on two-dimensional systems of quadrupole particles confined to a triangular lattice in order to determine the conditions that permit the formation of a limit-periodic phase. We have found that limit-periodic structures form only when the rotations of the particles are confined to a set of six orientations aligned with the lattice directions. Related structures including striped and unidirectional rattler phases form when π /π 6 rotations or continuous rotations are allowed. Order parameters signaling the formation of the limit-periodic structure and related structures are measured as a function of temperature. Our findings on the formation of the limit-periodic structure elucidate features relevant to the experimental creation of such a structure, which is expected to have interesting vibrational and electromagnetic modes.

  16. Macroscopically structured polymer formation governed by spatial patterns in the Belousov Zhabotinsky reaction

    NASA Astrophysics Data System (ADS)

    Kalishyn, Yevhen Yu.; Khavrus, Vyacheslav O.; Strizhak, Peter E.; Seipel, Michael; Münster, Arno F.

    2002-09-01

    We report the formation of macroscopically structured cross-linked polyacrylamide hydrogel in the Belousov-Zhabotinsky (BZ) system (oxidation of malonic acid by bromate catalyzed by ferroin). Here, acrylamide, the cross-linker bis-acrylamide, and polymerization initiator are added into the BZ system. We show that the formation of waves and ripples in the polymer is governed by spatial structures emerging in the BZ system. Without any spatial structures in the BZ system only the formation of a spatially uniform polymer is observed. Without cross-linker, a spatially uniform polymer was observed as well. Structured polymer formation is caused by the interaction of chemical reactions in the BZ system and the polymerization process including gelation and cross-linking of the monomer units.

  17. Structural Basis for TSC-1 TSC-2 Complex Formation

    DTIC Science & Technology

    2008-03-01

    three ankyrin repeats (residues 420-525), and two tandem BRCT domains (resi- dues 568-777) (5, 6). Germline and somatic mutations that affect the...ovarian cancers from patients negative for mutations in BRCA1 (7-9). Two missense mutations (C557S and Q564H) occur in the region between the ankyrin ... Haire , L. F., Yaffe, M. B., and Smerdon, S. J. (2004) Structure and mechanism of BRCA1 BRCT domain recognition of phosphory- lated BACH1 with

  18. Formation of Structure and Properties of Carbide-Free Bainite in Steel 30KhGSA

    NASA Astrophysics Data System (ADS)

    Panov, D. O.; Simonov, Yu. N.; Leont'ev, P. A.; Kaletin, A. Yu.; Georgiev, M. N.

    2016-05-01

    The process of formation of carbide-free bainite, its structure and properties in steel 30KhGSA are studied. The results of a dilatometric analysis are used to determine the temperature and time boundaries of formation of upper and lower carbide-free bainite. The methods of scanning and transmission electron microscopy are used to determine the special features of the structure of bainite as a function of the temperature of isothermal treatment.

  19. Dynamics of nanopore structure formation in the carbonization of carbon-containing materials

    SciTech Connect

    V.N. Antsiferov; V.N. Strel'nikov; V.F. Olontsev; I.A. Borisova

    2009-04-15

    The dynamics of nanopore structure formation in the carbonization of carbon-containing materials with various volatile matter contents was determined using physicochemical methods of analysis. The main stages of the formation of the nanopore structure of carbon adsorbents upon carbonization were demonstrated using black coals from the Kuznetsk Basin, brown coals from the Kansk-Achinsk Basin, Textolite wastes, nut shell wastes, woods and gazwarine.

  20. 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.

  1. Fuel Structure and Pressure Effects on the Formation of Soot Particles in Diffusion Flames

    DTIC Science & Technology

    1990-05-01

    higher values of the pressure power dependence appear to be related to fuel structure effects , the direct nature of which remains to be understood...61102F 2308 A2 11. TITLE (Include Security Classification) "Fuel Structure and Pressure Effects on the Formation of Soot Particlesin Diffusion Flames...block number) Studies emphasizing the effects of fuel concentration and operating pressure on the formation of soot particles have been conducted in a

  2. 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.

  3. 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.

  4. Geochemistry and structure of the Hawley Formation: Northwestern Massachusetts

    SciTech Connect

    Kim, J.; Jacobi, R. . Dept. of Geology)

    1993-03-01

    The Hawley Formation in northwestern Massachusetts is composed of mafic and felsic, (trondhjemitic) igneous units and black sulfidic schists and quartzites. The dominant lithology is a thinly foliated hbd-plag.-chi-qtz.-Fe carbonate schist with or without hornblende fasicules. Locally, this schist has alternating folia of chl/hbd and plag. and probably has a volcaniclastic protolith. Distinct pillows and tuffs are observed locally. In general, these schists have flat REE patterns at 10X chondrite and plot as IABs on discrimination diagrams. In the eastern part of the Hawley, some amphibolites show concave upward REE patterns, plot in the IAT or boninite field on discrimination diagrams, and appear to have boninitic affinities. The felsic lithologies are trondhjemitic and are intrusive into the IAT/boninite amphibolites. The intrusive nature is based on the presence of mafic xenoliths and intruded rafts of country rock in the trondhjemite as well as the occurrence of thin tabular trondhjemite bodies in sharp contact with the surrounding amphibolite. The trondhjemite varies from coarse-grained weakly foliated qtz-plag.-biotite gneiss with probable relict igneous zoned plagioclases to finer-grained well foliated qtz-plag.-garnet-hbd gneiss. REE patterns for the trondhjemites are weakly U-shaped with moderate to pronounced negative Eu anomalies. The trondhjemites, surrounding amphibolites, and black sulfidic schists and quartzites of the eastern part of the Hawley are intruded by massive, granular, medium grained, plagioclase phenocryst amphibolites with chilled margins. These intrusive sills predate or are coeval with the dominant foliation in the Hawley. Both sills and country rock contain a contact-parallel foliation as well as a later foliation at a low angle to the earlier foliation. The sill amphibolites are high TiO2 high Zr varieties that plot as MORBs to WPBs on discrimination diagrams and exhibit slightly LREE enriched MORB-like to T-MORB REE patterns.

  5. Comparison between structurally connected propellant formation flying and electromagnetic formation flying spacecraft configurations for Gen-X mission

    NASA Astrophysics Data System (ADS)

    Ahsun, Umair; Rodgers, Lennon; Miller, David W.

    2005-08-01

    Gen-X is a next generation concept x-ray telescope that would be approximately 1000-times more sensitive than current x-ray telescopes such as Chandra. Since Gen-X will require focal lengths greater than 50 meters, formation flying the detector module behind the primary mirror is a feasible option. This study investigates the viability of a novel approach referred to as Electromagnetic Formation Flight (EMFF). EMFF uses High Temperature Superconducting (HTS) coils to generate force and torque between the primary and detector modules. EMFF subsystems such as coils, thermal control and power are sized as a function of different system parameters such as slew rate, focal length and detector mass. To investigate the viability of EMFF, a comparison is made between three different techniques for keeping the detector at the focal length distance behind the primary mirror assembly. The first architecture uses a deployable truss to create a Structurally Connected X-ray telescope (SCX), the second uses propellant-based formation flying (PFF) and the third uses Electromagnetic Formation Flying (EMFF).

