Sample records for subapical cytoplasmic dense

  1. Polarized sphingolipid transport from the subapical compartment changes during cell polarity development

    NARCIS (Netherlands)

    van Ijzendoorn, SCD; Hoekstra, D

    The subapical compartment (SAC) plays an important role in the polarized transport of proteins and lipids. In hepatoma-derived HepG2 cells, fluorescent analogues of sphingomyelin and glucosylceramide are sorted in the SAG. Here, evidence is provided that shows that polarity development is regulated

  2. Apical endocytosis in rat hepatocytes In situ involves clathrin, traverses a subapical compartment, and leads to lysosomes. (United States)

    Rahner, C; Stieger, B; Landmann, L


    This study demonstrates and characterizes apical (canalicular) endocytic pathways in hepatocytes in situ. Endocytic markers were administered by retrograde infusion through the common bile duct. Colocalization with proteins that are specific for various endocytic compartments was performed on stacks of deconvoluted confocal immunofluorescence images. The subcellular distribution of marker proteins was assessed by electron microscopy (EM). Bulk-phase, as well as membrane-associated markers, were internalized readily at the apical cell pole. At the EM level, marker was found initially in 60-100-nm tubulovesicular structures and 150-200-nm cup-shaped vesicles, whereas multivesicular bodies and lysosomes became labeled after longer time intervals. Apical endocytosis involved clathrin and delivered marker to late endosomes (rab7(+), cathepsin D(+)), as well as lysosomes (rab7(-), cathepsin D(+)). Simultaneous labeling of the basolateral endocytic route resulted in overlap of both pathways in the late endosomal and lysosomal compartments. In addition, apical endocytosis involved a subapical compartment (endolyn-78(+), rab11(+), polymeric IgA receptor [pIgA-R(+)]) that is passed by the transcytotic route, thus constituting a crossroads. pIgA-R immunoreactivity, probably reflecting the cleaved receptor fragment, was associated with apical endocytic marker and colocalized with clathrin and later with cathepsin D. Apical endocytosis involves coated pits/vesicles, leads to a subapical compartment, and plays a role in the retrieval of canalicular plasma membrane components for lysosomal degradation.

  3. Strategic camouflage treatment of skeletal Class III malocclusion (mandibular prognathism) using bone-borne rapid maxillary expansion and mandibular anterior subapical osteotomy. (United States)

    Seo, Yu-Jin; Lin, Lu; Kim, Seong-Hun; Chung, Kyu-Rhim; Nelson, Gerald


    This case report presents the camouflage treatment that successfully improved the facial profile of a patient with a skeletal Class III malocclusion using bone-borne rapid maxillary expansion and mandibular anterior subapical osteotomy. The patient was an 18-year-old woman with chief complaints of crooked teeth and a protruded jaw. Camouflage treatment was chosen because she rejected orthognathic surgery under general anesthesia. A hybrid type of bone-borne rapid maxillary expander with palatal mini-implants was used to correct the transverse discrepancy, and a mandibular anterior subapical osteotomy was conducted to achieve proper overjet with normal incisal inclination and to improve her lip and chin profile. As a result, a Class I occlusion with a favorable inclination of the anterior teeth and a good esthetic profile was achieved with no adverse effects. Therefore, the hybrid type of bone-borne rapid maxillary expander and a mandibular anterior subapical osteotomy can be considered effective camouflage treatment of a skeletal Class III malocclusion, providing improved inclination of the dentition and lip profile. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

  4. Systematic analysis of clinical outcomes of anterior maxillary and mandibular subapical osteotomy with preoperative modeling in the treatment of bimaxillary protrusion. (United States)

    Xie, Fang; Teng, Li; Jin, Xiaolei; Zheng, Jinlong; Xu, Jiajie; Lu, Jianjian; Zhang, Chao; Xu, Meibang; Zeng, Haifeng; Li, Shuyuan; Sun, Xuejian


    The purpose of this study was to determine the changes in teeth and hard tissues after preoperative modeling and bimaxillary anterior subapical osteotomy for the treatment of bimaxillary protrusion. Cephalometric analysis was used to evaluate the aesthetic effects and occlusal relationships obtained. The subjects included 19 women and 1 man (aged 19-41 years; average, 29 years) with bimaxillary protrusion who underwent anterior subapical osteotomy of both the maxilla and mandible, with simultaneous genioplasty, if required. Based on a preoperative computer-aided manufacturing/design-assisted and model surgical design and an occlusal guide plate, new occlusal relationships were established for the patients. In addition, the preoperative and postoperative cephalometric radiographs were systematically analyzed. In all patients, the surgical incisions underwent primary healing, with no infection or osteonecrosis. Significant differences were observed in the preoperative and postoperative values of all hard tissue and teeth parameters, except for SGn-FH degrees and Co-MP. The most obvious significant differences were seen in L1-OP°, Id-Pog-Go°, IIA°, U1E-Apog, L1E-Apog, U1E-NA, and L1-NA° (P protrusion with satisfactory postoperative occlusal relationship and facial aesthetic appearance and minimal postoperative complications.

  5. Dense Breasts (United States)

    ... also appear white on mammography, they can be hidden by or within dense breast tissue. Other imaging ... understanding of the possible charges you will incur. Web page review process: This Web page is reviewed ...

  6. Relevância clínica e frequência de padrões citoplasmático e pontilhado fino denso observados em FAN-HEp-2 Clinical relevance and frequency of cytoplasmic and nuclear dense fine speckled patterns observed in ANA-HEp-2

    Directory of Open Access Journals (Sweden)

    Andréia Martini Pazini


    Full Text Available OBJETIVOS: O presente estudo procurou determinar a frequência e relacionar o título sorológico dos padrões de imunofluorescência para citoplasma celular e nuclear pontilhado fino denso com possível correlação clínica. MÉTODOS: No período entre 2007 a 2009 foram avaliados os resultados de 2.788 testes sorológicos para pesquisa de autoanticorpos pela técnica de imunofluorescência indireta (IFI, utilizando como substrato células HEp-2, realizados no LAC-HUSM/UFSM. RESULTADOS: Entre as amostras analisadas, 1.998 resultaram não reagentes para a pesquisa de autoanticorpos. Entre as amostras reagentes (n = 790 foram encontradas 57 (7,2% amostras apresentando padrão de reatividade descrita como pontilhado fino denso (SFD (3,8% ou fluorescência citoplasmática (Cit (3,4%. Nas amostras com padrão SFD (n = 29, nove apresentaram título 1/160 apenas um não apresentava DAI. Entre as amostras com padrão Cit (n = 27, 20 apresentavam título 1/160 tinham relato de DAI. CONCLUSÃO: Os resultados encontrados ratificam o valor de 1/160 como melhor ponto de corte para definição de presença de DAI, para qualquer um dos padrões de fluorescência avaliados. Contudo, deve-se prestar atenção a títulos inferiores, principalmente para IFI Cit, uma vez que apenas 40% não apresentavam relato de DAI presenteOBJECTIVES: This study aimed to determine the frequency and antibody titers of nuclear dense fine and cytoplasmic patterns with possible clinical correlation. METHODS: From 2007 to 2009, the results of 2,788 autoantibody serological tests were assessed by indirect immunofluorescence (IIF at LAC-HUSM/UFSM, using as substrate HEp-2. RESULTS: Among the analyzed samples, 1,998 of them were negative for autoantibodies. Among the positive samples (n = 790, we found 57 (7.2% showing reactivity pattern described as dense fine speckled (DFS (3.8%, or cytoplasmic (Cit fluorescence (3.4%. In samples with standard DFS (n = 29, nine had titers of 1

  7. The distribution of special cytoplasmic differentiations of the egg during early cleavage in Limnaea stagnalis

    NARCIS (Netherlands)

    Raven, Chr.P.

    Uncleaved eggs of Limnaea stagnalis show a pattern of cytoplasmic differentiations in which there are 6 “subcortical accumulations” (SCA) in the equatorial region. SCA consist of a dense cytoplasmic matrix, containing a special kind of small granules. At certain stages also lens-shaped bodies,

  8. The distribution of special cytoplasmic differentiations of the egg during early cleavage in Limnaea stagnalis

    NARCIS (Netherlands)

    Raven, Chr.P.


    Uncleaved eggs of Limnaea stagnalis show a pattern of cytoplasmic differentiations in which there are 6 “subcortical accumulations” (SCA) in the equatorial region. SCA consist of a dense cytoplasmic matrix, containing a special kind of small granules. At certain stages also lens-shaped bodies,

  9. Cellular Subcompartments through Cytoplasmic Streaming. (United States)

    Pieuchot, Laurent; Lai, Julian; Loh, Rachel Ann; Leong, Fong Yew; Chiam, Keng-Hwee; Stajich, Jason; Jedd, Gregory


    Cytoplasmic streaming occurs in diverse cell types, where it generally serves a transport function. Here, we examine streaming in multicellular fungal hyphae and identify an additional function wherein regimented streaming forms distinct cytoplasmic subcompartments. In the hypha, cytoplasm flows directionally from cell to cell through septal pores. Using live-cell imaging and computer simulations, we identify a flow pattern that produces vortices (eddies) on the upstream side of the septum. Nuclei can be immobilized in these microfluidic eddies, where they form multinucleate aggregates and accumulate foci of the HDA-2 histone deacetylase-associated factor, SPA-19. Pores experiencing flow degenerate in the absence of SPA-19, suggesting that eddy-trapped nuclei function to reinforce the septum. Together, our data show that eddies comprise a subcellular niche favoring nuclear differentiation and that subcompartments can be self-organized as a consequence of regimented cytoplasmic streaming. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules. (United States)

    Trovato, Fabio; Tozzini, Valentina


    Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1-10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.


    NARCIS (Netherlands)



    The cytoplasmic pH of Lactococcus lactis was studied with the fluorescent pH indicator 2',7'-bis-(2-carboxyethyl)-5 (and-6)-carboxyfluorescein (BCECF). A novel method was applied for loading bacterial cells with BCECF, which consists of briefly treating a dense cell suspension with acid in the

  12. Modelling dense relational data

    DEFF Research Database (Denmark)

    Herlau, Tue; Mørup, Morten; Schmidt, Mikkel Nørgaard


    Relational modelling classically consider sparse and discrete data. Measures of influence computed pairwise between temporal sources naturally give rise to dense continuous-valued matrices, for instance p-values from Granger causality. Due to asymmetry or lack of positive definiteness they are no......Relational modelling classically consider sparse and discrete data. Measures of influence computed pairwise between temporal sources naturally give rise to dense continuous-valued matrices, for instance p-values from Granger causality. Due to asymmetry or lack of positive definiteness...... they are not naturally suited for kernel K-means. We propose a generative Bayesian model for dense matrices which generalize kernel K-means to consider off-diagonal interactions in matrices of interactions, and demonstrate its ability to detect structure on both artificial data and two real data sets....

  13. Is dense codeswitching complex?

    NARCIS (Netherlands)

    Dorleijn, M.


    In this paper the question is raised to what extent dense code switching can be considered complex. Psycholinguistic experiments indicate that code switching involves cognitive costs, both in production and comprehension, a conclusion that could indicate that code switching is indeed complex. In

  14. Dense Plasma Focus Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Hui [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Li, Shengtai [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Jungman, Gerard [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hayes-Sterbenz, Anna Catherine [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    The mechanisms for pinch formation in Dense Plasma Focus (DPF) devices, with the generation of high-energy ions beams and subsequent neutron production over a relatively short distance, are not fully understood. Here we report on high-fidelity 2D and 3D numerical magnetohydrodynamic (MHD) simulations using the LA-COMPASS code to study the pinch formation dynamics and its associated instabilities and neutron production.

  15. Measurement of Cytoplasmic Streaming in Drosophila Melanogaster (United States)

    Ganguly, Sujoy; Williams, Lucy; Palacios, Isabel; Goldstein, Raymond


    During stage 9 of Drosophila melanogastor oogenesis flow of the oocyte cytoplasm, driven by kinesin 1 motor protein is observed. This cytoplasmic streaming is analyzed by PIV in both wild type and kinesin light chain mutants, revealing striking statistical differences. Further measurements of the rheology of the oocyte allow for estimations of the mechanical energy needed to generate the observed flows.

  16. Dense Axion Stars. (United States)

    Braaten, Eric; Mohapatra, Abhishek; Zhang, Hong


    If the dark matter particles are axions, gravity can cause them to coalesce into axion stars, which are stable gravitationally bound systems of axions. In the previously known solutions for axion stars, gravity and the attractive force between pairs of axions are balanced by the kinetic pressure. The mass of these dilute axion stars cannot exceed a critical mass, which is about 10^{-14}M_{⊙} if the axion mass is 10^{-4}  eV. We study axion stars using a simple approximation to the effective potential of the nonrelativistic effective field theory for axions. We find a new branch of dense axion stars in which gravity is balanced by the mean-field pressure of the axion Bose-Einstein condensate. The mass on this branch ranges from about 10^{-20}M_{⊙} to about M_{⊙}. If a dilute axion star with the critical mass accretes additional axions and collapses, it could produce a bosenova, leaving a dense axion star as the remnant.

  17. Hydrodynamic property of the cytoplasm is sufficient to mediate cytoplasmic streaming in the Caenorhabiditis elegans embryo (United States)

    Niwayama, Ritsuya; Shinohara, Kyosuke; Kimura, Akatsuki


    Cytoplasmic streaming is a type of intracellular transport widely seen in nature. Cytoplasmic streaming in Caenorhabditis elegans at the one-cell stage is bidirectional; the flow near the cortex (“cortical flow”) is oriented toward the anterior, whereas the flow in the central region (“cytoplasmic flow”) is oriented toward the posterior. Both cortical flow and cytoplasmic flow depend on non-muscle-myosin II (NMY-2), which primarily localizes in the cortex. The manner in which NMY-2 proteins drive cytoplasmic flow in the opposite direction from remote locations has not been fully understood. In this study, we demonstrated that the hydrodynamic properties of the cytoplasm are sufficient to mediate the forces generated by the cortical myosin to drive bidirectional streaming throughout the cytoplasm. We quantified the flow velocities of cytoplasmic streaming using particle image velocimetry (PIV) and conducted a three-dimensional hydrodynamic simulation using the moving particle semiimplicit method. Our simulation quantitatively reconstructed the quantified flow velocity distribution resolved through PIV analysis. Furthermore, our PIV analyses detected microtubule-dependent flows during the pronuclear migration stage. These flows were reproduced via hydrodynamic interactions between moving pronuclei and the cytoplasm. The agreement of flow dynamics in vivo and in simulation indicates that the hydrodynamic properties of the cytoplasm are sufficient to mediate cytoplasmic streaming in C. elegans embryos. PMID:21730185

  18. Hyperons in dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Dapo, Haris


    The hyperon-nucleon YN low momentum effective interaction (V{sub low} {sub k}) allows for an extensive study of the behavior of hyperons in dense matter, together with an investigation of effects of the presence of hyperons on dense matter. The first step towards this goal is the construction of the matrix elements for the hyperon-nucleon low momentum potential. In order to assess the different properties of hyperons within these potentials we calculate the hyperon single-particle potentials in the Hartree-Fock approximation for all of the interactions. Their dependence on both momentum and density, is studied. The single-particle potentials are then used to determine the chemical potential of hyperons in neutron stars. For nucleonic properties, the nucleon-nucleon V{sub low} {sub k} can be used with the caveat that the calculation of the ground-state energy of symmetric nuclear matter does not correctly reproduce the properties of matter at saturation. With the nucleon-nucleon V{sub low} {sub k} one is unable to reach the densities needed for the calculation of neutron star masses. To circumvent this problem we use two approaches: in the first one, we parametrize the entire nucleonic sector. In the second one, we replace only the three-body force. The former will enable us to study neutron star masses, and the latter for studying the medium's response to the external probe. In this thesis we take the external probe to be the neutrino. By combining this parametrization with the YN V{sub low} {sub k} potential, we calculate the equation of state of equilibrated matter. Performing the calculation in the Hartree-Fock approximation at zero temperature, the concentrations of all particles are calculated. From these we can ascertain at which densities hyperons appear for a wide range of parameters. Finally, we calculate the masses of neutron stars with these concentrations. For the calculation of the medium's response to an external probe, we replace the three

  19. Fractal organization of feline oocyte cytoplasm

    Directory of Open Access Journals (Sweden)

    G De Vico


    Full Text Available The present study aimed at verifying whether immature cat oocytes with morphologic irregular cytoplasm display selfsimilar features which can be analytically described by fractal analysis. Original images of oocytes collected by ovariectomy were acquired at a final magnification of 400 X with a CCD video camera connected to an optic microscope. After greyscale thresholding segmentation of cytoplasm, image profiles were submitted to fractal analysis using FANAL++, a program which provided an analytical standard procedure for determining the fractal dimension (FD. The presentation of the oocyte influenced the magnitude of the fractal dimension with the highest FD of 1.91 measured on grey-dark cytoplasm characterized by a highly connected network of lipid droplets and intracellular membranes. Fractal analysis provides an effective quantitative descriptor of the real cytoplasm morphology, which can influence the acquirement of in vitro developmental competence, without introducing any bias or shape approximation and thus contributes to an objective and reliable classification of feline oocytes.

  20. Cytoplasmic-anti-neutrophil cytoplasmic antibodies targeting myeloperoxidase in Wegener′s granulomatosis: A rare phenomenon

    Directory of Open Access Journals (Sweden)

    Bhavana M Venkatesh


    Full Text Available Wegener′s granulomatosis (WG patients can rarely have antineutrophil cytoplasmic antibodies (ANCAs directed against myeloperoxidase (MPO, producing a cytoplasmic pattern on indirect immunofluorescence (IIF. This has important implications in the diagnosis and pathophysiology of the disease. We present to you a report of three cases of WG, demonstrating a cytoplasmic-ANCA pattern on indirect IIF, but directed against MPO. It is necessary to diagnose a patient taking into account both the autoimmune test results and the clinical features.

  1. Dense MCA Sign

    Directory of Open Access Journals (Sweden)

    Richard J Chen


    Full Text Available History of present illness: A 77-year-old female presented to the emergency department after being found down at home, last seen normal 7 ½ hours prior to arrival. Patient had a history of hypertension, congestive heart failure, atrial fibrillation and breast cancer status post chemotherapy/radiation and lumpectomy. Physical exam showed right gaze preference, left facial droop and tongue deviation and flaccid left hemiplegia. Significant findings: A non-contrast computed tomography (CT scan showed a hyperdensity along the right middle cerebral artery (MCA consistent with acute thrombus. The red arrow highlights the hyperdensity in the annotated image. Discussion: The dense MCA sign can serve as an important tool in the diagnosis of acute stroke. It typically appears before other signs of infarct are apparent on CT imaging, and identifies an intracranial large artery occlusion and corresponding infarct, in the correct clinical setting.1 Calcifications in the same area of the brain could be mistaken for an MCA sign, but this sign carries a high specificity (95% and lower sensitivity (52% for arterial obstruction in ischemic stroke.2 Early identification allows for a wider array of treatment options for a patient with an ischemic stroke, including intra-venous or intra-arterial thrombolysis and mechanical thrombectomy. This patient was subsequently taken for mechanical thrombectomy. Mechanical thrombectomy was chosen for this patient because the resources were available, and recent clinical trials have shown that newer types of mechanical thrombectomy have a positive functional outcome in patients with an ischemic stroke from an intracranial large artery occlusion, as compared to intravenous tissue plasminogen activator (tPa alone.3,4,5,6 In facilities lacking the capability for mechanical thrombectomy, treatment considerations include rapid transfer to a facility with capability, or proceeding with intravenous tPa. After intervention, this

  2. Unified approach to dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Park, Byung-Yoon [CSSM, University of Adelaide, Adelaide 5005 (Australia); Lee, Hee-Jung [Departament de Fisica Teorica and Institut de Fisica Corpuscular Universitat de Valencia and Consejo Superior de Investigaciones Cientificas, E-46100 Burjassot (Valencia) (Spain); Vento, Vicente [Departament de Fisica Teorica and Institut de Fisica Corpuscular Universitat de Valencia and Consejo Superior de Investigaciones Cientificas, E-46100 Burjassot (Valencia) (Spain); Kim, Joon-Il [Department of Physics, Seoul National University, Seoul 151-742 (Korea, Republic of); Min, Dong-Pil [Department of Physics, Seoul National University, Seoul 151-742 (Korea, Republic of); Rho, Mannque [Department of Physics, Hanyang University, Seoul 133-791, Korea, and Service de Physique Theorique, CE Saclay, 91191 Gif-sur-Yvette (France)


    We apply the Skyrme model to dense hadronic matter, which provides a unified approach to high density, valid in the large N {sub c} limit. In our picture, dense hadronic matter is described by the classical soliton configuration with minimum energy for the given baryon number density. By incorporating the meson fluctuations on such ground state we obtain an effective Lagrangian for meson dynamics in a dense medium. Our starting point has been the Skyrme model defined in terms of pions, thereafter we have extended and improved the model by incorporating other degrees of freedom such as dilaton, kaons and vector mesons.

  3. Cytoplasmic Streaming in the Drosophila Oocyte. (United States)

    Quinlan, Margot E


    Objects are commonly moved within the cell by either passive diffusion or active directed transport. A third possibility is advection, in which objects within the cytoplasm are moved with the flow of the cytoplasm. Bulk movement of the cytoplasm, or streaming, as required for advection, is more common in large cells than in small cells. For example, streaming is observed in elongated plant cells and the oocytes of several species. In the Drosophila oocyte, two stages of streaming are observed: relatively slow streaming during mid-oogenesis and streaming that is approximately ten times faster during late oogenesis. These flows are implicated in two processes: polarity establishment and mixing. In this review, I discuss the underlying mechanism of streaming, how slow and fast streaming are differentiated, and what we know about the physiological roles of the two types of streaming.

  4. Densely crosslinked polycarbosiloxanes .1. Synthesis

    NARCIS (Netherlands)

    Flipsen, T.A C; Derks, R.; van der Vegt, H.A.; Pennings, A.J; Hadziioannou, G


    Novel densely crosslinked polycarbosiloxanes were obtained by using functional branched prepolymers. Two types of soluble prepolymers were prepared from di- and trifunctional alkoxysilane monomers via cohydrolysis/condensation and for both final crosslinking occurred via hydrosilylation. The

  5. How crowded is the prokaryotic cytoplasm?

    NARCIS (Netherlands)

    Spitzer, Jan; Poolman, Bert; Ferguson, Stuart


    We consider biomacromolecular crowding within the cytoplasm of prokaryotic cells as a two-phase system of 'supercrowded' cytogel and 'dilute' cytosol; we simplify and quantify this model for a coccoid cell over a wide range of biomacromolecular crowding. The key result shows that the supercrowded

  6. Electrochemical structure of the crowded cytoplasm

    NARCIS (Netherlands)

    Spitzer, JJ; Poolman, B


    The current view of the cytoplasm as a 'bustling and well-organized metropolitan city' raises the issue of how physicochemical forces control the macromolecular interactions and transport of metabolites and energy in the cell. Motivated by studies on bacterial osmosensors, we argue that charged

  7. Arrest of cytoplasmic streaming induces algal proliferation in green paramecia.

    Directory of Open Access Journals (Sweden)

    Toshiyuki Takahashi

    Full Text Available A green ciliate Paramecium bursaria, bearing several hundreds of endosymbiotic algae, demonstrates rotational microtubule-based cytoplasmic streaming, in which cytoplasmic granules and endosymbiotic algae flow in a constant direction. However, its physiological significance is still unknown. We investigated physiological roles of cytoplasmic streaming in P. bursaria through host cell cycle using video-microscopy. Here, we found that cytoplasmic streaming was arrested in dividing green paramecia and the endosymbiotic algae proliferated only during the arrest of cytoplasmic streaming. Interestingly, arrest of cytoplasmic streaming with pressure or a microtubule drug also induced proliferation of endosymbiotic algae independently of host cell cycle. Thus, cytoplasmic streaming may control the algal proliferation in P. bursaria. Furthermore, confocal microscopic observation revealed that a division septum was formed in the constricted area of a dividing paramecium, producing arrest of cytoplasmic streaming. This is a first report to suggest that cytoplasmic streaming controls proliferation of eukaryotic cells.

  8. The cytoplasmic face of cell contact sites. (United States)

    Pokutta, Sabine; Weis, William I


    The cytoplasmic face of cell contact sites comprises large macromolecular assemblies that link transmembrane cell adhesion molecules to the cytoskeleton. These assemblies are dynamic structures that are the targets of regulatory signals that control cell adhesiveness. Recent studies of the biochemistry and structure of the cadherin-catenin complex, vinculin and proteins of the ezrin/radixin/moesin family have begun to reveal the architecture of these assemblies and the mechanisms that are involved in their regulation.

  9. Cytoplasmic male sterility in Brassicaceae crops (United States)

    Yamagishi, Hiroshi; Bhat, Shripad R.


    Brassicaceae crops display strong hybrid vigor, and have long been subject to F1 hybrid breeding. Because the most reliable system of F1 seed production is based on cytoplasmic male sterility (CMS), various types of CMS have been developed and adopted in practice to breed Brassicaceae oil seed and vegetable crops. CMS is a maternally inherited trait encoded in the mitochondrial genome, and the male sterile phenotype arises as a result of interaction of a mitochondrial CMS gene and a nuclear fertility restoring (Rf) gene. Therefore, CMS has been intensively investigated for gaining basic insights into molecular aspects of nuclear-mitochondrial genome interactions and for practical applications in plant breeding. Several CMS genes have been identified by molecular genetic studies, including Ogura CMS from Japanese radish, which is the most extensively studied and most widely used. In this review, we discuss Ogura CMS, and other CMS systems, and the causal mitochondrial genes for CMS. Studies on nuclear Rf genes and the cytoplasmic effects of alien cytoplasm on general crop performance are also reviewed. Finally, some of the unresolved questions about CMS are highlighted. PMID:24987289

  10. Heterogeneous dynamics in the bacterial cytoplasm (United States)

    Parry, Brad

    The bacterial cytoplasm is a highly crowded environment, with estimates of excluded volume reaching 40 - 60%. A diverse array of highly polydisperse components is responsible for crowding and ranges from metabolites to compact proteins to large nucleic acid polymers and macromolecular assemblies. In contrast to eukaryotic cells, bacterial cells lack membrane delimited intracellular components. To measure the material properties of the Eschericia coli cytoplasm, I tracked foreign particles of different sizes in various cellular states. I found particle motion to be dependent on cellular metabolism at physiological pH and exhibited dynamical properties associated with glass-like materials, including particle caging and un-caging and heterogeneous dynamics in single cells. When particle mobility was compared across populations of cells, an enormous amount of heterogeneity was measured that increased over time. This inter-cellular heterogeneity could be separated into contributions from cellular components and differences in effective cytoplasmic viscosity between cells. These findings have implications for bacterial physiology and motivate experiments and simulations in colloid-polymer mixtures with high polydispersity.

  11. Dense Crowds of Virtual Humans

    NARCIS (Netherlands)

    Stüvel, S.A.


    This thesis presents a novel crowd simulation method `Torso Crowds', aimed at the simulation of dense crowds. The method is based on the results of user studies and a motion capture experiment, which are also described in this thesis. Torso Crowds introduces a capsule shape to represent people in

  12. Anti-neutrophil cytoplasm autoantibodies (ANCA) in autoimmune liver diseases

    NARCIS (Netherlands)

    Roozendaal, C.; Kallenberg, Cees


    Anti-neutrophil cytoplasm antibodies (ANCA) are autoantibodies directed against cytoplasmic constituents of neutrophil granulocytes and monocytes. ANCA have been detected in serum from patients with inflammatory bowel diseases (mainly ulcerative colitis) and autoimmune mediated liver diseases

  13. Warm Dense Matter: An Overview

    Energy Technology Data Exchange (ETDEWEB)

    Kalantar, D H; Lee, R W; Molitoris, J D


    This document provides a summary of the ''LLNL Workshop on Extreme States of Materials: Warm Dense Matter to NIF'' which was held on 20, 21, and 22 February 2002 at the Wente Conference Center in Livermore, CA. The warm dense matter regime, the transitional phase space region between cold material and hot plasma, is presently poorly understood. The drive to understand the nature of matter in this regime is sparking scientific activity worldwide. In addition to pure scientific interest, finite temperature dense matter occurs in the regimes of interest to the SSMP (Stockpile Stewardship Materials Program). So that obtaining a better understanding of WDM is important to performing effective experiments at, e.g., NIF, a primary mission of LLNL. At this workshop we examined current experimental and theoretical work performed at, and in conjunction with, LLNL to focus future activities and define our role in this rapidly emerging research area. On the experimental front LLNL plays a leading role in three of the five relevant areas and has the opportunity to become a major player in the other two. Discussion at the workshop indicated that the path forward for the experimental efforts at LLNL were two fold: First, we are doing reasonable baseline work at SPLs, HE, and High Energy Lasers with more effort encouraged. Second, we need to plan effectively for the next evolution in large scale facilities, both laser (NIF) and Light/Beam sources (LCLS/TESLA and GSI) Theoretically, LLNL has major research advantages in areas as diverse as the thermochemical approach to warm dense matter equations of state to first principles molecular dynamics simulations. However, it was clear that there is much work to be done theoretically to understand warm dense matter. Further, there is a need for a close collaboration between the generation of verifiable experimental data that can provide benchmarks of both the experimental techniques and the theoretical capabilities

  14. Dense, finely, grained composite materials (United States)

    Dunmead, Stephen D.; Holt, Joseph B.; Kingman, Donald D.; Munir, Zuhair A.


    Dense, finely grained composite materials comprising one or more ceramic phase or phase and one or more metallic and/or intermetallic phase or phases are produced by combustion synthesis. Spherical ceramic grains are homogeneously dispersed within the matrix. Methods are provided, which include the step of applying mechanical pressure during or immediately after ignition, by which the microstructures in the resulting composites can be controllably selected.

  15. Dilute and dense axion stars (United States)

    Visinelli, Luca; Baum, Sebastian; Redondo, Javier; Freese, Katherine; Wilczek, Frank


    Axion stars are hypothetical objects formed of axions, obtained as localized and coherently oscillating solutions to their classical equation of motion. Depending on the value of the field amplitude at the core |θ0 | ≡ | θ (r = 0) |, the equilibrium of the system arises from the balance of the kinetic pressure and either self-gravity or axion self-interactions. Starting from a general relativistic framework, we obtain the set of equations describing the configuration of the axion star, which we solve as a function of |θ0 |. For small |θ0 | ≲ 1, we reproduce results previously obtained in the literature, and we provide arguments for the stability of such configurations in terms of first principles. We compare qualitative analytical results with a numerical calculation. For large amplitudes |θ0 | ≳ 1, the axion field probes the full non-harmonic QCD chiral potential and the axion star enters the dense branch. Our numerical solutions show that in this latter regime the axions are relativistic, and that one should not use a single frequency approximation, as previously applied in the literature. We employ a multi-harmonic expansion to solve the relativistic equation for the axion field in the star, and demonstrate that higher modes cannot be neglected in the dense regime. We interpret the solutions in the dense regime as pseudo-breathers, and show that the life-time of such configurations is much smaller than any cosmological time scale.

  16. Antineutrophil cytoplasmic autoantibodies in ulcerative colitis

    Directory of Open Access Journals (Sweden)

    Vodjgani M


    Full Text Available Antineutrophil cytoplasmic autoanibodies (ANCA were detecte in patients with certain autoimmune vascular disease such as Wegner’s granulomatosis, polyarthrits nodosa and systemic luuc erythematous. Indirect immunofluorescence (IIF technique was employed to detec these autoantibodies.ANCA have been recently detected in some forms of inflammatory bowel disease (IBD, ulcerative colitis (U.C. Crohn’s disease (C.D and primary sclerosing cholangitis (PSC. By IIF method, two general patterns of ANCA were seen: a cytoplasmic (C-ANCA and perinuclear form (P-ANCA. In this study we evaluated the presece of ANCA in 52 U.C. patients and 69 matched normal control group by IIF technique, and it’s relationship with disease activity. Site of colon involvement and, lesion extent. The results showed that all control group were ANCA negative, but 58% of patients had ANCA, and most cases (70% had C- ANCA. The obtained results also revealed that there was no relationship between ANCA and disease activity

  17. Detection of antineutrophil cytoplasmic antibodies (ANCAs)

    DEFF Research Database (Denmark)

    Damoiseaux, Jan; Csernok, Elena; Rasmussen, Niels


    of diagnosis) from 251 patients with ANCA-associated vasculitis (AAV), including granulomatosis with polyangiitis and microscopic polyangiitis, and from 924 disease controls were tested for the presence of cytoplasmic pattern/perinuclear pattern and atypical ANCA (A-ANCA) by indirect immunofluorescence (IIF......) (at two sites) and for the presence of PR3-ANCA and MPO-ANCA by eight different immunoassays. RESULTS: The area under the curve (AUC) of the receiver operating characteristic curve to discriminate AAV from controls was 0.923 (95% CI 0.902 to 0.944) and 0.843 (95% CI 0.814 to 0.871) for the two IIF...... between the two IIF methods tested and (ii) a high diagnostic performance of PR3-ANCA and MPO-ANCA by immunoassay to discriminate AAV from disease controls. Consequently, dual IIF/antigen-specific immunoassay testing of each sample is not necessary for maximal diagnostic accuracy. These results indicate...

  18. Probing Cold Dense Nuclear Matter

    Energy Technology Data Exchange (ETDEWEB)

    Subedi, Ramesh; Shneor, R.; Monaghan, Peter; Anderson, Bryon; Aniol, Konrad; Annand, John; Arrington, John; Benaoum, Hachemi; Benmokhtar, Fatiha; Bertozzi, William; Boeglin, Werner; Chen, Jian-Ping; Choi, Seonho; Cisbani, Evaristo; Craver, Brandon; Frullani, Salvatore; Garibaldi, Franco; Gilad, Shalev; Gilman, Ronald; Glamazdin, Oleksandr; Hansen, Jens-Ole; Higinbotham, Douglas; Holmstrom, Timothy; Ibrahim, Hassan; Igarashi, Ryuichi; De Jager, Cornelis; Jans, Eddy; Jiang, Xiaodong; Kaufman, Lisa; Kelleher, Aidan; Kolarkar, Ameya; Kumbartzki, Gerfried; LeRose, John; Lindgren, Richard; Liyanage, Nilanga; Margaziotis, Demetrius; Markowitz, Pete; Marrone, Stefano; Mazouz, Malek; Meekins, David; Michaels, Robert; Moffit, Bryan; Perdrisat, Charles; Piasetzky, Eliazer; Potokar, Milan; Punjabi, Vina; Qiang, Yi; Reinhold, Joerg; Ron, Guy; Rosner, Guenther; Saha, Arunava; Sawatzky, Bradley; Shahinyan, Albert; Sirca, Simon; Slifer, Karl; Solvignon, Patricia; Sulkosky, Vince; Sulkosky, Vincent; Sulkosky, Vince; Sulkosky, Vincent; Urciuoli, Guido; Voutier, Eric; Watson, John; Weinstein, Lawrence; Wojtsekhowski, Bogdan; Wood, Stephen; Zheng, Xiaochao; Zhu, Lingyan


    The protons and neutrons in a nucleus can form strongly correlated nucleon pairs. Scattering experiments, in which a proton is knocked out of the nucleus with high-momentum transfer and high missing momentum, show that in carbon-12 the neutron-proton pairs are nearly 20 times as prevalent as proton-proton pairs and, by inference, neutron-neutron pairs. This difference between the types of pairs is due to the nature of the strong force and has implications for understanding cold dense nuclear systems such as neutron stars.

  19. Cytoplasmic peptidoglycan intermediate levels in Staphylococcus aureus. (United States)

    Vemula, Harika; Ayon, Navid J; Gutheil, William G


    Intracellular cytoplasmic peptidoglycan (PG) intermediate levels were determined in Staphylococcus aureus during log-phase growth in enriched media. Levels of UDP-linked intermediates were quantitatively determined using ion pairing LC-MS/MS in negative mode, and amine intermediates were quantitatively determined stereospecifically as their Marfey's reagent derivatives in positive mode. Levels of UDP-linked intermediates in S. aureus varied from 1.4 μM for UDP-GlcNAc-Enolpyruvyate to 1200 μM for UDP-MurNAc. Levels of amine intermediates (L-Ala, D-Ala, D-Ala-D-Ala, L-Glu, D-Glu, and L-Lys) varied over a range of from 860 μM for D-Ala-D-Ala to 30-260 mM for the others. Total PG was determined from the D-Glu content of isolated PG, and used to estimate the rate of PG synthesis (in terms of cytoplasmic metabolite flux) as 690 μM/min. The total UDP-linked intermediates pool (2490 μM) is therefore sufficient to sustain growth for 3.6 min. Comparison of UDP-linked metabolite levels with published pathway enzyme characteristics demonstrates that enzymes on the UDP-branch range from >80% saturation for MurA, Z, and C, to <5% saturation for MurB. Metabolite levels were compared with literature values for Escherichia coli, with the major difference in UDP-intermediates being the level of UDP-MurNAc, which was high in S. aureus (1200 μM) and low in E. coli (45 μM). Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  20. The molecular mechanism and physiological role of cytoplasmic streaming. (United States)

    Tominaga, Motoki; Ito, Kohji


    Cytoplasmic streaming occurs widely in plants ranging from algae to angiosperms. However, the molecular mechanism and physiological role of cytoplasmic streaming have long remained unelucidated. Recent molecular genetic approaches have identified specific myosin members (XI-2 and XI-K as major and XI-1, XI-B, and XI-I as minor motive forces) for the generation of cytoplasmic streaming among 13 myosin XIs in Arabidopsis thaliana. Simultaneous knockout of these myosin XI members led to a reduced velocity of cytoplasmic streaming and marked defects of plant development. Furthermore, the artificial modifications of myosin XI-2 velocity changed plant and cell sizes along with the velocity of cytoplasmic streaming. Therefore, we assume that cytoplasmic streaming is one of the key regulators in determining plant size. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  1. Internal sense of direction: sensing and signaling from cytoplasmic chemoreceptors. (United States)

    Collins, Kieran D; Lacal, Jesus; Ottemann, Karen M


    Chemoreceptors sense environmental signals and drive chemotactic responses in Bacteria and Archaea. There are two main classes of chemoreceptors: integral inner membrane and soluble cytoplasmic proteins. The latter were identified more recently than integral membrane chemoreceptors and have been studied much less thoroughly. These cytoplasmic chemoreceptors are the subject of this review. Our analysis determined that 14% of bacterial and 43% of archaeal chemoreceptors are cytoplasmic, based on currently sequenced genomes. Cytoplasmic chemoreceptors appear to share the same key structural features as integral membrane chemoreceptors, including the formations of homodimers, trimers of dimers, and 12-nm hexagonal arrays within the cell. Cytoplasmic chemoreceptors exhibit varied subcellular locations, with some localizing to the poles and others appearing both cytoplasmic and polar. Some cytoplasmic chemoreceptors adopt more exotic locations, including the formations of exclusively internal clusters or moving dynamic clusters that coalesce at points of contact with other cells. Cytoplasmic chemoreceptors presumably sense signals within the cytoplasm and bear diverse signal input domains that are mostly N terminal to the domain that defines chemoreceptors, the so-called MA domain. Similar to the case for transmembrane receptors, our analysis suggests that the most common signal input domain is the PAS (Per-Arnt-Sim) domain, but a variety of other N-terminal domains exist. It is also common, however, for cytoplasmic chemoreceptors to have C-terminal domains that may function for signal input. The most common of these is the recently identified chemoreceptor zinc binding (CZB) domain, found in 8% of all cytoplasmic chemoreceptors. The widespread nature and diverse signal input domains suggest that these chemoreceptors can monitor a variety of cytoplasmically based signals, most of which remain to be determined. Copyright © 2014, American Society for Microbiology. All

  2. Cytoplasmic Male Sterility in Nicotiana, Restoration of Fertility, and the Nucleolus. II. N. DEBNEYI Cytoplasm (United States)

    Burns, J. A.; Gerstel, D. U.; Sand, S. A.


    Previously, it was shown that a fragment chromosome, apparently derived from the Nicotiana repanda chromosomal complement, restores to normal the morphology and fertility of the abortive and feminized anthers produced by plants that possess the N. tabacum genome in cytoplasm from N. repanda. Furthermore, that restorer chromosome organizes the nucleolus and inhibits the nucleolus-forming activity of the nucleolar organizers of N. tabacum chromosomes present in the same cells, particularly in pollen mother cells. To determine whether these relations are basic or only coincidental, restorer chromosomes for other cytoplasms are now being investigated. The present paper describes a study of a chromosome, presumably derived from N. debneyi, with partial restoring power. Acting in the cytoplasm of N. debneyi, it directs formation of morphologically normal anthers, without, however, restoring pollen fertility. We find that this chromosome also has a functioning nucleolar organizer, but only slightly inhibits the nucleolus-forming capacity of N. tabacum chromosomes. The suggestion of a relationship between the nucleolar apparatus and restoration of normal anthers is thus strengthened by the observation that restorers are found on nucleolus-forming chromosomes from two very distinct Nicotiana species, as well as in several comparable cases cited from the Triticinae. The manner in which the nucleolus, or its organizer, may direct defeminization and restoration of anther morphology is not known; suggestions were offered in the preceding paper in this series (Gerstel, Burns and Burk 1978). PMID:17248855

  3. DPIS for warm dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Kondo, K.; Kanesue, T.; Horioka, K.; Okamura, M.


    Warm Dense Matter (WDM) offers an challenging problem because WDM, which is beyond ideal plasma, is in a low temperature and high density state with partially degenerate electrons and coupled ions. WDM is a common state of matter in astrophysical objects such as cores of giant planets and white dwarfs. The WDM studies require large energy deposition into a small target volume in a shorter time than the hydrodynamical time and need uniformity across the full thickness of the target. Since moderate energy ion beams ({approx} 0.3 MeV/u) can be useful tool for WDM physics, we propose WDM generation using Direct Plasma Injection Scheme (DPIS). In the DPIS, laser ion source is connected to the Radio Frequency Quadrupole (RFQ) linear accelerator directly without the beam transport line. DPIS with a realistic final focus and a linear accelerator can produce WDM.