  6. 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.

  7. Plasmonic Nanostructured Cellular Automata

    NASA Astrophysics Data System (ADS)

    Alkhazraji, Emad; Ghalib, A.; Manzoor, K.; Alsunaidi, M. A.

    2017-03-01

    In this work, we have investigated the scattering plasmonic resonance characteristics of silver nanospheres with a geometrical distribution that is modelled by Cellular Automata using time-domain numerical analysis. Cellular Automata are discrete mathematical structures that model different natural phenomena. Two binary one-dimensional Cellular Automata rules are considered to model the nanostructure, namely rule 30 and rule 33. The analysis produces three-dimensional scattering profiles of the entire plasmonic nanostructure. For the Cellular Automaton rule 33, the introduction of more Cellular Automata generations resulted only in slight red and blue shifts in the plasmonic modes with respect to the first generation. On the other hand, while rule 30 introduced significant red shifts in the resonance peaks at early generations, at later generations however, a peculiar effect is witnessed in the scattering profile as new peaks emerge as a feature of the overall Cellular Automata structure rather than the sum of the smaller parts that compose it. We strongly believe that these features that emerge as a result adopting the different 256 Cellular Automata rules as configuration models of nanostructures in different applications and systems might possess a great potential in enhancing their capability, sensitivity, efficiency, and power utilization.

  8. Structure formation upon barocryodeformation of a steel of austenitic class

    NASA Astrophysics Data System (ADS)

    Antoshina, I. A.; Khaymovich, P. A.; Chernyaeva, E. V.; Shulgin, N. A.

    2016-10-01

    Data are given concerning the opportunity of applying barocryodeformation (plastic deformation under the conditions of severe uniform compression at cryogenic temperatures) to produce ultrafine-disperse martensitic structure in Kh18N10T steel (≤0.08 C, 18 Cr, 10 Ni, <0.7 Ti, ≤2 Mn, ≤0.8 Si (wt %)), which ensures an increase in the physicomechanical characteristics of material that are unattainable when using other types of treatment. Experiments are described that make it possible to explain the high (in spite of the presence of large forces of uniform compression) rate of completion of the martensitic transition upon the deformation of the steel under such conditions.

  9. Structural characterization of casein micelles: shape changes during film formation

    NASA Astrophysics Data System (ADS)

    Gebhardt, R.; Vendrely, C.; Kulozik, U.

    2011-11-01

    The objective of this study was to determine the effect of size-fractionation by centrifugation on the film structure of casein micelles. Fractionated casein micelles in solution were asymmetrically distributed with a small distribution width as measured by dynamic light scattering. Films prepared from the size-fractionated samples showed a smooth surface in optical microscopy images and a homogeneous microstructure in atomic force micrographs. The nano- and microstructure of casein films was probed by micro-beam grazing incidence small angle x-ray scattering (μGISAXS). Compared to the solution measurements, the sizes determined in the film were larger and broadly distributed. The measured GISAXS patterns clearly deviate from those simulated for a sphere and suggest a deformation of the casein micelles in the film.

  10. Change of surface structure upon foam film formation.

    PubMed

    Ridings, Christiaan; Andersson, Gunther G

    2015-03-16

    The charge distribution and coverage with surfactant molecules at foam film surfaces plays an important role in determining foam film structure and stability. This work uses the concentration depth profiling technique neutral impact collision ion scattering spectroscopy to experimentally observe the charge distribution in a foam film for the first time. The charge distribution at the surface of a foam film and the surface of the corresponding bulk liquid were measured for a cationic surfactant solution and the surface excess as well as the electric potential were determined. Describing the internal pressure of foam films by using the electrochemical potential is introduced as a new concept. The foam film can be seen to have a more negative surface charge compared to the bulk liquid surface due to re-arranging of the surfactant molecules. It is discussed how the change in surface excess and electric potential change the electrochemical potential and the stability of the foam film.

  11. Structure and decomposition of the silver formate Ag(HCO2)

    NASA Astrophysics Data System (ADS)

    Puzan, Anna N.; Baumer, Vyacheslav N.; Mateychenko, Pavel V.

    2017-02-01

    Crystal structure of the silver formate Ag(HCO2) has been determined (orthorhombic, sp.gr. Pccn, a=7.1199(5), b=10.3737(4), c=6.4701(3)Å, V=477.88(4) Å3, Z=8). The structure contains isolated formate ions and the pairs Ag22+ which form the layers in (001) planes (the shortest Ag-Ag distances is 2.919 in the pair and 3.421 and 3.716 Å between the nearest Ag atoms of adjacent pairs). Silver formate is unstable compound which decompose spontaneously vs time. Decomposition was studied using Rietveld analysis of the powder diffraction patterns. It was concluded that the diffusion of Ag atoms leads to the formation of plate-like metal particles as nuclei in the (100) planes which settle parallel to (001) planes of the silver formate matrix.

  12. Structural characteristics of green tea catechins for formation of protein carbonyl in human serum albumin.

    PubMed

    Ishii, Takeshi; Mori, Taiki; Ichikawa, Tatsuya; Kaku, Maiko; Kusaka, Koji; Uekusa, Yoshinori; Akagawa, Mitsugu; Aihara, Yoshiyuki; Furuta, Takumi; Wakimoto, Toshiyuki; Kan, Toshiyuki; Nakayama, Tsutomu

    2010-07-15

    Catechins are polyphenolic antioxidants found in green tea leaves. Recent studies have reported that various polyphenolic compounds, including catechins, cause protein carbonyl formation in proteins via their pro-oxidant actions. In this study, we evaluate the formation of protein carbonyl in human serum albumin (HSA) by tea catechins and investigate the relationship between catechin chemical structure and its pro-oxidant property. To assess the formation of protein carbonyl in HSA, HSA was incubated with four individual catechins under physiological conditions to generate biotin-LC-hydrazide labeled protein carbonyls. Comparison of catechins using Western blotting revealed that the formation of protein carbonyl in HSA was higher for pyrogallol-type catechins than the corresponding catechol-type catechins. In addition, the formation of protein carbonyl was also found to be higher for the catechins having a galloyl group than the corresponding catechins lacking a galloyl group. The importance of the pyrogallol structural motif in the B-ring and the galloyl group was confirmed using methylated catechins and phenolic acids. These results indicate that the most important structural element contributing to the formation of protein carbonyl in HSA by tea catechins is the pyrogallol structural motif in the B-ring, followed by the galloyl group. The oxidation stability and binding affinity of tea catechins with proteins are responsible for the formation of protein carbonyl, and consequently the difference in these properties of each catechin may contribute to the magnitude of their biological activities.

  13. 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

  14. 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.

  15. Sunspot magnetic structure and interspot radio source formation

    NASA Astrophysics Data System (ADS)

    Solov'ev, A. A.

    2015-12-01

    The magnetic structure of a typical sunspot is represented as a set of three interacting magnetic fluxes. The first one, F1, escapes upward from the sunspot umbra and closes through the corona on the sunspot of opposite polarity. The second, F2, forms the sunspot penumbra. It includes Evershed flows emerging from the sunspot, the heavy photospheric plasma of which cannot be pulled up to the corona. For this reason, the F2 flux at the outer edge of the penumbra should close on the photosphere adjacent to the sunspot, i.e., here the F2 field changes sign. The third flux, F3, is the external magnetic field flux and has the same polarity as F1. Thus, magnetic fields of different signs occur near the outer boundary of the sunspot penumbra. Magnetic reconnections will inevitably take place there. Smalland multiscale current sheets in which particles are accelerated are formed. The latter fill short and low magnetic loops that connect sunspots of different polarity in the bipolar group and form interspot radio sources at the tops of these loops.

  16. 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.

  17. 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.

  18. Peculiarities of the structure formation of nanoscale coatings from the vacuum arc discharge plasma

    NASA Astrophysics Data System (ADS)

    Kostrin, D. K.; Pikus, M. I.; Smirnov, E. A.; Lisenkov, A. A.

    2017-01-01

    In this paper features of the structure formation of nanoscale coatings (TiN)–(AlN)– (Ti–Al–N) in the vacuum arc discharge plasma are considered. The composition and structure of the formed nanoscale coatings are studied. The main factors influencing the quality of the formed coatings are shown.

  19. Family Structure History: Links to Relationship Formation Behaviors in Young Adulthood

    ERIC Educational Resources Information Center

    Ryan, Suzanne; Franzetta, Kerry; Schelar, Erin; Manlove, Jennifer

    2009-01-01

    Using data from three waves of the National Longitudinal Study of Adolescent Health (N = 4,667), we examined the intergenerational link between parental family structure history and relationship formation in young adulthood. We investigated (a) whether parental family structure history is associated with young adults' own relationship formation…

  20. 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.

  1. 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.

  2. Cellular dynamics and embryonic morphogenesis

    NASA Astrophysics Data System (ADS)

    Zallen, Jennifer

    2007-11-01

    The elongated body axis is a characteristic feature of many multicellular animals. Axis elongation occurs largely through cell rearrangements that are coordinated across a large cell population and driven by an asymmetric distribution of cytoskeletal and junctional proteins [1]. To visualize cellular dynamics during this process, we performed time-lapse confocal imaging of cell behavior in the Drosophila embryo. These studies revealed that rearranging cells display a steady increase in topological disorder that is accompanied by the formation of transient structures where 5-11 cells meet [2,3]. These multicellular rosettes form and resolve in a directional fashion to produce a local change in the aspect ratio of the cellular assembly, contributing to an overall change in tissue structure. We propose that higher-order rosette structures link local cell interactions to global tissue reorganization during morphogenesis. [1] J. Zallen and E. Wieschaus, Developmental Cell 6, 343 (2004). [2] J. Zallen and R. Zallen, J. Phys.: Condens. Matter 16, S5073 (2004). [3] J. Blankenship et al., Developmental Cell 11, 459 (2006).

  3. Effect of mesa structure formation on the electrical properties of zinc oxide thin film transistors.

    PubMed

    Singh, Shaivalini; Chakrabarti, P

    2014-05-01

    ZnO based bottom-gate thin film transistor (TFT) with SiO2 as insulating layer has been fabricated with two different structures. The effect of formation of mesa structure on the electrical characteristics of the TFTs has been studied. The formation of mesa structure of ZnO channel region can definitely result in better control over channel region and enhance value of channel mobility of ZnO TFT. As a result, by fabricating a mesa structured TFT, a better value of mobility and on-state current are achieved at low voltages. A typical saturation current of 1.85 x 10(-7) A under a gate bias of 50 V is obtained for non mesa structure TFT while for mesa structured TFT saturation current of 5 x 10(-5) A can be obtained at comparatively very low gate bias of 6.4 V.

  4. 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.

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

    PubMed Central

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

    2016-01-01

    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

  6. 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.

  7. 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.

  8. The roles of tertiary amine structure, background organic matter and chloramine species on NDMA formation.

    PubMed

    Selbes, Meric; Kim, Daekyun; Ates, Nuray; Karanfil, Tanju

    2013-02-01

    N-nitrosodimethylamine (NDMA), a probable human carcinogen, is a disinfection by-product that has been detected in chloraminated and chlorinated drinking waters and wastewaters. Formation mechanisms and precursors of NDMA are still not well understood. The main objectives of this study were to systematically investigate (i) the effect of tertiary amine structure, (ii) the effect of background natural organic matter (NOM), and (iii) the roles of mono vs. dichloramine species on the NDMA formation. Dimethylamine (DMA) and 20 different tertiary aliphatic and aromatic amines were carefully examined based on their functional groups attached to the basic DMA structure. The wide range (0.02-83.9%) of observed NDMA yields indicated the importance of the structure of tertiary amines, and both stability and electron distribution of the leaving group of tertiary amines on NDMA formation. DMA associated with branched alkyl groups or benzyl like structures having only one carbon between the ring and DMA structure consistently gave higher NDMA yields. Compounds with electron withdrawing groups (EWG) reacted preferentially with monochloramine, whereas compounds with electron donating group (EDG) showed tendency to react with dichloramine to form NDMA. When the selected amines were present in NOM solutions, NDMA formation increased for compounds with EWG while decreased for compounds with EDG. This impact was attributed to the competitions between NOM and amines for chloramine species. The results provided additional information to the commonly accepted mechanism for NDMA formation including chloramine species reacting with tertiary amines and the role of the leaving group on overall NDMA conversion.

  9. Formation of the structures from dusty clusters in neon dc discharge under cooling

    NASA Astrophysics Data System (ADS)

    Polyakov, D. N.; Shumova, V. V.; Vasilyak, L. M.

    2016-11-01

    The formation of structures consisted of dusty clusters in plasma at the discharge tube cooling to a temperature of liquid nitrogen was discovered. The dependence of the reduced electric field in the positive column of a discharge on gas temperature was experimentally measured. Depending on the pressure of neon were observed the different structural transitions in the regions of growing current-voltage characteristics at low discharge currents ≤ 1 mA. It was found that the regions of existence of structured clusters and the regions of structural transitions were characterized by the higher values of the reduced electric field than the regions of destruction of ordered structures.

  10. Spatially Periodic Domain Structure in Coupled Reaction--Diffusion Equations for Segment Formation

    NASA Astrophysics Data System (ADS)

    Sakaguchi, Hidetsugu

    2012-02-01

    Segment formation is an important process of pattern formation in the developing vertebrate embryo. The mechanism of such pattern formation is considered to be different from that of Turing instability. We propose reaction--diffusion equations generating traveling pulses and coupled reaction--diffusion equations for two genes that generate a domain structure. Next, we construct a synthetic model for segment formation by combining the coupled reaction--diffusion equations. A spatially periodic domain structure is found in the numerical simulation of the model equation. It is shown that the wavelength of the spatially periodic pattern and the proportion of the sizes of the anterior and posterior domains in each segment can be controlled by adjusting some system parameters.