  4. Antineutrophil cytoplasm antibody: positivity and clinical correlation. (United States)

    Martínez Téllez, Goitybell; Torres Rives, Bárbara; Rangel Velázquez, Suchiquil; Sánchez Rodríguez, Vicky; Ramos Ríos, María Antonia; Fuentes Smith, Lisset Evelyn


    To determine positivity and clinical correlation of anti-neutrophil cytoplasmic antibodies (ANCA), taking into account the interference of antinuclear antibodies (ANA). A prospective study was conducted in the Laboratory of Immunology of the National Cuban Center of Medical Genetic during one year. Two hounded sixty-seven patients with indication for ANCA determination were included. ANCA and ANA determinations with different cut off points and assays were determined by indirect immunofluorescense. Anti proteinase 3 and antimyeloperoxidase antibodies were determined by ELISA. Most positivity for ANCA was seen in patients with ANCA associated, primary small-vessel vasculitides, rheumatoid arthritis and systemic lupus erythematosus. Presence of ANCA without positivity for proteinase 3 and myeloperoxidase was higher in patients with ANA and little relation was observed between the perinuclear pattern confirmed in formalin and specificity by myeloperoxidase. Highest sensibility and specificity values for vasculitides diagnostic were achieved by ANCA determination using indirect immunofluorescense with a cut off 1/80 and confirming antigenic specificities with ELISA. ANCA can be present in a great number of chronic inflammatory or autoimmune disorders in the population studied. This determination using indirect immunofluorescence and following by ELISA had a great value for vasculitis diagnosis. Anti mieloperoxidasa assay has a higher utility than the formalin assay when ANA is present. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

  5. A physical perspective on cytoplasmic streaming. (United States)

    Goldstein, Raymond E; van de Meent, Jan-Willem


    Organisms show a remarkable range of sizes, yet the dimensions of a single cell rarely exceed 100 µm. While the physical and biological origins of this constraint remain poorly understood, exceptions to this rule give valuable insights. A well-known counterexample is the aquatic plant Chara, whose cells can exceed 10 cm in length and 1 mm in diameter. Two spiralling bands of molecular motors at the cell periphery drive the cellular fluid up and down at speeds up to 100 µm s(-1), motion that has been hypothesized to mitigate the slowness of metabolite transport on these scales and to aid in homeostasis. This is the most organized instance of a broad class of continuous motions known as 'cytoplasmic streaming', found in a wide range of eukaryotic organisms-algae, plants, amoebae, nematodes and flies-often in unusually large cells. In this overview of the physics of this phenomenon, we examine the interplay between streaming, transport and cell size and discuss the possible role of self-organization phenomena in establishing the observed patterns of streaming.

  6. Optimal cytoplasmic transport in viral infections.

    Directory of Open Access Journals (Sweden)

    Maria R D'Orsogna


    Full Text Available For many viruses, the ability to infect eukaryotic cells depends on their transport through the cytoplasm and across the nuclear membrane of the host cell. During this journey, viral contents are biochemically processed into complexes capable of both nuclear penetration and genomic integration. We develop a stochastic model of viral entry that incorporates all relevant aspects of transport, including convection along microtubules, biochemical conversion, degradation, and nuclear entry. Analysis of the nuclear infection probabilities in terms of the transport velocity, degradation, and biochemical conversion rates shows how certain values of key parameters can maximize the nuclear entry probability of the viral material. The existence of such "optimal" infection scenarios depends on the details of the biochemical conversion process and implies potentially counterintuitive effects in viral infection, suggesting new avenues for antiviral treatment. Such optimal parameter values provide a plausible transport-based explanation of the action of restriction factors and of experimentally observed optimal capsid stability. Finally, we propose a new interpretation of how genetic mutations unrelated to the mechanism of drug action may nonetheless confer novel types of overall drug resistance.

  7. Cytoplasmic Dynein Promotes HIV-1 Uncoating

    Directory of Open Access Journals (Sweden)

    Paulina Pawlica


    Full Text Available Retroviral capsid (CA cores undergo uncoating during their retrograde transport (toward the nucleus, and/or after reaching the nuclear membrane. However, whether HIV-1 CA core uncoating is dependent upon its transport is not understood. There is some evidence that HIV-1 cores retrograde transport involves cytoplasmic dynein complexes translocating on microtubules. Here we investigate the role of dynein-dependent transport in HIV-1 uncoating. To interfere with dynein function, we depleted dynein heavy chain (DHC using RNA interference, and we over-expressed p50/dynamitin. In immunofluorescence microscopy experiments, DHC depletion caused an accumulation of CA foci in HIV-1 infected cells. Using a biochemical assay to monitor HIV-1 CA core disassembly in infected cells, we observed an increase in amounts of intact (pelletable CA cores upon DHC depletion or p50 over-expression. Results from these two complementary assays suggest that inhibiting dynein-mediated transport interferes with HIV-1 uncoating in infected cells, indicating the existence of a functional link between HIV-1 transport and uncoating.

  8. Breaking Dense Structures: Proving Stability of Densely Structured Hybrid Systems

    Directory of Open Access Journals (Sweden)

    Eike Möhlmann


    Full Text Available Abstraction and refinement is widely used in software development. Such techniques are valuable since they allow to handle even more complex systems. One key point is the ability to decompose a large system into subsystems, analyze those subsystems and deduce properties of the larger system. As cyber-physical systems tend to become more and more complex, such techniques become more appealing. In 2009, Oehlerking and Theel presented a (de-composition technique for hybrid systems. This technique is graph-based and constructs a Lyapunov function for hybrid systems having a complex discrete state space. The technique consists of (1 decomposing the underlying graph of the hybrid system into subgraphs, (2 computing multiple local Lyapunov functions for the subgraphs, and finally (3 composing the local Lyapunov functions into a piecewise Lyapunov function. A Lyapunov function can serve multiple purposes, e.g., it certifies stability or termination of a system or allows to construct invariant sets, which in turn may be used to certify safety and security. In this paper, we propose an improvement to the decomposing technique, which relaxes the graph structure before applying the decomposition technique. Our relaxation significantly reduces the connectivity of the graph by exploiting super-dense switching. The relaxation makes the decomposition technique more efficient on one hand and on the other allows to decompose a wider range of graph structures.

  9. Antineutrophil Cytoplasmic Antibodies, Autoimmune Neutropenia, and Vasculitis (United States)

    Grayson, Peter C.; Sloan, J. Mark; Niles, John L.; Monach, Paul A.; Merkel, Peter A.


    Objectives Reports of an association between antineutrophil cytoplasmic antibodies (ANCA) and autoimmune neutropenia have rarely included cases of proven vasculitis. A case of ANCA-associated vasculitis (AAV) with recurrent neutropenia is described and relevant literature on the association between ANCA, neutropenia, and vasculitis is reviewed. Methods Longitudinal clinical assessments and laboratory findings are described in a patient with AAV and recurrent episodes of profound neutropenia from December 2008 – October 2010. A PubMed database search of the medical literature was performed for papers published from 1960 through October 2010 to identify all reported cases of ANCA and neutropenia. Results A 49 year-old man developed recurrent neutropenia, periodic fevers, arthritis, biopsy-proven cutaneous vasculitis, sensorineural hearing loss, epididymitis, and positive tests for ANCA with specificity for antibodies to both proteinase 3 and myeloperoxidase. Antineutrophil membrane antibodies were detected during an acute neutropenic phase and were not detectable in a post-recovery sample, whereas ANCA titers did not seem to correlate with neutropenia. An association between ANCA and neutropenia has been reported in 74 cases from 24 studies in the context of drug/toxin exposure, underlying autoimmune disease, or chronic neutropenia without underlying autoimmune disease. In these cases, the presence of atypical ANCA patterns and other antibodies were common; however, vasculitis was uncommon and when it occurred was usually limited to the skin and in cases of underlying toxin exposure. Conclusions ANCA is associated with autoimmune neutropenia, but systemic vasculitis rarely occurs in association with ANCA and neutropenia. The interaction between neutrophils and ANCA may provide insight into understanding both autoimmune neutropenia and AAV. PMID:21507463

  10. Filter-Dense Multicolor Microscopy.

    Directory of Open Access Journals (Sweden)

    Siavash Kijani

    Full Text Available Immunofluorescence microscopy is a unique method to reveal the spatial location of proteins in tissues and cells. By combining antibodies that are labeled with different fluorochromes, the location of several proteins can simultaneously be visualized in one sample. However, because of the risk of bleed-through signals between fluorochromes, standard multicolor microscopy is restricted to a maximum of four fluorescence channels, including one for nuclei staining. This is not always enough to address common scientific questions. In particular, the use of a rapidly increasing number of marker proteins to classify functionally distinct cell populations and diseased tissues emphasizes the need for more complex multistainings. Hence, multicolor microscopy should ideally offer more channels to meet the current needs in biomedical science. Here we present an enhanced multi-fluorescence setup, which we call Filter-Dense Multicolor Microscopy (FDMM. FDMM is based on condensed filter sets that are more specific for each fluorochrome and allow a more economic use of the light spectrum. FDMM allows at least six independent fluorescence channels and can be applied to any standard fluorescence microscope without changing any operative procedures for the user. In the present study, we demonstrate an FDMM setup of six channels that includes the most commonly used fluorochromes for histology. We show that the FDMM setup is specific and robust, and we apply the technique on typical biological questions that require more than four fluorescence microscope channels.

  11. Pediatric Inflammatory Bowel Disease with Cytoplasmic Staining of Antineutrophil Cytoplasmic Antibodies

    Directory of Open Access Journals (Sweden)

    Omar I. Saadah


    Full Text Available Background. It is unusual for the antineutrophil cytoplasmic antibody with cytoplasmic pattern (cANCA to present in patients with inflammatory bowel disease (IBD without vasculitis. The purpose of this study was to describe the occurrence and characteristics of pediatrics IBD with cANCA. Methods. A retrospective review of pediatric IBD associated with cANCA serology in patients from King Abdulaziz University Hospital, Saudi Arabia, between September 2002 and February 2012. Results. Out of 131 patients with IBD screened for cANCAs, cANCA was positive in 7 (5.3% patients of whom 4 had ulcerative colitis and 3 had Crohn's disease. The median age was 8.8 years (2–14.8 years. Six (86% were males. Of the 7 patients, 5 (71% were Saudi Arabians and 2 were of Indian ethnicity. The most common symptoms were diarrhea, abdominal pain, weight loss, and rectal bleeding. None had family history or clinical features suggestive of vasculitis involving renal and respiratory systems. No difference in the disease location or severity was observed between cANCA positive and cANCA negative patients apart from male preponderance in cANCA positive patients. Conclusion. The occurrence of cANCA in pediatric IBD is rare. Apart from male preponderance, there were no peculiar characteristics for the cANCA positive patients.

  12. Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes. (United States)

    Christie, Joshua R; Beekman, Madeleine


    Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. CTP synthase forms cytoophidia in the cytoplasm and nucleus

    Energy Technology Data Exchange (ETDEWEB)

    Gou, Ke-Mian [MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT (United Kingdom); State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193 (China); Chang, Chia-Chun [Institute of Biotechnology, National Taiwan University, Taipei, Taiwan, ROC (China); Shen, Qing-Ji [MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT (United Kingdom); Sung, Li-Ying, E-mail: [Institute of Biotechnology, National Taiwan University, Taipei, Taiwan, ROC (China); Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan, ROC (China); Liu, Ji-Long, E-mail: [MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT (United Kingdom)


    CTP synthase is an essential metabolic enzyme responsible for the de novo synthesis of CTP. Multiple studies have recently showed that CTP synthase protein molecules form filamentous structures termed cytoophidia or CTP synthase filaments in the cytoplasm of eukaryotic cells, as well as in bacteria. Here we report that CTP synthase can form cytoophidia not only in the cytoplasm, but also in the nucleus of eukaryotic cells. Both glutamine deprivation and glutamine analog treatment promote formation of cytoplasmic cytoophidia (C-cytoophidia) and nuclear cytoophidia (N-cytoophidia). N-cytoophidia are generally shorter and thinner than their cytoplasmic counterparts. In mammalian cells, both CTP synthase 1 and CTP synthase 2 can form cytoophidia. Using live imaging, we have observed that both C-cytoophidia and N-cytoophidia undergo multiple rounds of fusion upon glutamine analog treatment. Our study reveals the coexistence of cytoophidia in the cytoplasm and nucleus, therefore providing a good opportunity to investigate the intracellular compartmentation of CTP synthase. - Highlights: • CTP synthase forms cytoophidia not only in the cytoplasm but also in the nucleus. • Glutamine deprivation and Glutamine analogs promotes cytoophidium formation. • N-cytoophidia exhibit distinct morphology when compared to C-cytoophidia. • Both CTP synthase 1 and CTP synthase 2 form cytoophidia in mammalian cells. • Fusions of cytoophidia occur in the cytoplasm and nucleus.

  14. Phase diagram of vertically vibrated dense suspensions

    NARCIS (Netherlands)

    von Kann, S.; Snoeijer, Jacobus Hendrikus; van der Meer, Roger M.


    When a hole is created in a layer of a dense, vertically vibrated suspension, phenomena are known to occur that defy the natural tendency of gravity to close the hole. Here, an overview is presented of the different patterns that we observed in a variety of dense particulate suspensions.

  15. Interference Coordination for Dense Wireless Networks

    DEFF Research Database (Denmark)

    Soret, Beatriz; Pedersen, Klaus I.; Jørgensen, Niels T.K.


    The promise of ubiquitous and super-fast connectivity for the upcoming years will be in large part fulfilled by the addition of base stations and spectral aggregation. The resulting very dense networks (DenseNets) will face a number of technical challenges. Among others, the interference emerges...

  16. Finding dense locations in indoor tracking data

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua


    Finding the dense locations in large indoor spaces is very useful for getting overloaded locations, security, crowd management, indoor navigation, and guidance. Indoor tracking data can be very large and are not readily available for finding dense locations. This paper presents a graph-based model...

  17. Heavy meson production in hot dense matter

    NARCIS (Netherlands)

    Tolos, Laura; Gamermann, Daniel; Garcia-Recio, Carmen; Molina, Raquel; Nieves, Juan; Oset, Eulogio; Ramos, Angels; Nieves, JM; Oset, E; Vacas, MJV


    The properties of charmed mesons in dense matter are studied using a unitary coupled-channel approach in the nuclear medium which takes into account Pauli-blocking effects and meson self-energies in a self-consistent manner. We obtain the open-charm meson spectral functions in this dense nuclear

  18. Dense image correspondences for computer vision

    CERN Document Server

    Liu, Ce


    This book describes the fundamental building-block of many new computer vision systems: dense and robust correspondence estimation. Dense correspondence estimation techniques are now successfully being used to solve a wide range of computer vision problems, very different from the traditional applications such techniques were originally developed to solve. This book introduces the techniques used for establishing correspondences between challenging image pairs, the novel features used to make these techniques robust, and the many problems dense correspondences are now being used to solve. The book provides information to anyone attempting to utilize dense correspondences in order to solve new or existing computer vision problems. The editors describe how to solve many computer vision problems by using dense correspondence estimation. Finally, it surveys resources, code, and data necessary for expediting the development of effective correspondence-based computer vision systems.   ·         Provides i...

  19. Refractory disease in antineutrophil cytoplasmic antibodies associated vasculitis

    NARCIS (Netherlands)

    Rutgers, Abraham; Kallenberg, Cornelis

    Purpose of review Induction treatment of antineutrophil cytoplasmic antibodies (ANCA) associated vasculitis (AAV) is not always successful and nonresponding patients are considered refractory. Recent findings Refractory disease should be subdefined to the treatment that was received.

  20. On the evolution of cytoplasmic incompatibility in haplodiploid species

    NARCIS (Netherlands)

    Egas, C.J.M.; de Freitas Vala Salvador, F.; Breeuwer, J.A.J.


    The most enigmatic sexual manipulation by Wolbachia endosymbionts is cytoplasmic incompatibility (CI): infected mates are reproductively incompatible with uninfected females. In this paper, we extend the theory on population dynamics and evolution of CI, with emphasis on haplodiploid species. First,

  1. Cytoplasmic ATR Activation Promotes Vaccinia Virus Genome Replication

    Directory of Open Access Journals (Sweden)

    Antonio Postigo


    Full Text Available In contrast to most DNA viruses, poxviruses replicate their genomes in the cytoplasm without host involvement. We find that vaccinia virus induces cytoplasmic activation of ATR early during infection, before genome uncoating, which is unexpected because ATR plays a fundamental nuclear role in maintaining host genome integrity. ATR, RPA, INTS7, and Chk1 are recruited to cytoplasmic DNA viral factories, suggesting canonical ATR pathway activation. Consistent with this, pharmacological and RNAi-mediated inhibition of canonical ATR signaling suppresses genome replication. RPA and the sliding clamp PCNA interact with the viral polymerase E9 and are required for DNA replication. Moreover, the ATR activator TOPBP1 promotes genome replication and associates with the viral replisome component H5. Our study suggests that, in contrast to long-held beliefs, vaccinia recruits conserved components of the eukaryote DNA replication and repair machinery to amplify its genome in the host cytoplasm.

  2. Internal sense of direction: Sensing and signaling from cytoplasmic chemoreceptors


    Collins, KD; Lacal, J; Ottemann, KM


    Copyright © 2014, American Society for Microbiology. All Rights Reserved. Chemoreceptors sense environmental signals and drive chemotactic responses in Bacteria and Archaea. There are two main classes of chemoreceptors: integral inner membrane and soluble cytoplasmic proteins. The latter were identified more recently than integral membrane chemoreceptors and have been studied much less thoroughly. These cytoplasmic chemoreceptors are the subject of this review. Our analysis determined that 14...

  3. Cytoplasmic chromatin triggers inflammation in senescence and cancer. (United States)

    Dou, Zhixun; Ghosh, Kanad; Vizioli, Maria Grazia; Zhu, Jiajun; Sen, Payel; Wangensteen, Kirk J; Simithy, Johayra; Lan, Yemin; Lin, Yanping; Zhou, Zhuo; Capell, Brian C; Xu, Caiyue; Xu, Mingang; Kieckhaefer, Julia E; Jiang, Tianying; Shoshkes-Carmel, Michal; Tanim, K M Ahasan Al; Barber, Glen N; Seykora, John T; Millar, Sarah E; Kaestner, Klaus H; Garcia, Benjamin A; Adams, Peter D; Berger, Shelley L


    Chromatin is traditionally viewed as a nuclear entity that regulates gene expression and silencing. However, we recently discovered the presence of cytoplasmic chromatin fragments that pinch off from intact nuclei of primary cells during senescence, a form of terminal cell-cycle arrest associated with pro-inflammatory responses. The functional significance of chromatin in the cytoplasm is unclear. Here we show that cytoplasmic chromatin activates the innate immunity cytosolic DNA-sensing cGAS-STING (cyclic GMP-AMP synthase linked to stimulator of interferon genes) pathway, leading both to short-term inflammation to restrain activated oncogenes and to chronic inflammation that associates with tissue destruction and cancer. The cytoplasmic chromatin-cGAS-STING pathway promotes the senescence-associated secretory phenotype in primary human cells and in mice. Mice deficient in STING show impaired immuno-surveillance of oncogenic RAS and reduced tissue inflammation upon ionizing radiation. Furthermore, this pathway is activated in cancer cells, and correlates with pro-inflammatory gene expression in human cancers. Overall, our findings indicate that genomic DNA serves as a reservoir to initiate a pro-inflammatory pathway in the cytoplasm in senescence and cancer. Targeting the cytoplasmic chromatin-mediated pathway may hold promise in treating inflammation-related disorders.

  4. Differentiation-dependent rearrangements of actin filaments and microtubules hinder apical endocytosis in urothelial cells. (United States)

    Tratnjek, Larisa; Romih, Rok; Kreft, Mateja Erdani


    During differentiation, superficial urothelial cells (UCs) of the urinary bladder form the apical surface, which is almost entirely covered by urothelial plaques containing densely packed uroplakin particles. These urothelial plaques are the main structural components of the blood-urine permeability barrier in the urinary bladder. We have shown previously that endocytosis from the apical plasma membrane decreases during urothelial cell differentiation. Here, we investigated the role of actin filament and microtubule rearrangements in apical endocytosis of differentiating UCs cells using hyperplastic and normoplastic porcine urothelial models. Partially differentiated normal porcine UCs contained actin filaments in the subapical cytoplasm, while microtubules had a net-like appearance. In highly differentiated UCs, actin filaments mostly disappeared from the subapical cytoplasm and microtubules remained as a thin layer close to the apical plasma membrane. Inhibition of actin filament formation with cytochalasin-D in partially differentiated UCs caused a decrease in apical endocytosis. Depolymerisation of microtubules with nocodazole did not prevent endocytosis of the endocytotic marker WGA into the subapical cytoplasm; however, it abolished WGA transport to endolysosomal compartments in the central cytoplasm. Cytochalasin-D or nocodazole treatment did not significantly change apical endocytosis in highly differentiated UCs. In conclusion, we showed that the physiological differentiation-dependent or chemically induced redistribution and reorganization of actin filaments and microtubules impair apical endocytosis in UCs. Importantly, reduced apical endocytosis due to cytoskeletal rearrangements in highly differentiated UCs, together with the formation of rigid urothelial plaques, reinforces the barrier function of the urothelium.

  5. Propagation Of Dense Plasma Jets (United States)

    Turchi, Peter J.; Davis, John F.


    A variety of schemes have been proposed over the last two decades for delivering lethal amounts of energy and/or momentum to targets such as missiles and high speed aircraft. Techniques have ranged from high energy lasers and high voltage charged-particle accelerators to less exotic but still challenging devices such as electromagnetic railguns. One class of technology involves the use of high speed plasmas. The primary attraction of such technology is the possibility of utilizing relatively compact accelerators and electrical power systems that could allow highly mobile and agile operation from rocket or aircraft platforms, or in special ordnance. Three years ago, R & D Associates examined the possibility of plasma propagation for military applications and concluded that the only viable approach consisted of long dense plasma jets, contained in radial equilibrium by the atmosphere, while propagating at speeds of about 10 km/s. Without atmospheric confinement the plasma density would diminish too rapidly for adequate range and lethality. Propagation of atmospherically-confined jets at speeds much greater than 10 km/s required significant increases in power levels and/or operating altitudes to achieve useful ranges. The present research effort has been developing the experimental conditions necessary to achieve reasonable comparison with theoretical predictions for plasma jet propagation in the atmosphere. Time-resolved measurements have been made of high speed argon plasma jets penetrating a helium background (simulating xenon jets propagating into air). Basic radial confinement of the jet has been observed by photography and spectroscopy and structures in the flow field resemble those predicted by numerical calculations. Results from our successful initial experiments have been used to design improved diagnostic procedures and arcjet source characteristics for further experiments. In experiments with a modified arcjet source, radial confinement of the jet is again

  6. Tissue composition of mammographically dense and non-dense breast tissue. (United States)

    Ghosh, Karthik; Brandt, Kathleen R; Reynolds, Carol; Scott, Christopher G; Pankratz, V S; Riehle, Darren L; Lingle, Wilma L; Odogwu, Tonye; Radisky, Derek C; Visscher, Daniel W; Ingle, James N; Hartmann, Lynn C; Vachon, Celine M


    Mammographic density is a strong risk factor for breast cancer but its underlying biology in healthy women is not well-defined. Using a novel collection of core biopsies from mammographically dense versus non-dense regions of the breasts of healthy women, we examined histologic and molecular differences between these two tissue types. Eligible participants were 40 + years, had a screening mammogram and no prior breast cancer or current endocrine therapy. Mammograms were used to identify dense and non-dense regions and ultrasound-guided core biopsies were performed to obtain tissue from these regions. Quantitative assessment of epithelium, stroma, and fat was performed on dense and non-dense cores. Molecular markers including Ki-67, estrogen receptor (ER) and progesterone receptor (PR) were also assessed for participants who had >0% epithelial area in both dense and non-dense tissue. Signed rank test was used to assess within woman differences in epithelium, stroma and fat between dense and non-dense tissue. Differences in molecular markers (Ki-67, ER, and PR) were analyzed using generalized linear models, adjusting for total epithelial area. Fifty-nine women, mean age 51 years (range: 40-82), were eligible for analyses. Dense tissue was comprised of greater mean areas of epithelium and stroma (1.1 and 9.2 mm(2) more, respectively) but less fat (6.0 mm(2) less) than non-dense tissue. There were no statistically significant differences in relative expression of Ki-67 (P = 0.82), ER (P = 0.09), or PR (P = 0.96) between dense and non-dense tissue. Consistent with prior reports, we found that mammographically dense areas of the breast differ histologically from non-dense areas, reflected in greater proportions of epithelium and stroma and lesser proportions of fat in the dense compared to non-dense breast tissue. Studies of both epithelial and stromal components are important in understanding the association between mammographic density and breast cancer risk.

  7. Dynamical theory of dense groups of galaxies (United States)

    Mamon, Gary A.


    It is well known that galaxies associate in groups and clusters. Perhaps 40% of all galaxies are found in groups of 4 to 20 galaxies (e.g., Tully 1987). Although most groups appear to be so loose that the galaxy interactions within them ought to be insignificant, the apparently densest groups, known as compact groups appear so dense when seen in projection onto the plane of the sky that their members often overlap. These groups thus appear as dense as the cores of rich clusters. The most popular catalog of compact groups, compiled by Hickson (1982), includes isolation among its selection critera. Therefore, in comparison with the cores of rich clusters, Hickson's compact groups (HCGs) appear to be the densest isolated regions in the Universe (in galaxies per unit volume), and thus provide in principle a clean laboratory for studying the competition of very strong gravitational interactions. The $64,000 question here is then: Are compact groups really bound systems as dense as they appear? If dense groups indeed exist, then one expects that each of the dynamical processes leading to the interaction of their member galaxies should be greatly enhanced. This leads us to the questions: How stable are dense groups? How do they form? And the related question, fascinating to any theorist: What dynamical processes predominate in dense groups of galaxies? If HCGs are not bound dense systems, but instead 1D change alignments (Mamon 1986, 1987; Walke & Mamon 1989) or 3D transient cores (Rose 1979) within larger looser systems of galaxies, then the relevant question is: How frequent are chance configurations within loose groups? Here, the author answers these last four questions after comparing in some detail the methods used and the results obtained in the different studies of dense groups.

  8. Cytoplasmic streaming velocity as a plant size determinant. (United States)

    Tominaga, Motoki; Kimura, Atsushi; Yokota, Etsuo; Haraguchi, Takeshi; Shimmen, Teruo; Yamamoto, Keiichi; Nakano, Akihiko; Ito, Kohji


    Cytoplasmic streaming is active transport widely occurring in plant cells ranging from algae to angiosperms. Although it has been revealed that cytoplasmic streaming is generated by organelle-associated myosin XI moving along actin bundles, the fundamental function in plants remains unclear. We generated high- and low-speed chimeric myosin XI by replacing the motor domains of Arabidopsis thaliana myosin XI-2 with those of Chara corallina myosin XI and Homo sapiens myosin Vb, respectively. Surprisingly, the plant sizes of the transgenic Arabidopsis expressing high- and low-speed chimeric myosin XI-2 were larger and smaller, respectively, than that of the wild-type plant. This size change correlated with acceleration and deceleration, respectively, of cytoplasmic streaming. Our results strongly suggest that cytoplasmic streaming is a key determinant of plant size. Furthermore, because cytoplasmic streaming is a common system for intracellular transport in plants, our system could have applications in artificial size control in plants. Copyright © 2013 Elsevier Inc. All rights reserved.

  9. Cytoplasmic RNA: a case of the tail wagging the dog. (United States)

    Norbury, Chris J


    The addition of poly(A) tails to eukaryotic nuclear mRNAs promotes their stability, export to the cytoplasm and translation. Subsequently, the balance between exonucleolytic deadenylation and selective re-establishment of translation-competent poly(A) tails by cytoplasmic poly(A) polymerases is essential for the appropriate regulation of gene expression from oocytes to neurons. In recent years, surprising roles for cytoplasmic poly(A) polymerase-related enzymes that add uridylyl, rather than adenylyl, residues to RNA 3' ends have also emerged. These terminal uridylyl transferases promote the turnover of certain mRNAs but also modify microRNAs, their precursors and other small RNAs to modulate their stability or biological functions.

  10. Asymmetric dense matter in holographic QCD

    Directory of Open Access Journals (Sweden)

    Shin Ik Jae


    Full Text Available We study asymmetric dense matter in holographic QCD.We construct asymmetric dense matter by considering two quark flavor branes with dierent quark masses in a D4/D6/D6 model. To calculate the symmetry energy in nuclear matter, we consider two quarks with equal masses and observe that the symmetry energy increases with the total charge showing the stiff dependence. This behavior is universal in the sense that the result is independent of parameters in the model. We also study strange (or hyperon matter with one light and one intermediate mass quarks. In addition to the vacuum properties of asymmetric matter, we calculate meson masses in asymmetric dense matter and discuss our results in the light of in-medium kaon masses.

  11. Controlled Dense Coding with the W State (United States)

    Yang, Xue; Bai, Ming-qiang; Mo, Zhi-wen


    The average amount of information is an important factor in implementing dense coding. Based on this, we propose two schemes for controlled dense coding by using the three-qubit entangled W state as the quantum channel in this paper. In these schemes, the controller (Charlie) can adjust the local measurement angle 𝜃 to modulate the entanglement, and consequently the average amount of information transmitted from the sender (Alice) to the receiver (Bob). Although the results for the average amounts of information are the same from the different two schemes, the second scheme has advantage over the first scheme.

  12. Accelerating Dense Linear Algebra on the GPU

    DEFF Research Database (Denmark)

    Sørensen, Hans Henrik Brandenborg

    GPUs have already become an integral part of high performance scientific computing, since they offer dedicated parallel hardware that can potentially accelerate the execution of many scientific applications. In this talk, I will consider the automatic performance acceleration of dense vector...... and matrix-vector operations on GPUs. Such operations form the backbone of level 1 and level 2 routines in the Basic Linear Algebra Subroutines (BLAS) library and are therefore of great importance in many scientific applications. The target hardware is the most recent NVIDIA Tesla 20-series (Fermi...... architecture). Most of the techniques I discuss for accelerating dense linear algebra are applicable to memory-bound GPU algorithms in general....

  13. Nuclear repulsion enables division autonomy in a single cytoplasm. (United States)

    Anderson, Cori A; Eser, Umut; Korndorf, Therese; Borsuk, Mark E; Skotheim, Jan M; Gladfelter, Amy S


    Current models of cell-cycle control, based on classic studies of fused cells, predict that nuclei in a shared cytoplasm respond to the same CDK activities to undergo synchronous cycling. However, synchrony is rarely observed in naturally occurring syncytia, such as the multinucleate fungus Ashbya gossypii. In this system, nuclei divide asynchronously, raising the question of how nuclear timing differences are maintained despite sharing a common milieu. We observe that neighboring nuclei are highly variable in division-cycle duration and that neighbors repel one another to space apart and demarcate their own cytoplasmic territories. The size of these territories increases as a nucleus approaches mitosis and can influence cycling rates. This nonrandom nuclear spacing is regulated by microtubules and is required for nuclear asynchrony, as nuclei that transiently come in very close proximity will partially synchronize. Sister nuclei born of the same mitosis are generally not persistent neighbors over their lifetimes yet remarkably retain similar division cycle times. This indicates that nuclei carry a memory of their birth state that influences their division timing and supports that nuclei subdivide a common cytosol into functionally distinct yet mobile compartments. These findings support that nuclei use cytoplasmic microtubules to establish "cells within cells." Individual compartments appear to push against one another to compete for cytoplasmic territory and insulate the division cycle. This provides a mechanism by which syncytial nuclei can spatially organize cell-cycle signaling and suggests size control can act in a system without physical boundaries. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Animal models of antineutrophil cytoplasm antibody-associated vasculitis.

    LENUS (Irish Health Repository)

    Salama, Alan D


    To provide an update on the experimental models that have been developed recapitulating clinical antineutrophil cytoplasm antibody (ANCA) associated vasculitis. The application of the models in the study of pathogenesis, and the therapeutic implications of this, are covered in the article by van Timmeren and Heeringa in this issue.

  15. Serine phosphorylation of syndecan-2 proteoglycan cytoplasmic domain

    DEFF Research Database (Denmark)

    Oh, E S; Couchman, J R; Woods, A


    Protein kinase C (PKC) is involved in cell-matrix and cell-cell adhesion, and the cytoplasmic domain of syndecan-2 contains two serines (residues 197 and 198) which lie in a consensus sequence for phosphorylation by PKC. Other serine and threonine residues are present but not in a consensus seque...

  16. Nuclear proteins hijacked by mammalian cytoplasmic plus strand RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Lloyd, Richard E., E-mail:


    Plus strand RNA viruses that replicate in the cytoplasm face challenges in supporting the numerous biosynthetic functions required for replication and propagation. Most of these viruses are genetically simple and rely heavily on co-opting cellular proteins, particularly cellular RNA-binding proteins, into new roles for support of virus infection at the level of virus-specific translation, and building RNA replication complexes. In the course of infectious cycles many nuclear-cytoplasmic shuttling proteins of mostly nuclear distribution are detained in the cytoplasm by viruses and re-purposed for their own gain. Many mammalian viruses hijack a common group of the same factors. This review summarizes recent gains in our knowledge of how cytoplasmic RNA viruses use these co-opted host nuclear factors in new functional roles supporting virus translation and virus RNA replication and common themes employed between different virus groups. - Highlights: • Nuclear shuttling host proteins are commonly hijacked by RNA viruses to support replication. • A limited group of ubiquitous RNA binding proteins are commonly hijacked by a broad range of viruses. • Key virus proteins alter roles of RNA binding proteins in different stages of virus replication.

  17. Molecular cloning and characterization of a cytoplasmic cyclophilin ...

    African Journals Online (AJOL)



    Aug 8, 2011 ... Cyclophilins are ubiquitous proteins with an enzymatic activity of peptidyl-prolyl cis-trans isomerase. (PPIase), which play important roles in a variety of stress responsiveness. In this study, we reported the cloning and characterization of a full-length cytoplasmic cyclophilin gene in sugarcane. Sequence.

  18. Curious Sex Ratios and Cytoplasmic Genes Microbes Can Distort ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 2; Issue 6. Curious Sex Ratios and Cytoplasmic Genes Microbes Can Distort the Sex Ratio of Populations. Stephen J Freeland Laurence D Hurst. General Article Volume 2 Issue 6 June 1997 pp 68-78 ...

  19. Magnetite nanoparticles as reporters for microcarrier processing in cytoplasm

    Energy Technology Data Exchange (ETDEWEB)

    Reibetanz, Uta, E-mail: [Translational Centre for Regenerative Medicine (TRM) Leipzig, Universitaet Leipzig, Philipp-Rosenthal-Strasse 55, 04103 Leipzig (Germany); Institute for Medical Physics and Biophysics, Medical Faculty, Universitaet Leipzig, Haertelstrasse 16-18, 04107 Leipzig (Germany); Jankuhn, Steffen, E-mail: [Division of Nuclear Solid State Physics, Faculty of Physics and Geosciences, Universitaet Leipzig, Linnestrasse 5, 04103 Leipzig (Germany); Office for Environmental Protection and Occupational Safety, Universitaet Leipzig, Ritterstrasse 24, 04109 Leipzig (Germany)


    The development and therapeutic application of drug delivery systems based on colloidal microcarriers layer-by-layer coated with biopolyelectrolytes requires the investigation of their processing inside the cell for the successful and efficient transport and release of the active agents. The present study is focused on the time-dependent multilayer decomposition and the subsequent release of active agents to the cytoplasm. Magnetite nanoparticles (MNP) were used as reporter agents integrated into the protamine sulfate/dextran sulfate basis multilayer on colloidal SiO{sub 2} cores. This functionalization allows the monitoring of the multilayer decomposition due to the detection of the MNP release, visualized by means of proton-induced X-ray emission (PIXE) by elemental distribution of Si and Fe. The direct correlation between the microcarrier localization in endolysosomes and cytoplasm of HEK293T/17 cells via confocal laser scanning microscopy (CLSM) and the elemental distribution (PIXE) allows tracing the fate of the MNP-coated microcarriers in cytoplasm, and thus the processing of the multilayer. Microcarrier/cell co-incubation experiments of 6 h, 24 h, 48 h, and 72 h show that a MNP release and a slight expansion into the cytoplasm occurs after a longer co-incubation of 72 h.

  20. Molecular cloning and characterization of a cytoplasmic cyclophilin ...

    African Journals Online (AJOL)

    Cyclophilins are ubiquitous proteins with an enzymatic activity of peptidyl-prolyl cis-trans isomerase (PPIase), which play important roles in a variety of stress responsiveness. In this study, we reported the cloning and characterization of a full-length cytoplasmic cyclophilin gene in sugarcane. Sequence analysis showed the ...

  1. Experimental Analysis of Cell Function Using Cytoplasmic Streaming (United States)

    Janssens, Peter; Waldhuber, Megan


    This laboratory exercise investigates the phenomenon of cytoplasmic streaming in the fresh water alga "Nitella". Students use the fungal toxin cytochalasin D, an inhibitor of actin polymerization, to investigate the mechanism of streaming. Students use simple statistical methods to analyze their data. Typical student data are provided. (Contains 3…

  2. Endoplasmic-reticulum-mediated microtubule alignment governs cytoplasmic streaming. (United States)

    Kimura, Kenji; Mamane, Alexandre; Sasaki, Tohru; Sato, Kohta; Takagi, Jun; Niwayama, Ritsuya; Hufnagel, Lars; Shimamoto, Yuta; Joanny, Jean-François; Uchida, Seiichi; Kimura, Akatsuki


    Cytoplasmic streaming refers to a collective movement of cytoplasm observed in many cell types. The mechanism of meiotic cytoplasmic streaming (MeiCS) in Caenorhabditis elegans zygotes is puzzling as the direction of the flow is not predefined by cell polarity and occasionally reverses. Here, we demonstrate that the endoplasmic reticulum (ER) network structure is required for the collective flow. Using a combination of RNAi, microscopy and image processing of C. elegans zygotes, we devise a theoretical model, which reproduces and predicts the emergence and reversal of the flow. We propose a positive-feedback mechanism, where a local flow generated along a microtubule is transmitted to neighbouring regions through the ER. This, in turn, aligns microtubules over a broader area to self-organize the collective flow. The proposed model could be applicable to various cytoplasmic streaming phenomena in the absence of predefined polarity. The increased mobility of cortical granules by MeiCS correlates with the efficient exocytosis of the granules to protect the zygotes from osmotic and mechanical stresses.

  3. The transmission of cytoplasmic genes in Aspergillus nidulans

    NARCIS (Netherlands)

    Coenen, A.



    This manuscript concerns the spread of selfish cytoplasmic genes in the fungus Aspergillus nidulans. A.nidulans is a common soil fungus that grows vegetatively by forming a network (mycelium) of hyphae and reproduces

  4. Evaluation of cytoplasmic genetic effects for production and ...

    African Journals Online (AJOL)



    sajas.v44i5.17. Evaluation of cytoplasmic genetic effects for production and reproduction traits in Afrikaner cattle. F.W.C. Neser1#, J.B. van Wyk1 & M.M. Scholtz1,2. 1 Department of Animal, Wildlife and Grassland Sciences, ...

  5. Evaluation of cytoplasmic genetic effects for production and ...

    African Journals Online (AJOL)

    The model used for WW include direct additive, maternal additive, the covariance between the animal-, permanent maternal environmental-, herd-year-season x sire- and damline effects, while the simplest model which include only direct- and damline effects were used for AFC. The contribution of the cytoplasmic effects to ...

  6. Neutrophil-activating potential of antineutrophil cytoplasm autoantibodies

    NARCIS (Netherlands)

    Rarok, Agnieszka; Limburg, Piet; Kallenberg, Cees

    Accumulating in vivo and in vitro evidence supports the hypothesis that antineutrophil cytoplasm autoantibodies (ANCA) with specificity for proteinase 3 (PR3) and myeloperoxidase (MPO) are involved in the pathophysiology of small-vessel vasculitis. The best-described effector function of these

  7. Actin-mediated cytoplasmic organization of plant cells

    NARCIS (Netherlands)

    Honing, van der H.S.


    In this thesis, I present results that give insight in the role of the actin cytoskeleton in the production of an organized cytoplasm in plant cells, which is, for instance, required for proper cell morphogenesis. Chapter 1 is a review in which we discuss the possible role of actin-based force

  8. [Sexual reproduction of insects is regulated by cytoplasmic bacteria]. (United States)

    Markov, A V; Zakharov, I A


    The effects have been considered that the intracellular symbiotic alpha-proteobacteria Wolbachia pipientis induces in its hosts, such as insects and other arthropods: cytoplasmic incompatibility upon mating, feminization, parthenogenesis, and androcide. Specific features of the bacterium genome and possible mechanisms of its action on hosts are discussed.

  9. Investigation of factors responsible for cell line cytoplasmic expression differences

    Directory of Open Access Journals (Sweden)

    Finn Jonathan D


    Full Text Available Abstract Background Previous work has described a novel cytoplasmic expression system that results in a 20-fold increase in the levels of gene expression over a standard CMV-based nuclear expression system, as compared with a 2–3 fold increase seen with previous similar systems. While this increase was seen with BHK and Neuro-2a cells, further studies revealed that some cell lines, such as COS-7, demonstrated relatively poor levels of cytoplasmic expression. The objective of this study was to determine what factors were responsible for the different expression levels between BHK (a high expressing cell line and COS-7 (a low expressing cell line. Results The main findings of this work are that the individual elements of the cytoplasmic expression system (such as the T7 RNAP gene and Internal Ribosome Entry Sequence are functioning similarly in both cell types. Both cell types were found to have the same amount of cytosolic nuclease activity, and that the cells appeared to have differences in the intra-cellular processing of DNA -cationic lipid complexes. Conclusion After exploring many factors, it was found that differences in the intra-cellular processing of the DNA-cationic lipid complex was the most probable factor responsible for the difference in cytoplasmic gene expression.