  11. Comparison of cellular architecture, axonal growth, and blood vessel formation through cell-loaded polymer scaffolds in the transected rat spinal cord.

    PubMed

    Madigan, Nicolas N; Chen, Bingkun K; Knight, Andrew M; Rooney, Gemma E; Sweeney, Eva; Kinnavane, Lisa; Yaszemski, Michael J; Dockery, Peter; O'Brien, Timothy; McMahon, Siobhan S; Windebank, Anthony J

    2014-11-01

    The use of multichannel polymer scaffolds in a complete spinal cord transection injury serves as a deconstructed model that allows for control of individual variables and direct observation of their effects on regeneration. In this study, scaffolds fabricated from positively charged oligo[poly(ethylene glycol)fumarate] (OPF(+)) hydrogel were implanted into rat spinal cords following T9 complete transection. OPF(+) scaffold channels were loaded with either syngeneic Schwann cells or mesenchymal stem cells derived from enhanced green fluorescent protein transgenic rats (eGFP-MSCs). Control scaffolds contained extracellular matrix only. The capacity of each scaffold type to influence the architecture of regenerated tissue after 4 weeks was examined by detailed immunohistochemistry and stereology. Astrocytosis was observed in a circumferential peripheral channel compartment. A structurally separate channel core contained scattered astrocytes, eGFP-MSCs, blood vessels, and regenerating axons. Cells double-staining with glial fibrillary acid protein (GFAP) and S-100 antibodies populated each scaffold type, demonstrating migration of an immature cell phenotype into the scaffold from the animal. eGFP-MSCs were distributed in close association with blood vessels. Axon regeneration was augmented by Schwann cell implantation, while eGFP-MSCs did not support axon growth. Methods of unbiased stereology provided physiologic estimates of blood vessel volume, length and surface area, mean vessel diameter, and cross-sectional area in each scaffold type. Schwann cell scaffolds had high numbers of small, densely packed vessels within the channels. eGFP-MSC scaffolds contained fewer, larger vessels. There was a positive linear correlation between axon counts and vessel length density, surface density, and volume fraction. Increased axon number also correlated with decreasing vessel diameter, implicating the importance of blood flow rate. Radial diffusion distances in vessels

  12. Comparison of Cellular Architecture, Axonal Growth, and Blood Vessel Formation Through Cell-Loaded Polymer Scaffolds in the Transected Rat Spinal Cord

    PubMed Central

    Madigan, Nicolas N.; Chen, Bingkun K.; Knight, Andrew M.; Rooney, Gemma E.; Sweeney, Eva; Kinnavane, Lisa; Yaszemski, Michael J.; Dockery, Peter; O'Brien, Timothy; McMahon, Siobhan S.

    2014-01-01

    The use of multichannel polymer scaffolds in a complete spinal cord transection injury serves as a deconstructed model that allows for control of individual variables and direct observation of their effects on regeneration. In this study, scaffolds fabricated from positively charged oligo[poly(ethylene glycol)fumarate] (OPF+) hydrogel were implanted into rat spinal cords following T9 complete transection. OPF+ scaffold channels were loaded with either syngeneic Schwann cells or mesenchymal stem cells derived from enhanced green fluorescent protein transgenic rats (eGFP-MSCs). Control scaffolds contained extracellular matrix only. The capacity of each scaffold type to influence the architecture of regenerated tissue after 4 weeks was examined by detailed immunohistochemistry and stereology. Astrocytosis was observed in a circumferential peripheral channel compartment. A structurally separate channel core contained scattered astrocytes, eGFP-MSCs, blood vessels, and regenerating axons. Cells double-staining with glial fibrillary acid protein (GFAP) and S-100 antibodies populated each scaffold type, demonstrating migration of an immature cell phenotype into the scaffold from the animal. eGFP-MSCs were distributed in close association with blood vessels. Axon regeneration was augmented by Schwann cell implantation, while eGFP-MSCs did not support axon growth. Methods of unbiased stereology provided physiologic estimates of blood vessel volume, length and surface area, mean vessel diameter, and cross-sectional area in each scaffold type. Schwann cell scaffolds had high numbers of small, densely packed vessels within the channels. eGFP-MSC scaffolds contained fewer, larger vessels. There was a positive linear correlation between axon counts and vessel length density, surface density, and volume fraction. Increased axon number also correlated with decreasing vessel diameter, implicating the importance of blood flow rate. Radial diffusion distances in vessels significantly

  13. 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.

  14. Multilayered and digitally structured presentation formats of trustworthy recommendations: a combined survey and randomised trial

    PubMed Central

    Vandvik, Per Olav; Alonso-Coello, Pablo; Akl, Elie A; Thornton, Judith; Rigau, David; Adams, Katie; O'Connor, Paul; Guyatt, Gordon; Kristiansen, Annette

    2017-01-01

    Objectives To investigate practicing physicians' preferences, perceived usefulness and understanding of a new multilayered guideline presentation format—compared to a standard format—as well as conceptual understanding of trustworthy guideline concepts. Design Participants attended a standardised lecture in which they were presented with a clinical scenario and randomised to view a guideline recommendation in a multilayered format or standard format after which they answered multiple-choice questions using clickers. Both groups were also presented and asked about guideline concepts. Setting Mandatory educational lectures in 7 non-academic and academic hospitals, and 2 settings involving primary care in Lebanon, Norway, Spain and the UK. Participants 181 practicing physicians in internal medicine (156) and general practice (25). Interventions A new digitally structured, multilayered guideline presentation format and a standard narrative presentation format currently in widespread use. Primary and secondary outcome measures Our primary outcome was preference for presentation format. Understanding, perceived usefulness and perception of absolute effects were secondary outcomes. Results 72% (95% CI 65 to 79) of participants preferred the multilayered format and 16% (95% CI 10 to 22) preferred the standard format. A majority agreed that recommendations (multilayered 86% vs standard 91%, p value=0.31) and evidence summaries (79% vs 77%, p value=0.76) were useful in the context of the clinical scenario. 72% of participants randomised to the multilayered format vs 58% for standard formats reported correct understanding of the recommendations (p value=0.06). Most participants elected an appropriate clinical action after viewing the recommendations (98% vs 92%, p value=0.10). 82% of the participants considered absolute effect estimates in evidence summaries helpful or crucial. Conclusions Clinicians clearly preferred a novel multilayered presentation format to the

  15. 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.

  16. A virtual structure approach to formation control of unicycle mobile robots using mutual coupling

    NASA Astrophysics Data System (ADS)

    Sadowska, Anna; van den Broek, Thijs; Huijberts, Henri; van de Wouw, Nathan; Kostić, Dragan; Nijmeijer, Henk

    2011-11-01

    In this article, the formation control problem for unicycle mobile robots is studied. A distributed virtual structure control strategy with mutual coupling between the robots is proposed. The rationale behind the introduction of the coupling terms is the fact that these introduce additional robustness of the formation with respect to perturbations as compared to typical leader-follower approaches. The applicability of the proposed approach is shown in simulations and experiments with a group of wirelessly controlled mobile robots.