  10. Nuclear and cytoplasmic LIMK1 enhances human breast cancer progression

    Directory of Open Access Journals (Sweden)

    Gutierrez-Hartmann Arthur


    Full Text Available Abstract Background LIM kinase 1 (LIMK1 is expressed in both cytoplasmic and nuclear compartments, and is a key regulator of cytoskeletal organization involved in cell migration and proliferation. LIMK1 levels are increased in several human cancers, with LIMK1 over-expression in prostate and breast cancer cells leading to tumor progression. While it has been presumed that the mechanism by which LIMK1 promotes cancer progression is via its cytoplasmic effects, the role of nuclear vs cytoplasmic LIMK1 in the tumorigenic process has not been examined. Results To determine if cytoplasmic or nuclear LIMK1 expression correlated with breast cancer, we performed immunohistochemical (IHC analysis of breast tissue microarrays (TMAs, The IHC analysis of breast TMAs revealed that 76% of malignant breast tissue samples strongly expressed LIMK1 in the cytoplasm, with 52% of these specimens also expressing nuclear LIMK1. Only 48% of benign breast samples displayed strong cytoplasmic LIMK1 expression and 27% of these expressed nuclear LIMK1. To investigate the respective roles of cytoplamsic and nuclear LIMK1 in breast cancer progression, we targeted GFP-LIMK1 to cytoplasmic and nuclear subcellular compartments by fusing nuclear export signals (NESs or nuclear localization sequences (NLS, respectively, to the amino-terminus of GFP-LIMK1. Stable pools of MDA-MB-231 cells were generated by retroviral transduction, and fluorescence microscopy revealed that GFP alone (control and GFP-LIMK1 were each expressed in both the cytoplasm and nucleus of MDA-MB-231 cells, whereas NLS-GFP-LIMK1 was expressed in the nucleus and NES-GFP-LIMK1 was expressed in the cytoplasm. Western blot analyses revealed equal expression of GFP-LIMK1 and NES-GFP-LIMK1, with NLS-GFP-LIMK1 expression being less but equal to endogenous LIMK1. Also, Western blotting revealed increased levels of phospho-cofilin, phospho-FAK, phospho-paxillin, phospho-Src, phospho-AKT, and phospho-Erk1/2 in cells

  11. Cytoplasmic flows as signatures for the mechanics of mitotic positioning. (United States)

    Nazockdast, Ehssan; Rahimian, Abtin; Needleman, Daniel; Shelley, Michael


    The proper positioning of mitotic spindle in the single-cell Caenorhabditis elegans embryo is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated astral microtubules (MTs). Pronuclear migration produces global cytoplasmic flows that couple the mechanics of all MTs, the PNC, and the cell periphery with each other through their hydrodynamic interactions (HIs). We present the first computational study that explicitly accounts for detailed HIs between the cytoskeletal components and demonstrate the key consequences of HIs for the mechanics of pronuclear migration. First, we show that, because of HIs between the MTs, the cytoplasm-filled astral MTs behave like a porous medium, with its permeability decreasing with increasing the number of MTs. We then directly study the dynamics of PNC migration under various force-transduction models, including the pushing or pulling of MTs at the cortex and the pulling of MTs by cytoplasmically bound force generators. Although achieving proper position and orientation on reasonable time scales does not uniquely choose a model, we find that each model produces a different signature in its induced cytoplasmic flow. We suggest that cytoplasmic flows can be used to differentiate between mechanisms. © 2017 Nazockdast et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (

  12. Dense ceramic membranes for methane conversion

    NARCIS (Netherlands)

    Bouwmeester, Henricus J.M.


    Dense ceramic membranes made from mixed oxygen-ionic and electronic conducting perovskite-related oxides allow separation of oxygen from an air supply at elevated temperatures (>700 °C). By combining air separation and catalytic partial oxidation of methane to syngas into a ceramic membrane reactor,

  13. Relaxation phenomena in dense glassy polymer membranes

    NARCIS (Netherlands)

    Bouma, R.H.B.; Bouma, Richard Hendrik Bouke


    Dense polymeric films can be used as permeation-selective barriers which change the composition of a fluid by differences in solubility and/or diffusivity of fluid components in the membrane material. In general glassy polymers show rather high selectivities, but usually in combination with low

  14. The Golgi apparatus in the endomembrane-rich gastric parietal cells exist as functional stable mini-stacks dispersed throughout the cytoplasm. (United States)

    Gunn, Priscilla A; Gliddon, Briony L; Londrigan, Sarah L; Lew, Andrew M; van Driel, Ian R; Gleeson, Paul A


    Acid-secreting gastric parietal cells are polarized epithelial cells that harbour highly abundant and specialized, H+,K+ ATPase-containing, tubulovesicular membranes in the apical cytoplasm. The Golgi apparatus has been implicated in the biogenesis of the tubulovesicular membranes; however, an unanswered question is how a typical Golgi organization could regulate normal membrane transport within the membrane-dense cytoplasm of parietal cells. Here, we demonstrate that the Golgi apparatus of parietal cells is not the typical juxta-nuclear ribbon of stacks, but rather individual Golgi units are scattered throughout the cytoplasm. The Golgi membrane structures labelled with markers of both cis- and trans-Golgi membrane, indicating the presence of intact Golgi stacks. The parietal cell Golgi stacks were closely aligned with the microtubule network and were shown to participate in both anterograde and retrograde transport pathways. Dispersed Golgi stacks were also observed in parietal cells from H+,K+ ATPase-deficient mice that lack tubulovesicular membranes. These results indicate that the unusual organization of individual Golgi stacks dispersed throughout the cytoplasm of these terminally differentiated cells is likely to be a developmentally regulated event.

  15. Chemical Dense Gas Modeling in Cities (United States)

    Brown, M. J.; Williams, M. D.; Nelson, M. A.; Streit, G. E.


    Many industrial facilities have on-site storage of chemicals and are within a few kilometers of residential population. Chemicals are transported around the country via trains and trucks and often go through populated areas on their journey. Many of the chemicals, like chlorine and phosgene, are toxic and when released into the air are heavier-than-air dense gases that hug the ground and result in high airborne concentrations at breathing level. There is considerable concern about the vulnerability of these stored and transported chemicals to terrorist attack and the impact a release could have on highly-populated urban areas. There is the possibility that the impacts of a dense gas release within a city would be exacerbated since the buildings might act to trap the toxic cloud at street level and channel it over a large area down side streets. However, no one is quite sure what will happen for a release in cities since there is a dearth of experimental data. There are a number of fast-running dense gas models used in the air pollution and emergency response community, but there are none that account for the complex flow fields and turbulence generated by buildings. As part of this presentation, we will discuss current knowledge regarding dense gas releases around buildings and other obstacles. We will present information from wind tunnel and field experiments, as well as computational fluid dynamics modeling. We will also discuss new fast response modeling efforts which are trying to account for dense gas transport and dispersion in cities.

  16. Anti-neutrophil cytoplasmic autoantibody pathogenicity revisited : pathogenic versus non-pathogenic anti-neutrophil cytoplasmic autoantibody

    NARCIS (Netherlands)

    Land, Judith; Rutgers, Abraham; Kallenberg, Cees G. M.

    Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is strongly associated with autoantibodies against myeloperoxidase (MPO) and proteinase 3 (PR3). No clear consensus has been reached on the pathogenicity of these autoantibodies. Animal models for MPO-ANCA, in vitro data

  17. Cytoplasmic inclusions within developing mouse retinal photoreceptor cells maintained in culture: possible type A retrovirus particles? (United States)

    Bird, M M


    Unusual cytoplasmic inclusions were consistently observed in photoreceptor cells of explants of embryonic mouse retina maintained in culture for 21 days or longer. The inclusions were chiefly spherical (some appeared to be short cylinders) and about 76 nm in diameter. They consisted of a granular/amorphous electron-dense periphery and an electron-lucent core and were usually in clusters, often close to the Golgi apparatus or plasma membrane. They were also commonly present in photoreceptor cell synaptic terminals in the outer plexiform layer. They displayed close relationships with cisterns and tubules of the endoplasmic reticulum and many were located within dilated sacs of reticulum. Narrow, smooth-surfaced tubules appeared to run into or through the cores of some of the inclusion bodies linking them to others. Similar inclusions were not seen in any other cell types in the explants and have not been reported in previous in vivo and in vitro studies of developing or adult mouse retina. The possibility that these inclusions represent Type A retrovirus particles is considered. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 Fig. 13 PMID:3417552

  18. Amorphous areas in the cytoplasm of Dendrobium tepal cells (United States)

    van Doorn, Wouter G.; Kirasak, Kanjana; Ketsa, Saichol


    In Dendrobium flowers some tepal mesophyll cells showed cytoplasmic areas devoid of large organelles. Such amorphous areas comprised up to about 40% of the cross-section of a cell. The areas were not bound by a membrane. The origin of these areas is not known. We show data suggesting that they can be formed from vesicle-like organelles. The data imply that these organelles and other material become degraded inside the cytoplasm. This can be regarded as a form of autophagy. The amorphous areas became surrounded by small vacuoles, vesicles or double membranes. These seemed to merge and thereby sequester the areas. Degradation of the amorphous areas therefore seemed to involve macroautophagy. PMID:23823702

  19. Nucleoporin Nup98 mediates galectin-3 nuclear-cytoplasmic trafficking

    Energy Technology Data Exchange (ETDEWEB)

    Funasaka, Tatsuyoshi, E-mail: [Laboratory of Molecular and Cellular Biology, Department of Biology, Faculty of Natural Systems, Institute of Science and Engineering, Kanazawa University, Ishikawa (Japan); Balan, Vitaly; Raz, Avraham [Department of Oncology and Pathology, Karmanos Cancer Institute, Wayne State University, School of Medicine, Detroit, MI (United States); Wong, Richard W., E-mail: [Laboratory of Molecular and Cellular Biology, Department of Biology, Faculty of Natural Systems, Institute of Science and Engineering, Kanazawa University, Ishikawa (Japan); Bio-AFM Frontier Research Center, Kanazawa Kanazawa University, Ishikawa (Japan)


    Highlights: •Nuclear pore protein Nup98 is a novel binding partner of galectin-3. •Nup98 transports galectin-3 into cytoplasm. •Nup98 depletion leads to galectin-3 nuclear transport and induces growth retardation. •Nup98 may involve in ß-catenin pathway through interaction with galectin-3. -- Abstract: Nucleoporin Nup98 is a component of the nuclear pore complex, and is important in transport across the nuclear pore. Many studies implicate nucleoporin in cancer progression, but no direct mechanistic studies of its effect in cancer have been reported. We show here that Nup98 specifically regulates nucleus–cytoplasm transport of galectin-3, which is a ß-galactoside-binding protein that affects adhesion, migration, and cancer progression, and controls cell growth through the ß-catenin signaling pathway in cancer cells. Nup98 interacted with galectin-3 on the nuclear membrane, and promoted galectin-3 cytoplasmic translocation whereas other nucleoporins did not show these functions. Inversely, silencing of Nup98 expression by siRNA technique localized galectin-3 to the nucleus and retarded cell growth, which was rescued by Nup98 transfection. In addition, Nup98 RNA interference significantly suppressed downstream mRNA expression in the ß-catenin pathway, such as cyclin D1 and FRA-1, while nuclear galectin-3 binds to ß-catenin to inhibit transcriptional activity. Reduced expression of ß-catenin target genes is consistent with the Nup98 reduction and the galectin-3–nucleus translocation rate. Overall, the results show Nup98’s involvement in nuclear–cytoplasm translocation of galectin-3 and ß-catenin signaling pathway in regulating cell proliferation, and the results depicted here suggest a novel therapeutic target/modality for cancers.

  20. CD248 facilitates tumor growth via its cytoplasmic domain

    Directory of Open Access Journals (Sweden)

    Janssens Tom


    Full Text Available Abstract Background Stromal fibroblasts participate in the development of a permissive environment for tumor growth, yet molecular pathways to therapeutically target fibroblasts are poorly defined. CD248, also known as endosialin or tumor endothelial marker 1 (TEM1, is a transmembrane glycoprotein expressed on activated fibroblasts. We recently showed that the cytoplasmic domain of CD248 is important in facilitating an inflammatory response in a mouse model of arthritis. Others have reported that CD248 gene inactivation in mice results in dampened tumor growth. We hypothesized that the conserved cytoplasmic domain of CD248 is important in regulating tumor growth. Methods Mice lacking the cytoplasmic domain of CD248 (CD248CyD/CyD were generated and evaluated in tumor models, comparing the findings with wild-type mice (CD248WT/WT. Results As compared to the response in CD248WT/WT mice, growth of T241 fibrosarcomas and Lewis lung carcinomas was significantly reduced in CD248CyD/CyD mice. Tumor size was similar to that seen with CD248-deficient mice. Conditioned media from CD248CyD/CyD fibroblasts were less effective at supporting T241 fibrosarcoma cell survival. In addition to our previous observation of reduced release of activated matrix metalloproteinase (MMP-9, CD248CyD/CyD fibroblasts also had impaired PDGF-BB-induced migration and expressed higher transcripts of tumor suppressor factors, transgelin (SM22α, Hes and Hey1. Conclusions The multiple pathways regulated by the cytoplasmic domain of CD248 highlight its potential as a therapeutic target to treat cancer.

  1. Highly Dense Isolated Metal Atom Catalytic Sites

    DEFF Research Database (Denmark)

    Chen, Yaxin; Kasama, Takeshi; Huang, Zhiwei


    Atomically dispersed noble-metal catalysts with highly dense active sites are promising materials with which to maximise metal efficiency and to enhance catalytic performance; however, their fabrication remains challenging because metal atoms are prone to sintering, especially at a high metal...... loading. A dynamic process of formation of isolated metal atom catalytic sites on the surface of the support, which was achieved starting from silver nanoparticles by using a thermal surface-mediated diffusion method, was observed directly by using in situ electron microscopy and in situ synchrotron X......-ray diffraction. A combination of electron microscopy images with X-ray absorption spectra demonstrated that the silver atoms were anchored on five-fold oxygen-terminated cavities on the surface of the support to form highly dense isolated metal active sites, leading to excellent reactivity in catalytic oxidation...

  2. Topological groups with dense compactly generated subgroups

    Directory of Open Access Journals (Sweden)

    Hiroshi Fujita


    Full Text Available A topological group G is: (i compactly generated if it contains a compact subset algebraically generating G, (ii -compact if G is a union of countably many compact subsets, (iii 0-bounded if arbitrary neighborhood U of the identity element of G has countably many translates xU that cover G, and (iv finitely generated modulo open sets if for every non-empty open subset U of G there exists a finite set F such that F  U algebraically generates G. We prove that: (1 a topological group containing a dense compactly generated subgroup is both 0-bounded and finitely generated modulo open sets, (2 an almost metrizable topological group has a dense compactly generated subgroup if and only if it is both 0-bounded and finitely generated modulo open sets, and (3 an almost metrizable topological group is compactly generated if and only if it is -compact and finitely generated modulo open sets.

  3. Dense deposit disease and C3 glomerulopathy. (United States)

    Barbour, Thomas D; Pickering, Matthew C; Terence Cook, H


    C3 glomerulopathy refers to those renal lesions characterized histologically by predominant C3 accumulation within the glomerulus, and pathogenetically by aberrant regulation of the alternative pathway of complement. Dense deposit disease is distinguished from other forms of C3 glomerulopathy by its characteristic appearance on electron microscopy. The extent to which dense deposit disease also differs from other forms of C3 glomerulopathy in terms of clinical features, natural history, and outcomes of treatment including renal transplantation is less clear. We discuss the pathophysiology of C3 glomerulopathy, with evidence for alternative pathway dysregulation obtained from affected individuals and complement factor H (Cfh)-deficient animal models. Recent linkage studies in familial C3 glomerulopathy have shown genomic rearrangements in the Cfh-related genes, for which the novel pathophysiologic concept of Cfh deregulation has been proposed. © 2013 Elsevier Inc. All rights reserved.

  4. The kinetic chemistry of dense interstellar clouds (United States)

    Graedel, T. E.; Langer, W. D.; Frerking, M. A.


    A model of the time-dependent chemistry of dense interstellar clouds is formulated to study the dominant chemical processes in carbon and oxygen isotope fractionation, the formation of nitrogen-containing molecules, and the evolution of product molecules as a function of cloud density and temperature. The abundances of the dominant isotopes of the carbon- and oxygen-bearing molecules are calculated. The chemical abundances are found to be quite sensitive to electron concentration since the electron concentration determines the ratio of H3(+) to He(+), and the electron density is strongly influenced by the metals abundance. For typical metal abundances and for H2 cloud density not less than 10,000 molecules/cu cm, nearly all carbon exists as CO at late cloud ages. At high cloud density, many aspects of the chemistry are strongly time dependent. Finally, model calculations agree well with abundances deduced from observations of molecular line emission in cold dense clouds.

  5. Dense Output for Strong Stability Preserving Runge–Kutta Methods

    KAUST Repository

    Ketcheson, David I.


    We investigate dense output formulae (also known as continuous extensions) for strong stability preserving (SSP) Runge–Kutta methods. We require that the dense output formula also possess the SSP property, ideally under the same step-size restriction as the method itself. A general recipe for first-order SSP dense output formulae for SSP methods is given, and second-order dense output formulae for several optimal SSP methods are developed. It is shown that SSP dense output formulae of order three and higher do not exist, and that in any method possessing a second-order SSP dense output, the coefficient matrix A has a zero row.

  6. Particle identification system based on dense aerogel

    Energy Technology Data Exchange (ETDEWEB)

    Barnyakov, A.Yu. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Barnyakov, M.Yu. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State Technical University, 20, Karl Marx prospect, Novosibirsk, 630092 (Russian Federation); Beloborodov, K.I., E-mail: [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Bobrovnikov, V.S.; Buzykaev, A.R. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Danilyuk, A.F. [Boreskov Institute of Catalysis, 5, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Golubev, V.B. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Gulevich, V.V. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Kononov, S.A.; Kravchenko, E.A. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); Onuchin, A.P.; Martin, K.A. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State Technical University, 20, Karl Marx prospect, Novosibirsk, 630092 (Russian Federation); Serednyakov, S.I. [Budker Institute of Nuclear Physics, 11, akademika Lavrentieva prospect, Novosibirsk 630090 (Russian Federation); Novosibirsk State University, 2, Pirogova Street, Novosibirsk 630090 (Russian Federation); and others


    A threshold Cherenkov counter based on dense aerogel with refraction index n=1.13 is described. This counter is used for kaon identification at momenta below 1 GeV/c in the SND detector, which takes data at the VEPP-2000 e{sup +}e{sup −} collider. The results of measurements of the counter efficiency using electrons, muons, pions, and kaons produced in e{sup +}e{sup −} annihilation are presented.

  7. Dense medium cyclone control - a reconsideration

    Energy Technology Data Exchange (ETDEWEB)

    Firth, B.A. [CSIRO Energy Technology, Kenmore, Qld (Australia)


    The current process management and control of dense medium cyclones is based on the measurement of feed medium density and pressure. This paper considers the relationships between the controlling factors and the relative density of separation and Ep. These relationships have been developed from the analysis of over 20 data sets on modern large cyclones in which important factors such as overflow and underflow densities, feed solids flow rate, medium to coal ratio, and loading to the spigot were recorded.

  8. Dense Aluminum Plasma Equation of State Measurements (United States)

    Workman, J.; Tierney, T.; Kyrala Benage, G., Jr.


    Knowledge of the equation of state for any material is essential to a full understanding of its intrinsic and dynamic properties. Accurate experimental measurements of the equation of state for strongly coupled plasmas (Γ >= 1), relevant to astrophysical, geologic and ICF applications, have been extremely difficult. We present preliminary results on a novel method for off-Hugoniot measurements of the equation of state for dense plasmas (3 Marx pulsed power device to create plasma densities of up to one-tenth solid and temperatures of a few eV from a 200 μm diameter aluminum wire. Density and temperature profiles of the dense aluminum plasma are determined using laser-produced temporally- and spatially-resolved x-ray backlighters and optical streak records. Simulations indicate that the use of a laser-generated shock wave in the dense plasma can provide megabar pressures at 10 eV temperatures with ion densities of up to 10 times the initial density. Future experiments will concentrate on the use of this laser-generated shock to determine the equation of state through accurate density and shock-speed measurements.

  9. Dense planetary rings and the viscous overstability (United States)

    Latter, Henrik N.; Ogilvie, Gordon I.


    This paper examines the onset of the viscous overstability in dense particulate rings. First, we formulate a dense gas kinetic theory that is applicable to the saturnian system. Our model is essentially that of Araki and Tremaine [Araki, S., Tremaine, S., 1986. Icarus 65, 83-109], which we show can be both simplified and generalised. Second, we put this model to work computing the equilibrium properties of dense planetary rings, which we subsequently compare with the results of N-body simulations, namely those of Salo [Salo, H., 1991. Icarus 90, 254-270]. Finally, we present the linear stability analyses of these equilibrium states, and derive criteria for the onset of viscous overstability in the self-gravitating and non-self-gravitating cases. These are framed in terms of particle size, orbital frequency, optical depth, and the parameters of the collision law. Our results compare favourably with the simulations of Salo et al. [Salo, H., Schmidt, J., Spahn, F., 2001. Icarus 153, 295-315]. The accuracy and practicality of the continuum model we develop encourages its general use in future investigations of nonlinear phenomena.

  10. CFD modeling of dense medium cyclone

    Energy Technology Data Exchange (ETDEWEB)

    Rajamani, R.K.; Delgadillo, J.; Kodukula, U.B.; Alkac, D. [University of Utah, Salt Lake City, UT (United States)


    A number of empirical models are in existence for the dense medium cyclone (DMC) and in recent years this subject has been broached with computational fluid dynamics (CFD). The dense medium presents a centrifugal field within the cyclone body. The coal particles separate in this field due to various forces acting on them. Hence, CFD is ideally suited for the modeling of the DMC. The Large Eddy Simulation (LES) method for resolving the turbulence was used in the CFD simulation of a 76mm dense medium cyclone. In particular, the magnetite was modeled as three granular fluids. In the simulation the diameter of the vortex finder and spigot are varied to compare with the experimental data of P. A. Verghese and T. C. Rao. The results obtained using LES turbulence model is found to be accurate in terms of the cut density and the slope of the distribution curves. Thus, the three granular fluid modeling of the magnetite stream is a computationally simpler method for the analysis of DMC.

  11. MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. (United States)

    Politz, Joan C Ritland; Zhang, Fan; Pederson, Thoru


    MicroRNAs are small, approximately 21- to 24-nt RNAs that have been found to regulate gene expression. miR-206 is a microRNA that is expressed at high levels in Drosophila, zebrafish, and mouse skeletal muscle and is thought to be involved in the attainment and/or maintenance of the differentiated state. We used locked nucleic acid probes for in situ hybridization analysis of the intracellular localization of miR-206 during differentiation of rat myogenic cells. Like most microRNAs, which are presumed to suppress translation of target mRNAs, we found that miR-206 occupies a cytoplasmic location in cultured myoblasts and differentiated myotubes and that its level increases in myotubes over the course of differentiation, consistent with previous findings in muscle tissue in vivo. However, to our surprise, we also observed miR-206 to be concentrated in nucleoli. A probe designed to be complementary to the precursor forms of miR-206 gave no nucleolar signal. We characterized the intracellular localization of miR-206 at higher spatial resolution and found that a substantial fraction colocalizes with 28S rRNA in both the cytoplasm and the nucleolus. miR-206 is not concentrated in either the fibrillar centers of the nucleolus or the dense fibrillar component, where ribosomal RNA transcription and early processing occur, but rather is localized in the granular component, the region of the nucleolus where final ribosome assembly takes place. These results suggest that miR-206 may associate both with nascent ribosomes in the nucleolus and with exported, functional ribosomes in the cytoplasm.

  12. FttC-Based Fronthaul for 5G Dense/Ultra-Dense Access Network: Performance and Costs in Realistic Scenarios


    Franco Mazzenga; Romeo Giuliano; Francesco Vatalaro


    One distinctive feature of the next 5G systems is the presence of a dense/ultra-dense wireless access network with a large number of access points (or nodes) at short distances from each other. Dense/ultra-dense access networks allow for providing very high transmission capacity to terminals. However, the deployment of dense/ultra-dense networks is slowed down by the cost of the fiber-based infrastructure required to connect radio nodes to the central processing units and then to the core net...

  13. Actin and myosin regulate cytoplasm stiffness in plant cells: a study using optical tweezers

    NARCIS (Netherlands)

    Honing, van der H.S.; Ruijter, de N.C.A.; Emons, A.M.C.; Ketelaar, T.


    Here, we produced cytoplasmic protrusions with optical tweezers in mature BY-2 suspension cultured cells to study the parameters involved in the movement of actin filaments during changes in cytoplasmic organization and to determine whether stiffness is an actin-related property of plant cytoplasm.

  14. DMPD: Negative regulation of cytoplasmic RNA-mediated antiviral signaling. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18703349 Negative regulation of cytoplasmic RNA-mediated antiviral signaling. Komur...Show Negative regulation of cytoplasmic RNA-mediated antiviral signaling. PubmedID 18703349 Title Negative r...egulation of cytoplasmic RNA-mediated antiviral signaling. Authors Komuro A, Bamm

  15. Leeuwpan fine coal dense medium plant

    CSIR Research Space (South Africa)

    Lundt, M


    Full Text Available as shown in Figure 5. When the circulating medium density is increased, the density of the feed to both the primary and secondary cyclones is increased, and relatively small increases in the circulating medium density causes fairly large increases... availability to treat the higher grade coal (the bottom layer of coal) from the no. 2 Seam for a local and export metallurgical market. Following the path of evolution, in 2007, Leeuwpan commissioned the first double stage ultra-fines dense medium cyclone...

  16. Gravity-driven dense granular flows

    Energy Technology Data Exchange (ETDEWEB)



    The authors report and analyze the results of numerical studies of dense granular flows in two and three dimensions, using both linear damped springs and Hertzian force laws between particles. Chute flow generically produces a constant density profile that satisfies scaling relations suggestive of a Bagnold grain inertia regime. The type for force law has little impact on the behavior of the system. Failure is not initiated at the surface, consistent with the absence of surface flows and different principal stress directions at vs. below the surface.

  17. Superfluid phase transitions in dense neutron matter. (United States)

    Khodel, V A; Clark, J W; Zverev, M V


    The phase transitions in a realistic system with triplet pairing, dense neutron matter, have been investigated. The spectrum of phases of the 3P2-3F2 model, which adequately describes pairing in this system, is analytically constructed with the aid of a separation method for solving BCS gap equations in states of arbitrary angular momentum. In addition to solutions involving a single value of the magnetic quantum number (and its negative), there exist ten real multicomponent solutions. Five of the corresponding angle-dependent order parameters have nodes, and five do not. In contrast to the case of superfluid 3He, transitions occur between phases with nodeless order parameters.

  18. Graph Quasicontinuous Functions and Densely Continuous Forms

    Directory of Open Access Journals (Sweden)

    Lubica Hola


    Full Text Available Let $X, Y$ be topological spaces. A function $f: X \\to Y$ is said to be graph quasicontinuous if there is a quasicontinuous function $g: X \\to Y$ with the graph of $g$ contained in the closure of the graph of $f$. There is a close relation between the notions of graph quasicontinuous functions and minimal usco maps as well as the notions of graph quasicontinuous functions and densely continuous forms. Every function with values in a compact Hausdorff space is graph quasicontinuous; more generally every locally compact function is graph quasicontinuous.

  19. Phase boundary of hot dense fluid hydrogen. (United States)

    Ohta, Kenji; Ichimaru, Kota; Einaga, Mari; Kawaguchi, Sho; Shimizu, Katsuya; Matsuoka, Takahiro; Hirao, Naohisa; Ohishi, Yasuo


    We investigated the phase transformation of hot dense fluid hydrogen using static high-pressure laser-heating experiments in a laser-heated diamond anvil cell. The results show anomalies in the heating efficiency that are likely to be attributed to the phase transition from a diatomic to monoatomic fluid hydrogen (plasma phase transition) in the pressure range between 82 and 106 GPa. This study imposes tighter constraints on the location of the hydrogen plasma phase transition boundary and suggests higher critical point than that predicted by the theoretical calculations.

  20. Cytoplasmic TRADD Confers a Worse Prognosis in Glioblastoma

    Directory of Open Access Journals (Sweden)

    Sharmistha Chakraborty


    Full Text Available Tumor necrosis factor receptor 1 (TNFR1-associated death domain protein (TRADD is an important adaptor in TNFR1 signaling and has an essential role in nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB activation and survival signaling. Increased expression of TRADD is sufficient to activate NF-κB. Recent studies have highlighted the importance of NF-κB activation as a key pathogenic mechanism in glioblastoma multiforme (GBM, the most common primary malignant brain tumor in adults.We examined the expression of TRADD by immunohistochemistry (IHC and find that TRADD is commonly expressed at high levels in GBM and is detected in both cytoplasmic and nuclear distribution. Cytoplasmic IHC TRADD scoring is significantly associated with worse progression-free survival (PFS both in univariate and multivariate analysis but is not associated with overall survival (n = 43 GBMs. PFS is a marker for responsiveness to treatment. We propose that TRADD-mediated NF-κB activation confers chemoresistance and thus a worse PFS in GBM. Consistent with the effect on PFS, silencing TRADD in glioma cells results in decreased NF-κB activity, decreased proliferation of cells, and increased sensitivity to temozolomide. TRADD expression is common in glioma-initiating cells. Importantly, silencing TRADD in GBM-initiating stem cell cultures results in decreased viability of stem cells, suggesting that TRADD may be required for maintenance of GBM stem cell populations. Thus, our study suggests that increased expression of cytoplasmic TRADD is both an important biomarker and a key driver of NF-κB activation in GBM and supports an oncogenic role for TRADD in GBM.

  1. Predicting diffusivities in dense fluid mixtures

    Directory of Open Access Journals (Sweden)



    Full Text Available In this work the Enskog solution of the Boltzmann equation, as corrected by Speedy, together with the Weeks-Chandler-Andersen (WCA perturbation theory of liquids is employed in correlating and predicting self-diffusivities of dense fluids. Afterwards this theory is used to estimate mutual diffusion coefficients of solutes at infinite dilution in sub and supercritical solvents. We have also investigated the behavior of Fick diffusion coefficients in the proximity of a binary vapor-liquid critical point since this subject is of great interest for extraction purposes. The approach presented here, which makes use of a density and temperature dependent hard-sphere diameter, is shown to be excellent for predicting diffusivities in dense pure fluids and fluid mixtures. The calculations involved highly nonideal mixtures as well as systems with high molecular asymmetry. The predicted diffusivities are in good agreement with the experimental data for the pure and binary systems. The methodology proposed here makes only use of pure component information and density of mixtures. The simple algebraic relations are proposed without any binary adjustable parameters and can be readily used for estimating diffusivities in multicomponent mixtures.

  2. Wireless Fractal Ultra-Dense Cellular Networks (United States)

    Hao, Yixue; Chen, Min; Hu, Long; Song, Jeungeun; Volk, Mojca; Humar, Iztok


    With the ever-growing number of mobile devices, there is an explosive expansion in mobile data services. This represents a challenge for the traditional cellular network architecture to cope with the massive wireless traffic generated by mobile media applications. To meet this challenge, research is currently focused on the introduction of a small cell base station (BS) due to its low transmit power consumption and flexibility of deployment. However, due to a complex deployment environment and low transmit power of small cell BSs, the coverage boundary of small cell BSs will not have a traditional regular shape. Therefore, in this paper, we discuss the coverage boundary of an ultra-dense small cell network and give its main features: aeolotropy of path loss fading and fractal coverage boundary. Simple performance analysis is given, including coverage probability and transmission rate, etc., based on stochastic geometry theory and fractal theory. Finally, we present an application scene and discuss challenges in the ultra-dense small cell network. PMID:28417927

  3. Solids flow rate measurement in dense slurries

    Energy Technology Data Exchange (ETDEWEB)

    Porges, K.G.; Doss, E.D.


    Accurate and rapid flow rate measurement of solids in dense slurries remains an unsolved technical problem, with important industrial applications in chemical processing plants and long-distance solids conveyance. In a hostile two-phase medium, such a measurement calls for two independent parameter determinations, both by non-intrusive means. Typically, dense slurries tend to flow in laminar, non-Newtonian mode, eliminating most conventional means that usually rely on calibration (which becomes more difficult and costly for high pressure and temperature media). These issues are reviewed, and specific solutions are recommended in this report. Detailed calculations that lead to improved measuring device designs are presented for both bulk density and average velocity measurements. Cross-correlation, chosen here for the latter task, has long been too inaccurate for practical applications. The cause and the cure of this deficiency are discussed using theory-supported modeling. Fluid Mechanics are used to develop the velocity profiles of laminar non-Newtonian flow in a rectangular duct. This geometry uniquely allows the design of highly accurate `capacitive` devices and also lends itself to gamma transmission densitometry on an absolute basis. An absolute readout, though of less accuracy, is also available from a capacitive densitometer and a pair of capacitive sensors yields signals suitable for cross-correlation velocity measurement.

  4. Quantum molecular dynamics simulations of dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Collins, L.; Kress, J.; Troullier, N.; Lenosky, T.; Kwon, I. [Los Alamos National Lab., Albuquerque, NM (United States)


    The authors have developed a quantum molecular dynamics (QMD) simulation method for investigating the properties of dense matter in a variety of environments. The technique treats a periodically-replicated reference cell containing N atoms in which the nuclei move according to the classical equations-of-motion. The interatomic forces are generated from the quantum mechanical interactions of the (between?) electrons and nuclei. To generate these forces, the authors employ several methods of varying sophistication from the tight-binding (TB) to elaborate density functional (DF) schemes. In the latter case, lengthy simulations on the order of 200 atoms are routinely performed, while for the TB, which requires no self-consistency, upwards to 1000 atoms are systematically treated. The QMD method has been applied to a variety cases: (1) fluid/plasma Hydrogen from liquid density to 20 times volume-compressed for temperatures of a thousand to a million degrees Kelvin; (2) isotopic hydrogenic mixtures, (3) liquid metals (Li, Na, K); (4) impurities such as Argon in dense hydrogen plasmas; and (5) metal/insulator transitions in rare gas systems (Ar,Kr) under high compressions. The advent of parallel versions of the methods, especially for fast eigensolvers, presage LDA simulations in the range of 500--1000 atoms and TB runs for tens of thousands of particles. This leap should allow treatment of shock chemistry as well as large-scale mixtures of species in highly transient environments.

  5. Redesigning Triangular Dense Matrix Computations on GPUs

    KAUST Repository

    Charara, Ali


    A new implementation of the triangular matrix-matrix multiplication (TRMM) and the triangular solve (TRSM) kernels are described on GPU hardware accelerators. Although part of the Level 3 BLAS family, these highly computationally intensive kernels fail to achieve the percentage of the theoretical peak performance on GPUs that one would expect when running kernels with similar surface-to-volume ratio on hardware accelerators, i.e., the standard matrix-matrix multiplication (GEMM). The authors propose adopting a recursive formulation, which enriches the TRMM and TRSM inner structures with GEMM calls and, therefore, reduces memory traffic while increasing the level of concurrency. The new implementation enables efficient use of the GPU memory hierarchy and mitigates the latency overhead, to run at the speed of the higher cache levels. Performance comparisons show up to eightfold and twofold speedups for large dense matrix sizes, against the existing state-of-the-art TRMM and TRSM implementations from NVIDIA cuBLAS, respectively, across various GPU generations. Once integrated into high-level Cholesky-based dense linear algebra algorithms, the performance impact on the overall applications demonstrates up to fourfold and twofold speedups, against the equivalent native implementations, linked with cuBLAS TRMM and TRSM kernels, respectively. The new TRMM/TRSM kernel implementations are part of the open-source KBLAS software library ( and are lined up for integration into the NVIDIA cuBLAS library in the upcoming v8.0 release.

  6. Wireless Fractal Ultra-Dense Cellular Networks. (United States)

    Hao, Yixue; Chen, Min; Hu, Long; Song, Jeungeun; Volk, Mojca; Humar, Iztok


    With the ever-growing number of mobile devices, there is an explosive expansion in mobile data services. This represents a challenge for the traditional cellular network architecture to cope with the massive wireless traffic generated by mobile media applications. To meet this challenge, research is currently focused on the introduction of a small cell base station (BS) due to its low transmit power consumption and flexibility of deployment. However, due to a complex deployment environment and low transmit power of small cell BSs, the coverage boundary of small cell BSs will not have a traditional regular shape. Therefore, in this paper, we discuss the coverage boundary of an ultra-dense small cell network and give its main features: aeolotropy of path loss fading and fractal coverage boundary. Simple performance analysis is given, including coverage probability and transmission rate, etc., based on stochastic geometry theory and fractal theory. Finally, we present an application scene and discuss challenges in the ultra-dense small cell network.

  7. Morphology and distribution of cytoplasmic inclusions in adrenoleukodystrophy. (United States)

    Ghatak, N R; Nochlin, D; Peris, M; Myer, E C


    We report some additional observations on the pathognomonic cytoplasmic inclusions in a typical case of adrenoleukodystrophy (ALD). Study of the linear inclusions by means of tilt-stage electron microscopy indicated that they represent trilaminar sheet-like structures distinct from materials seen in various other storage disorders. This study emphasizes that the inclusions in the adrenal and testicular parenchymal cells morphologically differ from those in the brain macrophages. In the latter they occur as membrane-bound discrete structures while in the parenchymal cells they are always seen lying free in the cytoplasm and associated with cleft-like spaces. This morphologic variation of the inclusions is noteworthy and probably reflects a biochemical difference in the storage materials in these two most severely affected organs. In addition, this study demonstrates the presence of linear inclusions within macrophages in otherwise normal-appearing liver, spleen, thymus and also in the renal tubular cells. These findings suggest that the abnormal materials containing very long chain fatty acids enter the blood stream and become sequestered in the reticuloendothelial system and possibly are also excreted in the urine. Detection of these abnormal fatty acids in blood and urine may simplify diagnosis of ALD.

  8. Mitochondrion role in molecular basis of cytoplasmic male sterility. (United States)

    Horn, Renate; Gupta, Kapuganti J; Colombo, Noemi


    Cytoplasmic male sterility and its fertility restoration via nuclear genes offer the possibility to understand the role of mitochondria during microsporogenesis. In most cases rearrangements in the mitochondrial DNA involving known mitochondrial genes as well as unknown sequences result in the creation of new chimeric open reading frames, which encode proteins containing transmembrane domains. So far, most of the CMS systems have been characterized via restriction fragment polymorphisms followed by transcript analysis. However, whole mitochondrial genome sequence analyses comparing male sterile and fertile cytoplasm open options for deeper insights into mitochondrial genome rearrangements. We more and more start to unravel how mitochondria are involved in triggering death of the male reproductive organs. Reduced levels of ATP accompanied by increased concentrations of reactive oxygen species, which are produced more under conditions of mitochondrial dysfunction, seem to play a major role in the fate of pollen production. Nuclear genes, so called restorer-of-fertility are able to restore the male fertility. Fertility restoration can occur via pentatricopeptide repeat (PPR) proteins or via different mechanisms involving non-PPR proteins. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  9. Endogenous Mouse Dicer Is an Exclusively Cytoplasmic Protein.

    Directory of Open Access Journals (Sweden)

    Christian Much


    Full Text Available Dicer is a large multi-domain protein responsible for the ultimate step of microRNA and short-interfering RNA biogenesis. In human and mouse cell lines, Dicer has been shown to be important in the nuclear clearance of dsRNA as well as the establishment of chromatin modifications. Here we set out to unambiguously define the cellular localization of Dicer in mice to understand if this is a conserved feature of mammalian Dicer in vivo. To this end, we utilized an endogenously epitope tagged Dicer knock-in mouse allele. From primary mouse cell lines and adult tissues, we determined with certainty by biochemical fractionation and confocal immunofluorescence microscopy that endogenous Dicer is exclusively cytoplasmic. We ruled out the possibility that a fraction of Dicer shuttles to and from the nucleus as well as that FGF or DNA damage signaling induce Dicer nuclear translocation. We also explored Dicer localization during the dynamic and developmental context of embryogenesis, where Dicer is ubiquitously expressed and strictly cytoplasmic in all three germ layers as well as extraembryonic tissues. Our data exclude a direct role for Dicer in the nuclear RNA processing in the mouse.

  10. Effects of cytoplasmic inheritance on preweaning traits of Hereford cattle

    Directory of Open Access Journals (Sweden)

    Mezzadra Carlos Alberto


    Full Text Available The influence of cytoplasmic inheritance on birth and weaning weight was evaluated in an experimental Hereford herd. Data on 1,720 records for birth and weaning weights from calves born between 1963 and 2002 were studied. Variance components were estimated using MTDFREML procedures and an animal model was fitted for each trait. Direct and maternal additive effects and permanent environment and maternal lineage effects were treated as random, while year and month of birth, age of dam and sex of the calf were treated as fixed. Identification of maternal lineages was based on pedigree information. The contribution to phenotypic variance of cytoplasmic lineages defined by pedigree information was negligible for both traits. Mitochondrial genotypes of cows present in the herd in 2002 were analyzed by single strand conformation polymorphism (SSCP analysis. Only five different genotypes were identified among 23 maternal lineages. All the animals with records were assigned to maternal genotypes based on pedigree information. The statistical analysis was repeated, removing maternal lineage from the model and including mitochondrial genotype as a fixed effect. No evidence of genotype effects was detected. These results suggest a negligible effect of the mitochondrial genome on the preweaning traits of this Hereford herd.