  17. 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.

  18. Structural Analysis of G-Quadruplex Formation at the Human MEST Promoter

    PubMed Central

    Kennedy, Martin A.

    2017-01-01

    The promoter region of the imprinted gene MEST contains several motifs capable of forming G-quadruplex (G4) structures, which appear to contribute to consistent allelic dropout during polymerase chain reaction (PCR) analysis of this region. Here, we extend our previous analysis of MEST G4 structures by applying fluorescent footprinting techniques to assess non B-DNA structure and topology in dsDNA from the full MEST promoter region, under conditions that mimic PCR. We demonstrate that the buffer used for PCR provides an extremely favourable milieu for G4 formation, and that cytosine methylation helps maintain G4 structures during PCR. Additionally, we demonstrate G4 formation at motifs not previously identified through bioinformatic analysis of the MEST promoter, and provide nucleotide level resolution for topological reconstruction of these structures. These observations increase our understanding of the mechanisms through which methylation and G4 contribute towards allelic drop-out during PCR. PMID:28052120

  19. Star formation, structure, and formation mechanism of cometary globules: near-infrared observations of CG 1 and CG 2

    NASA Astrophysics Data System (ADS)

    Mäkelä, M. M.; Haikala, L. K.

    2013-02-01

    Context. Cometary globule (CG) 1 and CG 2 are "classic" cometary globules in the Gum Nebula. They have compact heads and long dusty tails that point away from the centre of the Gum Nebula. Aims: We study the structure of CG 1 and CG 2 and the star formation in them to find clues to the CG formation mechanism. The two possible CG formation mechanisms, radiation-driven implosion (RDI) and a supernova blast wave, produce a characteristic mass distribution where the major part of the mass is situated in either the head (RDI) or the tail (supernova blast). Methods: CG 1 and CG 2 were imaged in the near infrared (NIR) JsHKs bands. NIR photometry was used to locate NIR excess objects and to create visual extinction maps of the CGs. The AV maps allow us to analyse the large-scale structure of CG 1 and CG 2. Archival images from the WISE and Spitzer satellites and HIRES-processed IRAS images were used to study the globule's small-scale structure. Fits were made to the spectral energy distribution plots of the NIR-excess stars to estimate their age and mass. Results: In addition to the previously known CG 1 IRS 1 we discovered three new NIR-excess objects in IR imaging, two in CG 1 and one in CG 2. CG 2 IRS 1 is the first detection of star formation in CG 2. The objects are young low-mass stars. CG 1 IRS 1 is probably a class I protostar in the head of CG 1. CG 1 IRS 1 drives a bipolar outflow, which is very weak in CO, but the cavity walls are seen in reflected light in our NIR and in the Spitzer 3.6 and 4.5 μm images. Strong emission from excited polycyclic aromatic hydrocarbon particles and very small grains were detected in the CG 1 tail. The total mass of CG 1 in the observed area is 41.9 M⊙ of which 16.8 M⊙ lies in the head. For CG 2 these values are 31.0 M⊙ total and 19.1 M⊙ in the head. The observed mass distribution does not offer a firm conclusion for the formation mechanism of the two CGs: CG 1 is in too evolved a state, and in CG 2 part of the globule

  20. Controlling branching structure formation of the salivary gland by the degree of chitosan deacetylation.

    PubMed

    Hsiao, Ya-Chuan; Chen, Chun-Nan; Chen, You-Tzung; Yang, Tsung-Lin

    2013-09-01

    The salivary gland is characterized by ramified epithelial branches, a specific tissue structure responsible for saliva production and regulation. To regenerate the salivary gland function, it is important to establish the tissue structure. Chitosan is a deacetylated derivative of chitin with wide biomedical applications. Because of its deacetylated nature, chitosan has different properties when prepared with different degrees of deacetylation (DDA). However, the impact of chitosan DDA on the effect of regulating tissue structure formation remains unexplored. In this study, the embryonic murine submandibular gland (SMG) was used as a model to investigate the role of chitosan DDA in regulating tissue structure formation of the salivary gland. When chitin substrates with different DDA were used, the branching numbers of cultured SMG explants changed. Similar effects were observed in the culture with chitosan prepared using different degrees of acetylation. The mRNA expressions of type I and type III collagen were elevated in SMG explants with enhanced branching morphogenesis, as was the protein level. In addition to the amounts of collagen, type I and type III collagen fibers were spatially present in the epithelial-mesenchymal junction of developing branches in the culture with chitosan of a specific range of DDA. The branch-promoting effect of chitosan DDA was abolished when SMG explants were treated with collagenase, both early in the stage of branch initiation and with the establishment of the branching structure. The branch-promoting effect of chitosan DDA disappeared when antisense oligonucleotides were applied to specifically block type III collagen. This study demonstrates for the first time that DDA of chitosan affects tissue structure formation. The different proportions of side-chain components of chitin derivatives regulate structural formation of cultured SMG, indicating that DDA is an important parameter using chitosan as a biomaterial for tissue

  1. 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.

  2. 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.

  3. Formation of abnormal structures and their effects on the ductility of eutectoid steel

    NASA Astrophysics Data System (ADS)

    An, Kang-Suk; Jeong, Shin Woong; Bea, Hyeong Jun; Nam, Won Jong

    2016-11-01

    The formation of abnormal structures and their effects on reduction of area (RA) were investigated in eutectoid steels transformed at different temperatures ranging from 560 °C-650 °C. The occurrence of abnormal structures, such as upper bainite, degenerate pearlite, free ferrite, and grain boundary cementite, was confirmed. The volume fraction of upper bainite and degenerate pearlite decreased on increasing the transformation temperature, while the amount of free ferrite increased. As the transformation temperature increased, RA increased, reached a maximum, and then decreased, while the tensile strength continuously decreased. The crack formations during the tensile test could be classified into three types: tearing, shear cracking, and void formation/ coalescence. The decrease of the ductility at low transformation temperatures was attributed to the increased amount of upper bainite and degenerate pearlite, since the formation of cracks occurred by tearing interfaces or by void formation at abnormal structures during the tensile test. Meanwhile, the decrease in RA at high transformation temperatures was attributed to the occurrence of shear cracking rather than the presence of abnormal structures.

  4. Cellular prion protein localizes to the nucleus of endocrine and neuronal cells and interacts with structural chromatin components.

    PubMed

    Strom, Alexander; Wang, Gen-Sheng; Picketts, David J; Reimer, Rudolph; Stuke, Andreas W; Scott, Fraser W

    2011-05-01

    Several physiological processes have been purported for cellular prion protein (PrP(C)). However, the physiological function of PrP(C) is still unclear and the cellular localization of PrP(C) remains a subject of debate. PrP(C) is expressed in a wide range of tissues including islets of Langerhans. We previously demonstrated that the function of PrP(C) is associated with blood glucose regulation. Little is known of the function of PrP(C) in islet cells and specifically in β-cells. To get first insight into the putative role of PrP(C) in β-cells, we used far-Western immunoblotting and MS to identify candidate PrP(C)-interacting proteins. We also used Western blot, immunofluorescence (IF) and protein overlay IF to characterize the sub-cellular localization of PrP(C). Here we demonstrate in vivo that PrP(C) is abundant in the nuclear lamina of endocrine and neuronal cells and interacts with histone H1(0), histone H3 and lamin B1. The interaction of PrP(C) with histone H3 suggests that it is involved in transcriptional regulation in the nucleus. This study reveals new avenues for the elucidation of the physiological function of PrP(C) in endocrine and neuronal cells as well as the molecular mechanisms leading to prion diseases.

  5. Dynamic Modulation of HIV-1 Integrase Structure and Function by Cellular Lens Epithelium-derived Growth Factor (LEDGF) Protein*S⃞

    PubMed Central

    McKee, Christopher J.; Kessl, Jacques J.; Shkriabai, Nikolozi; Dar, Mohd Jamal; Engelman, Alan; Kvaratskhelia, Mamuka

    2008-01-01

    The mandatory integration of the reverse-transcribed HIV-1 genome into host chromatin is catalyzed by the viral protein integrase (IN), and IN activity can be regulated by numerous viral and cellular proteins. Among these, LEDGF has been identified as a cellular cofactor critical for effective HIV-1 integration. The x-ray crystal structure of the catalytic core domain (CCD) of IN in complex with the IN binding domain (IBD) of LEDGF has furthermore revealed essential protein-protein contacts. However, mutagenic studies indicated that interactions between the full-length proteins were more extensive than the contacts observed in the co-crystal structure of the isolated domains. Therefore, we have conducted detailed biochemical characterization of the interactions between full-length IN and LEDGF. Our results reveal a highly dynamic nature of IN subunit-subunit interactions. LEDGF strongly stabilized these interactions and promoted IN tetramerization. Mass spectrometric protein footprinting and molecular modeling experiments uncovered novel intra- and inter-protein-protein contacts in the full-length IN-LEDGF complex that lay outside of the observable IBD-CCD structure. In particular, our studies defined the IN tetramer interface important for enzymatic activities and high affinity LEDGF binding. These findings provide new insight into how LEDGF modulates HIV-1 IN structure and function, and highlight the potential for exploiting the highly dynamic structure of multimeric IN as a novel therapeutic target. PMID:18801737

  6. Microsized structures assisted nanostructure formation on ZnSe wafer by femtosecond laser irradiation

    SciTech Connect

    Wang, Shutong; Feng, Guoying E-mail: zhoush@scu.edu.cn

    2014-12-22

    Micro/nano patterning of ZnSe wafer is demonstrated by femtosecond laser irradiation through a diffracting pinhole. The irradiation results obtained at fluences above the ablation threshold are characterized by scanning electron microscopy. The microsized structure with low spatial frequency has a good agreement with Fresnel diffraction theory. Laser induced periodic surface structures and laser-induced periodic curvelet surface structures with high spatial frequency have been found on the surfaces of microsized structures, such as spikes and valleys. We interpret its formation in terms of the interference between the reflected laser field on the surface of the valley and the incident laser pulse.

  7. Formation and atomic structure of boron nitride nanotubes with a cup-stacked structure

    NASA Astrophysics Data System (ADS)

    Oku, Takeo; Koi, Naruhiro; Suganuma, Katsuaki; Belosludov, Rodion V.; Kawazoe, Yoshiyuki

    2007-08-01

    Boron nitride (BN) nanotubes were synthesized by annealing Fe 4N/B powder at 1000 ∘C for 1 h in a nitrogen gas atmosphere, and large amounts of BN nanotubes with a cup-stacked structure were obtained after a purification process. The atomic structures of the cup-stacked BN nanotubes were investigated by high-resolution electron microscopy as well as molecular mechanics calculations, and compared with double walled BN nanotubes. The present results indicate that the cup-stacked structure with a cone angle of 20 ∘ is more stable than the structure with an angle of 38 ∘ and ordinary nanotube structures.

  8. Irregular Cellular Learning Automata.

    PubMed

    Esnaashari, Mehdi; Meybodi, Mohammad Reza

    2015-08-01

    Cellular learning automaton (CLA) is a recently introduced model that combines cellular automaton (CA) and learning automaton (LA). The basic idea of CLA is to use LA to adjust the state transition probability of stochastic CA. This model has been used to solve problems in areas such as channel assignment in cellular networks, call admission control, image processing, and very large scale integration placement. In this paper, an extension of CLA called irregular CLA (ICLA) is introduced. This extension is obtained by removing the structure regularity assumption in CLA. Irregularity in the structure of ICLA is needed in some applications, such as computer networks, web mining, and grid computing. The concept of expediency has been introduced for ICLA and then, conditions under which an ICLA becomes expedient are analytically found.

  9. 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

  10. HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation.

    PubMed

    Park, Jihye; Lammers, Fabienne; Herr, Winship; Song, Ji-Joon

    2012-10-23

    Host-cell factor 1 (HCF-1) is an unusual transcriptional regulator that undergoes a process of proteolytic maturation to generate N- (HCF-1(N)) and C- (HCF-1(C)) terminal subunits noncovalently associated via self-association sequence elements. Here, we present the crystal structure of the self-association sequence 1 (SAS1) including the adjacent C-terminal HCF-1 nuclear localization signal (NLS). SAS1 elements from each of the HCF-1(N) and HCF-1(C) subunits form an interdigitated fibronectin type 3 (Fn3) tandem repeat structure. We show that the C-terminal NLS recruited by the interdigitated SAS1 structure is required for effective formation of a transcriptional regulatory complex: the herpes simplex virus VP16-induced complex. Thus, HCF-1(N)-HCF-1(C) association via an integrated Fn3 structure permits an NLS to facilitate formation of a transcriptional regulatory complex.

  11. Kinetic and Structural Analysis of Coxsackievirus B3 Receptor Interactions and Formation of the A-Particle

    PubMed Central

    Organtini, Lindsey J.; Makhov, Alexander M.; Conway, James F.