  11. A Balance between Nuclear and Cytoplasmic Volumes Controls Spindle Length (United States)

    Novakova, Lucia; Kovacovicova, Kristina; Dang-Nguyen, Thanh Quang; Sodek, Martin; Skultety, Michal; Anger, Martin


    Proper assembly of the spindle apparatus is crucially important for faithful chromosome segregation during anaphase. Thanks to the effort over the last decades, we have very detailed information about many events leading to spindle assembly and chromosome segregation, however we still do not understand certain aspects, including, for example, spindle length control. When tight regulation of spindle size is lost, chromosome segregation errors emerge. Currently, there are several hypotheses trying to explain the molecular mechanism of spindle length control. The number of kinetochores, activity of molecular rulers, intracellular gradients, cell size, limiting spindle components, and the balance of the spindle forces seem to contribute to spindle size regulation, however some of these mechanisms are likely specific to a particular cell type. In search for a general regulatory mechanism, in our study we focused on the role of cell size and nuclear to cytoplasmic ratio in this process. To this end, we used relatively large cells isolated from 2-cell mouse embryos. Our results showed that the spindle size upper limit is not reached in these cells and suggest that accurate control of spindle length requires balanced ratio between nuclear and cytoplasmic volumes. PMID:26886125

  12. Microfluidics of cytoplasmic streaming and its implications for intracellular transport (United States)

    Goldstein, Raymond E.; Tuval, Idan; van de Meent, Jan-Willem


    Found in many large eukaryotic cells, particularly in plants, cytoplasmic streaming is the circulation of their contents driven by fluid entrainment from particles carried by molecular motors at the cell periphery. In the more than two centuries since its discovery, streaming has frequently been conjectured to aid in transport and mixing of molecular species in the cytoplasm and, by implication, in cellular homeostasis, yet no theoretical analysis has been presented to quantify these processes. We show by a solution to the coupled dynamics of fluid flow and diffusion appropriate to the archetypal “rotational streaming” of algal species such as Chara and Nitella that internal mixing and the transient dynamical response to changing external conditions can indeed be enhanced by streaming, but to an extent that depends strongly on the pitch of the helical flow. The possibility that this may have a developmental consequence is illustrated by the coincidence of the exponential growth phase of Nitella and the point of maximum enhancement of those processes. PMID:18310326

  13. Dynamics and molecular determinants of cytoplasmic lipid droplet clustering and dispersion.

    Directory of Open Access Journals (Sweden)

    David J Orlicky

    Full Text Available Perilipin-1 (Plin1, a prominent cytoplasmic lipid droplet (CLD binding phosphoprotein and key physiological regulator of triglyceride storage and lipolysis in adipocytes, is thought to regulate the fragmentation and dispersion of CLD that occurs in response to β-adrenergic activation of adenylate cyclase. Here we investigate the dynamics and molecular determinants of these processes using cell lines stably expressing recombinant forms of Plin1 and/or other members of the perilipin family. Plin1 and a C-terminal CLD-binding fragment of Plin1 (Plin1CT induced formation of single dense CLD clusters near the microtubule organizing center, whereas neither an N-terminal CLD-binding fragment of Plin1, nor Plin2 or Plin3 induced clustering. Clustered CLD coated by Plin1, or Plin1CT, dispersed in response to isoproterenol, or other agents that activate adenylate cyclase, in a process inhibited by the protein kinase A inhibitor, H89, and blocked by microtubule disruption. Isoproterenol-stimulated phosphorylation of CLD-associated Plin1 on serine 492 preceded their dispersion, and live cell imaging showed that cluster dispersion involved initial fragmentation of tight clusters into multiple smaller clusters, which then fragmented into well-dispersed individual CLD. siRNA knockdown of the cortical actin binding protein, moesin, induced disaggregation of tight clusters into multiple smaller clusters, and inhibited the reaggregation of dispersed CLD into tight clusters. Together these data suggest that the clustering and dispersion processes involve a complex orchestration of phosphorylation-dependent, microtubule-dependent and independent, and microfilament dependent steps.

  14. Frontiers and challenges in warm dense matter

    CERN Document Server

    Desjarlais, Michael; Redmer, Ronald; Trickey, Samuel


    Warm Dense Matter (WDM) occupies a loosely defined region of phase space intermediate between solid, liquid, gas, and plasma, and typically shares characteristics of two or more of these phases. WDM is generally associated with the combination of strongly coupled ions and moderately degenerate electrons, and careful attention to quantum physics and electronic structure is essential. The lack of a small perturbation parameter greatly limits approximate attempts at its accurate description. Since WDM resides at the intersection of solid state and high energy density physics, many high energy density physics (HEDP) experiments pass through this difficult region of phase space. Thus, understanding and modeling WDM is key to the success of experiments on diverse facilities. These include the National Ignition Campaign centered on the National Ignition Facility (NIF), pulsed-power driven experiments on the Z machine, ion-beam-driven WDM experiments on the NDCX-II, and fundamental WDM research at the Linear Coherent...

  15. Superfluid Phase Transitions in Dense Neutron Matter

    Energy Technology Data Exchange (ETDEWEB)

    Khodel, V. A.; Clark, J. W.; Zverev, M. V.


    The phase transitions in a realistic system with triplet pairing, dense neutron matter, have been investigated. The spectrum of phases of the P{sub 2}{sup 3}- F{sub 2}{sup 3} model, which adequately describes pairing in this system, is analytically constructed with the aid of a separation method for solving BCS gap equations in states of arbitrary angular momentum. In addition to solutions involving a single value of the magnetic quantum number (and its negative), there exist ten real multicomponent solutions. Five of the corresponding angle-dependent order parameters have nodes, and five do not. In contrast to the case of superfluid {sup 3}He , transitions occur between phases with nodeless order parameters.

  16. Binary Black Holes from Dense Star Clusters (United States)

    Rodriguez, Carl


    The recent detections of gravitational waves from merging binary black holes have the potential to revolutionize our understanding of compact object astrophysics. But to fully utilize this new window into the universe, we must compare these observations to detailed models of binary black hole formation throughout cosmic time. In this talk, I will review our current understanding of cluster dynamics, describing how binary black holes can be formed through gravitational interactions in dense stellar environments, such as globular clusters and galactic nuclei. I will review the properties and merger rates of binary black holes from the dynamical formation channel. Finally, I will describe how the spins of a binary black hole are determined by its formation history, and how we can use this to discriminate between dynamically-formed binaries and those formed from isolated evolution in galactic fields.

  17. Charmonium propagation through a dense medium

    Directory of Open Access Journals (Sweden)

    Kopeliovich B.Z.


    Full Text Available Attenuation of a colourless c̄c dipole propagating with a large momentum through a hot medium originates from two sources, Debye screening (melting, and inelastic collisions with surrounding scattering centres (absorption. The former never terminates completely production of a bound charmonium in heavy ion collisions, even at very high temperatures. The latter, is controlled my the magnitude of the dipole cross section, related to the transport coefficient, which is the rate of transverse momentum broadening in the medium. A novel procedure of Lorentz boosting of the Schrödinger equation is developed, which allows to calculate the charmonium survival probability employing the path-integral technique, incorporating both melting and absorption. A novel mechanism of charmonium regeneration in a dense medium is proposed.

  18. Properties of industrial dense gas plumes (United States)

    Shaver, E. M.; Forney, L. J.

    Hazardous gases and vapors are often discharged into the atmosphere from industrial plants during catastrophic events (e.g. Union Carbide incident in Bhopal, India). In many cases the discharged components are more dense than air and settle to the ground surface downstream from the stack exit. In the present paper, the buoyant plume model of Hoult, Fay and Forney (1969, J. Air Pollut. Control Ass. 19, 585-590.) has been altered to predict the properties of hazardous discharges. In particular, the plume impingement point, radius and concentration are predicted for typical stack exit conditions, wind speeds and temperature profiles. Asymptotic expressions for plume properties at the impingement point are also derived for a constant crosswind and neutral temperature profile. These formulae are shown to be useful for all conditions.

  19. Anisotropic hydrodynamic function of dense confined colloids (United States)

    Nygârd, Kim; Buitenhuis, Johan; Kagias, Matias; Jefimovs, Konstantins; Zontone, Federico; Chushkin, Yuriy


    Dense colloidal dispersions exhibit complex wave-vector-dependent diffusion, which is controlled by both direct particle interactions and indirect nonadditive hydrodynamic interactions mediated by the solvent. In bulk the hydrodynamic interactions are probed routinely, but in confined geometries their studies have been hitherto hindered by additional complications due to confining walls. Here we solve this issue by combining high-energy x-ray photon correlation spectroscopy and small-angle x-ray-scattering experiments on colloid-filled microfluidic channels to yield the confined fluid's hydrodynamic function in the short-time limit. Most importantly, we find the confined fluid to exhibit a strongly anisotropic hydrodynamic function, similar to its anisotropic structure factor. This observation is important in order to guide future theoretical research.

  20. Classification of mammographic patterns: beyond fraction of dense tissue (United States)

    Judy, Philip F.; Nawfel, Richard; Jacobson, Francine L.; Smith, Darrel N.; Seltzer, Steven E.


    Women with mammograms that radiologists classify as dense have been found to have an increased risk of breast cancer. The purpose to this investigation was to determine whether human readers are willing and able to make reliable comparisons of five attributes of pairs of mammograms matched by a quantitative estimate of the fraction of dense tissue (FDT). Forty pairs of CC projections were digitized and presented using a computer workstation. The 40 pairs of mammograms had the same FDT as measured by a visual threshold procedure. Each breast image was from a different woman. The difference in the following 5 attributes were rated: (1) fraction of dense tissue, (2) fraction of homogeneous of the dense tissue, (3) fraction of ductal dense tissue, (4) prominence of scalloping of dense tissue, and (5) prominence of subareolar structures. The rating were replicated to evaluate their reliability. Spearman rank-order correlations of replicated measurements ranged from 0.89 to 0.65 (p was less than 0.0001). Homogeneous dense tissue ratings were negatively correlated with ductal dense tissue ratings (-0.59, p equals 0.0001). The prominence of scalloping rating was not significantly correlated with other attributes. The ratings of the attributes, except scalloping, were significantly correlated to differences mean gray level of breast parenchyma. Readers can make reliable judgments regarding the differences in attributes of mammograms that are matched by FDT. The negative correlation between the homogeneous dense and the ductal dense tissue ratings suggest that homogeneous dense and ductal dense tissues contend for perceived dense breast area. The absence of correlation between scalloping and other image attributes suggests further investigation of scalloping as an independent, breast-cancer risk factor is warranted.

  1. Embedded binaries and their dense cores (United States)

    Sadavoy, Sarah I.; Stahler, Steven W.


    We explore the relationship between young, embedded binaries and their parent cores, using observations within the Perseus Molecular Cloud. We combine recently published Very Large Array observations of young stars with core properties obtained from Submillimetre Common-User Bolometer Array 2 observations at 850 μm. Most embedded binary systems are found towards the centres of their parent cores, although several systems have components closer to the core edge. Wide binaries, defined as those systems with physical separations greater than 500 au, show a tendency to be aligned with the long axes of their parent cores, whereas tight binaries show no preferred orientation. We test a number of simple, evolutionary models to account for the observed populations of Class 0 and I sources, both single and binary. In the model that best explains the observations, all stars form initially as wide binaries. These binaries either break up into separate stars or else shrink into tighter orbits. Under the assumption that both stars remain embedded following binary break-up, we find a total star formation rate of 168 Myr-1. Alternatively, one star may be ejected from the dense core due to binary break-up. This latter assumption results in a star formation rate of 247 Myr-1. Both production rates are in satisfactory agreement with current estimates from other studies of Perseus. Future observations should be able to distinguish between these two possibilities. If our model continues to provide a good fit to other star-forming regions, then the mass fraction of dense cores that becomes stars is double what is currently believed.

  2. Dense gas dispersion in the atmosphere

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Morten


    Dense gas dispersion is characterized by buoyancy induced gravity currents and reduction of the vertical mixing. Liquefied gas releases from industrial accidents are cold because of the heat of evaporation which determines the density for a given concentration and physical properties. The temperature deficit is moderated by the heat flux from the ground, and this convection is an additional source of turbulence which affects the mixing. A simple model as the soil heat flux is used to estimate the ability of the ground to sustain the heat flux during release. The initial enthalpy, release rate, initial entrainment and momentum are discussed for generic source types and the interaction with obstacles is considered. In the MTH project BA experiments source with and without momentum were applied. The continuously released propane gas passed a two-dimensional removable obstacle perpendicular to the wind direction. Ground-level gas concentrations and vertical profiles of concentration, temperature, wind speed and turbulence were measured in front of and behind the obstacle. Ultrasonic anemometers providing fast velocity and concentration signals were mounted at three levels on the masts. The observed turbulence was influenced by the stability and the initial momentum of the jet releases. Additional information were taken from the `Dessert tortoise` ammonia jet releases, from the `Fladis` experiment with transition from dense to passive dispersion, and from the `Thorney Island` continuous releases of isothermal freon mixtures. The heat flux was found to moderate the negative buoyancy in both the propane and ammonia experiments. The heat flux measurements are compared to an estimate by analogy with surface layer theory. (au) 41 tabs., 146 ills., 189 refs.

  3. Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm (United States)

    Weber, Stephanie C.; Spakowitz, Andrew J.; Theriot, Julie A.


    Tracking of fluorescently labeled chromosomal loci in live bacterial cells reveals a robust scaling of the mean square displacement (MSD) as τ0.39. Brownian dynamics simulations show that this anomalous behavior cannot be fully accounted for by the classic Rouse or reptation models for polymer dynamics. Instead, the observed motion arises from the characteristic relaxation of the Rouse modes of the DNA polymer within the viscoelastic environment of the cytoplasm. To demonstrate these physical effects, we exploit our general analytical solution of the subdiffusive scaling for a monomer in a polymer embedded in a viscoelastic medium. The time-averaged and ensemble-averaged MSD of chromosomal loci exhibit ergodicity, and the velocity autocorrelation function is negative at short time lags. These observations are most consistent with fractional Brownian motion and rule out a continuous time random walk model as an explanation for anomalous motion in vivo. PMID:20867274

  4. Cytoplasmic flows as signatures for the mechanics of mitotic positioning

    CERN Document Server

    Nazockdast, Ehssan; Needleman, Daniel; Shelley, Michael


    The proper positioning of the mitotic spindle is crucial for asymmetric cell division and generating cell diversity during development. Proper position in the single-cell embryo of Caenorhabditis elegans is achieved initially by the migration and rotation of the pronuclear complex (PNC) and its two associated centrosomal arrays of microtubules (MTs). We present here the first systematic theoretical study of how these $O(1000)$ centrosomal microtubules (MTs) interact through the immersing cytoplasm, the cell periphery and PNC, and with each other, to achieve proper position. This study is made possible through our development of a highly efficient and parallelized computational framework that accounts explicitly for long-ranged hydrodynamic interactions (HIs) between the MTs, while also capturing their flexibility, dynamic instability, and interactions with molecular motors and boundaries. First, we show through direct simulation that previous estimates of the PNC drag coefficient, based on either ignoring or ...

  5. [Antineutrophil cytoplasmic antibodies associated with infective endocarditis: Literature review]. (United States)

    Langlois, V; Marie, I


    Antineutrophil cytoplasmic antibodies (ANCA) associated with infective endocarditis are a rare disorder. The condition can mimic primary systemic vasculitis (i.e. granulomatosis with polyangiitis, microscopic polyangiitis, and eosinophilic granulomatosis with polyangiitis). Thus, a wrong diagnosis of valvular involvement related to primary systemic vasculitis can be made in patients exhibiting ANCA associated with infective endocarditis. Because treatment of both conditions is different, this wrong diagnosis will lead to dramatic consequences in these latter patients. This review reports the state of knowledge and proposes an algorithm to follow when confronted to a possible case of ANCA associated with infective endocarditis. Copyright © 2016 Société Nationale Française de Médecine Interne (SNFMI). Published by Elsevier SAS. All rights reserved.

  6. Rearrangements of sea urchin egg cytoplasmic membrane domains at fertilization. (United States)

    Collas, P; Barona, T; Poccia, D L


    Fertilization in the sea urchin is accompanied by rapid reorganization of the egg endoplasmic reticulum (ER). ER-derived vesicles contribute to one of three classes of membranes used in assembling the male pronuclear envelope in vitro. We provide here biochemical evidence for the rearrangement of sea urchin egg cytoplasmic membrane domains at fertilization up to the first mitosis, with respect to two nuclear envelope markers, lamin B and lamin B receptor (LBR), using purified vesicles prepared from homogenates fractionated by floatation on sucrose gradients. In unfertilized eggs, immunoprecipitation data indicate that most of lamin B and LBR are localized in the same vesicles but do not interact. By 3 min post-fertilization, both proteins are more widely distributed across the gradients and by 12 min most of lamin B and LBR are localized in vesicles of different densities. This partitioning is maintained throughout S phase. At mitosis, most lamin B and LBR remain in distinct vesicles, while a small proportion of lamin B and LBR, likely derived from the disassembled nuclear envelope, associate in a minor subset of vesicles. The results illustrate a dynamic reorganization of egg cytoplasmic membranes at fertilization, and the establishment of distinct membrane domains enriched in specific nuclear envelope markers during the first cell cycle of sea urchin development. Additionally, we demonstrate that male pro-nuclear membrane assembly occurs only when both cytosol and membranes originate from fertilized but not unfertilized eggs, suggesting that fertilization-induced membrane rearrangements contribute to the ability of the egg to assemble the male pronuclear envelope.

  7. Experimental analysis of dense multipath components in an industrial environment


    Tanghe, Emmeric; Gaillot, Davy P.; Liénard, Martine; Martens, Luc; Joseph, Wout


    This work presents an analysis of dense multipath components (DMC) in an industrial workshop. Radio channel sounding was performed with a vector network analyzer and virtual antenna arrays. The specular and dense multipath components were estimated with the RiMAX algorithm. The DMC covariance structure of the RiMAX data model was validated. Two DMC parameters were studied: the distribution of radio channel power between specular and dense multipath, and the DMC reverberation time. The DMC pow...

  8. Breast cancer screening in Korean woman with dense breast tissue

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Hee Jung [Dept. of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of); Ko, Eun Sook [Dept. of Radiology, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul (Korea, Republic of); Yi, Ann [Dept. of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul (Korea, Republic of)


    Asian women, including Korean, have a relatively higher incidence of dense breast tissue, compared with western women. Dense breast tissue has a lower sensitivity for the detection of breast cancer and a higher relative risk for breast cancer, compared with fatty breast tissue. Thus, there were limitations in the mammographic screening for women with dense breast tissue, and many studies for the supplemental screening methods. This review included appropriate screening methods for Korean women with dense breasts. We also reviewed the application and limitation of supplemental screening methods, including breast ultrasound, digital breast tomosynthesis, and breast magnetic resonance imaging; and furthermore investigated the guidelines, as well as the study results.

  9. Changes in chloroplastic and cytoplasmic ribosomal protein after GA3-treatment of Zea mays leaves

    Directory of Open Access Journals (Sweden)

    P. Masłowski


    Full Text Available Protein was isolated from chioroplastic and cytoplasmic ribosomes of 14-day-old maize leaves subjected to the action of gibberellic acid. The proteins were separated electrophoretically on polyacrylamide gel. Fourteen fractions of ribosomal protein were obtained exhibiting wide electrophoretic differences. Qualitative differences were found between the chloroplastic and cytoplasmic ribosomes. Gibberellic acid caused the appearance of an additional protein Traction in cytoplasmic ribosomes. It did not, however, affect the qualitative composition of ribosome proteins from chloroplasts.

  10. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes


    Lee, Ji-Ann; Damianov, Andrey; Lin, Chia-Ho; Fontes, Mariana; Parikshak, Neelroop N.; Anderson, Erik S.; Geschwind, Daniel H.; Black, Douglas L.; Martin, Kelsey C.


    Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytop...

  11. Dense colloidal fluids form denser amorphous sediments. (United States)

    Liber, Shir R; Borohovich, Shai; Butenko, Alexander V; Schofield, Andrew B; Sloutskin, Eli


    We relate, by simple analytical centrifugation experiments, the density of colloidal fluids with the nature of their randomly packed solid sediments. We demonstrate that the most dilute fluids of colloidal hard spheres form loosely packed sediments, where the volume fraction of the particles approaches in frictional systems the random loose packing limit, ϕRLP = 0.55. The dense fluids of the same spheres form denser sediments, approaching the so-called random close packing limit, ϕRCP = 0.64. Our experiments, where particle sedimentation in a centrifuge is sufficiently rapid to avoid crystallization, demonstrate that the density of the sediments varies monotonically with the volume fraction of the initial suspension. We reproduce our experimental data by simple computer simulations, where structural reorganizations are prohibited, such that the rate of sedimentation is irrelevant. This suggests that in colloidal systems, where viscous forces dominate, the structure of randomly close-packed and randomly loose-packed sediments is determined by the well-known structure of the initial fluids of simple hard spheres, provided that the crystallization is fully suppressed.

  12. Thermochemistry of dense hydrous magnesium silicates (United States)

    Bose, Kunal; Burnley, Pamela; Navrotsky, Alexandra


    Recent experimental investigations under mantle conditions have identified a suite of dense hydrous magnesium silicate (DHMS) phases that could be conduits to transport water to at least the 660 km discontinuity via mature, relatively cold, subducting slabs. Water released from successive dehydration of these phases during subduction could be responsible for deep focus earthquakes, mantle metasomatism and a host of other physico-chemical processes central to our understanding of the earth's deep interior. In order to construct a thermodynamic data base that can delineate and predict the stability ranges for DHMS phases, reliable thermochemical and thermophysical data are required. One of the major obstacles in calorimetric studies of phases synthesized under high pressure conditions has been limitation due to the small (less than 5 mg) sample mass. Our refinement of calorimeter techniques now allow precise determination of enthalpies of solution of less than 5 mg samples of hydrous magnesium silicates. For example, high temperature solution calorimetry of natural talc (Mg(0.99) Fe(0.01)Si4O10(OH)2), periclase (MgO) and quartz (SiO2) yield enthalpies of drop solution at 1044 K to be 592.2 (2.2), 52.01 (0.12) and 45.76 (0.4) kJ/mol respectively. The corresponding enthalpy of formation from oxides at 298 K for talc is minus 5908.2 kJ/mol agreeing within 0.1 percent to literature values.

  13. Improved models of dense anharmonic lattices

    Energy Technology Data Exchange (ETDEWEB)

    Rosenau, P., E-mail:; Zilburg, A.


    We present two improved quasi-continuous models of dense, strictly anharmonic chains. The direct expansion which includes the leading effect due to lattice dispersion, results in a Boussinesq-type PDE with a compacton as its basic solitary mode. Without increasing its complexity we improve the model by including additional terms in the expanded interparticle potential with the resulting compacton having a milder singularity at its edges. A particular care is applied to the Hertz potential due to its non-analyticity. Since, however, the PDEs of both the basic and the improved model are ill posed, they are unsuitable for a study of chains dynamics. Using the bond length as a state variable we manipulate its dispersion and derive a well posed fourth order PDE. - Highlights: • An improved PDE model of a Newtonian lattice renders compacton solutions. • Compactons are classical solutions of the improved model and hence amenable to standard analysis. • An alternative well posed model enables to study head on interactions of lattices' solitary waves. • Well posed modeling of Hertz potential.

  14. Order and instabilities in dense bacterial colonies (United States)

    Tsimring, Lev


    The structure of cell colonies is governed by the interplay of many physical and biological factors, ranging from properties of surrounding media to cell-cell communication and gene expression in individual cells. The biomechanical interactions arising from the growth and division of individual cells in confined environments are ubiquitous, yet little work has focused on this fundamental aspect of colony formation. By combining experimental observations of growing monolayers of non-motile strain of bacteria Escherichia coli in a shallow microfluidic chemostat with discrete-element simulations and continuous theory, we demonstrate that expansion of a dense colony leads to rapid orientational alignment of rod-like cells. However, in larger colonies, anisotropic compression may lead to buckling instability which breaks perfect nematic order. Furthermore, we found that in shallow cavities feedback between cell growth and mobility in a confined environment leads to a novel cell streaming instability. Joint work with W. Mather, D. Volfson, O. Mondrag'on-Palomino, T. Danino, S. Cookson, and J. Hasty (UCSD) and D. Boyer, S. Orozco-Fuentes (UNAM, Mexico).

  15. Elemental nitrogen partitioning in dense interstellar clouds. (United States)

    Daranlot, Julien; Hincelin, Ugo; Bergeat, Astrid; Costes, Michel; Loison, Jean-Christophe; Wakelam, Valentine; Hickson, Kevin M


    Many chemical models of dense interstellar clouds predict that the majority of gas-phase elemental nitrogen should be present as N(2), with an abundance approximately five orders of magnitude less than that of hydrogen. As a homonuclear diatomic molecule, N(2) is difficult to detect spectroscopically through infrared or millimeter-wavelength transitions. Therefore, its abundance is often inferred indirectly through its reaction product N(2)H(+). Two main formation mechanisms, each involving two radical-radical reactions, are the source of N(2) in such environments. Here we report measurements of the low temperature rate constants for one of these processes, the N + CN reaction, down to 56 K. The measured rate constants for this reaction, and those recently determined for two other reactions implicated in N(2) formation, are tested using a gas-grain model employing a critically evaluated chemical network. We show that the amount of interstellar nitrogen present as N(2) depends on the competition between its gas-phase formation and the depletion of atomic nitrogen onto grains. As the reactions controlling N(2) formation are inefficient, we argue that N(2) does not represent the main reservoir species for interstellar nitrogen. Instead, elevated abundances of more labile forms of nitrogen such as NH(3) should be present on interstellar ices, promoting the eventual formation of nitrogen-bearing organic molecules.

  16. Load Designs For MJ Dense Plasma Foci (United States)

    Link, A.; Povlius, A.; Anaya, R.; Anderson, M. G.; Angus, J. R.; Cooper, C. M.; Falabella, S.; Goerz, D.; Higginson, D.; Holod, I.; McMahon, M.; Mitrani, J.; Koh, E. S.; Pearson, A.; Podpaly, Y. A.; Prasad, R.; van Lue, D.; Watson, J.; Schmidt, A. E.


    Dense plasma focus (DPF) Z-pinches are compact pulse power driven devices with coaxial electrodes. The discharge of DPF consists of three distinct phases: first generation of a plasma sheath, plasma rail gun phase where the sheath is accelerated down the electrodes and finally an implosion phase where the plasma stagnates into a z-pinch geometry. During the z-pinch phase, DPFs can produce MeV ion beams, x-rays and neutrons. Megaampere class DPFs with deuterium fills have demonstrated neutron yields in the 1012 neutrons/shot range with pulse durations of 10-100 ns. Kinetic simulations using the code Chicago are being used to evaluate various load configurations from initial sheath formation to the final z-pinch phase for DPFs with up to 5 MA and 1 MJ coupled to the load. Results will be presented from the preliminary design simulations. LLNL-ABS-734785 This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 and with support from the Computing Grand Challenge program at LLNL.

  17. Kinetic Simulations of Dense Plasma Focus Breakdown (United States)

    Schmidt, A.; Higginson, D. P.; Jiang, S.; Link, A.; Povilus, A.; Sears, J.; Bennett, N.; Rose, D. V.; Welch, D. R.


    A dense plasma focus (DPF) device is a type of plasma gun that drives current through a set of coaxial electrodes to assemble gas inside the device and then implode that gas on axis to form a Z-pinch. This implosion drives hydrodynamic and kinetic instabilities that generate strong electric fields, which produces a short intense pulse of x-rays, high-energy (>100 keV) electrons and ions, and (in deuterium gas) neutrons. A strong factor in pinch performance is the initial breakdown and ionization of the gas along the insulator surface separating the two electrodes. The smoothness and isotropy of this ionized sheath are imprinted on the current sheath that travels along the electrodes, thus making it an important portion of the DPF to both understand and optimize. Here we use kinetic simulations in the Particle-in-cell code LSP to model the breakdown. Simulations are initiated with neutral gas and the breakdown modeled self-consistently as driven by a charged capacitor system. We also investigate novel geometries for the insulator and electrodes to attempt to control the electric field profile. The initial ionization fraction of gas is explored computationally to gauge possible advantages of pre-ionization which could be created experimentally via lasers or a glow-discharge. Prepared by LLNL under Contract DE-AC52-07NA27344.

  18. Casimir Friction between Dense Polarizable Media

    Directory of Open Access Journals (Sweden)

    Johan S. Høye


    Full Text Available The present paper—a continuation of our recent series of papers on Casimir friction for a pair of particles at low relative particle velocity—extends the analysis, so as to include dense media. The situation becomes, in this case, more complex, due to induced dipolar correlations, both within planes and between planes. We show that the structure of the problem can be simplified by regarding the two half-planes as a generalized version of a pair of particles. It turns out that macroscopic parameters, such as permittivity, suffice to describe the friction, also in the finite density case. The expression for the friction force per unit surface area becomes mathematically well-defined and finite at finite temperature. We give numerical estimates and compare them with those obtained earlier by Pendry (1997 and by Volokitin and Persson (2007. We also show in an appendix how the statistical methods that we are using correspond to the field theoretical methods more commonly in use.

  19. Matching Cost Filtering for Dense Stereo Correspondence

    Directory of Open Access Journals (Sweden)

    Yimin Lin


    Full Text Available Dense stereo correspondence enabling reconstruction of depth information in a scene is of great importance in the field of computer vision. Recently, some local solutions based on matching cost filtering with an edge-preserving filter have been proved to be capable of achieving more accuracy than global approaches. Unfortunately, the computational complexity of these algorithms is quadratically related to the window size used to aggregate the matching costs. The recent trend has been to pursue higher accuracy with greater efficiency in execution. Therefore, this paper proposes a new cost-aggregation module to compute the matching responses for all the image pixels at a set of sampling points generated by a hierarchical clustering algorithm. The complexity of this implementation is linear both in the number of image pixels and the number of clusters. Experimental results demonstrate that the proposed algorithm outperforms state-of-the-art local methods in terms of both accuracy and speed. Moreover, performance tests indicate that parameters such as the height of the hierarchical binary tree and the spatial and range standard deviations have a significant influence on time consumption and the accuracy of disparity maps.

  20. Dense chlorinated solvents and other DNAPLs in groundwater

    DEFF Research Database (Denmark)

    Broholm, K.


    Anmeldelse af Pankow,J.F. & Cherry,J.A.: Dense chlorinated solvents and other DNAPLs in groundwater. Waterloo Press, Portland, Oregon, USA, 1996......Anmeldelse af Pankow,J.F. & Cherry,J.A.: Dense chlorinated solvents and other DNAPLs in groundwater. Waterloo Press, Portland, Oregon, USA, 1996...

  1. Finding dense locations in symbolic indoor tracking data

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua


    Finding the dense locations in large indoor spaces is very useful for many applications such as overloaded area detection, security control, crowd management, indoor navigation, and so on. Indoor tracking data can be enormous and are not immediately ready for finding dense locations. This paper p...

  2. Dense fibrillar collagen is a master activator of invadopodia


    Artym, Vira V.


    Tumor stroma is characterized by abnormal accumulation of dense fibrillar collagen, which promotes tumor progression and metastasis. However, the effect of desmoplastic collagen on cells has been unclear. Our recent findings demonstrate that dense fibrillar collagen activates a novel phosphosignaling mechanism for robust induction of invadopodia in tumor cells and normal fibroblasts.

  3. Dense fibrillar collagen is a master activator of invadopodia. (United States)

    Artym, Vira V


    Tumor stroma is characterized by abnormal accumulation of dense fibrillar collagen, which promotes tumor progression and metastasis. However, the effect of desmoplastic collagen on cells has been unclear. Our recent findings demonstrate that dense fibrillar collagen activates a novel phosphosignaling mechanism for robust induction of invadopodia in tumor cells and normal fibroblasts.

  4. Dry processing versus dense medium processing for preparing thermal coal

    CSIR Research Space (South Africa)

    De Korte, GJ


    Full Text Available of the final product. The separation efficiency of dry processes is, however, not nearly as good as that of dense medium and, as a result, it is difficult to effectively beneficiate coals with a high near-dense content. The product yield obtained from some raw...

  5. Effects of alien and intraspecies cytoplasms on manifestation of nuclear genes for wheat resistance to brown rust: II. Specificity of cytoplasm influence on different Lr genes

    Energy Technology Data Exchange (ETDEWEB)

    Voluevich, E.A.; Buloichik, A.A.; Palilova, A.N. [Institute of Genetics and Cytology, Minsk (Belarus)


    Specificity of expression of the major nuclear genes Lr to two brown rust clones in hybrids with the same maternal cytoplasm was analyzed. It was evaluated by a resistant: susceptible ratio in the F{sub 2}. Reciprocal hybrids were obtained from the cross between the progeny of homozygous susceptible plants of the cultivar Penjamo 62 and its alloplasmatic lines carrying cytoplasms of Triticum dicoccoides var. fulvovillosum, Aegilops squarrosa var. typical, Agropyron trichophorum, and isogenic lines of the cultivar Thatcher (Th) with the Lr1, Lr9, Lr15, and Lr19 genes. It was shown that the effect of the Lr1 gene in the cytoplasm of cultivar Thatcher and in eu-, and alloplasmatic forms of Penjamo 62 was less expressed than that of other Lr genes. Cytoplasm of the alloplasmatic line (dicoccoides)-Penjamo 62 was the only exception: in the F{sub 2}, hybrids with Th (Lr1) had a higher yield of resistant forms than those with Th (Lr15). In the hybrid combinations studied, expression and/or transmission of the Lr19 gene was more significant than that of other genes. This gene had no advantages over Lr15 and Lr19 only in cytoplasm of the alloplasmatic line (squarrosa)-Penjamo 62. In certain hybrid cytoplasms, the display of the Lr1, Lr15, and Lr19 genes, in contrast to Lr9, varied with the virulence of the pathogen clones. 15 refs., 5 tabs.

  6. Does a parthenogenesis-inducing Wolbachia induce vestigial cytoplasmic incompatibility? (United States)

    Kraaijeveld, Ken; Reumer, Barbara M.; Mouton, Laurence; Kremer, Natacha; Vavre, Fabrice; van Alphen, Jacques J. M.


    Wolbachia is a maternally inherited bacterium that manipulates the reproduction of its host. Recent studies have shown that male-killing strains can induce cytoplasmic incompatibility (CI) when introgressed into a resistant host. Phylogenetic studies suggest that transitions between CI and other Wolbachia phenotypes have also occurred frequently, raising the possibility that latent CI may be widespread among Wolbachia. Here, we investigate whether a parthenogenesis-inducing Wolbachia strain can also induce CI. Parthenogenetic females of the parasitoid wasp Asobara japonica regularly produce a small number of males that may be either infected or not. Uninfected males were further obtained through removal of the Wolbachia using antibiotics and from a naturally uninfected strain. Uninfected females that had mated with infected males produced a slightly, but significantly more male-biased sex ratio than uninfected females that had mated with uninfected males. This effect was strongest in females that mated with males that had a relatively high Wolbachia titer. Quantitative PCR indicated that infected males did not show higher ratios of nuclear versus mitochondrial DNA content. Wolbachia therefore does not cause diploidization of cells in infected males. While these results are consistent with CI, other alternatives such as production of abnormal sperm by infected males cannot be completely ruled out. Overall, the effect was very small (9%), suggesting that if CI is involved it may have degenerated through the accumulation of mutations.

  7. Cytoplasmic lipid bodies in eosinophils: Central roles in eicosanoid generation

    Directory of Open Access Journals (Sweden)

    Peter F Weller


    Full Text Available Lipid bodies are non-membrane bound, lipid-rich cytoplasmic inclusions that form in diverse cell types. Characteristically, lipid body numbers increase when eosinophils and other leukocytes are participating in inflammatory processes. Moreover, lipid bodies are numerous in other sites active in eicosanoid formation, such as the amnion epithelium at parturition. Our interests in lipid bodies relate to the roles that these structures play in arachidonate metabolism by eosinophils and other leukocytes involved in inflammation. Findings indicate that lipid bodies in these leukocytes can function as intracellular domains that are both depots of esterified arachidonate and sites at which regulated enzymatic events relevant to arachidonate metabolism can occur. Lipid bodies are discrete intracellular structures whose formation is specifically inducible early, whose increased numbers correlate with the 'priming' responses of leukocytes to form enhanced amounts of both cyclooxygenase- and lipoxygenase-derived eicosanoids and whose inhibition of formation correlates with reduced synthesis of these eicosanoids. Inhibition of lipid body formation represents a novel pharmacologic target to block the formation of eicosanoid mediators of inflammation.

  8. Novel clinical and diagnostic aspects of antineutrophil cytoplasmic antibodies. (United States)

    Schulte-Pelkum, Johannes; Radice, Antonella; Norman, Gary L; Lόpez Hoyos, Marcos; Lakos, Gabriella; Buchner, Carol; Musset, Lucile; Miyara, Makoto; Stinton, Laura; Mahler, Michael


    Antineutrophil cytoplasmic antibodies (ANCA) are the serological hallmark of some idiopathic systemic vasculitides. Besides the investigation of ANCA-associated vasculitis (AAV) and constant effort for a standardized nomenclature and classification of the AAV, a main focus of research during the last few years has been to constantly improve the performance of enzyme immunoassays. With the latest so called third generation ELISA, this goal seemed to be fulfilled. The International Consensus Statement on Testing and Reporting of ANCA gave recommendations for standardized strategies for the serological diagnosis of ANCA. New developments now target the system immanent drawbacks of the respective diagnostic methods, be it the need for batching and the long time to result for ELISA, or the high likelihood of error and subjectivity of indirect immunofluorescence (IIF). Random access technology and multiplexing for solid phase assays as well as digital imaging for IIF are tools which may help to expedite and simplify routine diagnostics in the lab and in emergency settings. Recent findings indicate that PR3-ANCA have clinical utility beyond the diagnosis of AAV. PR3-ANCA can also serve as an aid for the differentiation between ulcerative colitis (UC) and Crohn's disease (CrD) and the stratification of UC patients. This review provides a detailed review of what is known about ANCA and highlights the latest research and state-of-the-art developments in this area.

  9. Bacterial conjugation in the cytoplasm of mouse cells. (United States)

    Lim, Yin Mei; de Groof, Ad J C; Bhattacharjee, Mrinal K; Figurski, David H; Schon, Eric A


    Intracellular pathogenic organisms such as salmonellae and shigellae are able to evade the effects of many antibiotics because the drugs are not able to penetrate the plasma membrane. In addition, these bacteria may be able to transfer genes within cells while protected from the action of drugs. The primary mode by which virulence and antibiotic resistance genes are spread is bacterial conjugation. Salmonellae have been shown to be competent for conjugation in the vacuoles of cultured mammalian cells. We now show that the conjugation machinery is also functional in the mammalian cytosol. Specially constructed Escherichia coli strains expressing Shigella flexneri plasmid and chromosomal virulence factors for escape from vacuoles and synthesizing the invasin protein from Yersinia pseudotuberculosis to enhance cellular entry were able to enter 3T3 cells and escape from the phagocytic vacuole. One bacterial strain (the donor) of each pair to be introduced sequentially into mammalian cells had a conjugative plasmid. We found that this plasmid could be transferred at high frequency. Conjugation in the cytoplasm of cells may well be a general phenomenon.

  10. Anti-neutrophil cytoplasmic antibodies stimulate release of neutrophil microparticles.

    LENUS (Irish Health Repository)

    Hong, Ying


    The mechanisms by which anti-neutrophil cytoplasmic antibodies (ANCAs) may contribute to the pathogenesis of ANCA-associated vasculitis are not well understood. In this study, both polyclonal ANCAs isolated from patients and chimeric proteinase 3-ANCA induced the release of neutrophil microparticles from primed neutrophils. These microparticles expressed a variety of markers, including the ANCA autoantigens proteinase 3 and myeloperoxidase. They bound endothelial cells via a CD18-mediated mechanism and induced an increase in endothelial intercellular adhesion molecule-1 expression, production of endothelial reactive oxygen species, and release of endothelial IL-6 and IL-8. Removal of the neutrophil microparticles by filtration or inhibition of reactive oxygen species production with antioxidants abolished microparticle-mediated endothelial activation. In addition, these microparticles promoted the generation of thrombin. In vivo, we detected more neutrophil microparticles in the plasma of children with ANCA-associated vasculitis compared with that in healthy controls or those with inactive vasculitis. Taken together, these results support a role for neutrophil microparticles in the pathogenesis of ANCA-associated vasculitis, potentially providing a target for future therapeutics.

  11. Sexy sons: a dead end for cytoplasmic genes. (United States)

    Zeh, Jeanne A


    Critics of sexual conflict theory argue that females may gain a net reproductive benefit from mating with manipulative males because the direct costs that they suffer may be offset by the production of sexy, i.e. manipulative, sons. However, this exclusive focus on nuclear gene effects represents an incomplete view of female fitness. Females differ fundamentally from males in transmitting not only nuclear genes but also a wide range of cytoplasmic genetic elements (CGEs) that can have profound effects, from male killing to influencing development of the nervous system and cognitive ability. Maternal transmission of CGEs has two major implications for sexual selection. First, the evolution of male fitness traits, such as sperm competitive ability, may be constrained because response to selection on mitochondrial genomes can occur only through the female line. Second, CGEs bear the direct costs of male manipulation but gain no indirect benefits when females produce sexy sons. This should result in perpetual antagonistic coevolution between nuclear genes involved in male manipulation and CGEs that promote female resistance to male sexually selected traits. Explicit consideration of the consequences of selection acting on CGEs is therefore necessary for a better understanding of the relationship between sexual selection and sexual conflict.

  12. Cardinium symbionts cause cytoplasmic incompatibility in spider mites. (United States)

    Gotoh, T; Noda, H; Ito, S


    Intracellular symbiotic bacteria belonging to the Cytophaga-Flavobacterium-Bacteroides lineage have recently been described and are widely distributed in arthropod species. The newly discovered bacteria, named Cardinium sp, cause the expression of various reproductive alterations in their arthropod hosts, including cytoplasmic incompatibility (CI), induction of parthenogenesis and feminization of genetic males. We detected 16S ribosomal DNA sequences similar to those of Cardinium from seven populations of five spider mite species, suggesting a broad distribution of infection of Cardinium in spider mites. To clarify the effect of Cardinium on the reproductive traits of the infected spider mites, infected mites were crossed with uninfected mites for each population. In one of the populations, Eotetranychus suginamensis, CI was induced when infected males were crossed with uninfected females. The other six populations of four species showed no reproductive abnormalities in the F(1) generation, but the possibility of CI effects in the F(2) generation remains to be tested. One species of spider mite, Tetranychus pueraricola, harbored both Cardinium and Wolbachia, but these symbionts seemed to have no effect on the reproduction of the host, even when the host was infected independently with each symbiont.

  13. Eculizumab in Pediatric Dense Deposit Disease. (United States)

    Oosterveld, Michiel J S; Garrelfs, Mark R; Hoppe, Bernd; Florquin, Sandrine; Roelofs, Joris J T H; van den Heuvel, L P; Amann, Kerstin; Davin, Jean-Claude; Bouts, Antonia H M; Schriemer, Pietrik J; Groothoff, Jaap W


    Dense deposit disease (DDD), a subtype of C3 glomerulopathy, is a rare disease affecting mostly children. Treatment options are limited. Debate exists whether eculizumab, a monoclonal antibody against complement factor C5, is effective in DDD. Reported data are scarce, especially in children. The authors analyzed clinical and histologic data of five pediatric patients with a native kidney biopsy diagnosis of DDD. Patients received eculizumab as therapy of last resort for severe nephritic or nephrotic syndrome with alternative pathway complement activation; this therapy was given only when the patients had not or only marginally responded to immunosuppressive therapy. Outcome measures were kidney function, proteinuria, and urine analysis. In all, seven disease episodes were treated with eculizumab (six episodes of severe nephritic syndrome [two of which required dialysis] and one nephrotic syndrome episode). Median age at treatment start was 8.4 (range, 5.9-13) years. For three treatment episodes, eculizumab was the sole immunosuppressive treatment. In all patients, both proteinuria and renal function improved significantly within 12 weeks of treatment (median urinary protein-to-creatinine ratio of 8.5 [range, 2.2-17] versus 1.1 [range, 0.2-2.0] g/g, P<0.005, and eGFR of 58 [range, 17-114] versus 77 [range, 50-129] ml/min per 1.73 m(2), P<0.01). A striking finding was the disappearance of leukocyturia within 1 week after the first eculizumab dose in all five episodes with leukocyturia at treatment initiation. In this case series of pediatric patients with DDD, eculizumab treatment was associated with reduction in proteinuria and increase in eGFR. Leukocyturia resolved within 1 week of initiation of eculizumab treatment. These results underscore the need for a randomized trial of eculizumab in DDD. Copyright © 2015 by the American Society of Nephrology.

  14. FttC-Based Fronthaul for 5G Dense/Ultra-Dense Access Network: Performance and Costs in Realistic Scenarios

    Directory of Open Access Journals (Sweden)

    Franco Mazzenga


    Full Text Available One distinctive feature of the next 5G systems is the presence of a dense/ultra-dense wireless access network with a large number of access points (or nodes at short distances from each other. Dense/ultra-dense access networks allow for providing very high transmission capacity to terminals. However, the deployment of dense/ultra-dense networks is slowed down by the cost of the fiber-based infrastructure required to connect radio nodes to the central processing units and then to the core network. In this paper, we investigate the possibility for existing FttC access networks to provide fronthaul capabilities for dense/ultra-dense 5G wireless networks. The analysis is realistic in that it is carried out considering an actual access network scenario, i.e., the Italian FttC deployment. It is assumed that access nodes are connected to the Cabinets and to the corresponding distributors by a number of copper pairs. Different types of cities grouped in terms of population have been considered. Results focus on fronthaul transport capacity provided by the FttC network and have been expressed in terms of the available fronthaul bit rate per node and of the achievable coverage.

  15. Human anti-neutrophil cytoplasm autoantibodies to proteinase 3 (PR3-ANCA) bind to neutrophils

    NARCIS (Netherlands)

    Van Rossum, AP; van der Geld, YM; Limburg, PC; Kallenberg, CGM

    Human anti-neutrophil cytoplasm autoantibodies to proteinase 3 (PR3-ANCA) bind to neutrophils. Background. Recently, the in vivo pathogenic role of anti-neutrophil cytoplasm autoantibodies (ANCA) in ANCA-associated vasculitis has been challenged by Abdel-Salam et al. In their report, they observed

  16. Sequential closure of the cytoplasm and then the periplasm during cell division in Escherichia coli. (United States)

    Skoog, Karl; Söderström, Bill; Widengren, Jerker; von Heijne, Gunnar; Daley, Daniel O


    To visualize the latter stages of cell division in live Escherichia coli, we have carried out fluorescence recovery after photobleaching (FRAP) on 121 cells expressing cytoplasmic green fluorescent protein and periplasmic mCherry. Our data show conclusively that the cytoplasm is sealed prior to the periplasm during the division event.

  17. Anti-neutrophil cytoplasm autoantibodies (ANCA). The need for specific and sensitive assays

    DEFF Research Database (Denmark)

    Baslund, B; Petersen, J


    Anti-neutrophil cytoplasm antibodies (ANCA) are a group of autoantibodies primarily associated with systemic vasculitis. Hitherto, the method of choice for ANCA detection has been indirect immunofluorescence (IIF). By this method two major patterns can be seen: a cytoplasmic pattern (cANCA) or a ...... to use assays with these highly purified antigens instead of an unspecific method like IIF....

  18. High viscosity and anisotropy characterize the cytoplasm of fungal dormant stress-resistant spores

    NARCIS (Netherlands)

    Dijksterhuis, J; Nijsse, J; Hoekstra, F A; Golovina, E A

    Ascospores of the fungus Talaromyces macrosporus are dormant and extremely stress resistant, whereas fungal conidia--the main airborne vehicles of distribution--are not. Here, physical parameters of the cytoplasm of these types of spores were compared. Cytoplasmic viscosity and level of anisotropy

  19. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. (United States)

    Lee, Ji-Ann; Damianov, Andrey; Lin, Chia-Ho; Fontes, Mariana; Parikshak, Neelroop N; Anderson, Erik S; Geschwind, Daniel H; Black, Douglas L; Martin, Kelsey C


    Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that Rbfox1 bound predominantly to introns in nascent RNA, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and Rbfox1 and miRNA binding sites overlapped significantly. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

    DEFF Research Database (Denmark)

    Joseph, Bindu; Corwin, Jason A.; Li, Baohua


    affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation...... was a central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation......Understanding genome to phenotype linkages has been greatly enabled by genomic sequencing. However, most genome analysis is typically confined to the nuclear genome. We conducted a metabolomic QTL analysis on a reciprocal RIL population structured to examine how variation in the organelle genomes...

  1. Flow microfluorometric and light-scatter measurement of nuclear and cytoplasmic size in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Steinkamp, J.A.; Hansen, K.M.; Crissman, H.A.


    A technique for rapid measurement of nuclear and cytoplasmic size relationships in mammalian cell populations has been developed. Based on fluorescence staining of either the nucleus alone or in combination with the cytoplasm using two-color fluorescence methods, this technique permits the simultaneous determination of nuclear and cytoplasmic diameters from fluorescence and light-scatter measurements. Cells stained in liquid suspension pass through a flow chamber at a constant velocity, intersecting a laser beam which excites cell fluorescence and causes light scatter. Depending upon which analysis procedure is used, optical sensors measure nuclear fluorescence and light scatter (whole cell size) or two-color nuclear and cytoplasmic fluorescence from individual cells crossing the laser beam. The time durations of signals generated by the nucleus and cytoplasm are converted electronically into signals proportional to the respective diameters and are displayed as frequency distribution histograms. Illustrative examples of measurements on uniform microspheres, cultured mammalian cells and human exfoliated gynecologic cells are presented.

  2. [Wegener's granulomatosis with anti-neutrophil cytoplasmic antibodies against anti-cathepsin G antigen]. (United States)

    Ocaña Pérez, E; Peña Casas, A M; del Campo Muñoz, T; Avila Casas, A; Luque Barona, R


    Wegener's granulomatosis belongs to the group of small vessel vasculitis associated with anti-neutrophil cytoplasmic antibodies characterized by granulomatous inflammation and necrotising vasculitis in various organs with particular involvement of the upper and lower respiratory tracts and kidneys. Wegener's granulomatosis is a rare disorder in childhood and early diagnosis of this disease is critical to the long-term prognosis of the disease. The presence of positive cytoplasmic antineutrophil cytoplasmic antibody staining or a high titre of proteinase 3 antibodies were added as new criteria of vasculitis in childhood. This article presents a case of Wegener's granulomatosis, with the presence of anti-neutrophil cytoplasm antibodies with cytoplasmic pattern with absence of anti-proteinase 3 antibodies and presence of high levels of anti-cathepsin G antibodies, rarely described in Wegener's granulomatosis. Copyright © 2012 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

  3. Regulation of Cytoplasmic and Vacuolar Volumes by Plant Cells in Suspension Culture

    DEFF Research Database (Denmark)

    Owens, Trevor; Poole, Ronald J


    Quantitative microscopical measurements have been made of the proportion of cell volume occupied by cytoplasm in a cell suspension culture derived from cotyledons of bush bean (cv. Contender). On a 7-day culture cycle, the content of cytoplasm varies from 25% at the time of transfer to 45......% at the start of the phase of rapid cell division. If the culture is continued beyond 7 days, the vacuole volume reaches 90% of cell volume by day 12.Attempts to measure relative cytoplasmic volumes by compartmental analysis of nonelectrolyte efflux were unsuccessful. The proportion of cell volume occupied...... by cytoplasm is roughly correlated with protein content, but shows no correlation with cell size or with intracellular concentrations of K or Na. The most striking observation is that the growth of cytoplasmic volume for the culture as a whole appears to be constant throughout the culture cycle, despite...

  4. Tubulin dynamics during the cytoplasmic cohesiveness cycle in artificially activated sea urchin eggs. (United States)

    Coffe, G; Foucault, G; Raymond, M N; Pudles, J


    Sedimentation studies and [3H]colchicine-binding assays have demonstrated a relationship between the cytoplasmic cohesiveness cycles and the changes in tubulin organization in Paracentrotus lividus eggs activated by 2.5 mM procaine. The same amount of tubulin (20-25% of the total egg tubulin) is involved in these cyclic process and appears to undergo polymerization and depolymerization cycles. Electron microscopy studies reveal that the microtubules formed during these cytoplasmic cohesiveness cycles are under a particulate form which is sedimentable at low speed. Activation experiments carried out in the presence of cytochalasin B (CB) show that the increase in the cytoplasmic cohesiveness is highly reduced while tubulin polymerization and depolymerization cycles and pronuclear centration are not affected. Although tubulin or actin polymerization can be independently triggered in procaine-activated eggs, the increase in cytoplasmic cohesiveness requires the polymerization of both proteins. However, the cytoplasmic cohesiveness cycles appear to be regulated by tubulin polymerization and depolymerization cycles.

  5. Neutrino reactions in hot and dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Lohs, Andreas


    In this thesis, neutrino reactions in hot and dense matter are studied. In particular, this work is concerned with neutrino-matter interactions that are relevant for neutrino transport in core-collapse supernovae (CCSNe). The majority of the energy from a CCSN is released in the form of neutrinos. Accurate understanding and computation of these interactions is most relevant to achieve sufficiently reliable predictions for the evolution of CCSNe and other related question such as the production of heavy elements or neutrino oscillations. For this purpose this work follows the combined approach of searching for new important neutrino reactions and improving the computation of those reactions that are already implemented. First we estimate the relevance of charged-current weak interactions that include muon-neutrinos or muons, as well as the role of neutron decay for neutrino transport in CCSNe. All of these reactions were previously neglected in CCSN-simulations. We derive and compute the matrix element and subsequent semi-analytic expressions for transport properties like the inverse mean free path of the new reactions. It is found that these reactions are important for muon neutrinos and low energy electron antineutrinos at very high densities in the protoneutron star surface. Consequently their implementation might lead to several changes in the prediction of CCSNe signatures such as the nucleosynthesis yields. Second we improve the precision in the computation of well known neutrino-nucleon reactions like neutrino absorption on neutrons. We derive semi-analytic expressions for transport properties that use less restrictive approximations while keeping the computational demand constant. Therefore we consider the full relativistic kinematics of all participating particles i.e. allowing for relativistic nucleons and finite lepton masses. Also the weak magnetism terms of the matrix elements are explicitly included to all orders. From our results we suggest that the

  6. Anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus. (United States)

    Su, Fang; Xiao, Weiguo; Yang, Pingting; Chen, Qingyan; Sun, Xiaojie; Li, Tienan


    The clinical significance of anti-neutrophil cytoplasmic antibodies in patients with new-onset systemic lupus erythematosus, especially in systemic disease accompanied by interstitial lung disease remains to be elucidated. This study was designed to investigate the role of anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus patients. A hundred and seven patients with new-onset SLE were enrolled. Presence of anti-neutrophil cytoplasmic antibodies in the sera was assessed by indirect immunofluorescence as well as enzyme linked immunosorbent assay against proteinase-3 and myeloperoxidase. Clinical features and laboratory parameters of patients were also recorded. All patients were subjected to chest X-ray, chest high-resolution computed tomography and pulmonary function test. Forty-five systemic lupus erythematosus patients (45/107, 42%) were seropositive for anti-neutrophil cytoplasmic antibodies. Compared with anti-neutrophil cytoplasmic antibodies-negative patients, the anti-neutrophil cytoplasmic antibodies-positive patients had significantly higher incidence of renal involvement, anemia, and Raynaud's phenomenon as well as decreased serum level of complement 3/complement 4 and elevated erythrocyte sedimentation rate. In addition, there was a positive correlation between serum anti-neutrophil cytoplasmic antibodies level and disease activity of systemic lupus erythematosus. Furthermore, prevalence of interstitial lung disease in the anti-neutrophil cytoplasmic antibodies -positive patients (25/45, 55.6%) was obviously higher than that in the anti-neutrophil cytoplasmic antibodies-negative patients (15/62, 24.2%). The sample size was limited and the criteria for screening new-onset systemic lupus erythematosus patients might produce bias. The level of anti-neutrophil cytoplasmic antibodies in new-onset systemic lupus erythematosus patients correlates positively with the disease activity and the prevalence of interstitial lung disease.

  7. Finding Hierarchical and Overlapping Dense Subgraphs using Nucleus Decompositions

    Energy Technology Data Exchange (ETDEWEB)

    Seshadhri, Comandur [The Ohio State Univ., Columbus, OH (United States); Pinar, Ali [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sariyuce, Ahmet Erdem [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Catalyurek, Umit [The Ohio State Univ., Columbus, OH (United States)


    Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique, k-densest subgraph) are NP-hard. Furthermore, the goal is rarely to nd the \\true optimum", but to identify many (if not all) dense substructures, understand their distribution in the graph, and ideally determine a hierarchical structure among them. Current dense subgraph nding algorithms usually optimize some objective, and only nd a few such subgraphs without providing any hierarchy. It is also not clear how to account for overlaps in dense substructures. We de ne the nucleus decomposition of a graph, which represents the graph as a forest of nuclei. Each nucleus is a subgraph where smaller cliques are present in many larger cliques. The forest of nuclei is a hierarchy by containment, where the edge density increases as we proceed towards leaf nuclei. Sibling nuclei can have limited intersections, which allows for discovery of overlapping dense subgraphs. With the right parameters, the nuclear decomposition generalizes the classic notions of k-cores and k-trusses. We give provable e cient algorithms for nuclear decompositions, and empirically evaluate their behavior in a variety of real graphs. The tree of nuclei consistently gives a global, hierarchical snapshot of dense substructures, and outputs dense subgraphs of higher quality than other state-of-theart solutions. Our algorithm can process graphs with tens of millions of edges in less than an hour.

  8. Formation of antiviral cytoplasmic granules during orthopoxvirus infection. (United States)

    Simpson-Holley, M; Kedersha, N; Dower, K; Rubins, K H; Anderson, P; Hensley, L E; Connor, J H


    Vaccinia virus (VV) mutants lacking the double-stranded RNA (dsRNA)-binding E3L protein (ΔE3L mutant VV) show restricted replication in most cell types, as dsRNA produced by VV activates protein kinase R (PKR), leading to eIF2α phosphorylation and impaired translation initiation. Here we show that cells infected with ΔE3L mutant VV assemble cytoplasmic granular structures which surround the VV replication factories at an early stage of the nonproductive infection. These structures contain the stress granule-associated proteins G3BP, TIA-1, and USP10, as well as poly(A)-containing RNA. These structures lack large ribosomal subunit proteins, suggesting that they are translationally inactive. Formation of these punctate structures correlates with restricted replication, as they occur in >80% of cells infected with ΔE3L mutant VV but in only 10% of cells infected with wild-type VV. We therefore refer to these structures as antiviral granules (AVGs). Formation of AVGs requires PKR and phosphorylated eIF2α, as mouse embryonic fibroblasts (MEFs) lacking PKR displayed reduced granule formation and MEFs lacking phosphorylatable eIF2α showed no granule formation. In both cases, these decreased levels of AVG formation correlated with increased ΔE3L mutant VV replication. Surprisingly, MEFs lacking the AVG component protein TIA-1 supported increased replication of ΔE3L mutant VV, despite increased eIF2α phosphorylation and the assembly of AVGs that lacked TIA-1. These data indicate that the effective PKR-mediated restriction of ΔE3L mutant VV replication requires AVG formation subsequent to eIF2α phosphorylation. This is a novel finding that supports the hypothesis that the formation of subcellular protein aggregates is an important component of the successful cellular antiviral response.

  9. Impaired cytoplasmic ionized calcium mobilization in inherited platelet secretion defects

    Energy Technology Data Exchange (ETDEWEB)

    Rao, A.K.; Kowalska, M.A.; Disa, J. (Temple Univ. School of Medicine, Philadelphia, PA (USA))


    Defects in platelet cytoplasmic Ca++ mobilization have been postulated but not well demonstrated in patients with inherited platelet secretion defects. We describe studies in a 42-year-old white woman, referred for evaluation of easy bruising, and her 23-year-old son. In both subjects, aggregation and {sup 14}C-serotonin secretion responses in platelet-rich plasma (PRP) to adenosine diphosphate (ADP), epinephrine, platelet activating factor (PAF), arachidonic acid (AA), U46619, and ionophore A23187 were markedly impaired. Platelet ADP and adenosine triphosphate (ATP), contents and thromboxane synthesis induced by thrombin and AA were normal. In quin2-loaded platelets, the basal intracellular Ca++ concentration, (Ca++)i, was normal; however, peak (Ca++)i measured in the presence of 1 mmol/L external Ca++ was consistently diminished following activation with ADP (25 mumol/L), PAF (20 mumol/L), collagen (5 micrograms/mL), U46619 (1 mumol/L), and thrombin (0.05 to 0.5 U/mL). In aequorin-loaded platelets, the peak (Ca++)i studied following thrombin (0.05 and 0.5 U/mL) stimulation was diminished. Myosin light chain phosphorylation following thrombin (0.05 to 0.5 U/mL) stimulation was comparable with that in the normal controls, while with ADP (25 mumol/L) it was more strikingly impaired in the propositus. We provide direct evidence that at least in some patients with inherited platelet secretion defects, agonist-induced Ca++ mobilization is impaired. This may be related to defects in phospholipase C activation. These patients provide a unique opportunity to obtain new insights into Ca++ mobilization in platelets.

  10. Cytoplasmic molecular delivery with shock waves: importance of impulse. (United States)

    Kodama, T; Hamblin, M R; Doukas, A G


    Cell permeabilization using shock waves may be a way of introducing macromolecules and small polar molecules into the cytoplasm, and may have applications in gene therapy and anticancer drug delivery. The pressure profile of a shock wave indicates its energy content, and shock-wave propagation in tissue is associated with cellular displacement, leading to the development of cell deformation. In the present study, three different shock-wave sources were investigated; argon fluoride excimer laser, ruby laser, and shock tube. The duration of the pressure pulse of the shock tube was 100 times longer than the lasers. The uptake of two fluorophores, calcein (molecular weight: 622) and fluorescein isothiocyanate-dextran (molecular weight: 71,600), into HL-60 human promyelocytic leukemia cells was investigated. The intracellular fluorescence was measured by a spectrofluorometer, and the cells were examined by confocal fluorescence microscopy. A single shock wave generated by the shock tube delivered both fluorophores into approximately 50% of the cells (p shock waves from the lasers did not. The cell survival fraction was >0.95. Confocal microscopy showed that, in the case of calcein, there was a uniform fluorescence throughout the cell, whereas, in the case of FITC-dextran, the fluorescence was sometimes in the nucleus and at other times not. We conclude that the impulse of the shock wave (i.e., the pressure integrated over time), rather than the peak pressure, was a dominant factor for causing fluorophore uptake into living cells, and that shock waves might have changed the permeability of the nuclear membrane and transferred molecules directly into the nucleus.

  11. Dense deposit disease in a child with febrile sore throat

    Directory of Open Access Journals (Sweden)

    Giovanni Conti


    Full Text Available Dense deposit disease or membranoproliferative glomerulonephritis type II is a rare glomerulopathy characterized on renal biopsy by deposition of abnormal electron-dense material in the glomerular basement membrane. The pathophysiologic basis is uncontrolled systemic activation of the alternate pathway of the complement cascade. C3 nephritic factor, an autoantibody directed against the C3 convertase of the alternate pathway, plays a key role. In some patients, complement gene mutations have been identified. We report the case of a child who had persistent microscopic hematuria, proteinuria, and hypocomplementemia C3 for over 2 months. Renal biopsy confirmed the diagnosis of dense deposit disease.

  12. Dense deposit disease in a child with febrile sore throat. (United States)

    Conti, Giovanni; De Vivo, Dominique; Vitale, Agata; Fede, Carmelo; Santoro, Domenico


    Dense deposit disease or membranoproliferative glomerulonephritis type II is a rare glomerulopathy characterized on renal biopsy by deposition of abnormal electron-dense material in the glomerular basement membrane. The pathophysiologic basis is uncontrolled systemic activation of the alternate pathway of the complement cascade. C3 nephritic factor, an autoantibody directed against the C3 convertase of the alternate pathway, plays a key role. In some patients, complement gene mutations have been identified. We report the case of a child who had persistent microscopic hematuria, proteinuria, and hypocomplementemia C3 for over 2 months. Renal biopsy confirmed the diagnosis of dense deposit disease.


    Energy Technology Data Exchange (ETDEWEB)

    Timothy L. Ward


    Mixed-conducting ceramics have the ability to conduct oxygen with perfect selectivity at elevated temperatures, making them extremely attractive as membrane materials for oxygen separation and membrane reactor applications. While the conductivity of these materials can be quite high at elevated temperatures (typically 800-1000 C), much higher oxygen fluxes, or, alternatively, equivalent fluxes at lower temperatures, could be provided by supported thin or thick film membrane layers. Based on that motivation, the objective of this project was to explore the use of ultrafine aerosol-derived powder of a mixed-conducting ceramic material for fabrication of supported thick-film dense membranes. The project focused on the mixed-conducting ceramic composition SrCo{sub 0.5}FeO{sub x} (SCFO) because of the desirable permeability and stability of that material, as reported in the literature. Appropriate conditions to produce the submicron SrCo{sub 0.5}FeO{sub x} powder using aerosol pyrolysis were determined. Porous supports of the same composition were produced by partial sintering of a commercially obtained powder that possessed significantly larger particle size than the aerosol-derived powder. The effects of sintering conditions (temperature, atmosphere) on the porosity and microstructure of the porous discs were studied, and a standard support fabrication procedure was adopted. Subsequently, a variety of paste and slurry formulations were explored utilizing the aerosol-derived SCFO powder. These formulations were applied to the porous SCFO support by a doctor blade or spin coating procedure. Sintering of the supported membrane layer was then conducted, and additional layers were deposited and sintered in some cases. The primary characterization methods were X-ray diffraction and scanning electron microscopy, and room-temperature nitrogen permeation was used to assess defect status of the membranes.We found that non-aqueous paste/slurry formulations incorporating

  14. Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants. (United States)

    Soltani, Ali; Kumar, Ajay; Mergoum, Mohamed; Pirseyedi, Seyed Mostafa; Hegstad, Justin B; Mazaheri, Mona; Kianian, Shahryar F


    Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines.

  15. Exploring interspace: open space opportunities in dense urban areas (United States)

    Paul H. Gobster; Kathleen E. Dickhut


    Using ideas from landscape ecology, this paper explores how small open spaces can aid urban forestry efforts in dense urban areas. A case study in Chicago illustrates the physical and social lessons learned in dealing with these spaces.

  16. Densely crosslinked polycarbosiloxanes .2. Thermal and mechanical properties

    NARCIS (Netherlands)

    Flipsen, T.A C; Derks, R.; van der Vegt, H.A.; Stenekes, R.; Pennings, A.J; Hadziioannou, G


    The thermal and mechanical properties of two densely crosslinked polycarbosiloxane systems were investigated in relation to the molecular structure. The networks were prepared from functional branched prepolymers and crosslinked via a hydrosilylation curing reaction. The prepolymers having only

  17. Automated Motion Estimation for 2D Cine DENSE MRI (United States)

    Gilliam, Andrew D.; Epstein, Frederick H.


    Cine displacement encoding with stimulated echoes (DENSE) is a magnetic resonance (MR) method that directly encodes tissue displacement into MR phase images. This technique has successfully interrogated many forms of tissue motion, but is most commonly used to evaluate cardiac mechanics. Currently, motion analysis from cine DENSE images requires manually delineated anatomical structures. An automated analysis would improve measurement throughput, simplify data interpretation, and potentially access important physiological information during the MR exam. In this article, we present the first fully automated solution for the estimation of tissue motion and strain from 2D cine DENSE data. Results using both simulated and human cardiac cine DENSE data indicate good agreement between the automated algorithm and the standard semi-manual analysis method. PMID:22575669

  18. Simulation of Radiowave Propagation in a Dense Urban Environment

    National Research Council Canada - National Science Library

    Chung, Chris V


    One objective of this thesis was to investigate the effect of details, such as the windows of high-rise buildings, on the radio wave propagation in the dense urban environment through modeling and simulations...

  19. A Sparse Multi-Scale Algorithm for Dense Optimal Transport


    Schmitzer, Bernhard


    International audience; Discrete optimal transport solvers do not scale well on dense large problems since they do not explicitly exploit the geometric structure of the cost function. In analogy to continuous optimal transport, we provide a framework to verify global optimality of a discrete transport plan locally. This allows the construction of an algorithm to solve large dense problems by considering a sequence of sparse problems instead. The algorithm lends itself to being combined with a...

  20. Neutrinos and Nucleosynthesis in Hot and Dense Matter

    Energy Technology Data Exchange (ETDEWEB)

    Fuller, George [Univ. of California, San Diego, CA (United States)


    The Topical Collaboration for Neutrinos and Nucleosynthesis in Hot and Dense matter brought together researchers from a variety of nuclear science specialties and a number of institutions to address nuclear physics and neutrino physics problems associated with dense matter and the origin of the elements. See attached final technical reports for (1) the UCSD award and (2) a copy of the report for the whole TC

  1. Relating quantum discord with the quantum dense coding capacity

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xin; Qiu, Liang, E-mail:; Li, Song; Zhang, Chi [China University of Mining and Technology, School of Sciences (China); Ye, Bin [China University of Mining and Technology, School of Information and Electrical Engineering (China)


    We establish the relations between quantum discord and the quantum dense coding capacity in (n + 1)-particle quantum states. A necessary condition for the vanishing discord monogamy score is given. We also find that the loss of quantum dense coding capacity due to decoherence is bounded below by the sum of quantum discord. When these results are restricted to three-particle quantum states, some complementarity relations are obtained.

  2. Object detection in surveillance video from dense trajectories


    Zhai, Mengyao


    Detecting objects such as humans or vehicles is a central problem in surveillance video. Myriad standard approaches exist for this problem. At their core, approaches consider either the appearance of people, patterns of their motion, or differences from the background. In this paper we build on dense trajectories, a state-of-the-art approach for describing spatio-temporal patterns in video sequences. We demonstrate an application of dense trajectories to object detection in surveillance video...

  3. Increased dense erythrocytes in flame-burned patients. (United States)

    Saavedra, Arturo P; Warth, James A; Burke, John F; Norton, Kathryn J; Gelfand, Jeffrey A


    We have studied dense erythrocytes separated on Arabinogalactan (Stractan) ultracentrifuged gradients in flame-burned patients and in normal individuals. In each case, the percentage of erythrocytes in the densest layers was increased when compared to age and sex matched controls. Using an in vitro system, we showed that as human whole blood is warmed to 48.6°C, the number of dense erythrocytes increases. In addition, the reduced glutathionine (GSH) content of the densest red blood cells is decreased compared to those in lighter fractions on the same gradient or to dense erythrocytes separated from blood incubated at room temperature. These dense red cells were largely composed of spherocytes and spheroechynocytes, two forms of erythrocytes which have been shown by others to have markedly abnormal flow characteristics in vitro. We have demonstrated that in vivo dense erythrocytes can be generated in the setting of flame burns. Thus, the underlying reason may be oxidant injury as represented by the reduced level of GSH that we found in association with the generation of dense erythrocytes.

  4. Characterization of Novel Cytoplasmic PARP in the Brain of Octopus vulgaris (United States)



    Recent investigation has focused on the participation of the poly (ADP-ribose) polymerase (PARP) reaction in the invertebrate central nervous system (CNS) during the process of long-term memory (LTM). In this paper, we characterize, localize, and assign a possible role to a cytoplasmic PARP in the brain of Octopus vulgaris. PARP activity was assayed in optic lobes, supraesophageal mass, and optic nerves. The highest levels of enzyme were found in the cytoplasmic fraction. Hyper-activation of the enzyme was detected in Octopus brain after visual discrimination training. Finally, cytoplasmic PARP was found to inhibit Octopus vulgaris actin polymerization. We propose that the cytoplasmic PARP plays a role in vivo to induce the cytoskeletonal reorganization that occurs during learning-induced neuronal plasticity. PMID:22815366


    NARCIS (Netherlands)


    The immunopathogenic importance of neutrophil cytoplasmic autoantibodies in ulcerative colitis and primary sclerosing cholangitis is unknown. These autoantibodies were investigated before and after liver transplantation in 9 patients with primary sclerosing cholangitis. Sera from 10 patients


    NARCIS (Netherlands)

    Haagsma, E.B.; MULDER, A.H.L.; Gouw, A.S.H.; MEERMAN, L.; Slooff, M.JH; Kallenberg, Cees; Horst, G.


    The immunopathogenic importance of neutrophil cytoplasmic autoantibodies in ulcerative colitis and primary sclerosing cholangitis is unknown. These autoantibodies were investigated before and after liver transplantation in 9 patients with primary sclerosing cholangitis. Sera from 10 patients

  7. Probing the stochastic, motor-driven properties of the cytoplasm using force spectrum microscopy (United States)

    Guo, Ming; Ehrlicher, Allen J.; Jensen, Mikkel H.; Renz, Malte; Moore, Jeffrey R.; Goldman, Robert D.; Lippincott-Schwartz, Jennifer; Mackintosh, Frederick C.; Weitz, David A.


    SUMMARY Molecular motors in cells typically produce highly directed motion; however, the aggregate, incoherent effect of all active processes also creates randomly fluctuating forces, which drive diffusive-like, non-thermal motion. Here we introduce force-spectrum-microscopy (FSM) to directly quantify random forces within the cytoplasm of cells and thereby probe stochastic motor activity. This technique combines measurements of the random motion of probe particles with independent micromechanical measurements of the cytoplasm to quantify the spectrum of force fluctuations. Using FSM, we show that force fluctuations substantially enhance intracellular movement of small and large components. The fluctuations are three times larger in malignant cells than in their benign counterparts. We further demonstrate that vimentin acts globally to anchor organelles against randomly fluctuating forces in the cytoplasm, with no effect on their magnitude. Thus, FSM has broad applications for understanding the cytoplasm and its intracellular processes in relation to cell physiology in healthy and diseased states. PMID:25126787

  8. Anticorpos contra o citoplasma de neutrófilos Antineutrophil cytoplasmic antibodies

    Directory of Open Access Journals (Sweden)

    Ari Stiel Radu


    Full Text Available A descoberta do marcador sorológico denominado anticorpo anticitoplasma de neutrófilos revolucionou o diagnóstico e o seguimento das vasculites pulmonares, especialmente da granulomatose de Wegener. Seu padrão pode ser citoplasmático e perinuclear. Sua titulação auxilia no diagnóstico e no seguimento das vasculites pulmonares.The discovery of the serological markers known as antineutrophil cytoplasmic antibodies revolutionized the diagnosis and follow-up treatment of the various forms of pulmonary vasculitis, especially that of Wegener's granulomatosis. The antineutrophil cytoplasmic antibodies pattern can be cytoplasmic or perinuclear. Determination of antineutrophil cytoplasmic antibodies titers aids the diagnosis and follow-up treatment of pulmonary vasculitis.

  9. Formin DAAM1 Organizes Actin Filaments in the Cytoplasmic Nodal Actin Network

    National Research Council Canada - National Science Library

    Weiwei Luo; Zi Zhao Lieu; Ed Manser; Alexander D Bershadsky; Michael P Sheetz


    .... DAAM1 was found to be distributed between the cytoplasm and the plasma membrane. The membrane binding likely occurs through an interaction with lipid rafts, but is not required for F-actin assembly...

  10. Organization of the cytoplasmic reticulum in the central vacuole of parenchyma cells in Allium cepa L.

    Directory of Open Access Journals (Sweden)

    Tomasz J. Wodzicki


    Full Text Available An elaborate and complex cytoplasmic reticulum composed of fine filaments and lamellae ranging from 0.1 to 4 microns in size is revealed by viewing the central vacuole of onion bulb parenchyma cells with the scanning election microscope. The larger cytoplasmic strands, visible with the light microscope, are composed of numerous smaller filaments (some tubular which might explain the observed bidirectional movement of particles in these larger strands. The finely divided cytoplasmic network of filaments is continuous with the parietal cytoplasm inclosing the vacuolar sap. In these highly vacuolated cells the mass of the protoplast is in the form of an intravacuolar reticulum immersed in the cell sap. The probable significance of the vacuolar sap in relation to physiological processes of the cell is discussed.

  11. Evaluation of antineutrophil cytoplasmic antibody seroconversion induced by minocycline, sulfasalazine, or penicillamine

    NARCIS (Netherlands)

    Choi, HK; Slot, MC; Pan, GL; Weissbach, CA; Niles, JL; Merkel, PA


    Objective, Case reports have suggested that minocycline, sulfasalazine, and penicillamine are associated with antineutrophil cytoplasmic antibody (ANCA)-positive vasculitis, This study evaluated ANCA seroconversion due to these agents in serum samples prospectively collected in randomized,

  12. Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants (United States)

    Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversi...

  13. Microtubule–microtubule sliding by kinesin-1 is essential for normal cytoplasmic streaming in Drosophila oocytes (United States)

    Lu, Wen; Winding, Michael; Lakonishok, Margot; Wildonger, Jill


    Cytoplasmic streaming in Drosophila oocytes is a microtubule-based bulk cytoplasmic movement. Streaming efficiently circulates and localizes mRNAs and proteins deposited by the nurse cells across the oocyte. This movement is driven by kinesin-1, a major microtubule motor. Recently, we have shown that kinesin-1 heavy chain (KHC) can transport one microtubule on another microtubule, thus driving microtubule–microtubule sliding in multiple cell types. To study the role of microtubule sliding in oocyte cytoplasmic streaming, we used a Khc mutant that is deficient in microtubule sliding but able to transport a majority of cargoes. We demonstrated that streaming is reduced by genomic replacement of wild-type Khc with this sliding-deficient mutant. Streaming can be fully rescued by wild-type KHC and partially rescued by a chimeric motor that cannot move organelles but is active in microtubule sliding. Consistent with these data, we identified two populations of microtubules in fast-streaming oocytes: a network of stable microtubules anchored to the actin cortex and free cytoplasmic microtubules that moved in the ooplasm. We further demonstrated that the reduced streaming in sliding-deficient oocytes resulted in posterior determination defects. Together, we propose that kinesin-1 slides free cytoplasmic microtubules against cortically immobilized microtubules, generating forces that contribute to cytoplasmic streaming and are essential for the refinement of posterior determinants. PMID:27512034

  14. Localization and function of KLF4 in cytoplasm of vascular smooth muscle cell

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yan [Department of Biochemistry and Molecular Biology, The Key Laboratory of Neurobiology and Vascular Biology (China); The Third Hospital of Hebei Medical University, Shijazhuang (China); Zheng, Bin; Zhang, Xin-hua; Nie, Chan-juan; Li, Yong-hui [Department of Biochemistry and Molecular Biology, The Key Laboratory of Neurobiology and Vascular Biology (China); Wen, Jin-kun, E-mail: [Department of Biochemistry and Molecular Biology, The Key Laboratory of Neurobiology and Vascular Biology (China)


    Highlights: •PDGF-BB prompts the translocation of KLF4 to the cytoplasm. •PDGF-BB promotes interaction between KLF4 and actin in the cytoplasm. •Phosphorylation and SUMOylation of KLF4 participates in regulation of cytoskeletal organization. •KLF4 regulates cytoskeleton by promoting the expression of contraction-associated genes. -- Abstract: The Krüppel-like factor 4 is a DNA-binding transcriptional regulator that regulates a diverse array of cellular processes, including development, differentiation, proliferation, and apoptosis. The previous studies about KLF4 functions mainly focused on its role as a transcription factor, its functions in the cytoplasm are still unknown. In this study, we found that PDGF-BB could prompt the translocation of KLF4 to the cytoplasm through CRM1-mediated nuclear export pathway in vascular smooth muscle cells (VSMCs) and increased the interaction of KLF4 with actin in the cytoplasm. Further study showed that both KLF4 phosphorylation and SUMOylation induced by PDGF-BB participates in regulation of cytoskeletal organization by stabilizing the actin cytoskeleton in VSMCs. In conclusion, these results identify that KLF4 participates in the cytoskeletal organization by stabilizing cytoskeleton in the cytoplasm of VSMCs.

  15. Experimental Studies of the Transport Parameters of Warm Dense Matter

    Energy Technology Data Exchange (ETDEWEB)

    Chouffani, Khalid [Idaho State Univ., Pocatello, ID (United States)


    There is a need to establish fundamental properties of matter and energy under extreme physical conditions. Although high energy density physics (HEDP) research spans a wide range of plasma conditions, there is one unifying regime that is of particular importance and complexity: that of warm dense matter, the transitional state between solid state condensed matter and energetic plasmas. Most laboratory experimental conditions, including inertial confinement implosion, fall into this regime. Because all aspects of laboratory-created high-energy-density plasmas transition through the warm dense matter regime, understanding the fundamental properties to determine how matter and energy interact in this regime is an important aspect of major research efforts in HEDP. Improved understanding of warm dense matter would have significant and wide-ranging impact on HEDP science, from helping to explain wire initiation studies on the Sandia Z machine to increasing the predictive power of inertial confinement fusion modeling. The central goal or objective of our proposed research is to experimentally determine the electrical resistivity, temperature, density, and average ionization state of a variety of materials in the warm dense matter regime, without the use of theoretical calculations. Since the lack of an accurate energy of state (EOS) model is primarily due to the lack of experimental data, we propose an experimental study of the transport coefficients of warm dense matter.

  16. Application of a Dense Gas Technique for Sterilizing Soft Biomaterials (United States)

    Karajanagi, Sandeep S.; Yoganathan, Roshan; Mammucari, Raffaella; Park, Hyoungshin; Cox, Julian; Zeitels, Steven M.; Langer, Robert; Foster, Neil R.


    Sterilization of soft biomaterials such as hydrogels is challenging because existing methods such as gamma irradiation, steam sterilization, or ethylene oxide sterilization, while effective at achieving high sterility assurance levels (SAL), may compromise their physicochemical properties and biocompatibility. New methods that effectively sterilize soft biomaterials without compromising their properties are therefore required. In this report, a dense-carbon dioxide (CO2)-based technique was used to sterilize soft polyethylene glycol (PEG)-based hydrogels while retaining their structure and physicochemical properties. Conventional sterilization methods such as gamma irradiation and steam sterilization severely compromised the structure of the hydrogels. PEG hydrogels with high water content and low elastic shear modulus (a measure of stiffness) were deliberately inoculated with bacteria and spores and then subjected to dense CO2. The dense CO2-based methods effectively sterilized the hydrogels achieving a SAL of 10−7 without compromising the viscoelastic properties, pH, water-content, and structure of the gels. Furthermore, dense CO2-treated gels were biocompatible and non-toxic when implanted subcutaneously in ferrets. The application of novel dense CO2-based methods to sterilize soft biomaterials has implications in developing safe sterilization methods for soft biomedical implants such as dermal fillers and viscosupplements. PMID:21337339

  17. Hydrophobization of dense and fine concrete by polysulfide solutions

    Directory of Open Access Journals (Sweden)

    MASSALIMOV Ismail Alexandrovich


    Full Text Available The results of research on hydrophobic impregnation of dense concrete with composition «Aquastat» designed for manufacture of road and airfield plates are presented. It was found that after having been treated with waterrepellent agent the concrete sample is resistant to wetting, i.e. it gets hydrophobic properties. At the same time the water absorption of the samples treated for 24 hours at atmospheric pressure is reduced in three times, and soaked for 0.5 hours under vacuum decreases 5.5 times. It was revealed that the hydrophobic properties of fine-grained concrete impregnated with «Aquastat» may be at the same level of those of dense concrete based on coarse filler. Substantially increased hydrophobic properties of dense concrete (more than 5 times allow authors to forecast twice increased service life of road and airfield plates treated by «Aquastat» composition.

  18. Spatial and temporal segmented dense trajectories for gesture recognition (United States)

    Yamada, Kaho; Yoshida, Takeshi; Sumi, Kazuhiko; Habe, Hitoshi; Mitsugami, Ikuhisa


    Recently, dense trajectories [1] have been shown to be a successful video representation for action recognition, and have demonstrated state-of-the-art results with a variety of datasets. However, if we apply these trajectories to gesture recognition, recognizing similar and fine-grained motions is problematic. In this paper, we propose a new method in which dense trajectories are calculated in segmented regions around detected human body parts. Spatial segmentation is achieved by body part detection [2]. Temporal segmentation is performed for a fixed number of video frames. The proposed method removes background video noise and can recognize similar and fine-grained motions. Only a few video datasets are available for gesture classification; therefore, we have constructed a new gesture dataset and evaluated the proposed method using this dataset. The experimental results show that the proposed method outperforms the original dense trajectories.

  19. Holographic stereogram using camera array in dense arrangement (United States)

    Yamamoto, Kenji; Oi, Ryutaro; Senoh, Takanori; Ichihashi, Yasuyuki; Kurita, Taiichiro


    Holographic stereograms can display 3D objects by using ray information. To display high quality representations of real 3D objects by using holographic stereograms, relatively dense ray information must be prepared as the 3D object information. One promising method of obtaining this information uses a combination of a camera array and view interpolation which is signal processing technique. However, it is still technically difficult to synthesize ray information without visible error by using view interpolation. Our approach uses a densely arranged camera array to reduce this difficulty. Even though view interpolation is a simple signal processing technique, the synthesized ray information produced by this camera array should be adequate. We designed and manufactured a densely arranged camera array and used it to generate holographic stereograms.

  20. Warm dense matter and Thomson scattering at FLASH

    Energy Technology Data Exchange (ETDEWEB)

    Faeustlin, Roland Rainer


    X-ray free electron lasers are powerful tools to investigate moderately to strongly correlated solid density low temperature plasmas, named warm dense matter. These plasmas are of most interest for astrophysics and laser plasma interaction, particularly inertial confinement fusion. This work utilizes the ultrashort soft x-ray pulse duration and high brilliance of the free electron laser in Hamburg, FLASH, to generate warm dense matter and to study its ultrafast processes. The techniques applied are absorption measurement, emission spectroscopy and Thomson scattering. Radiative hydrodynamics and Thomson scattering simulations are used to investigate the impact of temperature and density gradients in the sample and to fit the experimental data. The measurements result in a comprehensive picture of soft x-ray matter interaction related to warm dense matter and yield insight into ultrafast equilibration and relaxation mechanisms, in particular impact ionization and radiative recombination. (orig.)