    2014-01-01

    ABSTRACT The coxsackievirus and adenovirus receptor (CAR) has been identified as the cellular receptor for group B coxsackieviruses, including serotype 3 (CVB3). CAR mediates infection by binding to CVB3 and catalyzing conformational changes in the virus that result in formation of the altered, noninfectious A-particle. Kinetic analyses show that the apparent first-order rate constant for the inactivation of CVB3 by soluble CAR (sCAR) at physiological temperatures varies nonlinearly with sCAR concentration. Cryo-electron microscopy (cryo-EM) reconstruction of the CVB3-CAR complex resulted in a 9.0-Å resolution map that was interpreted with the four available crystal structures of CAR, providing a consensus footprint for the receptor binding site. The analysis of the cryo-EM structure identifies important virus-receptor interactions that are conserved across picornavirus species. These conserved interactions map to variable antigenic sites or structurally conserved regions, suggesting a combination of evolutionary mechanisms for receptor site preservation. The CAR-catalyzed A-particle structure was solved to a 6.6-Å resolution and shows significant rearrangement of internal features and symmetric interactions with the RNA genome. IMPORTANCE This report presents new information about receptor use by picornaviruses and highlights the importance of attaining at least an ∼9-Å resolution for the interpretation of cryo-EM complex maps. The analysis of receptor binding elucidates two complementary mechanisms for preservation of the low-affinity (initial) interaction of the receptor and defines the kinetics of receptor-catalyzed conformational change to the A-particle. PMID:24623425

  12. The Structural Formation and Physical Behaviour of Cross-Linked Epoxy Resins

    DTIC Science & Technology

    1981-04-01

    and by dicyandiamide or by catalytic polymerization are discussed and compared with those obtained by amine or anhydride curing. The highest...system. (e) Dicyandiamide cross-linking Structure formation reactions with dicyandiamide follow a complex pattern. Not only is one concerned with the...investigation4s one must consider cleavage of the dicyandiamide with the production of 2-aminooxazoline derivatives, in accordance with Fig 5. The structural

  13. Optical formation of stable waveguiding structures from a photopolymerisable composition with a nonpolymerisable component

    SciTech Connect

    Mensov, Sergei N; Polushtaitsev, Yu V

    2012-06-30

    We report formation of stable dielectric waveguiding structures from a photopolymerisable composition containing a nonpolymerisable component by optical radiation. A computer simulation has shown that the use of nonpolymerisable additives not only retains the self-trapping modes of incident radiation but also provides matching conditions for the synthesised waveguiding structure with standard optical fibres at telecommunication wavelengths. The efficiency of these nonlinear wave processes for connecting single-mode fibres SMF-28 is experimentally confirmed.

  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 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

  15. 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.

  16. Annular structures as intermediates in fibril formation of Alzheimer Abeta17-42.

    PubMed

    Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Nussinov, Ruth

    2008-06-05

    We report all-atom molecular dynamics simulations of annular beta-amyloid (17-42) structures, single- and double-layered, in solution. We assess the structural stability and association force of Abeta annular oligomers associated through different interfaces, with a mutated sequence (M35A), and with the oxidation state (M35O). Simulation results show that single-layered annular models display inherent structural instability: one is broken down into linear-like oligomers, and the other collapses. On the other hand, a double-layered annular structure where the two layers interact through their C-termini to form an NC-CN interface (where N and C are the N and C termini, respectively) exhibits high structural stability over the simulation time due to strong hydrophobic interactions and geometrical constraints induced by the closed circular shape. The observed dimensions and molecular weight of the oligomers from atomic force microscopy (AFM) experiments are found to correspond well to our stable double-layered model with the NC-CN interface. Comparison with K3 annular structures derived from the beta 2-microglobulin suggests that the driving force for amyloid formation is sequence specific, strongly dependent on side-chain packing arrangements, structural morphologies, sequence composition, and residue positions. Combined with our previous simulations of linear-like Abeta, K3 peptide, and sup35-derived GNNQQNY peptide, the annular structures provide useful insight into oligomeric structures and driving forces that are critical in amyloid fibril formation.

  17. A standard format for reporting atomic positions in measured or calculated surface structures: The CIF file

    NASA Astrophysics Data System (ADS)

    Marks, Laurence D.

    2010-06-01

    In his editorial in this issue, the editor-in-chief emphasizes the editorial policy that any paper which involves a crystallographic structure (whether experimentally measured or theoretically calculated) must also include a complete listing of all the atomic positions within the crystal structure, either as supporting information or directly within the paper itself. He also strongly recommends that the complete crystallographic data set be included as supporting information. At the request of the editor-in-chief, I outline here the reasons why this is scientifically desirable. Furthermore, I propose here that the Surface Science community adopt the same standard format for reporting these as is already widely used in bulk crystallography publications, namely the inclusion of a Crystallographic Information Format file (or CIF file) as supporting information. Finally, I describe the details of this specific file format, with illustrative examples.

  18. Effect of fuel molecular structure on soot formation in gas turbine engines

    NASA Technical Reports Server (NTRS)

    Naegeli, D. W.; Moses, C. A.

    1980-01-01

    A high-pressure research combustor operating over a wide range of burner inlet conditions was used to determine the effects of fuel molecular structure on soot formation. Six test fuels with equal hydrogen content (12.8 percent) were blended to stress different molecular components and final boiling points. The fuels containing high concentrations (20 percent) of poly-cyclic aromatics and partially saturated polycyclic structures such as tetralin, produced more soot than would be expected from a hydrogen content correlation for typical petroleum based fuels. However, fuels containing naphthenes, such as decalin, agreed with the hydrogen content correlation. The contribution of polycylic aromatics to soot formation was equivalent to a reduction in fuel hydrogen content of about 1%. The fuel sensitivity to soot formation due to the polycyclic aromatic contribution decreased as burner inlet pressure and fuel/air ratio increased.

  19. How relevant are assembled equilibrium samples in understanding structure formation during lipid digestion?

    PubMed

    Phan, Stephanie; Salentinig, Stefan; Hawley, Adrian; Boyd, Ben J

    2015-10-01

    Lipid-based formulations are gaining interest for use as drug delivery systems for poorly water-soluble drug compounds. During digestion, the lipolysis products self-assemble with endogenous surfactants in the gastrointestinal tract to form colloidal structures, enabling enhanced drug solubilisation. Although earlier studies in the literature focus on assembled equilibrium systems, little is known about structure formation under dynamic lipolysis conditions. The purpose of this study was to investigate the likely colloidal structure formation in the small intestine after the ingestion of lipids, under equilibrium and dynamic conditions. The structural aspects were studied using small angle X-ray scattering and dynamic light scattering, and were found to depend on lipid composition, lipid chain length, prandial state and emulsification. Incorporation of phospholipids and lipolysis products into bile salt micelles resulted in swelling of the structure. At insufficient bile salt concentrations, a co-existing lamellar phase was observed, due to a reduction in the solubilisation capacity for lipolysis products. Emulsification accelerated the rate of lipolysis and structure formation.

  20. Large-scale magnetic structure formation in three-dimensional magnetohydrodynamic turbulence

    SciTech Connect

    Malapaka, Shiva Kumar; Müller, Wolf-Christian

    2013-11-20

    The inverse cascade of magnetic helicity in three-dimensional magnetohydrodynamic (3D-MHD) turbulence is believed to be one of the processes responsible for large-scale magnetic structure formation in astrophysical systems. In this work, we present an exhaustive set of high-resolution direct numerical simulations of both forced and decaying 3D-MHD turbulence, to understand this structure formation process. It is first shown that an inverse cascade of magnetic helicity in small-scale driven turbulence does not necessarily generate coherent large-scale magnetic structures. The observed large-scale magnetic field, in this case, is severely perturbed by magnetic fluctuations generated by the small-scale forcing. In the decaying case, coherent large-scale structures form similarly to those observed astronomically. Based on the numerical results, the formation of large-scale magnetic structures in some astrophysical systems is suggested to be the consequence of an initial forcing that imparts the necessary turbulent energy into the system, which, after the forcing shuts off, decays to form the large-scale structures. This idea is supported by representative examples, e.g., clusters of galaxies.

  1. Fibronectin alters the rate of formation and structure of the fibrin matrix.

    PubMed

    Ramanathan, Anand; Karuri, Nancy

    2014-01-10

    Plasma fibronectin is a vital component of the fibrin clot; however its role on clot structure is not clearly understood. The goal of this study was to examine the influence of fibronectin on the kinetics of formation, structural characteristics and composition of reconstituted fibrin clots or fibrin matrices. Fibrin matrices were formed by adding thrombin to 1, 2 or 4 mg/ml fibrinogen supplemented with 0-0.4 mg/ml fibronectin. The rate of fibrin matrix formation was then monitored by measuring light absorbance properties at different time points. Confocal microscopy of fluorescein conjugated fibrinogen was used to visualize the structural characteristics of fibrin matrices. The amount of fibronectin in fibrin matrices was determined through electrophoresis and immunoblotting of solubilized matrices. Fibronectin concentration positively correlated with the initial rate of fibrin matrix formation and with steady state light absorbance values of fibrin matrices. An increase in fibronectin concentration resulted in thinner and denser fibers in the fibrin matrices. Electrophoresis and immunoblotting showed that fibronectin was covalently and non-covalently bound to fibrin matrices and in the form of high molecular weight multimers. The formation of fibronectin multimers was attributed to cross-linking of fibronectin by trace amounts Factor XIIIa. These findings are novel because they link results from light absorbance studies to microcopy analyses and demonstrate an influence of fibronectin on fibrin matrix structural characteristics. This data is important in developing therapies that destabilize fibrin clots.

  2. EGCG Inhibited Lipofuscin Formation Based on Intercepting Amyloidogenic β-Sheet-Rich Structure Conversion

    PubMed Central

    Cai, Shuxian; Yang, Heng; Zeng, Kewu; Zhang, Jing; Zhong, Ni; Wang, Yingzi; Ye, Jing; Tu, Pengfei; Liu, Zhonghua

    2016-01-01

    Background Lipofuscin (LF) is formed during lipid peroxidation and sugar glycosylation by carbonyl-amino crosslinks with biomacrolecules, and accumulates slowly within postmitotic cells. The environmental pollution, modern dietary culture and lifestyle changes have been found to be the major sources of reactive carbonyl compounds in vivo. Irreversible carbonyl-amino crosslinks induced by carbonyl stress are essentially toxiferous for aging-related functional losses in modern society. Results show that (-)-epigallocatechin gallate (EGCG), the main polyphenol in green tea, can neutralize the carbonyl-amino cross-linking reaction and inhibit LF formation, but the underlying mechanism is unknown. Methods and Results We explored the mechanism of the neutralization process from protein, cell, and animal levels using spectrofluorometry, infrared spectroscopy, conformation antibodies, and electron microscopy. LF demonstrated an amyloidogenic β-sheet-rich with antiparallel structure, which accelerated the carbonyl-amino crosslinks formation and disrupted proteolysis in both PC12 cells and D-galactose (D-gal)-induced brain aging mice models. Additionally, EGCG effectively inhibited the formation of the amyloidogenic β-sheet-rich structure of LF, and prevented its conversion into toxic and on-pathway aggregation intermediates, thereby cutting off the carbonyl-amino crosslinks. Conclusions Our study indicated that the amyloidogenic β-sheet structure of LF may be the core driving force for carbonyl-amino crosslinks further formation, which mediates the formation of amyloid fibrils from native state of biomacrolecules. That EGCG exhibits anti-amyloidogenic β-sheet-rich structure properties to prevent the LF formation represents a novel strategy to impede the development of degenerative processes caused by ageing or stress-induced premature senescence in modern environments. PMID:27030967

  3. Recycling of inorganic waste in monolithic and cellular glass-based materials for structural and functional applications.

    PubMed

    Rincón, Acacio; Marangoni, Mauro; Cetin, Suna; Bernardo, Enrico

    2016-07-01

    The stabilization of inorganic waste of various nature and origin, in glasses, has been a key strategy for environmental protection for the last decades. When properly formulated, glasses may retain many inorganic contaminants permanently, but it must be acknowledged that some criticism remains, mainly concerning costs and energy use. As a consequence, the sustainability of vitrification largely relies on the conversion of waste glasses into new, usable and marketable glass-based materials, in the form of monolithic and cellular glass-ceramics. The effective conversion in turn depends on the simultaneous control of both starting materials and manufacturing processes. While silica-rich waste favours the obtainment of glass, iron-rich wastes affect the functionalities, influencing the porosity in cellular glass-based materials as well as catalytic, magnetic, optical and electrical properties. Engineered formulations may lead to important reductions of processing times and temperatures, in the transformation of waste-derived glasses into glass-ceramics, or even bring interesting shortcuts. Direct sintering of wastes, combined with recycled glasses, as an example, has been proven as a valid low-cost alternative for glass-ceramic manufacturing, for wastes with limited hazardousness. The present paper is aimed at providing an up-to-date overview of the correlation between formulations, manufacturing technologies and properties of most recent waste-derived, glass-based materials. © 2016 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  4. Recycling of inorganic waste in monolithic and cellular glass‐based materials for structural and functional applications

    PubMed Central

    Rincón, Acacio; Marangoni, Mauro; Cetin, Suna

    2016-01-01

    Abstract The stabilization of inorganic waste of various nature and origin, in glasses, has been a key strategy for environmental protection for the last decades. When properly formulated, glasses may retain many inorganic contaminants permanently, but it must be acknowledged that some criticism remains, mainly concerning costs and energy use. As a consequence, the sustainability of vitrification largely relies on the conversion of waste glasses into new, usable and marketable glass‐based materials, in the form of monolithic and cellular glass‐ceramics. The effective conversion in turn depends on the simultaneous control of both starting materials and manufacturing processes. While silica‐rich waste favours the obtainment of glass, iron‐rich wastes affect the functionalities, influencing the porosity in cellular glass‐based materials as well as catalytic, magnetic, optical and electrical properties. Engineered formulations may lead to important reductions of processing times and temperatures, in the transformation of waste‐derived glasses into glass‐ceramics, or even bring interesting shortcuts. Direct sintering of wastes, combined with recycled glasses, as an example, has been proven as a valid low‐cost alternative for glass‐ceramic manufacturing, for wastes with limited hazardousness. The present paper is aimed at providing an up‐to‐date overview of the correlation between formulations, manufacturing technologies and properties of most recent waste‐derived, glass‐based materials. © 2016 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:27818564