  1. Collaborative Research: Neutrinos & Nucleosynthesis in Hot Dense Matter

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Sanjay


    It is now firmly established that neutrinos, which are copiously produced in the hot and dense core of the supernova, play a role in the supernova explosion mechanism and in the synthesis of heavy elements through a phenomena known as r-process nucleosynthesis. They are also detectable in terrestrial neutrino experiments, and serve as a probe of the extreme environment and complex dynamics encountered in the supernova. The major goal of the UW research activity relevant to this project was to calculate the neutrino interaction rates in hot and dense matter of relevance to core collapse supernova. These serve as key input physics in large scale computer simulations of the supernova dynamics and nucleosynthesis being pursued at national laboratories here in the United States and by other groups in Europe and Japan. Our calculations show that neutrino production and scattering rate are altered by the nuclear interactions and that these modifications have important implications for nucleosynthesis and terrestrial neutrino detection. The calculation of neutrino rates in dense matter are difficult because nucleons in the dense matter are strongly coupled. A neutrino interacts with several nucleons and the quantum interference between scattering off different nucleons depends on the nature of correlations between them in dense matter. To describe these correlations we used analytic methods based on mean field theory and hydrodynamics, and computational methods such as Quantum Monte Carlo. We found that due to nuclear effects neutrino production rates at relevant temperatures are enhanced, and that electron neutrinos are more easily absorbed than anti-electron neutrinos in dense matter. The latter, was shown to favor synthesis of heavy neutron-rich elements in the supernova.

  2. Eculizumab for dense deposit disease and C3 glomerulonephritis. (United States)

    Bomback, Andrew S; Smith, Richard J; Barile, Gaetano R; Zhang, Yuzhou; Heher, Eliot C; Herlitz, Leal; Stokes, M Barry; Markowitz, Glen S; D'Agati, Vivette D; Canetta, Pietro A; Radhakrishnan, Jai; Appel, Gerald B


    The principle defect in dense deposit disease and C3 glomerulonephritis is hyperactivity of the alternative complement pathway. Eculizumab, a monoclonal antibody that binds to C5 to prevent formation of the membrane attack complex, may prove beneficial. In this open-label, proof of concept efficacy and safety study, six subjects with dense deposit disease or C3 glomerulonephritis were treated with eculizumab every other week for 1 year. All had proteinuria >1 g/d and/or AKI at enrollment. Subjects underwent biopsy before enrollment and repeat biopsy at the 1-year mark. The subjects included three patients with dense deposit disease (including one patient with recurrent dense deposit disease in allograft) and three patients with C3 glomerulonephritis (including two patients with recurrent C3 glomerulonephritis in allograft). Genetic and complement function testing revealed a mutation in CFH and MCP in one subject each, C3 nephritic factor in three subjects, and elevated levels of serum membrane attack complex in three subjects. After 12 months, two subjects showed significantly reduced serum creatinine, one subject achieved marked reduction in proteinuria, and one subject had stable laboratory parameters but histopathologic improvements. Elevated serum membrane attack complex levels normalized on therapy and paralleled improvements in creatinine and proteinuria. Clinical and histopathologic data suggest a response to eculizumab in some but not all subjects with dense deposit disease and C3 glomerulonephritis. Elevation of serum membrane attack complex before treatment may predict response. Additional research is needed to define the subgroup of dense deposit disease/C3 glomerulonephritis patients in whom eculizumab therapy can be considered.

  3. Interference Management with Successive Cancellation for Dense Small Cell Networks

    DEFF Research Database (Denmark)

    Lopez, Victor Fernandez; Pedersen, Klaus I.; Steiner, Jens


    , known as Symbol-Level Interference Cancellation (SLIC), with respect to a baseline Minimum Mean Square Error-Interference Rejection Combining (MMSE-IRC) receiver. The study is carried out on a dense, clusterized small cell network, illustrating to which extent NAICS can overcome the additional......Network-Assisted Interference Cancellation and Suppression (NAICS) receivers have appeared as a promising way to curb inter-cell interference in future dense network deployments. This investigation compares the performance of a NAICS receiver with successive interference cancellation capabilities...

  4. Electromagnetic solitary structures in dense electron-positron-ion magnetoplasmas

    Energy Technology Data Exchange (ETDEWEB)

    Masood, W; Hussain, S; Rizvi, H; Mushtaq, A [TPPD, PINSTECH, PO Nilore, Islamabad (Pakistan); Ayub, M, E-mail: [Government College University (GCU), Lahore (Pakistan)


    The linear and nonlinear propagation characteristics of low-frequency obliquely propagating magnetoacoustic waves in dense electron-positron-ion magnetoplasmas are studied in this paper by using the quantum magnetohydrodynamic (QMHD) model. A quantum Kadomtsev-Petviashvili (KP) equation is derived by using the reductive perturbation technique. The dependence of the fast and slow magnetoacoustic solitary waves on the positron concentration, the obliqueness parameter {theta} and the magnetic field is also investigated. The present investigation may have relevance to dense astrophysical environments where the quantum effects are expected to dominate.

  5. Dose-dependent relationship between oocyte cytoplasmic volume and transformation of sperm nuclei to metaphase chromosomes. (United States)

    Clarke, H J; Masui, Y


    We have studied the chromosome condensation activity of mouse oocytes that have been inseminated during meiotic maturation. These oocytes remain unactivated, and in those penetrated by up to three or four sperm, each sperm nucleus is transformed, without prior development of a pronucleus, into metaphase chromosomes. However, those penetrated by more than four sperm never transform any of the nuclei into metaphase chromosomes (Clarke, H. J., and Y. Masui, 1986, J. Cell Biol. 102:1039-1046). We report here that, when the cytoplasmic volume of oocytes was doubled or tripled by cell fusion, up to five or eight sperm nuclei, respectively, could be transformed into metaphase chromosomes. Conversely, when the cytoplasmic volume was reduced by bisection of oocytes after the germinal vesicle (GV) had broken down, no more than two sperm could be transformed into metaphase chromosomes. Thus, the capacity of the oocyte cytoplasm to transform sperm nuclei to metaphase chromosomes was proportional to its volume. The contribution of the nucleoplasm of the GV and the cytoplasm outside the GV to the chromosome condensation activity was investigated by bisecting oocytes that contained a GV and then inseminating the nucleate and anucleate fragments. The anucleate fragments never induced sperm chromosome formation, indicating that GV nucleoplasm is required for this activity. In the nucleate fragments, the capacity to induce sperm chromosome formation was reduced as compared with whole oocytes, in spite of the fact that the fragments contained the entire GV nucleoplasm. This implies that non-GV cytoplasmic material also was required for chromosome condensation activity. When inseminated oocytes were incubated in the presence of puromycin, the sperm nuclei were transformed into interphase-like nuclei, but no metaphase chromosomes developed. However, when protein synthesis resumed, the interphase nuclei were transformed to metaphase chromosomes. These results suggest that the

  6. The peripheral cytoplasm of adrenocortical cells: zone-specific responses to ACTH. (United States)

    Loesser, K E; Cain, L D; Malamed, S


    Differences in the cytoskeletal protein actin in cells from the zona glomerulosa and zona fasciculata would be of considerable interest because there is persuasive evidence that rat corticosteroids are secreted by mechanisms that are somewhat zone-specific. We have previously shown evidence that actin may be involved in steroid secretion, possibly in connection with changes in adrenocortical microvilli. However, the cells upon which the data were based were not separated according to zone of origin. Immunogold electron microscopy and morphometric procedures were used to determine whether ACTH-induced changes in the peripheral cytoplasm of isolated adrenocortical cells occur in both zona fasciculata and zona glomerulosa cells. Actin immunoreactivity was more concentrated in the cytoplasm adjacent to the plasma membrane (including the cytoplasm within the microvilli) than it was in the internal cytoplasm in cells from both zones (4-6 times more concentrated in zona glomerulosa cells and 3-6 times more concentrated in zona fasciculata cells). However, the mean aggregate microvillar surface length (microvillar index) of untreated zona fasciculata cells (previously reported (Loesser and Malamed, 1987)) was 23% greater than that of untreated zona glomerulosa cells. Although ACTH (at a maximal steroidogenic concentration) had no effect on the peripheral cytoplasmic actin concentration of zona glomerulosa cells, there was a 24% increase in the aggregate microvillar length. In contrast, in zona fasciculata cells, ACTH treatment was accompanied by an increase in peripheral cytoplasmic actin concentration of 58-64% and an increase in aggregate microvillar surface length of 40% (previously reported (Loesser and Malamed, 1987)), almost twice that for zona glomerulosa cells. The results suggest that ACTH-induced hormone release from zona fasciculata cells is mediated by increases in peripheral cytoplasmic actin and aggregate microvillar length; in zona glomerulosa cells such

  7. Predictions of x-ray scattering spectra in warm dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Starrett, Charles E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Saumon, Didier [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Souza, Andre N. [Univ. of Michigan, Ann Arbor, MI (United States); Perkins, David J. [Univ. of California, Los Angeles, CA (United States); Hansen, Stephanie B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)


    This presentation gives an Introduction to our model of warm dense matter; How x-ray scattering spectra are calculated from it; Comparisons with experiments: Room temperature/pressure beryllium Warm dense beryllium Warm dense aluminum; Predictions for warm dense beryllium and titanium; and, Conclusions.

  8. Phase separation between nucleoid and cytoplasm in Escherichia coli as defined by immersive refractometry. (United States)

    Valkenburg, J A; Woldringh, C L


    The refractive indices of nucleoid and cytoplasm in Escherichia coli were derived theoretically and experimentally. For the theoretical estimates, we made use of the known macromolecular composition of E. coli B/r (G. Churchward and H. Bremer, J. Theor. Biol. 94:651-670, 1982) and of estimates of cell and nucleoid volumes. These were obtained from micrographs of living bacteria made with a confocal scanning light microscope. The theoretical values were calculated, assuming that all DNA occurred in the nucleoid and that all protein and RNA occurred in the cytoplasm. Comparison with experimental refractive index values directly obtained by immersive refractometry showed that, besides its DNA, the nucleoid must contain an additional amount of solids equivalent to 8.6% (wt/vol) protein. With the nucleoid containing 6.8% (wt/vol) DNA and 8.6% (wt/vol) protein and the cytoplasm containing 21% (wt/vol) protein and 4% (wt/vol) RNA, a mass difference is obtained, which accounts for the phase separation observed between the nucleoid and cytoplasm in living cells by phase-contrast microscopy. The decrease in the refractive index of the nucleoid relative to that of the cytoplasm observed upon, for instance, OsO4 fixation was interpreted as being indicative of the loss of protein content in the nucleoid. Images PMID:6389508

  9. Detection of beta-tubulin in the cytoplasm of the interphasic Entamoeba histolytica trophozoites. (United States)

    Gómez-Conde, Eduardo; Vargas-Mejía, Miguel Ángel; Díaz-Orea, María Alicia; Hernández-Rivas, Rosaura; Cárdenas-Perea, María Elena; Guerrero-González, Tayde; González-Barrios, Juan Antonio; Montiel-Jarquín, Álvaro José


    It is known that the microtubules (MT) of Entamoeba histolytica trophozoites form an intranuclear mitotic spindle. However, electron microscopy studies and the employment of anti-beta-tubulin (β-tubulin) antibodies have not exhibited these cytoskeletal structures in the cytoplasm of these parasites. The purpose of this work was to detect β-tubulin in the cytoplasm of interphasic E. histolytica trophozoites. Activated or non-activated HMI-IMSS-strain E. histolytica trophozoites were used and cultured for 72 h at 37 °C in TYI-S-33 medium, and then these were incubated with the anti-β-tubulin antibody of E. histolytica. The anti-β-tubulin antibody reacted with the intranuclear mitotic spindle of E. histolytica-activated trophozoites as control. In contrast, in non-activated interphasic parasites, anti-β-tubulin antibody reacted with diverse puntiform structures in the cytoplasm and with ring-shaped structures localized in the cytoplasm, cellular membrane and endocytic stomas. In this work, for the first time, the presence of β-tubulin is shown in the cytoplasm of E. histolytica trophozoites. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Cytoplasmic flows as signatures for the mechanics of mitotic spindle positioning (United States)

    Nazockdast, Ehssan; Rahimian, Abtin; Needleman, Daniel; Shelley, Michael


    The proper positioning of the mitotic spindle is crucial for asymmetric cell division and generating cell diversity during development. We use dynamic simulations to study the cytoplasmic flows generated by three possible active forcing mechanisms involved in positioning of the mitotic spindle in the first cell division of C.elegans embryo namely cortical pulling, cortical pushing, and cytoplasmic pulling mechanisms. The numerical platform we have developed for simulating cytoskeletal assemblies is the first to incorporate the interactions between the fibers and other intracellular bodies with the cytoplasmic fluid, while also accounting for their polymerization, and interactions with motor proteins. The hydrodynamic interactions are computed using boundary integral methods in Stokes flow coupled with highly efficient fast summation techniques that reduce the computational cost to scale linearly with the number of fibers and other bodies. We show that although all three force transduction mechanisms predict proper positioning and orientation of the mitotic spindle, each model produces a different signature in its induced cytoplasmic flow and MT conformation. We suggest that cytoplasmic flows and MT conformation can be used to differentiate between these mechanisms.

  11. Sumoylation is Required for the Cytoplasmic Accumulation of a Subset of mRNAs

    Directory of Open Access Journals (Sweden)

    Hui Zhang


    Full Text Available In order to discover novel proteins that promote the nuclear export of newly synthesized mRNAs in mammalian cells, we carried out a limited RNAi screen for proteins required for the proper cytoplasmic distribution of a model intronless mRNA. From this screen we obtained two hits, Ubc9 (SUMO-conjugating E2 enzyme and GANP (germinal center-associated nuclear protein. Depletion of Ubc9 inhibited the proper cytoplasmic distribution of certain overexpressed intronless mRNAs, while depletion of GANP affected all tested mRNAs. Depletion of Sae1, which is also required for sumoylation, partially inhibited the cytoplasmic distribution of our model mRNA. Interestingly, the block in cytoplasmic accumulation in Ubc9-depleted cells could be overcome if an intron was incorporated into the mRNA. Surprisingly, Ubc9-depleted cells had normal nuclear export of newly synthesized intronless mRNAs, indicating that the observed accumulation of the model mRNA in the nuclei of transfected cells was likely due to some more general perturbation. Indeed, depletion of Ubc9, coupled with the overexpression of the intronless mRNAs, caused the redistribution of the nuclear speckle protein SC35 to cytoplasmic foci. Our results suggest that sumoylation may play a role in the proper assembly of mRNPs and/or the distribution of key RNA binding proteins, and may thus contribute to general protein expression patterns.

  12. Bayesian Inference of Forces Causing Cytoplasmic Streaming in Caenorhabditis elegans Embryos and Mouse Oocytes. (United States)

    Niwayama, Ritsuya; Nagao, Hiromichi; Kitajima, Tomoya S; Hufnagel, Lars; Shinohara, Kyosuke; Higuchi, Tomoyuki; Ishikawa, Takuji; Kimura, Akatsuki


    Cellular structures are hydrodynamically interconnected, such that force generation in one location can move distal structures. One example of this phenomenon is cytoplasmic streaming, whereby active forces at the cell cortex induce streaming of the entire cytoplasm. However, it is not known how the spatial distribution and magnitude of these forces move distant objects within the cell. To address this issue, we developed a computational method that used cytoplasm hydrodynamics to infer the spatial distribution of shear stress at the cell cortex induced by active force generators from experimentally obtained flow field of cytoplasmic streaming. By applying this method, we determined the shear-stress distribution that quantitatively reproduces in vivo flow fields in Caenorhabditis elegans embryos and mouse oocytes during meiosis II. Shear stress in mouse oocytes were predicted to localize to a narrower cortical region than that with a high cortical flow velocity and corresponded with the localization of the cortical actin cap. The predicted patterns of pressure gradient in both species were consistent with species-specific cytoplasmic streaming functions. The shear-stress distribution inferred by our method can contribute to the characterization of active force generation driving biological streaming.

  13. P granules phase transition induced by cytoplasmic streaming in Caenorhabditis elegans embryo (United States)

    Wang, Hang; Hu, GuoHui


    P granules are germ granules contained in Caenorhabditis elegans germ cells. The first germ cell is specified by the one-cell embryo in which P granules localize to the posterior. Previous studies suggested that the mechanism of the localization phenomena is induced by liquid-liquid phase transition (LLPT), in which the polarity proteins control the saturation point of P granules. In the present study, we propose that the P granules phase transition can be triggered by the cytoplasmic streaming. A two-phase flow model is employed to simulate the localization of P granules, i.e., the cytoplasm is considered as a liquid phase, and the droplet-like P granules are another liquid phase. With the presence of the cytoplasmic streaming, P granules, initially distributing uniformly in the entire one-cell embryo, eventually condense/dissolve in the cytoplasm phase, regulated by difference between the saturation pressure and the hydrodynamic pressure. The numerical results reveal that the cytoplasmic streaming has significant effects on the localization of P granules, as well as the embryo division.

  14. Export of Precursor tRNAIle from the Nucleus to the Cytoplasm in Human Cells.

    Directory of Open Access Journals (Sweden)

    Min Wei

    Full Text Available In the current concept, tRNA maturation in vertebrate cells, including splicing of introns, trimming of 5' leader and 3' trailer, and adding of CCA, is thought to occur exclusively in the nucleus. Here we provide evidence to challenge this concept. Unspliced intron-containing precursor tRNAIle was identified in Human Immunodeficiency Virus type 1 (HIV-1 virions, which are synthesized in the cytoplasm. Northern blot, confocal microscopy and quantitative RT-PCR further verified enrichment of this unspliced tRNAIle within the cytoplasm in human cells. In addition to containing an intron, the cytoplasmic precursor tRNAIle also contains a short incompletely processed 5´ leader and a 3´ trailer, which abundance is around 1000 fold higher than the nuclear precursor tRNAIle with long 5' leader and long 3' trailer. In vitro data also suggest that the cytoplasmic unspliced end-immature precursor tRNAIle could be processed by short isoform of RNase Z, but not long isoform of RNase Z. These data suggest that precursor tRNAs could export from the nucleus to the cytoplasm in human cells, instead of be processed only in the nucleus.

  15. Cytoplasmic and Nuclear TAZ Exert Distinct Functions in Regulating Primed Pluripotency

    Directory of Open Access Journals (Sweden)

    Xingliang Zhou


    Full Text Available Mouse epiblast stem cells (mEpiSCs and human embryonic stem cells (hESCs are primed pluripotent stem cells whose self-renewal can be maintained through cytoplasmic stabilization and retention of β-catenin. The underlying mechanism, however, remains largely unknown. Here, we show that cytoplasmic β-catenin interacts with and retains TAZ, a Hippo pathway effector, in the cytoplasm. Cytoplasmic retention of TAZ promotes mEpiSC self-renewal in the absence of nuclear β-catenin, whereas nuclear translocation of TAZ induces mEpiSC differentiation. TAZ is dispensable for naive mouse embryonic stem cell (mESC self-renewal but required for the proper conversion of mESCs to mEpiSCs. The self-renewal of hESCs, like that of mEpiSCs, can also be maintained through the cytoplasmic retention of β-catenin and TAZ. Our study indicates that how TAZ regulates cell fate depends on not only the cell type but also its subcellular localization.

  16. Cleavage, incomplete inversion, and cytoplasmic bridges in Gonium pectorale (Volvocales, Chlorophyta). (United States)

    Iida, Hitoshi; Ota, Shuhei; Inouye, Isao


    Multicellularity arose several times in evolution of eukaryotes. The volvocine algae have full range of colonial organization from unicellular to colonies, and thus these algae are well-known models for examining the evolution and mechanisms of multicellularity. Gonium pectorale is a multicellular species of Volvocales and is thought to be one of the first small colonial organisms among the volvocine algae. In these algae, a cytoplasmic bridge is one of the key traits that arose during the evolution of multicellularity. Here, we observed the inversion process and the cytoplasmic bridges in G. pectorale using time-lapse, fluorescence, and electron microscopy. The cytoplasmic bridges were located in the middle region of the cell in 2-, 4-, 8-, and 16-celled stages and in inversion stages. However, there were no cytoplasmic bridges in the mature adult stage. Cytoplasmic bridges and cortical microtubules in G. pectorale suggest that a mechanism of kinesin-microtubule machinery similar to that in other volvocine algae is responsible for inversion in this species.

  17. Atrazine-resistant cytoplasmic male-sterile-nigra broccoli obtained by protoplast fusion between cytoplasmic male-sterile Brassica oleracea and atrazine-resistant Brassica campestris. (United States)

    Christey, M C; Makaroff, C A; Earle, E D


    Protoplast fusion was used to combine the cytoplasmic traits of atrazine resistance and male sterility in Brassica oleracea var. italica (broccoli). Leaf protoplasts from broccoli with the petaloid B. nigra type of cytoplasmic male sterility were fused with hypocotyl protoplasts from an atrazine-resistant biotype of B. campestris var. oleifera cv Candle (oilseed rape). A total of 19 colonies regenerated shoots, all of which were broccolilike in phenotype, i.e., lacked trichomes. Four shoots, all from one colony, were atrazine resistant, surviving and growing in the presence of 25 μM atrazine. A leaf piece assay also confirmed that they were atrazine resistant. Molecular analysis showed that they contain chloroplasts from the atrazine-resistant B. campestris parent and mitochondria from the B. nigra parent. No recombination or rearrangement of the mitochondrial genomes in the fusion products was detected. These four plants and their progeny all showed the petaloid B. nigra type of male sterility.

  18. Cytoplasmic Skp2 expression is associated with p-Akt1 and predicts poor prognosis in human breast carcinomas.

    Directory of Open Access Journals (Sweden)

    Jing Liu

    Full Text Available BACKGROUND: S-phase kinase protein 2 (Skp2, an oncogenic protein, is a key regulator in different cellular and molecular processes, through ubiquitin-proteasome degradation pathway. Increased levels of Skp2 are observed in various types of cancer and associated with poor prognosis. However, in human breast carcinomas, the underlying mechanism and prognostic significance of cytoplasmic Skp2 is still undefined. METHODS: To investigate the role of cytoplasmic Skp2 expression in human breast carcinomas, we immnohistochemically assessed cytoplasmic Skp2, p-Akt1, and p27 expression in 251 patients with invasive ductal carcinomas of the breast. Association of cytoplasmic Skp2 expression with p-Akt1 and p27 was analyzed as well as correspondence with other clinicopathological parameters. Disease-free survival and overall survival were determined based on the Kaplan-Meier method and Cox regression models. RESULTS: Cytoplasmic of Skp2 was detected in 165 out of 251 (65.7% patients. Cytoplasmic Skp2 expression was associated with larger tumor size, more advanced histological grade, and positive HER2 expression. Increased cytoplasmic Skp2 expression correlated with p-Akt1 expression, with 54.2% (51/94 of low p-Akt1-expressing breast carcinomas, but 72.6% (114/157 of high p-Akt1-expressing breast carcinomas exhibiting cytoplasmic Skp2 expression. Elevated cytoplasmic Skp2 expression with low p-Akt1 expression was associated with poor disease-free and overall survival (DFS and OS, and Cox regression models demonstrated that cytoplasmic Skp2 expression was an independent prognostic marker for invasive breast carcinomas. CONCLUSION: Cytoplasmic Skp2 expression is associated with aggressive prognostic factors, such as larger tumor size, and advanced histological grade of the breast cancers. Results demonstrate that combined cytoplasmic Skp2 and p-Akt1 expression may be prognostic for patients with invasive breast carcinomas, and cytoplasmic Skp2 may serve as a

  19. Fine coal processing with dense-medium cyclones

    CSIR Research Space (South Africa)

    De Korte, GJ


    Full Text Available Dense medium cyclones have been used for many years in a number of countries to beneficiate fine coal. The use of cyclones in this application is, however, not widespread and at present, the process is in use only in South Africa and China...

  20. Subtle Monte Carlo Updates in Dense Molecular Systems

    DEFF Research Database (Denmark)

    Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.


    a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule...

  1. Force Statistics and Correlations in Dense Granular Packings

    NARCIS (Netherlands)

    Müller, M.K; Luding, Stefan; Pöschel, Thorsten


    In dense, static, polydisperse granular media under isotropic pressure, the probability density and the correlations of particle-wall contact forces are studied. Furthermore, the probability density functions of the populations of pressures measured with different sized circular pressure cells are

  2. Directly calculating electrical conductivities of dense hydrogen from molecular dynamics (United States)

    Ma, Qian; Kang, Dongdong; Dai, Jiayu


    The transport properties are important in warm and hot dense matter in which the Coulomb interaction is dominated in the scattering process. Density functional theory (DFT) is considered as an effective method to investigate the transport properties, but the dynamical collisions between particles are missed. Here we use an electron force field (eFF) method based molecular dynamics (MD) to include the electronic quantum effects to investigate the transport properties of warm dense hydrogen. The eFF method can be regarded as the development of wave packets molecular dynamics and it has been successfully used to describe the thermodynamics of hydrogen, Auger process in diamondoids, the equation of states for dense lithium. The most important point of eFF method is assuming that each electron is considered as a Gaussian wave packet controlled by position and size while ions are still charged points. The electrical conductivity is calculated via the correlation of electrical current. The results show that electronic quantum effects are important for the transport properties in warm dense hydrogen such as diffusion coefficient and electrical conductivity, which are much smaller than the results from DFT calculations.

  3. Sparse symmetric preconditioners for dense linear systems in electromagnetism

    NARCIS (Netherlands)

    Carpentieri, Bruno; Duff, Iain S.; Giraud, Luc; Monga Made, M. Magolu


    We consider symmetric preconditioning strategies for the iterative solution of dense complex symmetric non-Hermitian systems arising in computational electromagnetics. In particular, we report on the numerical behaviour of the classical incomplete Cholesky factorization as well as some of its recent

  4. Dense and accurate whole-chromosome haplotyping of individual genomes

    NARCIS (Netherlands)

    Porubsky, David; Garg, Shilpa; Sanders, Ashley D.; Korbel, Jan O.; Guryev, Victor; Lansdorp, Peter M.; Marschall, Tobias


    The diploid nature of the human genome is neglected in many analyses done today, where a genome is perceived as a set of unphased variants with respect to a reference genome. This lack of haplotype-level analyses can be explained by a lack of methods that can produce dense and accurate

  5. Spaces in which every dense subset is a G δ

    African Journals Online (AJOL)

    A topological space X is called a DG-space if every subset of X is a G-set in its closure. In this paper we study DG-spaces that contains subspaces in which every dense subset is open and spaces in which every subset is a G. We give some new results in these classes of topological spaces.

  6. Dilution in a Dense Bottom Jet in Cross Currents

    DEFF Research Database (Denmark)

    Petersen, O.; Larsen, Torben


    A 3-dimensional numerical model describing the dilution in the near field around dense vertical jets in a cross flow is formulated and validated against laboratory experiments. The validation shows that the model reproduces the flow pattern well, though the dilution is underestimated by 20%. The ...

  7. Neutrino-electron scattering in a dense strongly magnetized plasma

    Directory of Open Access Journals (Sweden)

    Kuznetsov Alexander


    Full Text Available We investigate the process of neutrino-electron scattering in a dense plasma and magnetic field of arbitrary strength, where electrons can occupy the states corresponding to excited Landau levels. We calculate the total probability of this process, summarized over all initial states of the plasma electrons which is only physically meaningful. Possible astrophysical manifestations of the process are briefly discussed.

  8. Numerical simulation of the fast dense gas Ludwieg tube experiment

    NARCIS (Netherlands)

    Zamfirescu, C.; Guerdone, A.; Collona, P.


    The preliminary design of a Ludwieg tube experiment for the verification of the existence of nonclassical rarefaction shock waves in dense vapors is here critically analyzed by means of real gas numerical simulations of the experimental setup. The Flexible Asymmetric Shock Tube (FAST) setup is a

  9. Hugoniot measurements of double-shocked precompressed dense xenon plasmas. (United States)

    Zheng, J; Chen, Q F; Gu, Y J; Chen, Z Y


    The current partially ionized plasmas models for xenon show substantial differences since the description of pressure and thermal ionization region becomes a formidable task, prompting the need for an improved understanding of dense xenon plasmas behavior at above 100 GPa. We performed double-shock compression experiments on dense xenon to determine accurately the Hugoniot up to 172 GPa using a time-resolved optical radiation method. The planar strong shock wave was produced using a flyer plate impactor accelerated up to ∼6 km/s with a two-stage light-gas gun. The time-resolved optical radiation histories were acquired by using a multiwavelength channel optical transience radiance pyrometer. Shock velocity was measured and mass velocity was determined by the impedance-matching methods. The experimental equation of state of dense xenon plasmas are compared with the self-consistent fluid variational calculations of dense xenon in the region of partial ionization over a wide range of pressures and temperatures.

  10. Dense Descriptors for Optical Flow Estimation: A Comparative Study

    Directory of Open Access Journals (Sweden)

    Ahmadreza Baghaie


    Full Text Available Estimating the displacements of intensity patterns between sequential frames is a very well-studied problem, which is usually referred to as optical flow estimation. The first assumption among many of the methods in the field is the brightness constancy during movements of pixels between frames. This assumption is proven to be not true in general, and therefore, the use of photometric invariant constraints has been studied in the past. One other solution can be sought by use of structural descriptors rather than pixels for estimating the optical flow. Unlike sparse feature detection/description techniques and since the problem of optical flow estimation tries to find a dense flow field, a dense structural representation of individual pixels and their neighbors is computed and then used for matching and optical flow estimation. Here, a comparative study is carried out by extending the framework of SIFT-flow to include more dense descriptors, and comprehensive comparisons are given. Overall, the work can be considered as a baseline for stimulating more interest in the use of dense descriptors for optical flow estimation.

  11. Interaction of ultrarelativistic electron and proton bunches with dense plasmas

    CERN Document Server

    Rukhadze, A A


    Here we discuss the possibility of employment of ultrarelativistic electron and proton bunches for generation of high plasma wakefields in dense plasmas due to the Cherenkov resonance plasma-bunch interaction. We estimate the maximum amplitude of such a wake and minimum system length at which the maximum amplitude can be generated at the given bunch parameters.

  12. Dense 3D Map Construction for Indoor Search and Rescue

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Huang, Shoudong; Miró, Jaime Valls


    The main contribution of this paper is a new simultaneous localization and mapping  SLAM algorithm for building dense three-dimensional maps using information ac- quired from a range imager and a conventional camera, for robotic search and rescue in unstructured indoor environments. A key challenge...

  13. Influence of Food Packaging on Children's Energy-dense Snack ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Childhood obesity is a major global public health concern. Rates of obese and overweight children have increased in low- and middle-income countries such as Guatemala. This research will study the influence of food packaging on Guatemalan preschool and school-aged children's energy-dense snack (EDS) food ...

  14. Obtaining and some properties of dense corundum-zirconium ceramics

    Energy Technology Data Exchange (ETDEWEB)

    Baranova, T.F.; Grishina, N.E.; Prokhorova, G.N.


    A dense pressed and cast corundum-zirconium ceramics is developed. The material is produced at relatively low calcination temperatures (1580 deg C). Cermics has a high compression strength (450 and 320 MPa at 950 and 1050 deg C, respectively) and it can be used as a structural material for small-size stamp insertions.

  15. A comparative study of fast dense stereo vision algorithms

    NARCIS (Netherlands)

    Sunyoto, H.; Mark, W. van der; Gavrila, D.M.


    With recent hardware advances, real-time dense stereo vision becomes increasingly feasible for general-purpose processors. This has important benefits for the intelligent vehicles domain, alleviating object segmentation problems when sensing complex, cluttered traffic scenes. In this paper, we

  16. Rapid haplotype reconstruction in predigrees with dense marker maps

    NARCIS (Netherlands)

    Windig, J.J.; Meuwissen, T.H.E.


    Reconstruction of marker phases is not straightforward when parents are untyped. In these cases information from other relatives has to be used. In dense marker maps, however, the space of possible haplotype configurations tends to be too large for procedures such as Monte Carlo Markov chains (MCMC)

  17. Dense Focal Plane Arrays for Pushbroom Satellite Radiometers

    DEFF Research Database (Denmark)

    Iupikov, O. A.; Ivashina, M. V.; Pontoppidan, K.


    Performance of a dense focal plane array feeding an offset toroidal reflector antenna system is studied and discussed in the context of a potential application in multi-beam radiometers for ocean surveillance. We present a preliminary design of the array feed for the 5-m diameter antenna at X-ban...

  18. Complete mitochondrial genome sequence and identification of a candidate gene responsible for cytoplasmic male sterility in radish (Raphanus sativus L.) containing DCGMS cytoplasm. (United States)

    Park, Jee Young; Lee, Young-Pyo; Lee, Jonghoon; Choi, Beom-Soon; Kim, Sunggil; Yang, Tae-Jin


    A novel cytoplasmic male sterility (CMS) conferred by Dongbu cytoplasmic and genic male-sterility (DCGMS) cytoplasm and its restorer-of-fertility gene (Rfd1) was previously reported in radish (Raphanus sativus L.). Its inheritance of fertility restoration and profiles of mitochondrial DNA (mtDNA)-based molecular markers were reported to be different from those of Ogura CMS, the first reported CMS in radish. The complete mitochondrial genome sequence (239,186 bp; GenBank accession No. KC193578) of DCGMS mitotype is reported in this study. Thirty-four protein-coding genes and three ribosomal RNA genes were identified. Comparative analysis of a mitochondrial genome sequence of DCGMS and previously reported complete sequences of normal and Ogura CMS mitotypes revealed various recombined structures of seventeen syntenic sequence blocks. Short-repeat sequences were identified in almost all junctions between syntenic sequence blocks. Phylogenetic analysis of three radish mitotypes showed that DCGMS was more closely related to the normal mitotype than to the Ogura mitotype. A single 1,551-bp unique region was identified in DCGMS mtDNA sequences and a novel chimeric gene, designated orf463, consisting of 128-bp partial sequences of cox1 gene and 1,261-bp unidentified sequences were found in the unique region. No other genes with a chimeric structure, a major feature of most characterized CMS-associated genes in other plant species, were found in rearranged junctions of syntenic sequence blocks. Like other known CMS-associated mitochondrial genes, the predicted gene product of orf463 contained 12 transmembrane domains. Thus, this gene product might be integrated into the mitochondrial membrane. In total, the results indicate that orf463 is likely to be a casual factor for CMS induction in radish containing the DCGMS cytoplasm.

  19. Secretion of Cpn0796 from Chlamydia pneumoniae into the host cell cytoplasm by an autotransporter mechanism

    DEFF Research Database (Denmark)

    Vandahl, Brian B S; Stensballe, Allan; Roepstorff, Peter


    By comparison of proteome profiles of purified Chlamydia pneumoniae and whole lysates of C. pneumoniae infected HEp-2 cells, an N-terminal fragment of the previously uncharacterized chlamydial protein Cpn0796 was identified as a secreted protein. A 38 kDa cleavage product of Cpn0796 was present...... of C. pneumoniae infected HEp-2 and BHK cells. Furthermore, Cpn0796 was detected in the cytoplasm of infected cells in the lungs of C. pneumoniae infected C57Bl mice. When cleavage was inhibited, Cpn0796 was retained in the chlamydiae. We propose that Cpn0796 is an autotransporter the N......-terminal of which is translocated to the host cell cytoplasm. This is the first example of secretion of a Chlamydia autotransporter passenger domain into the host cell cytoplasm. Cpn0796 is specific for C. pneumoniae, where five homologous proteins are encoded by clustered genes. None of these five proteins were...

  20. An FNA pitfall: Mammary analog secretory carcinoma mistaken for acinic cell carcinoma due to cytoplasmic granules

    Directory of Open Access Journals (Sweden)

    Nouf Hijazi, MD


    Full Text Available In the salivary gland, a key differential feature of Mammary analog secretory carcinoma (MASC from acinic cell carcinoma (ACC is the lack of cytoplasmic granules. We report a case of a parotid mass incorrectly diagnosed on fine needle aspirate as acinic cell carcinoma due to many cells with basophilic granules suggesting serous acinar differention. Tumor resection revealed a tumor consistent with low grade adenocarcinoma that had eosinophilic, microvacuolar cytoplasm with distinct basophilic granules staining with PASD and mucicarmine. The diagnosis of MASC was confirmed with stains for GCDF-15, mammoglobin, and S100 and FISH consistent with a t(12;15 translocation. Relying on the absence of cytoplasmic granules as a feature to distinguish ACC from MASC is a diagnostic pitfall.

  1. Essential role of cytoplasmic cdk5 and Prx2 in multiple ischemic injury models, in vivo. (United States)

    Rashidian, Juliet; Rousseaux, Maxime W; Venderova, Katerina; Qu, Dianbo; Callaghan, Steve M; Phillips, Maryam; Bland, Ross J; During, Matthew J; Mao, Zixu; Slack, Ruth S; Park, David S


    Recent evidence suggests that abnormal activation of cyclin-dependent kinase 5 (cdk5) is a critical prodeath signal in stroke. However, the mechanism(s) by which cdk5 promotes death is unclear. Complicating the role of cdk5 are the observations that cdk5 can exist in multiple cellular regions and possess both prosurvival and prodeath characteristics. In particular, the critical role of cytoplasmic or nuclear cdk5 in neuronal jury, in vivo, is unclear. Therefore, we determined where cdk5 was activated in models of ischemia and how manipulation of cdk5 in differing compartments may affect neuronal death. Here, we show a critical function for cytoplasmic cdk5 in both focal and global models of stroke, in vivo. Cdk5 is activated in the cytoplasm and expression of DNcdk5 localized to the cytoplasm is protective. Importantly, we also demonstrate the antioxidant enzyme Prx2 (peroxiredoxin 2) as a critical cytoplasmic target of cdk5. In contrast, the role of cdk5 in the nucleus is context-dependent. Following focal ischemia, nuclear cdk5 is activated and functionally relevant while there is no evidence for such activation following global ischemia. Importantly, myocyte enhancer factor 2D (MEF2D), a previously described nuclear target of cdk5 in vitro, is also phosphorylated by cdk5 following focal ischemia. In addition, MEF2D expression in this paradigm ameliorates death. Together, our results address the critical issue of cdk5 activity compartmentalization, as well as define critical substrates for both cytoplasmic and nuclear cdk5 activity in adult models of stroke.

  2. Distinct cytoplasmic and nuclear functions of the stress induced protein DDIT3/CHOP/GADD153.

    Directory of Open Access Journals (Sweden)

    Alexandra Jauhiainen

    Full Text Available DDIT3, also known as GADD153 or CHOP, encodes a basic leucine zipper transcription factor of the dimer forming C/EBP family. DDIT3 is known as a key regulator of cellular stress response, but its target genes and functions are not well characterized. Here, we applied a genome wide microarray based expression analysis to identify DDIT3 target genes and functions. By analyzing cells carrying tamoxifen inducible DDIT3 expression constructs we show distinct gene expression profiles for cells with cytoplasmic and nuclear localized DDIT3. Of 175 target genes identified only 3 were regulated by DDIT3 in both cellular localizations. More than two thirds of the genes were downregulated, supporting a role for DDIT3 as a dominant negative factor that could act by either cytoplasmic or nuclear sequestration of dimer forming transcription factor partners. Functional annotation of target genes showed cell migration, proliferation and apoptosis/survival as the most affected categories. Cytoplasmic DDIT3 affected more migration associated genes, while nuclear DDIT3 regulated more cell cycle controlling genes. Cell culture experiments confirmed that cytoplasmic DDIT3 inhibited migration, while nuclear DDIT3 caused a G1 cell cycle arrest. Promoters of target genes showed no common sequence motifs, reflecting that DDIT3 forms heterodimers with several alternative transcription factors that bind to different motifs. We conclude that expression of cytoplasmic DDIT3 regulated 94 genes. Nuclear translocation of DDIT3 regulated 81 additional genes linked to functions already affected by cytoplasmic DDIT3. Characterization of DDIT3 regulated functions helps understanding its role in stress response and involvement in cancer and degenerative disorders.

  3. Comparative assessment of genetic diversity in cytoplasmic and nuclear genome of upland cotton. (United States)

    Egamberdiev, Sharof S; Saha, Sukumar; Salakhutdinov, Ilkhom; Jenkins, Johnie N; Deng, Dewayne; Y Abdurakhmonov, Ibrokhim


    The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.

  4. A Mechanism for Cytoplasmic Streaming: Kinesin-Driven Alignment of Microtubules and Fast Fluid Flows. (United States)

    Monteith, Corey E; Brunner, Matthew E; Djagaeva, Inna; Bielecki, Anthony M; Deutsch, Joshua M; Saxton, William M


    The transport of cytoplasmic components can be profoundly affected by hydrodynamics. Cytoplasmic streaming in Drosophila oocytes offers a striking example. Forces on fluid from kinesin-1 are initially directed by a disordered meshwork of microtubules, generating minor slow cytoplasmic flows. Subsequently, to mix incoming nurse cell cytoplasm with ooplasm, a subcortical layer of microtubules forms parallel arrays that support long-range, fast flows. To analyze the streaming mechanism, we combined observations of microtubule and organelle motions with detailed mathematical modeling. In the fast state, microtubules tethered to the cortex form a thin subcortical layer and undergo correlated sinusoidal bending. Organelles moving in flows along the arrays show velocities that are slow near the cortex and fast on the inward side of the subcortical microtubule layer. Starting with fundamental physical principles suggested by qualitative hypotheses, and with published values for microtubule stiffness, kinesin velocity, and cytoplasmic viscosity, we developed a quantitative coupled hydrodynamic model for streaming. The fully detailed mathematical model and its simulations identify key variables that can shift the system between disordered (slow) and ordered (fast) states. Measurements of array curvature, wave period, and the effects of diminished kinesin velocity on flow rates, as well as prior observations on f-actin perturbation, support the model. This establishes a concrete mechanistic framework for the ooplasmic streaming process. The self-organizing fast phase is a result of viscous drag on kinesin-driven cargoes that mediates equal and opposite forces on cytoplasmic fluid and on microtubules whose minus ends are tethered to the cortex. Fluid moves toward plus ends and microtubules are forced backward toward their minus ends, resulting in buckling. Under certain conditions, the buckling microtubules self-organize into parallel bending arrays, guiding varying directions

  5. Analysis of cytoplasmic effects and fine-mapping of a genic male sterile line in rice.

    Directory of Open Access Journals (Sweden)

    Peng Qin

    Full Text Available Cytoplasm has substantial genetic effects on progeny and is important for yield improvement in rice breeding. Studies on the cytoplasmic effects of cytoplasmic male sterility (CMS show that most types of CMS have negative effects on yield-related traits and that these negative effects vary among CMS. Some types of genic male sterility (GMS, including photo-thermo sensitive male sterility (PTMS, have been widely used in rice breeding, but the cytoplasmic effects of GMS remain unknown. Here, we identified a GMS mutant line, h2s, which exhibited small, white anthers and failed to produce mature pollen. Unlike CMS, the h2s had significant positive cytoplasmic effects on the seed set rate, weight per panicle, yield, and general combining ability (GCA for plant height, seed set rate, weight per panicle, and yield. These effects indicated that h2s cytoplasm may show promise for the improvement of rice yield. Genetic analysis suggested that the phenotype of h2s was controlled by a single recessive locus. We mapped h2s to a 152 kb region on chromosome 6, where 22 candidate genes were predicted. None of the 22 genes had previously been reported to be responsible for the phenotypes of h2s. Sequencing analysis showed a 12 bp deletion in the sixth exon of Loc_Os06g40550 in h2s in comparison to wild type, suggesting that Loc_Os06g40550 is the best candidate gene. These results lay a strong foundation for cloning of the H2S gene to elucidate the molecular mechanism of male reproduction.

  6. Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps (United States)

    Tennessen, Jacob A.; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron


    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420

  7. A special fructose bisphosphate functions as a cytoplasmic regulatory metabolite in green leaves


    Cséke, Csaba; Weeden, Norman F.; Buchanan, Bob B.; Uyeda, Kosaku


    Fructose 2,6-bisphosphate (Fru-2,6-P2), a regulatory metabolite discovered in animal cells and recently reported to occur in etiolated seedlings, was found to be present in the cytoplasmic fraction of leaves of spinach and peas (typical C3 plants, in which a three-carbon carboxylic acid is a major early photosynthetic product). At concentrations approximating those calculated to occur physiologically, Fru-2,6-P2 modulated two enzymes of the leaf cytoplasm: (i) Fructose-1,6-bisphosphatase (EC ...

  8. Wild Nicotiana Species as a Source of Cytoplasmic Male Sterility in Nicotianatabacum

    Directory of Open Access Journals (Sweden)

    Nikova V


    Full Text Available The results of our experiments executed to obtain tobacco male sterile lines through interspecific hybridization are summarized. Ten wild species from the genus Nicotiana: N. excelsior (exc, N. amplexicaulis (amp, N. rustica (rus, Nicotianaglauca (gla, N. velutina (vel, N. benthamiana (ben, N. maritima (mar, N. paniculata (pan, N. longiflora (lon and N. africana (afr were used as cytoplasmic donors and N. tabacum, cv. HarmanliiskaBasma (HB as a donor of the nucleus. Genetic effects of cytoplasmic-nuclear interaction of the studied species are discussed. Our results suggested that cytoplasmic male sterility (CMS was expressed when the cytoplasms of the above mentioned wild Nicotiana species were combined with the nucleus of N. tabacum. The 10 sources of CMS obtained in tobacco were characterized by altered flower phenotypes. Flowers are classified into types according the stamen, pistil and corolla modification. All these CMS sources were backcrossed to Oriental tobaccos, cvs. Tekne, Nevrokop B-12, Kroumovgrad 90 and Djebel 576, to develop corresponding CMS lines. The investigated cytoplasms produced compete male sterility in all those cultivars. The CMS lines preserved flower types, specific for every “sterile” cytoplasm. The extent of male organ modifications varied from apparently normal (but pollenless stamens in CMS (pan, (afr, some plants of (vel (mar through different degrees of malformations (shriveled anther on shortened filaments (lon, pinnate-like anthers on filaments of normal length (amp, petal - (ben, pistil- or stigma-like structures (rus, (gla to lack of male reproductive organs in (exc and in some plants of (vel, (mar, (rus and (gla. Most of the above mentioned cytoplasms had normal female gametophyte and good seed productivity. Alterations of the pistils were observed in CMS (rus, (exc and (ben causing reduction of the seed set. Electrophoresis of seed proteins of the tobacco cultivars and their CMS lines also suggested that

  9. A cytoplasmic protein-protein interaction detection method based on reporter translation. (United States)

    Renaut, Laurence; Bouayadi, Khalil; Kharrat, Hakim; Mondon, Philippe


    One approach to drug discovery involves the targeting of abnormal protein-protein interactions that lead to pathology. We present a new technology allowing the detection of such interactions within the cytoplasm in a yeast-based system. The interaction detection is based on the sequestration of a translation termination factor involved in stop codon recognition. This sequestration inhibits the activity of the factor, thereby permitting the translation of a reporter gene harboring a premature stop codon. This novel cytoplasmic protein-protein interaction (CPPI) detection system should prove to be useful in the characterization of proteins as well as in partner identification, interaction mapping, and drug discovery applications.

  10. Spatial Organization of the Cell Cytoplasm by Position-Dependent Phase Separation (United States)

    Lee, Chiu Fan; Brangwynne, Clifford P.; Gharakhani, Jöbin; Hyman, Anthony A.; Jülicher, Frank


    During asymmetric cell division, cytoplasmic components are segregated to opposite sides of the cell. We discuss how the observed segregation can be achieved by a position-dependent phase separation mechanism controlled by a protein concentration gradient. We show that effects of even a weak gradient can be amplified by the phase transition to achieve strong segregation. We compare our theory to the segregation of germ granules observed during the divisions in the C. elegans embryo. Our study demonstrates how liquid-liquid phase separation can play a key role in the organization of the cytoplasm.

  11. Model studies of dense water overflows in the Faroese Channels (United States)

    Cuthbertson, Alan; Davies, Peter; Stashchuk, Nataliya; Vlasenko, Vasiliy


    The overflow of dense water from the Nordic Seas through the Faroese Channel system was investigated through combined laboratory experiments and numerical simulations using the Massachusetts Institute of Technology General Circulation Model. In the experimental study, a scaled, topographic representation of the Faroe-Shetland Channel, Wyville-Thomson Basin and Ridge and Faroe Bank Channel seabed bathymetry was constructed and mounted in a rotating tank. A series of parametric experiments was conducted using dye-tracing and drogue-tracking techniques to investigate deep-water overflow pathways and circulation patterns within the modelled region. In addition, the structure of the outflowing dense bottom water was investigated through density profiling along three cross-channel transects located in the Wyville-Thomson Basin and the converging, up-sloping approach to the Faroe Bank Channel. Results from the dye-tracing studies demonstrate a range of parametric conditions under which dense water overflow across the Wyville-Thomson Ridge is shown to occur, as defined by the Burger number, a non-dimensional length ratio and a dimensionless dense water volume flux parameter specified at the Faroe-Shetland Channel inlet boundary. Drogue-tracking measurements reveal the complex nature of flow paths and circulations generated in the modelled topography, particularly the development of a large anti-cyclonic gyre in the Wyville-Thompson Basin and up-sloping approach to the Faroe Bank Channel, which diverts the dense water outflow from the Faroese shelf towards the Wyville-Thomson Ridge, potentially promoting dense water spillage across the ridge itself. The presence of this circulation is also indicated by associated undulations in density isopycnals across the Wyville-Thomson Basin. Numerical simulations of parametric test cases for the main outflow pathways and density structure in a similarly-scaled Faroese Channels model domain indicate excellent qualitative agreement with

  12. Dense Plasma X-ray Scattering: Methods and Applications

    Energy Technology Data Exchange (ETDEWEB)

    Glenzer, S H; Lee, H J; Davis, P; Doppner, T; Falcone, R W; Fortmann, C; Hammel, B A; Kritcher, A L; Landen, O L; Lee, R W; Munro, D H; Redmer, R; Weber, S


    We have developed accurate x-ray scattering techniques to measure the physical properties of dense plasmas. Temperature and density are inferred from inelastic x-ray scattering data whose interpretation is model-independent for low to moderately coupled systems. Specifically, the spectral shape of the non-collective Compton scattering spectrum directly reflects the electron velocity distribution. In partially Fermi degenerate systems that have been investigated experimentally in laser shock-compressed beryllium, the Compton scattering spectrum provides the Fermi energy and hence the electron density. We show that forward scattering spectra that observe collective plasmon oscillations yield densities in agreement with Compton scattering. In addition, electron temperatures inferred from the dispersion of the plasmon feature are consistent with the ion temperature sensitive elastic scattering feature. Hence, theoretical models of the static ion-ion structure factor and consequently the equation of state of dense matter can be directly tested.

  13. The electron-atom interaction in partially ionized dense plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Omarbakiyeva, Yu A; Ramazanov, T S; Roepke, G [IETP, Al Farabi Kazakh National University, Tole Bi 96a, Almaty 050012 (Kazakhstan)], E-mail:


    The electron-atom interaction is considered in dense partially ionized plasmas. The separable potential is constructed from scattering data using effective radius theory. Parameters of the interaction potential were obtained from phase shifts, scattering length and effective radius. The binding energy of the electron in the H{sup -} ion is determined for the singlet channel on the basis of the reconstructed separable potential. In dense plasmas, the influence of the Pauli exclusion principle on the phase shifts and the binding energy is considered. Due to the Pauli blocking, the binding energy vanishes at the Mott density. At that density the behavior of the phase shifts is drastically changed. This leads to modifications of macroscopic properties such as composition and transport coefficients.

  14. Diagnosis of Choroidal Melanoma in Dense Asteroid Hyalosis. (United States)

    Motiani, Meghna V; McCannel, Colin A; Almanzor, Robert; McCannel, Tara A


    To demonstrate the utility of Optos ultra-wide field imaging in the diagnosis and management of choroidal melanoma in the setting of asteroid hyalosis. Observational case report. A 52-year-old female was referred for evaluation of floaters, photopsias, and blurry vision in the right eye. Clinical examination revealed dense asteroid hyalosis obscuring the fundus, and a limited view of a pigmented choroidal lesion in the nasal periphery. Optos ultra-wide field fluorescein angiography and ultrasonography facilitated the diagnosis of a choroidal melanoma. The patient underwent Iodine-125 brachytherapy for local tumor control and excellent tumor response was confirmed with serial follow-up Optos imaging and ultrasonography. Ultra-wide field fundus fluorescein angiography facilitated the diagnosis of a choroidal melanoma, which was obscured by dense asteroid hyalosis, allowing for local tumor control with brachytherapy. Optos wide-field imaging may be a valuable tool for detecting potentially life-threatening lesions in the setting of asteroid hyalosis.

  15. Dynamic Conductivity and Partial Ionization in Warm, Dense Hydrogen (United States)

    Zaghoo, M.; Silvera, I. F.


    A theoretical description for optical conduction experiments in dense fluid hydrogen is presented. Different quantum statistical approaches are used to describe the mechanism of electron transport in hydrogen's high-temperature dense phase. We show that at the onset of the metallic transition, optical conduction could be described by a strong rise in the atomic polarizability, resulting from increased ionization; whereas in the highly degenerate limit, the Ziman weak-scattering model better describes the observed saturation of reflectance. In the highly degenerate region, the inclusion of partial ionization effects provides excellent agreement with experimental results. Hydrogen's fluid metallic state is revealed to be a partially ionized free-electron plasma. These results provide a crucial benchmark for ab initio calculations as well as an important guide for future experiments. Research supported by DOE Stockpile Stewardship Academic Alliance Program, Grant DE-FG52-10NA29656, and NASA Earth and Space Science Fellowship Program, Award NNX14AP17H.

  16. Distributed Wi-Fi Interference Coordination for Dense Deployments

    DEFF Research Database (Denmark)

    Abinader, Fuad; Choudhury, Sayantan; Souza Jr., Vicente A.


    Unlicensed spectrum is increasingly being used by mobile operators to meet the mobile traffic demand, and Wi-Fi is foreseen as one of the technologies for implementing mobile traffic offloading. However, Wi-Fi efficiency does not scale well as node density increases, and IEEE 802.11ax Task Group...... (TGax) was created in 2014 for developing WiFi technology enhancements in dense deployments. This paper investigates Wi-Fi performance in the presence of Overlapping Basic Subscriber Set (OBSS) Wi-Fi networks in indoor dense deployments. We observe that Wi-Fi could benefit from scheduled operation...... with proper OBSS interference coordination. We propose a novel distributed interference coordination scheme for Wi-Fi scheduled mode operation, and evaluate it through system level simulations. Results indicate that the proposed scheme provides significant improvements over Enhanced Distributed Channel Access...

  17. Equation of state and correlation energy of dense plasmas

    CERN Document Server

    Schlanges, M; DeWitt, H E; Kraeft, W D


    In this paper, the method of thermodynamic Green's functions is applied to investigate thermodynamic properties of dense weakly coupled plasmas. First, we present results for the equation of state for fully ionized hydrogen and compare our results with path integral Monte Carlo simulation data. Densities and temperatures are considered where correlations as well as Fermi statistics have to be taken into account. Then, the correlation energy and the mean value of the kinetic energy of dense plasmas are considered. Usually one finds that the kinetic energy is larger than that of an ideal system due to the interaction. However, in agreement with results from quantum simulations, we found, for certain densities and temperatures, a lowering of the kinetic energy.

  18. Numerical Simulation of Cold Dense Plasma Sputtering with VORPAL (United States)

    Zhou, Chuandong; Stoltz, Peter; Veitzer, Seth


    Sputtering is an evaporation process that physically removes atoms from a solid target material. This process takes place under bombardment of the target surface by energetic ions. Sputtering is widely applied in material processing and coating, such as etching and thin film deposition. Numerical simulation of sputtering process requires both accurate models of nuclear stopping in materials, particle dynamics and consistent electromagnetic fields. The particle in cell code VORPAL can simulate cold dense plasma under many different electromagnetic configurations. The dynamics of both incident particles and sputtered neutral atoms are simulated in VORPAL, and the sputtering yield is calculated from a standalone numerical library for a variety of materials that are commonly used in industrial applications. Numerical simulation of the spatial distribution of sputtering resulting from a cold dense plasma under externally applied magnetic field and self-consistent electric field is presented.

  19. MADMX: A Novel Strategy for Maximal Dense Motif Extraction (United States)

    Grossi, Roberto; Pietracaprina, Andrea; Pisanti, Nadia; Pucci, Geppino; Upfal, Eli; Vandin, Fabio

    We develop, analyze and experiment with a new tool, called madmx, which extracts frequent motifs, possibly including don’t care characters, from biological sequences. We introduce density, a simple and flexible measure for bounding the number of don’t cares in a motif, defined as the ratio of solid (i.e., different from don’t care) characters to the total length of the motif. By extracting only maximal dense motifs, madmx reduces the output size and improves performance, while enhancing the quality of the discoveries. The efficiency of our approach relies on a newly defined combining operation, dubbed fusion, which allows for the construction of maximal dense motifs in a bottom-up fashion, while avoiding the generation of nonmaximal ones. We provide experimental evidence of the efficiency and the quality of the motifs returned by madmx.

  20. Reduction of Classical Measurement Noise via Quantum-Dense Metrology. (United States)

    Ast, Melanie; Steinlechner, Sebastian; Schnabel, Roman


    Quantum-dense metrology constitutes a special case of quantum metrology in which two orthogonal phase space projections of a signal are simultaneously sensed beyond the shot-noise limit. Previously, it was shown that the additional sensing channel that is provided by quantum-dense metrology contains information that can be used to identify and to discard corrupted segments from the measurement data. Here, we propose and demonstrate a new method in which this information is used for improving the sensitivity without discarding any measurement segments. Our measurement reached sub-shot-noise performance, although initially strong classical noise polluted the data. The new method has high potential for improving the noise spectral density of gravitational-wave detectors at signal frequencies of high astrophysical relevance.

  1. Collective waves in dense and confined microfluidic droplet arrays. (United States)

    Schiller, Ulf D; Fleury, Jean-Baptiste; Seemann, Ralf; Gompper, Gerhard


    Excitation mechanisms for collective waves in confined dense one-dimensional microfluidic droplet arrays are investigated by experiments and computer simulations. We demonstrate that distinct modes can be excited by creating specific 'defect' patterns in flowing droplet trains. Excited longitudinal modes exhibit a short-lived cascade of pairs of laterally displacing droplets. Transversely excited modes obey the dispersion relation of microfluidic phonons and induce a coupling between longitudinal and transverse modes, whose origin is the hydrodynamic interaction of the droplets with the confining walls. Moreover, we investigate the long-time behaviour of the oscillations and discuss possible mechanisms for the onset of instabilities. Our findings demonstrate that the collective dynamics of microfluidic droplet ensembles can be studied particularly well in dense and confined systems. Experimentally, the ability to control microfluidic droplets may allow the modulation of the refractive index of optofluidic crystals, which is a promising approach for the production of dynamically programmable metamaterials.

  2. Traveling salesman problem, conformal invariance, and dense polymers. (United States)

    Jacobsen, J L; Read, N; Saleur, H


    We propose that the statistics of the optimal tour in the planar random Euclidean traveling salesman problem is conformally invariant on large scales. This is exhibited in the power-law behavior of the probabilities for the tour to zigzag repeatedly between two regions, and in subleading corrections to the length of the tour. The universality class should be the same as for dense polymers and minimal spanning trees. The conjectures for the length of the tour on a cylinder are tested numerically.

  3. Memory-efficient analysis of dense functional connectomes

    Directory of Open Access Journals (Sweden)

    Kristian Loewe


    Full Text Available The functioning of the human brain relies on the interplay and integration of numerous individual units within a complex network. To identify network configurations characteristic of specific cognitive tasks or mental illnesses, functional connectomes can be constructed based on the assessment of synchronous fMRI activity at separate brain sites, and then analyzed using graph-theoretical concepts. In most previous studies, relatively coarse parcellations of the brain were used to define regions as graphical nodes. Such parcellated connectomes are highly dependent on parcellation quality because regional and functional boundaries need to be relatively consistent for the results to be interpretable. In contrast, dense connectomes are not subject to this limitation, since the parcellation inherent to the data is used to define graphical nodes, also allowing for a more detailed spatial mapping of connectivity patterns. However, dense connectomes are associated with considerable computational demands in terms of both time and memory requirements. The memory required to explicitly store dense connectomes in main memory can render their analysis infeasible, especially when considering high-resolution data or analyses across multiple subjects or conditions. Here, we present an object-based matrix representation that achieves a very low memory footprint by computing matrix elements on demand instead of explicitly storing them. In doing so, memory required for a dense connectome is reduced to the amount needed to store the underlying time series data. Based on theoretical considerations and benchmarks, different matrix object implementations and additional programs (based on available Matlab functions and Matlab-based third-party software are compared with regard to their computational efficiency in terms of memory requirements and computation time. The matrix implementation based on on-demand computations has very low memory requirements thus enabling

  4. Composition and thermodynamic properties of dense alkali metal plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Gabdullin, M.T. [NNLOT, al-Farabi Kazakh National University, 71 al-Farabi Str., Almaty 050035 (Kazakhstan); Ramazanov, T.S.; Dzhumagulova, K.N. [IETP, al-Farabi Kazakh National University, 71 al-Farabi Str., Almaty 050035 (Kazakhstan)


    In this work composition and thermodynamic properties of dense alkali metal plasmas (Li, Na) were investigated. Composition was derived by solving the Saha equations with corrections due to nonideality. The lowering of the ionization potentials was calculated on the basis of pseudopotentials by taking screening and quantum effects into account (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  5. The EOS and neutrino interactions in dense matter

    Energy Technology Data Exchange (ETDEWEB)

    Prakash, M.; Reddy, S. [Dept. of Physics and Astronomy, SUNY at Stony Brook, Stony Brook, NY (United States)


    The deleptonization and cooling times of a newly born neutron star depend on the equation of state (EOS) and neutrino opacities in dense matter. Through model calculations we show that effects of Pauli blocking and many-body correlations due to strong interactions reduce both the neutral and charged current neutrino cross sections by large factors compared to the case in which these effects are ignored. (orig.)

  6. Distributed Downlink Power Control for Dense Networks with Carrier Aggregation


    Fazliu, Zana Limani; Chiasserini, Carla-Fabiana; Dell'Aera, Gian Michele; Hamiti, Enver


    Given the proven benefits cell densification brings in terms of capacity and coverage, it is certain that 5G networks will be even more heterogeneous and dense. However, as smaller cells are introduced in the network, interference will inevitably become a serious problem as they are expected to share the same radio resources. Another central feature envisioned for future cellular networks is carrier aggregation (CA), which allows users to simultaneously use several component carriers of vario...

  7. Topical Collaboration "Neutrinos and Nucleosynthesis in Hot and Dense Matter"

    Energy Technology Data Exchange (ETDEWEB)

    Allahverdi, Rouzbeh [Univ. of New Mexico, Albuquerque, NM (United States)


    This is the final technical report describing contributions from the University of New Mexico to Topical Collaboration on "Neutrinos and Nucleosynthesis in Hot and Dense Matter" in the period June 2010 through May 2015. During the funding period, the University of New Mexico successfully hired Huaiyu Duan as a new faculty member with the support from DOE, who has contributed to the Topical Collaboration through his research and collaborations.

  8. Studies of RF Breakdown of Metals in Dense Gases

    CERN Document Server

    Hanlet, Pierrick M; Ankenbrandt, Charles; Johnson, Rolland P; Kaplan, Daniel; Kuchnir, Moyses; Moretti, Alfred; Paul, Kevin; Popovic, Milorad; Yarba, Victor; Yonehara, Katsuya


    A study of RF breakdown of metals in gases has begun as part of a program to develop RF cavities filled with dense hydrogen gas to be used for muon ionization cooling. A pressurized 800 MHz test cell has been used at Fermilab to compare the conditioning and breakdown behavior of copper, molybdenum, chromium, and beryllium electrodes as functions of hydrogen and helium gas density. These results are compared to the predicted or known RF breakdown behavior of these metals in vacuum.

  9. Recent progress on dense nuclear matter in skyrmion approaches (United States)

    Ma, YongLiang; Rho, Mannque


    The Skyrme model provides a novel unified approach to nuclear physics. In this approach, single baryon, baryonic matter and medium-modified hadron properties are treated on the same footing. Intrinsic density dependence (IDD) reflecting the change of vacuum by compressed baryonic matter figures naturally in the approach. In this article, we review the recent progress on accessing dense nuclear matter by putting baryons treated as solitons, namely, skyrmions, on crystal lattice with accents on the implications in compact stars.

  10. Dense Suspension Splat: Monolayer Spreading and Hole Formation after Impact (United States)

    Lubbers, Luuk A.; Xu, Qin; Wilken, Sam; Zhang, Wendy W.; Jaeger, Heinrich M.


    We use experiments and minimal numerical models to investigate the rapidly expanding monolayer formed by the impact of a dense suspension drop against a smooth solid surface. The expansion creates a lacelike pattern of particle clusters separated by particle-free regions. Both the expansion and the development of the spatial inhomogeneity are dominated by particle inertia and, therefore, are robust and insensitive to details of the surface wetting, capillarity, and viscous drag.

  11. Molecular analysis of a new cytoplasmic male sterile genotype in sunflower

    NARCIS (Netherlands)

    Spassova, Mariana; Christov, Michail; Bohorova, Natasha; Petrov, Peter; Dudov, Kalin; Atanassov, Atanas; Nijkamp, H. John J.; Hille, Jaques


    Mitochondrial DNA from 1 fertile and 6 cytoplasmic male sterile (CMS) sunflower genotypes was studied. The CMS genotypes had been obtained either by specific crosses between different Helianthus species or by mutagenesis. CMS-associated restriction fragment length polymorphisms (RFLPs) were found in

  12. Clinical significance of anti-neutrophil cytoplasmic antibodies (ANCA) in autoimmune liver diseases

    NARCIS (Netherlands)

    Roozendaal, C; de Jong, MA; van den Berg, AP; Limburg, PC; Kallenberg, CGM; van Wijk, R.

    Background/Aims: The clinical relevance of anti-neutrophil cytoplasmic antibodies (ANCA) in autoimmune liver disease is unclear. Defining the antigenic specificities of ANCA in these diseases may improve their clinical significance. Methods: We studied the target antigens of ANCA in 88 patients with

  13. Dynamics of vegetative cytoplasm during generative cell formation and pollen maturation in Arabidopsis thaliana (United States)

    Kuang, A.; Musgrave, M. E.


    Ultrastructural changes of pollen cytoplasm during generative cell formation and pollen maturation in Arabidopsis thaliana were studied. The pollen cytoplasm develops a complicated ultrastructure and changes dramatically during these stages. Lipid droplets increase after generative cell formation and their organization and distribution change with the developmental stage. Starch grains in amyloplasts increase in number and size during generative and sperm cell formation and decrease at pollen maturity. The shape and membrane system of mitochondria change only slightly. Dictyosomes become very prominent, and numerous associated vesicles are observed during and after sperm cell formation. Endoplasmic reticulum appears extensively as stacks during sperm cell formation. Free and polyribosomes are abundant in the cytoplasm at all developmental stages although they appear denser at certain stages and in some areas. In mature pollen, all organelles are randomly distributed throughout the vegetative cytoplasm and numerous small particles appear. Organization and distribution of storage substances and appearance of these small particles during generative and sperm cell formation and pollen maturation are discussed.

  14. Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis : where to go?

    NARCIS (Netherlands)

    Kallenberg, C. G. M.

    Enormous progress has been made during the last 25 years in our understanding of the aetiopathogenesis of the anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides (AAV). This has led to improvements in early diagnosis, treatment and secondary prevention of these diseases.

  15. Genetic loci of Staphylococcus aureus associated with anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides

    NARCIS (Netherlands)

    C. Glasner (Corinna); M.C. De Goffau (Marcus C.); M.M. Van Timmeren (Mirjan M.); Schulze, M.L. (Mirja L.); Jansen, B. (Benita); M. Tavakol (Mehri); W.J.B. van Wamel (Willem); C.A. Stegeman; C.G.M. Kallenberg (Cees G. M.); J.W. Arends (Jan Willem); J.W. Rossen (John); P. Heeringa (Peter); J.M. Dijl (Jan Maarten)


    textabstractThe proteinase 3 (PR3)-positive anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) granulomatosis with polyangiitis (GPA) has been associated with chronic nasal S. aureus carriage, which is a risk factor for disease relapse. The present study was aimed at

  16. Pathogenesis of antineutrophil cytoplasmic autoantibody-associated vasculitis and potential targets for biologic treatment

    NARCIS (Netherlands)

    Sanders, J.S.F.; Abdulahad, W H; Stegeman, C A; Kallenberg, C G M


    Antineutrophil cytoplasmic autoantibody (ANCA)-associated vasculitides (AAV) are autoimmune diseases in which the small vessels are inflamed. Clinical observations suggest a pathogenic role for ANCA. Such a role is supported by in vitro experimental data and animal models, particularly for

  17. The early noncoding region of human papillomavirus type 16 is regulated by cytoplasmic polyadenylation factors

    DEFF Research Database (Denmark)

    Glahder, Jacob-Andreas Harald; Kristiansen, Karen; Durand, Marjorie


    All human papillomavirus type 16 (HPV-16) early mRNAs are polyadenylated at the poly(A) signal within the early 3' untranslated region (3'UTR). The 3'end of the early E5 open reading frame and the 3'UTR of HPV-16 is very AU-rich, with five regions similar to cytoplasmic polyadenylation elements (...

  18. pH-Responsive Micelle-Based Cytoplasmic Delivery System for Induction of Cellular Immunity. (United States)

    Yuba, Eiji; Sakaguchi, Naoki; Kanda, Yuhei; Miyazaki, Maiko; Koiwai, Kazunori


    (1) Background: Cytoplasmic delivery of antigens is crucial for the induction of cellular immunity, which is an important immune response for the treatment of cancer and infectious diseases. To date, fusogenic protein-incorporated liposomes and pH-responsive polymer-modified liposomes have been used to achieve cytoplasmic delivery of antigen via membrane rupture or fusion with endosomes. However, a more versatile cytoplasmic delivery system is desired for practical use. For this study, we developed pH-responsive micelles composed of dilauroyl phosphatidylcholine (DLPC) and deoxycholic acid and investigated their cytoplasmic delivery performance and immunity-inducing capability. (2) Methods: Interaction of micelles with fluorescence dye-loaded liposomes, intracellular distribution of micelles, and antigenic proteins were observed. Finally, antigen-specific cellular immune response was evaluated in vivo using ELIspot assay. (3) Results: Micelles induced leakage of contents from liposomes via lipid mixing at low pH. Micelles were taken up by dendritic cells mainly via macropinocytosis and delivered ovalbumin (OVA) into the cytosol. After intradermal injection of micelles and OVA, OVA-specific cellular immunity was induced in the spleen. (4) Conclusions: pH-responsive micelles composed of DLPC and deoxycholic acid are promising as enhancers of cytosol delivery of antigens and the induction capability of cellular immunity for the treatment of cancer immunotherapy and infectious diseases.

  19. Enhanced electroporation in plant tissues via low frequency pulsed electric fields: influence of cytoplasmic streaming. (United States)

    Asavasanti, Suvaluk; Stroeve, Pieter; Barrett, Diane M; Jernstedt, Judith A; Ristenpart, William D


    Pulsed electric fields (PEF) are known to be effective at permeabilizing plant tissues. Prior research has demonstrated that lower pulse frequencies induce higher rates of permeabilization, but the underlying reason for this response is unclear. Intriguingly, recent microscopic observations with onion tissues have also revealed a correlation between PEF frequency and the subsequent speed of intracellular convective motion, i.e., cytoplasmic streaming. In this paper, we investigate the effect of cytoplasmic streaming on the efficacy of plant tissue permeabilization via PEF. Onion tissue samples were treated with Cytochalasin B, a known inhibitor of cytoplasmic streaming, and changes in cellular integrity and viability were measured over a wide range of frequencies and field strengths. We find that at low frequencies (f streaming results in a 19% decrease in the conductivity disintegration index compared with control samples. Qualitatively, similar results were observed using a microscopic cell viability assay. The results suggest that at low frequencies convection plays a statistically significant role in distributing more conductive fluid throughout the tissue, making subsequent pulses more efficacious. The key practical implication is that PEF pretreatment at low frequency can increase the rate of tissue permeabilization in dehydration or extraction processes, and that the treatment will be most effective when cytoplasmic streaming is most active, i.e., with freshly prepared plant tissues. Copyright © 2012 American Institute of Chemical Engineers (AIChE).

  20. Alternative complement pathway in the pathogenesis of disease mediated by anti-neutrophil cytoplasmic autoantibodies

    NARCIS (Netherlands)

    Xiao, Hong; Schreiber, Adrian; Heeringa, Peter; Falk, Ronald J.; Jennette, J. Charles

    Clinical and experimental data indicate that anti-neutrophil cytoplasmic autoantibodies (ANCAs) cause glomerulonephritis and vasculitis. Here we report the first evidence that complement is an important mediator of ANCA disease. Transfer of anti-myeloperoxidase (MPO) IgG into wild-type mice or

  1. Effect of thapsigargin on cytoplasmic Ca2+ and proliferation of human lymphocytes in relation to AIDS

    DEFF Research Database (Denmark)

    Scharff, O; Foder, B; Thastrup, Ole


    The tumor-promoting sesquiterpene lactone, thapsigargin, induced a dose-dependent increase of the cytoplasmic Ca2+ concentration ([ Ca2+]i) in human lymphocytes from a resting level between 100 and 150 nM up to about 1 microM. Half-maximum response was found at about 1 nM of thapsigargin, full re...

  2. Making it big : how characean algae use cytoplasmic streaming to enhance transport in giant cells

    NARCIS (Netherlands)

    Meent, Jan Willem van de


    Organisms show a remarkable variation in sizes, yet cell sizes are surprisingly similar across species, typically ranging from 10 μm to 100 μm. A striking exception are the giant cells of the algal weed Chara, which can exceed 10 cm in length and 1 mm in diameter. A circulation known as cytoplasmic

  3. Genetics of Male-Sterility in Gynodioecious Plantago-Coronopus .1. Cytoplasmic Variation

    NARCIS (Netherlands)

    Koelewijn, H.P.; Van Damme, J.M.M.


    Inheritance of male sterility was studied in the gynodioecious species plantago coronophus using five plants and their descendants from an area of similar to 50 m(2) in each of six locations. The crosses were planned to test for cytoplasmic inheritance of male sterility. In four locations

  4. Congenital cytoplasmic body myopathy with survival motor neuron gene deletion or Werdnig-Hoffmann disease

    DEFF Research Database (Denmark)

    Vajsar, J; Balslev, T; Ray, P N


    bodies. However, molecular analysis revealed a homozygous deletion of exons 7 and 8 of the survival motor neuron (SMN) gene, suggesting that the patient had Werdnig-Hoffmann disease. We recommend that every patient with congenital cytoplasmic body myopathy be tested for SMN gene deletion....


    Marshak, A.


    1. Egg albumin when injected into an ameba or discharged into the solution about it raises the apparent pH of the cytoplasm of the ameba. 2. With time the cytoplasm returns to the original pH 6.9 if the nucleus is present. Amebae that have received repeated injections of albumin in some cases extrude their nuclei. In these cells the cytoplasm remains at the more alkaline pH induced by the albumin for at least 12 hours. 3. When a 2 per cent solution of albumin is introduced into a suspension of amebae there is a temporary marked rise in the rate at which CO2 is given off with no corresponding rise in O2 uptake. 4. The results observed can be explained if the albumin discharged onto the surface of the ameba rapidly enters the cell and there becomes distributed in a phase of the cytoplasm other than the one which contains the phenol red. PMID:19873412

  6. MscL of Bacillus subtilis prevents selective release of cytoplasmic proteins in a hypotonic environment

    NARCIS (Netherlands)

    Kouwen, Thijs R. H. M.; Antelmann, Haike; van der Ploeg, Rene; Denham, Emma L.; Hecker, Michael; van Dijl, Jan Maarten

    Bacillus subtilis serves as an excellent model to study protein secretion at a proteomic scale. Most of the extracellular proteins are exported from the cytoplasm via the secretory (Sec) pathway. Despite extensive studies, the secretion mechanisms of about 25% of the extracellular proteins are

  7. Probing the biology of cell boundary conditions through confinement of Xenopus cell-free cytoplasmic extracts. (United States)

    Bermudez, Jessica G; Chen, Hui; Einstein, Lily C; Good, Matthew C


    Cell-free cytoplasmic extracts prepared from Xenopus eggs and embryos have for decades provided a biochemical system with which to interrogate complex cell biological processes in vitro. Recently, the application of microfabrication and microfluidic strategies in biology has narrowed the gap between in vitro and in vivo studies by enabling formation of cell-size compartments containing functional cytoplasm. These approaches provide numerous advantages over traditional biochemical experiments performed in a test tube. Most notably, the cell-free cytoplasm is confined using a two- or three-dimensional boundary, which mimics the natural configuration of a cell. This strategy enables characterization of the spatial organization of a cell, and the role that boundaries play in regulating intracellular assembly and function. In this review, we describe the marriage of Xenopus cell-free cytoplasm and confinement technologies to generate synthetic cell-like systems, the recent biological insights they have enabled, and the promise they hold for future scientific discovery. © 2017 Wiley Periodicals, Inc.

  8. Cytoplasmic male sterility in Petunia hybrida : a structural and histochemical analysis

    NARCIS (Netherlands)

    Bino, R.J.


    This thesis presents an analysis of the structural and histochemical aspects of cytoplasmic male sterility (cms) in Petuniahybrida . In petunia and in other crops, cms is the most commonly used tool for hybrid seed production. Application of the trait

  9. pH-Responsive Micelle-Based Cytoplasmic Delivery System for Induction of Cellular Immunity

    Directory of Open Access Journals (Sweden)

    Eiji Yuba


    Full Text Available (1 Background: Cytoplasmic delivery of antigens is crucial for the induction of cellular immunity, which is an important immune response for the treatment of cancer and infectious diseases. To date, fusogenic protein-incorporated liposomes and pH-responsive polymer-modified liposomes have been used to achieve cytoplasmic delivery of antigen via membrane rupture or fusion with endosomes. However, a more versatile cytoplasmic delivery system is desired for practical use. For this study, we developed pH-responsive micelles composed of dilauroyl phosphatidylcholine (DLPC and deoxycholic acid and investigated their cytoplasmic delivery performance and immunity-inducing capability. (2 Methods: Interaction of micelles with fluorescence dye-loaded liposomes, intracellular distribution of micelles, and antigenic proteins were observed. Finally, antigen-specific cellular immune response was evaluated in vivo using ELIspot assay. (3 Results: Micelles induced leakage of contents from liposomes via lipid mixing at low pH. Micelles were taken up by dendritic cells mainly via macropinocytosis and delivered ovalbumin (OVA into the cytosol. After intradermal injection of micelles and OVA, OVA-specific cellular immunity was induced in the spleen. (4 Conclusions: pH-responsive micelles composed of DLPC and deoxycholic acid are promising as enhancers of cytosol delivery of antigens and the induction capability of cellular immunity for the treatment of cancer immunotherapy and infectious diseases.

  10. Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress

    NARCIS (Netherlands)

    Mika, Jacek T.; van den Bogaart, Geert; Veenhoff, Liesbeth; Krasnikov, Victor; Poolman, Bert

    We determined the diffusion coefficients (D) of (macro)molecules of different sizes (from ~0.5 to 600 kDa) in the cytoplasm of live Escherichia coli cells under normal osmotic conditions and osmotic upshift. D values decreased with increasing molecular weight of the molecules. Upon osmotic upshift,

  11. Cytoplasmic fatty acid-binding protein facilitates fatty acid utilization by skeletal muscle

    NARCIS (Netherlands)

    Glatz, J. F. C.; Schaap, F. G.; Binas, B.; Bonen, A.; van der Vusse, G. J.; Luiken, J. J. F. P.


    The intracellular transport of long-chain fatty acids in muscle cells is facilitated to a great extent by heart-type cytoplasmic fatty acid-binding protein (H-FABP). By virtue of the marked affinity of this 14.5-kDa protein for fatty acids, H-FABP dramatically increases their concentration in the

  12. Cytoplasmic dynein and its regulatory proteins in Golgi pathology in nervous system disorders

    NARCIS (Netherlands)

    Jaarsma, Dick; Hoogenraad, Casper C


    The Golgi apparatus is a dynamic organelle involved in processing and sorting of lipids and proteins. In neurons, the Golgi apparatus is important for the development of axons and dendrites and maintenance of their highly complex polarized morphology. The motor protein complex cytoplasmic dynein has

  13. Mitochondrial DNA variation within P-type cytoplasmic male sterility of Plantago lanceolata L

    NARCIS (Netherlands)

    Groenendijk, C.F.M.; Sandbrink, J.M.; Van Brederode, J.; Van Damme, J.M.M.


    MtDNA restriction fragment polymorphisms were found between cytoplasmic male-sterility types P and R of Plantago lanceolata with the homologous probe pPl311 and maize mtDNA fragments derived from the regions of atp1, cox1 and cox2. No mtDNA differences were observed between male-sterile and restored

  14. Production of ABA responses requires both the nuclear and cytoplasmic functional involvement of PYR1. (United States)

    Park, EunJoo; Kim, Tae-Houn


    Abscisic acid (ABA) enhances stress tolerant responses in plants against unfavorable environmental conditions. In Arabidopsis, ABA promotes interactions between PYR/PYL/RCARs and PP2C, thereby allowing SnRK2s to phosphorylate downstream components required for the regulation of gene expression or for gating ion channels. Because PYR1 is known to localize to nucleus and cytoplasm it is a question whether nuclear or cytoplasmic PYR1 confer different functions to the ABA signaling pathway, as has been previously shown for regulatory proteins. In order to answer this question, transgenic lines expressing nuclear PYR1 were generated in an ABA insensitive mutant background. Enforced nuclear expression of PYR1 was examined by confocal microscopy and western blot analysis. Physiological analyses of the transgenic lines demonstrated that nuclear PYR1 is sufficient to generate ABA responses, such as, the inhibition of seed germination, root growth inhibition, the induction of gene expression, and stomatal closing movement. However, for the full recovery of ABA responses in the mutant background cytoplasmic PYR1 was required. The study suggests both nuclear and cytoplasmic PYR1 participate in the control of ABA signal transduction. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Bacterial cytoplasmic display platform Retained Display (ReD) identifies stable human germline antibody frameworks. (United States)

    Beasley, Matthew D; Niven, Keith P; Winnall, Wendy R; Kiefel, Ben R


    Conventional antibody surface display requires fusion protein export through at least one cellular membrane, constraining the yield and occasioning difficulties in achieving scaled production. To circumvent this limitation, we developed a novel cytoplasmic display platform, Retained Display (ReD), and used it to screen for human scFv frameworks that are highly soluble and stable in the bacterial cytoplasm. ReD, based on the retention of high-molecular weight complexes within detergent-permeabilized Escherichia coli, enabled presentation of exogenous targets to antibodies that were expressed and folded in the cytoplasm. All human λ and κ light chain family genes were expressed as IGHV3-23 fusions. Members of the λ subfamilies 1, 3 and 6 were soluble cytoplasmic partners of IGHV3-23. Contrary to previous in vivo screens for soluble reduced scFvs, the pairings identified by ReD were identical to the human germline sequences for the framework, CDR1 and CDR2 regions. Using the most soluble scFv scaffold identified, we demonstrated tolerance to CDR3 diversification and isolated a binding scFv to an exogenous protein target. This screening system has the potential to rapidly produce antibodies to target threats such as emerging infectious diseases and bioterror agents. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Rheology of dense suspensions of non colloidal particles

    Directory of Open Access Journals (Sweden)

    Guazzelli Élisabeth


    Full Text Available Dense suspensions are materials with broad applications both in industrial processes (e.g. waste disposal, concrete, drilling muds, metalworking chip transport, and food processing and in natural phenomena (e.g. flows of slurries, debris, and lava. Despite its long research history and its practical relevance, the mechanics of dense suspensions remain poorly understood. The major difficulty is that the grains interact both by hydrodynamic interactions through the liquid and by mechanical contact. These systems thus belong to an intermediate regime between pure suspensions and granular flows. We show that we can unify suspension and granular rheology under a common framework by transferring the frictional approach of dry granular media to wet suspensions of spherical particles. We also discuss non-Newtonian behavior such as normal-stress differences and shear-induced migration. Beyond the classical problem of dense suspension of hard spheres which is far from being completely resolved, there are also entirely novel avenues of study concerning more complex mixtures of particles and fluids such as those involving other types of particles (e.g. fibers or non-Newtonian fluids that we will also address.

  17. Ab initio thermodynamic results for warm dense matter (United States)

    Bonitz, Michael


    Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.

  18. Ultra-dense deuterium and cold fusion claims (United States)

    Winterberg, F.


    An attempt is made to explain the recently reported occurrence of 14 MeV neutron induced nuclear reactions in deuterium metal hydrides as the manifestation of a slightly radioactive ultra-dense form of deuterium, with a density of 130,000 g/cm 3 observed by a Swedish research group through the collapse of deuterium Rydberg matter. In accordance with this observation it is proposed that a large number of deuterons form a “linear-atom” supermolecule. By the Madelung transformation of the Schrödinger equation, the linear deuterium supermolecule can be described by a quantized line vortex. A vortex lattice made up of many such supermolecules is possible only with deuterium, because deuterons are bosons, and the same is true for the electrons, which by the electron-phonon interaction in a vortex lattice form Cooper pairs. It is conjectured that the latent heat released by the collapse into the ultra-dense state has been misinterpreted as cold fusion. Hot fusion though, is here possible through the fast ignition of a thermonuclear detonation wave from a hot spot made with a 1 kJ 10 petawatt laser in a thin slice of the ultra-dense deuterium.

  19. Rheology of dense suspensions of non colloidal particles (United States)

    Guazzelli, Élisabeth


    Dense suspensions are materials with broad applications both in industrial processes (e.g. waste disposal, concrete, drilling muds, metalworking chip transport, and food processing) and in natural phenomena (e.g. flows of slurries, debris, and lava). Despite its long research history and its practical relevance, the mechanics of dense suspensions remain poorly understood. The major difficulty is that the grains interact both by hydrodynamic interactions through the liquid and by mechanical contact. These systems thus belong to an intermediate regime between pure suspensions and granular flows. We show that we can unify suspension and granular rheology under a common framework by transferring the frictional approach of dry granular media to wet suspensions of spherical particles. We also discuss non-Newtonian behavior such as normal-stress differences and shear-induced migration. Beyond the classical problem of dense suspension of hard spheres which is far from being completely resolved, there are also entirely novel avenues of study concerning more complex mixtures of particles and fluids such as those involving other types of particles (e.g. fibers) or non-Newtonian fluids that we will also address.

  20. Approximate hard-sphere method for densely packed granular flows. (United States)

    Guttenberg, Nicholas


    The simulation of granular media is usually done either with event-driven codes that treat collisions as instantaneous but have difficulty with very dense packings, or with molecular dynamics (MD) methods that approximate rigid grains using a stiff viscoelastic spring. There is a little-known method that combines several collision events into a single timestep to retain the instantaneous collisions of event-driven dynamics, but also be able to handle dense packings. However, it is poorly characterized as to its regime of validity and failure modes. We present a modification of this method to reduce the introduction of overlap error, and test it using the problem of two-dimensional (2D) granular Couette flow, a densely packed system that has been well characterized by previous work. We find that this method can successfully replicate the results of previous work up to the point of jamming, and that it can do so a factor of 10 faster than comparable MD methods.

  1. Exotic x-ray emission from dense plasmas (United States)

    Rosmej, F. B.; Dachicourt, R.; Deschaud, B.; Khaghani, D.; Dozières, M.; Šmíd, M.; Renner, O.


    Exotic x-ray emission from dense matter is identified as the complex high intensity satellite emission from autoionizing states of highly charged ions. Among a vast amount of possible transitions, double K-hole hollow ion (HI) x-ray emission K0L X → K1L X-1 + hν hollow is of exceptional interest due to its advanced diagnostic potential for matter under extreme conditions where opacity and radiation fields play important roles. Transient ab initio simulations identify intense short pulse radiation fields (e.g., those emitted by x-ray free electron lasers) as possible driving mechanisms of HI x-ray emission via two distinct channels: first, successive photoionization of K-shell electrons, second, photoionization followed by resonant photoexciation among various ionic charge states that are simultaneously present in high density matter. We demonstrated that charge exchange of intermixing inhomogenous plasmas as well as collisions driven by suprathermal electrons are possible mechanisms to populate HIs to observable levels in dense plasmas, particularly in high current Z-pinch plasmas and high intensity field-ionized laser produced plasmas. Although the HI x-ray transitions were repeatedly identified in many other cases of dense optical laser produced plasmas on the basis of atomic structure calculations, their origin is far from being understood and remains one of the last holy grails of high intensity laser-matter interaction.

  2. Enhanced Productivity of Chemical Processes Using Dense Fluidized Beds

    Energy Technology Data Exchange (ETDEWEB)

    Sibashis Banerjee; Alvin Chen; Rutton Patel; Dale Snider; Ken Williams; Timothy O' Hern; Paul Tortora


    The work detailed in this report addresses Enabling Technologies within Computational Technology by integrating a “breakthrough” particle-fluid computational technology into traditional Process Science and Engineering Technology. The work completed under this DOE project addresses five major development areas 1) gas chemistry in dense fluidized beds 2) thermal cracking of liquid film on solids producing gas products 3) liquid injection in a fluidized bed with particle-to-particle liquid film transport 4) solid-gas chemistry and 5) first level validation of models. Because of the nature of the research using tightly coupled solids and fluid phases with a Lagrangian description of the solids and continuum description of fluid, the work provides ground-breaking advances in reactor prediction capability. This capability has been tested against experimental data where available. The commercial product arising out of this work is called Barracuda and is suitable for a wide (dense-to-dilute) range of industrial scale gas-solid flows with and without reactions. Commercial applications include dense gas-solid beds, gasifiers, riser reactors and cyclones.

  3. Cytoplasmic CUG RNA foci are insufficient to elicit key DM1 features.

    Directory of Open Access Journals (Sweden)

    Warunee Dansithong

    Full Text Available The genetic basis of myotonic dystrophy type I (DM1 is the expansion of a CTG tract located in the 3' untranslated region of DMPK. Expression of mutant RNAs encoding expanded CUG repeats plays a central role in the development of cardiac disease in DM1. Expanded CUG tracts form both nuclear and cytoplasmic aggregates, yet the relative significance of such aggregates in eliciting DM1 pathology is unclear. To test the pathophysiology of CUG repeat encoding RNAs, we developed and analyzed mice with cardiac-specific expression of a beta-galactosidase cassette in which a (CTG(400 repeat tract was positioned 3' of the termination codon and 5' of the bovine growth hormone polyadenylation signal. In these animals CUG aggregates form exclusively in the cytoplasm of cardiac cells. A key pathological consequence of expanded CUG repeat RNA expression in DM1 is aberrant RNA splicing. Abnormal splicing results from the functional inactivation of MBNL1, which is hypothesized to occur due to MBNL1 sequestration in CUG foci or from elevated levels of CUG-BP1. We therefore tested the ability of cytoplasmic CUG foci to elicit these changes. Aggregation of CUG RNAs within the cytoplasm results both in Mbnl1 sequestration and in approximately a two fold increase in both nuclear and cytoplasmic Cug-bp1 levels. Significantly, despite these changes RNA splice defects were not observed and functional analysis revealed only subtle cardiac dysfunction, characterized by conduction defects that primarily manifest under anesthesia. Using a human myoblast culture system we show that this transgene, when expressed at similar levels to a second transgene, which encodes expanded CTG tracts and facilitates both nuclear focus formation and aberrant splicing, does not elicit aberrant splicing. Thus the lack of toxicity of cytoplasmic CUG foci does not appear to be a consequence of low expression levels. Our results therefore demonstrate that the cellular location of CUG RNA

  4. Dual roles of p82, the clam CPEB homolog, in cytoplasmic polyadenylation and translational masking. (United States)

    Minshall, N; Walker, J; Dale, M; Standart, N


    In the transcriptionally inert maturing oocyte and early embryo, control of gene expression is largely mediated by regulated changes in translational activity of maternal mRNAs. Some mRNAs are activated in response to poly(A) tail lengthening; in other cases activation results from de-repression of the inactive or masked mRNA. The 3' UTR cis-acting elements that direct these changes are defined, principally in Xenopus and mouse, and the study of their trans-acting binding factors is just beginning to shed light on the mechanism and regulation of cytoplasmic polyadenylation and translational masking. In the marine invertebrate, Spisula solidissima, the timing of activation of three abundant mRNAs (encoding cyclin A and B and the small subunit of ribonucleotide reductase, RR) in fertilized oocytes correlates with their cytoplasmic polyadenylation. However, in vitro, mRNA-specific unmasking occurs in the absence of polyadenylation. In Walker et al. (in this issue) we showed that p82, a protein defined as selectively binding the 3' UTR masking elements, is a homolog of Xenopus CPEB (cytoplasmic polyadenylation element binding protein). In functional studies reported here, the elements that support polyadenylation in clam egg lysates include multiple U-rich CPE-like motifs as well as the nuclear polyadenylation signal AAUAAA. This represents the first detailed analysis of invertebrate cis-acting cytoplasmic polyadenylation signals. Polyadenylation activity correlates with p82 binding in wild-type and CPE-mutant RR 3' UTR RNAs. Moreover, since anti-p82 antibodies specifically neutralize polyadenylation in egg lysates, we conclude that clam p82 is a functional homolog of Xenopus CPEB, and plays a positive role in polyadenylation. Anti-p82 antibodies also result in specific translational activation of masked mRNAs in oocyte lysates, lending support to our original model of clam p82 as a translational repressor. We propose therefore that clam p82/CPEB has dual functions in

  5. Myosin-Powered Membrane Compartment Drives Cytoplasmic Streaming, Cell Expansion and Plant Development. (United States)

    Peremyslov, Valera V; Cole, Rex A; Fowler, John E; Dolja, Valerian V


    Using genetic approaches, particle image velocimetry and an inert tracer of cytoplasmic streaming, we have made a mechanistic connection between the motor proteins (myosins XI), cargo transported by these motors (distinct endomembrane compartment defined by membrane-anchored MyoB receptors) and the process of cytoplasmic streaming in plant cells. It is shown that the MyoB compartment in Nicotiana benthamiana is highly dynamic moving with the mean velocity of ~3 μm/sec. In contrast, Golgi, mitochondria, peroxisomes, carrier vesicles and a cytosol flow tracer share distinct velocity profile with mean velocities of 0.6-1.5 μm/sec. Dominant negative inhibition of the myosins XI or MyoB receptors using overexpression of the N. benthamiana myosin cargo-binding domain or MyoB myosin-binding domain, respectively, resulted in velocity reduction for not only the MyoB compartment, but also each of the tested organelles, vesicles and cytoplasmic streaming. Furthermore, the extents of this reduction were similar for each of these compartments suggesting that MyoB compartment plays primary role in cytosol dynamics. Using gene knockout analysis in Arabidopsis thaliana, it is demonstrated that inactivation of MyoB1-4 results in reduced velocity of mitochondria implying slower cytoplasmic streaming. It is also shown that myosins XI and MyoB receptors genetically interact to contribute to cell expansion, plant growth, morphogenesis and proper onset of flowering. These results support a model according to which myosin-dependent, MyoB receptor-mediated transport of a specialized membrane compartment that is conserved in all land plants drives cytoplasmic streaming that carries organelles and vesicles and facilitates cell growth and plant development.

  6. Critical role of the fusion protein cytoplasmic tail sequence in parainfluenza virus assembly.

    Directory of Open Access Journals (Sweden)

    Raychel Stone

    Full Text Available Interactions between viral glycoproteins, matrix protein and nucleocapsid sustain assembly of parainfluenza viruses at the plasma membrane. Although the protein interactions required for virion formation are considered to be highly specific, virions lacking envelope glycoprotein(s can be produced, thus the molecular interactions driving viral assembly and production are still unclear. Sendai virus (SeV and human parainfluenza virus type 1 (hPIV1 are highly similar in structure, however, the cytoplasmic tail sequences of the envelope glycoproteins (HN and F are relatively less conserved. To unveil the specific role of the envelope glycoproteins in viral assembly, we created chimeric SeVs whose HN (rSeVhHN or HN and F (rSeVh(HN+F were replaced with those of hPIV1. rSeVhHN grew as efficiently as wt SeV or hPIV1, suggesting that the sequence difference in HN does not have a significant impact on SeV replication and virion production. In sharp contrast, the growth of rSeVh(HN+F was significantly impaired compared to rSeVhHN. rSeVh(HN+Fstail which expresses a chimeric hPIV1 F with the SeV cytoplasmic tail sequence grew similar to wt SeV or rSeVhHN. Further analysis indicated that the F cytoplasmic tail plays a critical role in cell surface expression/accumulation of HN and F, as well as NP and M association at the plasma membrane. Trafficking of nucelocapsids in infected cells was not significantly affected by the origin of F, suggesting that F cytoplasmic tail is not involved in intracellular movement. These results demonstrate the role of the F cytoplasmic tail in accumulation of structural components at the plasma membrane assembly sites.

  7. Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML. (United States)

    Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D; Bader, Gary D; Laposa, Rebecca; Schimmer, Aaron D


    Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2'3'-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2'3'-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. © 2017 by The American Society of Hematology.

  8. Human B cells fail to secrete type I interferons upon cytoplasmic DNA exposure. (United States)

    Gram, Anna M; Sun, Chenglong; Landman, Sanne L; Oosenbrug, Timo; Koppejan, Hester J; Kwakkenbos, Mark J; Hoeben, Rob C; Paludan, Søren R; Ressing, Maaike E


    Most cells are believed to be capable of producing type I interferons (IFN I) as part of an innate immune response against, for instance, viral infections. In macrophages, IFN I is potently induced upon cytoplasmic exposure to foreign nucleic acids. Infection of these cells with herpesviruses leads to triggering of the DNA sensors interferon-inducible protein 16 (IFI16) and cyclic GMP-AMP (cGAMP) synthase (cGAS). Thereby, the stimulator of interferon genes (STING) and the downstream molecules TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) are sequentially activated culminating in IFN I secretion. Human gamma-herpesviruses, such as Epstein-Barr virus (EBV), exploit B cells as a reservoir for persistent infection. In this study, we investigated whether human B cells, similar to macrophages, engage the cytoplasmic DNA sensing pathway to induce an innate immune response. We found that the B cells fail to secrete IFN I upon cytoplasmic DNA exposure, although they express the DNA sensors cGAS and IFI16 and the signaling components TBK1 and IRF3. In primary human B lymphocytes and EBV-negative B cell lines, this deficiency is explained by a lack of detectable levels of the central adaptor protein STING. In contrast, EBV-transformed B cell lines did express STING, yet both these lines as well as STING-reconstituted EBV-negative B cells did not produce IFN I upon dsDNA or cGAMP stimulation. Our combined data show that the cytoplasmic DNA sensing pathway is dysfunctional in human B cells. This exemplifies that certain cell types cannot induce IFN I in response to cytoplasmic DNA exposure providing a potential niche for viral persistence. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Prediction of a Densely Loaded Particle-Laden Jet using a Euler-Lagrange Dense Spray Model (United States)

    Pakseresht, Pedram; Apte, Sourabh V.


    Modeling of a dense spray regime using an Euler-Lagrange discrete-element approach is challenging because of local high volume loading. A subgrid cluster of droplets can lead to locally high void fractions for the disperse phase. Under these conditions, spatio-temporal changes in the carrier phase volume fractions, which are commonly neglected in spray simulations in an Euler-Lagrange two-way coupling model, could become important. Accounting for the carrier phase volume fraction variations, leads to zero-Mach number, variable density governing equations. Using pressure-based solvers, this gives rise to a source term in the pressure Poisson equation and a non-divergence free velocity field. To test the validity and predictive capability of such an approach, a round jet laden with solid particles is investigated using Direct Numerical Simulation and compared with available experimental data for different loadings. Various volume fractions spanning from dilute to dense regimes are investigated with and without taking into account the volume displacement effects. The predictions of the two approaches are compared and analyzed to investigate the effectiveness of the dense spray model. Financial support was provided by National Aeronautics and Space Administration (NASA).

  10. Integrin cytoplasmic domain-associated protein-1 (ICAP-1) interacts with the ROCK-I kinase at the plasma membrane

    NARCIS (Netherlands)

    Stroeken, Peter J. M.; Alvarez, Belén; van Rheenen, Jacco; Wijnands, Yvonne M.; Geerts, Dirk; Jalink, Kees; Roos, Ed


    The integrin cytoplasmic domain-associated protein-1 (ICAP-1) binds via its C-terminal PTB (phosphotyrosine-binding) domain to the cytoplasmic tails of beta1 but not other integrins. Using the yeast two-hybrid assay, we found that ICAP-1 binds the ROCK-I kinase, an effector of the RhoA GTPase. By

  11. Characterisation and expression of the mitochondrial genome of a new type of cytoplasmic male-sterile sunflower

    NARCIS (Netherlands)

    Spassova, Mariana; Moneger, Françoise; Leaver, Christopher J.; Petrov, Peter; Atanassov, Atanas; Nijkamp, H. John J.; Hille, Jacques


    A new cytoplasmic male sterile sunflower, CMS3, was characterised in relation to the Petiolaris (PET1) cytoplasmic male-sterile sunflower, CMS89. Southern blot analysis showed that the mitochondrial genome of CMS3 contains unique rearrangements in at least five loci (atp6, atp9, atpA, nad1 + 5 and

  12. The molecularly crowded cytoplasm of bacterialcCells : Dividing cells contrasted with viable but non-culturable (VBNC) bacterial cells

    NARCIS (Netherlands)

    Trevors, J. T.; van Elsas, J. D.; Bej, A. K.


    In this perspective, we discuss the cytoplasm in actively growing bacterial cells contrasted with viable but non-culturable (VBNC) cells. Actively growing bacterial cells contain a more molecularly crowded and organized cytoplasm, and are capable of completing their cell cycle resulting in cell

  13. The dynamics of gynodioecy in Plantago lanceolata L. .1. Frequencies of male-steriles and their cytoplasmic male sterility types

    NARCIS (Netherlands)

    De Haan, A.A.; Luyten, R.M.J.M.; Bakx-Schotman, Tanja; Van Damme, J.M.M.


    The maintenance of a gynodioecious breeding system (hermaphrodites and male-steriles) was studied in Plantago lanceolata. Cytoplasmic-nuclear inheritance is important in the maintenance of male-steriles. The male-sterile trait is cytoplasmically based (CMS), and male fertility can be restored by

  14. Homologous Transcription Factors DUX4 and DUX4c Associate with Cytoplasmic Proteins during Muscle Differentiation.

    Directory of Open Access Journals (Sweden)

    Eugénie Ansseau

    Full Text Available Hundreds of double homeobox (DUX genes map within 3.3-kb repeated elements dispersed in the human genome and encode DNA-binding proteins. Among these, we identified DUX4, a potent transcription factor that causes facioscapulohumeral muscular dystrophy (FSHD. In the present study, we performed yeast two-hybrid screens and protein co-purifications with HaloTag-DUX fusions or GST-DUX4 pull-down to identify protein partners of DUX4, DUX4c (which is identical to DUX4 except for the end of the carboxyl terminal domain and DUX1 (which is limited to the double homeodomain. Unexpectedly, we identified and validated (by co-immunoprecipitation, GST pull-down, co-immunofluorescence and in situ Proximal Ligation Assay the interaction of DUX4, DUX4c and DUX1 with type III intermediate filament protein desmin in the cytoplasm and at the nuclear periphery. Desmin filaments link adjacent sarcomere at the Z-discs, connect them to sarcolemma proteins and interact with mitochondria. These intermediate filament also contact the nuclear lamina and contribute to positioning of the nuclei. Another Z-disc protein, LMCD1 that contains a LIM domain was also validated as a DUX4 partner. The functionality of DUX4 or DUX4c interactions with cytoplasmic proteins is underscored by the cytoplasmic detection of DUX4/DUX4c upon myoblast fusion. In addition, we identified and validated (by co-immunoprecipitation, co-immunofluorescence and in situ Proximal Ligation Assay as DUX4/4c partners several RNA-binding proteins such as C1QBP, SRSF9, RBM3, FUS/TLS and SFPQ that are involved in mRNA splicing and translation. FUS and SFPQ are nuclear proteins, however their cytoplasmic translocation was reported in neuronal cells where they associated with ribonucleoparticles (RNPs. Several other validated or identified DUX4/DUX4c partners are also contained in mRNP granules, and the co-localizations with cytoplasmic DAPI-positive spots is in keeping with such an association. Large muscle RNPs

  15. Antibody-mediated enzyme replacement therapy targeting both lysosomal and cytoplasmic glycogen in Pompe disease. (United States)

    Yi, Haiqing; Sun, Tao; Armstrong, Dustin; Borneman, Scott; Yang, Chunyu; Austin, Stephanie; Kishnani, Priya S; Sun, Baodong


    Pompe disease is characterized by accumulation of both lysosomal and cytoplasmic glycogen primarily in skeletal and cardiac muscles. Mannose-6-phosphate receptor-mediated enzyme replacement therapy (ERT) with recombinant human acid α-glucosidase (rhGAA) targets the enzyme to lysosomes and thus is unable to digest cytoplasmic glycogen. Studies have shown that anti-DNA antibody 3E10 penetrates living cells and delivers "cargo" proteins to the cytosol or nucleus via equilibrative nucleoside transporter ENT2. We speculate that 3E10-mediated ERT with GAA will target both lysosomal and cytoplasmic glycogen in Pompe disease. A fusion protein (FabGAA) containing a humanized Fab fragment derived from the murine 3E10 antibody and the 110 kDa human GAA precursor was constructed and produced in CHO cells. Immunostaining with an anti-Fab antibody revealed that the Fab signals did not co-localize with the lysosomal marker LAMP2 in cultured L6 myoblasts or Pompe patient fibroblasts after incubation with FabGAA. Western blot with an anti-GAA antibody showed presence of the 150 kDa full-length FabGAA in the cell lysates, in addition to the 95- and 76 kDa processed forms of GAA that were also seen in the rhGAA-treated cells. Blocking of mannose-6-phosphate receptor with mannose-6-phosphate markedly reduced the 95- and the 76 kDa forms but not the 150 kDa form. In GAA-KO mice, FabGAA achieved similar treatment efficacy as rhGAA at an equal molar dose in reducing tissue glycogen contents. Our data suggest that FabGAA retains the ability of rhGAA to treat lysosomal glycogen accumulation and has the beneficial potential over rhGAA to reduce cytoplasmic glycogen storage in Pompe disease. FabGAA can be delivered to both the cytoplasm and lysosomes in cultured cells. FabGAA equally reduced lysosomal glycogen accumulation as rhGAA in GAA-KO mice. FabGAA has the beneficial potential over rhGAA to clear cytoplasmic glycogen. This study suggests a novel antibody-enzyme fusion protein therapy

  16. Crystal structures and dynamical properties of dense CO2 (United States)

    Yong, Xue; Liu, Hanyu; Wu, Min; Yao, Yansun; Tse, John S.; Dias, Ranga; Yoo, Choong-Shik


    Structural polymorphism in dense carbon dioxide (CO2) has attracted significant attention in high-pressure physics and chemistry for the past two decades. Here, we have performed high-pressure experiments and first-principles theoretical calculations to investigate the stability, structure, and dynamical properties of dense CO2. We found evidence that CO2-V with the 4-coordinated extended structure can be quenched to ambient pressure below 200 K—the melting temperature of CO2-I. CO2-V is a fully coordinated structure formed from a molecular solid at high pressure and recovered at ambient pressure. Apart from confirming the metastability of CO2-V (I-42d) at ambient pressure at low temperature, results of ab initio molecular dynamics and metadynamics (MD) simulations provided insights into the transformation processes and structural relationship from the molecular to the extended phases. In addition, the simulation also predicted a phase V′(Pna21) in the stability region of CO2-V with a diffraction pattern similar to that previously assigned to the CO2-V (P212121) structure. Both CO2-V and -V′ are predicted to be recoverable and hard with a Vicker hardness of ∼20 GPa. Significantly, MD simulations found that the CO2 in phase IV exhibits large-amplitude bending motions at finite temperatures and high pressures. This finding helps to explain the discrepancy between earlier predicted static structures and experiments. MD simulations clearly indicate temperature effects are critical to understanding the high-pressure behaviors of dense CO2 structures—highlighting the significance of chemical kinetics associated with the transformations. PMID:27647887

  17. Dense motion field estimation from myocardial boundary displacements. (United States)

    Morais, Pedro; Queirós, Sandro; Ferreira, Adriano; Rodrigues, Nuno F; Baptista, Maria J; D'hooge, Jan; Vilaça, João L; Barbosa, Daniel


    Minimally invasive cardiovascular interventions guided by multiple imaging modalities are rapidly gaining clinical acceptance for the treatment of several cardiovascular diseases. These images are typically fused with richly detailed pre-operative scans through registration techniques, enhancing the intra-operative clinical data and easing the image-guided procedures. Nonetheless, rigid models have been used to align the different modalities, not taking into account the anatomical variations of the cardiac muscle throughout the cardiac cycle. In the current study, we present a novel strategy to compensate the beat-to-beat physiological adaptation of the myocardium. Hereto, we intend to prove that a complete myocardial motion field can be quickly recovered from the displacement field at the myocardial boundaries, therefore being an efficient strategy to locally deform the cardiac muscle. We address this hypothesis by comparing three different strategies to recover a dense myocardial motion field from a sparse one, namely, a diffusion-based approach, thin-plate splines, and multiquadric radial basis functions. Two experimental setups were used to validate the proposed strategy. First, an in silico validation was carried out on synthetic motion fields obtained from two realistic simulated ultrasound sequences. Then, 45 mid-ventricular 2D sequences of cine magnetic resonance imaging were processed to further evaluate the different approaches. The results showed that accurate boundary tracking combined with dense myocardial recovery via interpolation/diffusion is a potentially viable solution to speed up dense myocardial motion field estimation and, consequently, to deform/compensate the myocardial wall throughout the cardiac cycle. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  18. Parallel Access of Out-Of-Core Dense Extendible Arrays

    Energy Technology Data Exchange (ETDEWEB)

    Otoo, Ekow J; Rotem, Doron


    Datasets used in scientific and engineering applications are often modeled as dense multi-dimensional arrays. For very large datasets, the corresponding array models are typically stored out-of-core as array files. The array elements are mapped onto linear consecutive locations that correspond to the linear ordering of the multi-dimensional indices. Two conventional mappings used are the row-major order and the column-major order of multi-dimensional arrays. Such conventional mappings of dense array files highly limit the performance of applications and the extendibility of the dataset. Firstly, an array file that is organized in say row-major order causes applications that subsequently access the data in column-major order, to have abysmal performance. Secondly, any subsequent expansion of the array file is limited to only one dimension. Expansions of such out-of-core conventional arrays along arbitrary dimensions, require storage reorganization that can be very expensive. Wepresent a solution for storing out-of-core dense extendible arrays that resolve the two limitations. The method uses a mapping function F*(), together with information maintained in axial vectors, to compute the linear address of an extendible array element when passed its k-dimensional index. We also give the inverse function, F-1*() for deriving the k-dimensional index when given the linear address. We show how the mapping function, in combination with MPI-IO and a parallel file system, allows for the growth of the extendible array without reorganization and no significant performance degradation of applications accessing elements in any desired order. We give methods for reading and writing sub-arrays into and out of parallel applications that run on a cluster of workstations. The axial-vectors are replicated and maintained in each node that accesses sub-array elements.

  19. Neutron Star Dense Matter Equation of State Constraints with NICER (United States)

    Bogdanov, Slavko; Arzoumanian, Zaven; Chakrabarty, Deepto; Guillot, Sebastien; Kust Harding, Alice; Ho, Wynn C. G.; Lamb, Frederick K.; Mahmoodifar, Simin; Miller, M. Coleman; Morsink, Sharon; Ozel, Feryal; Psaltis, Dimitrios; Ray, Paul S.; Riley, Tom; Strohmayer, Tod E.; Watts, Anna; Wolff, Michael Thomas; Gendreau, Keith


    One of the principal goals of the Neutron Star Interior Composition Explorer (NICER) is to place constraints on the dense matter equation of state through sensitive X-ray observations of neutron stars. The NICER mission will focus on measuring the masses and radii of several relatively bright, thermally-emitting, rotation-powered millisecond pulsars, by fitting models that incorporate all relevant relativistic effects and atmospheric radiation transfer processes to their periodic soft X-ray modulations. Here, we provide an overview of the targets NICER will observe and tthe technique and models that have been developed by the NICER team to estimate the masses and radii of these pulsars.

  20. Superheating effects in line broadening of dense alkali vapors (United States)

    Pichler, G.; Makdisi, Y.; Kokaj, J.; Mathew, J.; Rakić, M.; Beuc, R.


    We used the superheating of the dense alkali vapor in order to separate atomic from the molecular photoionization spectrum. Homonuclear and heteronuclear alkali molecules are essentially two electron systems and therefore simultaneous excitation of two atoms above the ionization limit will form autoionizing potential curves which will bring about new bands in the photoionization spectrum. We present a satisfactory comparison between experimental and theoretical emission coefficient function of diffuse bands (cesium dimer excimer) at temperatures up to 1000 °C, where the metal vapor was heavily superheated. New results for Rb2 photoionization process reveal similar structured photoionization continuum but with reduced number of photoionization bands.

  1. Performance analysis of simultaneous dense coding protocol under decoherence (United States)

    Huang, Zhiming; Zhang, Cai; Situ, Haozhen


    The simultaneous dense coding (SDC) protocol is useful in designing quantum protocols. We analyze the performance of the SDC protocol under the influence of noisy quantum channels. Six kinds of paradigmatic Markovian noise along with one kind of non-Markovian noise are considered. The joint success probability of both receivers and the success probabilities of one receiver are calculated for three different locking operators. Some interesting properties have been found, such as invariance and symmetry. Among the three locking operators we consider, the SWAP gate is most resistant to noise and results in the same success probabilities for both receivers.

  2. Plasmon-polariton modes of dense Au nanowire arrays

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Hongdan; Lemmens, Peter; Wulferding, Dirk; Cetin, Mehmet Fatih [IPKM, TU-BS, Braunschweig (Germany); Tornow, Sabine; Zwicknagl, Gertrud [IMP, TU-BS, Braunschweig (Germany); Krieg, Ulrich; Pfnuer, Herbert [IFP, LU Hannover (Germany); Daum, Winfried; Lilienkamp, Gerhard [IEPT, TU Clausthal (Germany); Schilling, Meinhard [EMG, TU-BS, Braunschweig (Germany)


    Using optical absorption and other techniques we study plasmon-polariton modes of dense Au nanowire arrays as function of geometrical parameters and coupling to molecular degrees of freedom. For this instance we electrochemically deposit Au nanowires in porous alumina with well controlled morphology and defect concentration. Transverse and longitudinal modes are observed in the absorption spectra resulting from the anisotropic plasmonic structure. The longitudinal mode shows a blue shift of energy with increasing length of the wires due to the more collective nature of this response. We compare our observations with model calculations and corresponding results on 2D Ag nanowire lattices.

  3. A continuous stochastic model for non-equilibrium dense gases (United States)

    Sadr, M.; Gorji, M. H.


    While accurate simulations of dense gas flows far from the equilibrium can be achieved by direct simulation adapted to the Enskog equation, the significant computational demand required for collisions appears as a major constraint. In order to cope with that, an efficient yet accurate solution algorithm based on the Fokker-Planck approximation of the Enskog equation is devised in this paper; the approximation is very much associated with the Fokker-Planck model derived from the Boltzmann equation by Jenny et al. ["A solution algorithm for the fluid dynamic equations based on a stochastic model for molecular motion," J. Comput. Phys. 229, 1077-1098 (2010)] and Gorji et al. ["Fokker-Planck model for computational studies of monatomic rarefied gas flows," J. Fluid Mech. 680, 574-601 (2011)]. The idea behind these Fokker-Planck descriptions is to project the dynamics of discrete collisions implied by the molecular encounters into a set of continuous Markovian processes subject to the drift and diffusion. Thereby, the evolution of particles representing the governing stochastic process becomes independent from each other and thus very efficient numerical schemes can be constructed. By close inspection of the Enskog operator, it is observed that the dense gas effects contribute further to the advection of molecular quantities. That motivates a modelling approach where the dense gas corrections can be cast in the extra advection of particles. Therefore, the corresponding Fokker-Planck approximation is derived such that the evolution in the physical space accounts for the dense effects present in the pressure, stress tensor, and heat fluxes. Hence the consistency between the devised Fokker-Planck approximation and the Enskog operator is shown for the velocity moments up to the heat fluxes. For validation studies, a homogeneous gas inside a box besides Fourier, Couette, and lid-driven cavity flow setups is considered. The results based on the Fokker-Planck model are

  4. Warm, Dense Plasma Characterization by X-ray Thomson Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Landen, O L; Glenzer, S H; Cauble, R C; Lee, R W; Edwards, J E; Degroot, J S


    We describe how the powerful technique of spectrally resolved Thomson scattering can be extended to the x-ray regime, for direct measurements of the ionization state, density, temperature, and the microscopic behavior of dense cool plasmas. Such a direct measurement of microscopic parameters of solid density plasmas could eventually be used to properly interpret laboratory measurements of material properties such as thermal and electrical conductivity, EUS and opacity. In addition, x-ray Thomson scattering will provide new information on the characteristics of rarely and hitherto difficult to diagnose Fermi degenerate and strongly coupled plasmas.

  5. Gamma-ray burst interaction with dense interstellar medium


    Barkov, Maxim; Bisnovatyi-Kogan, Gennady


    Interaction of cosmological gamma ray burst radiation with the dense interstellar medium of host galaxy is considered. Gas dynamical motion of interstellar medium driven by gamma ray burst is investigated in 2D approximation for different initial density distributions of host galaxy matter and different total energy of gamma ray burst. The maximum velocity of motion of interstellar medium is $1.8\\cdot10^4$ km/s. Light curves of gamma ray burst afterglow are calculated for set of non homogeneo...

  6. Mesoscopic length scale controls the rheology of dense suspensions. (United States)

    Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric


    From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

  7. Shocks in Dense Clouds in the Vela Supernova Remnant: FUSE (United States)

    Nichols, Joy; Sonneborn, George (Technical Monitor)


    We have obtained 8 LWRS FUSE spectra to study a recently identified interaction of the Vela supernova remnant with a dense cloud region along its western edge. The goal is to quantify the temperature, ionization, density, and abundance characteristics associated with this shock/dense cloud interface by means of UV absorption line studies. Our detection of high-velocity absorption line C I at +90 to +130 km/s with IUE toward a narrow region interior to the Vela SNR strongly suggests the Vela supernova remnant is interacting with a dense ISM or molecular cloud. The shock/dense cloud interface is suggested by (1) the rarity of detection of high-velocity C I seen in IUE spectra, (2) its very limited spatial distribution in the remnant, and (3) a marked decrease in X-ray emission in the region immediately west of the position of these stars where one also finds a 100 micron emission ridge in IRAS images. We have investigated the shock physics and general properties of this interaction region through a focussed UV absorption line study using FUSE spectra. We have FUSE data on OVI absorption lines observed toward 8 stars behind the Vela supernova remnant (SNR). We compare the OVI observations with IUE observations of CIV absorption toward the same stars. Most of the stars, which are all B stars, have complex continua making the extraction of absorption lines difficult. Three of the stars, HD 72088, HD 72089 and HD 72350, however, are rapid rotators (v sin i less than 100 km/s) making the derivation of absorption column densities much easier. We have measured OVI and CIV column densities for the "main component" (i.e. the low velocity component) for these stars. In addition, by removing the H2 line at 1032.35A (121.6 km/s relative to OVI), we find high velocity components of OVI at approximately 150 km/s that we attribute to the shock in the Vela SNR. The column density ratios and magnitudes are compared to both steady shock models and results of hydrodynamical SNR

  8. Generation and characterisation of warm dense matter with intense lasers (United States)

    Riley, D.


    In this paper I discuss the subject of warm dense matter (WDM), which, apart from being of academic interest and relevant to inertial fusion capsules, is a subject of importance to those who wish to understand the formation and structure of planetary interiors and other astrophysical bodies. I broadly outline some key properties of WDM and go on to discuss various methods of generating samples in the laboratory using large laser facilities and outline some common techniques of diagnosis. It is not intended as a comprehensive review but rather a brief outline for scientists new to the field and those with an interest but not working in the field directly.

  9. Atomic Transport in Dense, Multi-Component Metallic Liquids


    Meyer, A


    Pd43Ni10Cu27P0 has been investigated in its equilibrium liquid state with incoherent, inelastic neutron scattering. As compared to simple liquids, liquid PdNiCuP is characterized by a dense packing with a packing fraction above 0.5. The intermediate scattering function exhibits a fast relaxation process that precedes structural relaxation. Structural relaxation obeys a time-temperature superposition that extends over a temperature range of 540K. The mode-coupling theory of the liquid to glass...

  10. Interaction of CO2 laser radiation with dense plasma


    Abdel-Raoof, Wasfi Sharkawy


    The instabilities which occur in the interaction of CO2 laser radiation with a dense plasma have been studied. A TEA CO2 laser provided pulses of up to 30 joules of energy with a duration of 50 nanoseconds. By focussing the radiation on to a plane target a focal spot of about 180 micrometers diameter was formed with a irradiance of 10 to 10 W cm. The scattered radiation was collected by a laser focussing lens and analysed with a grating spectrometer. Linear relationships have been found betwe...

  11. Laterally cyclic loading of monopile in dense sand

    DEFF Research Database (Denmark)

    Klinkvort, Rasmus Tofte; Hededal, Ole; Svensson, M.


    the loading conditions. In these tests the load conditions are controlled by two load characteristics, one controlling the level of the cyclic loading and one controlling the characteristic of the cyclic loading. The centrifuge tests were performed in dense dry sand on a pile with prototype dimensions...... used for wind turbine foundation. This is important in order to get the right failure mechanism in the sand. The load frame is controlled with a feedback system which enables force controlled load series. A total number of 8 tests have been carried. In all of the tests, the pile was loaded with 500...

  12. The Use of Living Cancer Cells Expressing Green Fluorescent Protein in the Nucleus and Red Fluorescence Protein in the Cytoplasm for Real-time Confocal Imaging of Chromosome and Cytoplasmic Dynamics During Mitosis. (United States)

    Suetsugu, Atsushi; Jiang, Ping; Yang, Meng; Yamamoto, Norio; Moriwaki, Hisataka; Saji, Shigetoyo; Hoffman, Robert M


    A library of dual-color fluorescent cancer cells with green fluorescent protein (GFP), linked to histone H2B, expressed in the nucleus and red fluorescent protein (RFP) expressed in the cytoplasm was previously genetically engineered. The aim of the current study was to use the dual-color cancer cells to visualize chromosome and cytoplasmic dynamics during mitosis. Using an Olympus FV1000 confocal microscope, a library of dual-color cells from the major cancer types was cultured on plastic. The cells were imaged by confocal microscopy to demonstrate chromosome and cytoplasmic dynamics during mitosis. Nuclear GFP expression enabled visualization of chromosomes behavior, whereas simultaneous cytoplasmic RFP expression enabled visualization of cytoplasmic behavior during mitosis. Thus, total cellular dynamics can be visualized at high resolution, including individual chromosomes in some cases, in living dual-color cells in real time. Dual-color cancer cells expressing H2B-GFP in the nucleus and RFP in the cytoplasm provide unique tools for visualizing subcellular nuclear and cytoplasm dynamics, including the behavior of individual chromosomes during mitosis. The dual-color cells can be used to evaluate chromosomal loss or gain in real time during treatment with a variety of agents or as the cells are selected for increased or decreased malignancy in culture or in vivo. The dual color cells will be a useful tool to discover and evaluate novel strategies for killing cancer cells. Copyright© 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  13. Enabling cytoplasmic delivery and organelle targeting by surface modification of nanocarriers (United States)

    Parodi, Alessandro; Corbo, Claudia; Cevenini, Armando; Molinaro, Roberto; Palomba, Roberto; Pandolfi, Laura; Agostini, Marco; Salvatore, Francesco; Tasciotti, Ennio


    Nanocarriers are designed to specifically accumulate in diseased tissues. In this context, targeting of intracellular compartments was shown to enhance the efficacy of many drugs and to offer new and more effective therapeutic approaches. This is especially true for therapies based on biologicals that must be encapsulated to favor cell internalization, and to avoid intracellular endosomal sequestration and degradation of the payload. In this review, we discuss specific surface modifications designed to achieve cell cytoplasm delivery and to improve targeting of major organelles; we also discuss the therapeutic applications of these approaches. Last, we describe some integrated strategies designed to sequentially overcome the biological barriers that separate the site of administration from the cell cytoplasm, which is the drug's site of action. PMID:26139126

  14. A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus.

    Directory of Open Access Journals (Sweden)

    Mattia Gazzola


    Full Text Available Cytoplasmic transport of organelles, nucleic acids and proteins on microtubules is usually bidirectional with dynein and kinesin motors mediating the delivery of cargoes in the cytoplasm. Here we combine live cell microscopy, single virus tracking and trajectory segmentation to systematically identify the parameters of a stochastic computational model of cargo transport by molecular motors on microtubules. The model parameters are identified using an evolutionary optimization algorithm to minimize the Kullback-Leibler divergence between the in silico and the in vivo run length and velocity distributions of the viruses on microtubules. The present stochastic model suggests that bidirectional transport of human adenoviruses can be explained without explicit motor coordination. The model enables the prediction of the number of motors active on the viral cargo during microtubule-dependent motions as well as the number of motor binding sites, with the protein hexon as the binding site for the motors.

  15. The cytoplasmic structure hypothesis for ribosome assembly, vertical inheritance, and phylogeny. (United States)

    Thaler, David S


    Fundamental questions in evolution concern deep divisions in the living world and vertical versus horizontal information transfer. Two contrasting views are: (i) three superkingdoms Archaea, Eubacteria, and Eukarya based on vertical inheritance of genes encoding ribosomes; versus (ii) a prokaryotic/eukaryotic dichotomy with unconstrained horizontal gene transfer (HGT) among prokaryotes. Vertical inheritance implies continuity of cytoplasmic and structural information whereas HGT transfers only DNA. By hypothesis, HGT of the translation machinery is constrained by interaction between new ribosomal gene products and vertically inherited cytoplasmic structure made largely of preexisting ribosomes. Ribosomes differentially enhance the assembly of new ribosomes made from closely related genes and inhibit the assembly of products from more distal genes. This hypothesis suggests experiments for synthetic biology: the ability of synthetic genomes to "boot," i.e., establish hereditary continuity, will be constrained by the phylogenetic closeness of the cell "body" into which genomes are placed.

  16. Parvovirus particles and movement in the cellular cytoplasm and effects of the cytoskeleton

    Energy Technology Data Exchange (ETDEWEB)

    Lyi, Sangbom Michael; Tan, Min Jie Alvin, E-mail:; Parrish, Colin R., E-mail:


    Cell infection by parvoviruses requires that capsids be delivered from outside the cell to the cytoplasm, followed by genome trafficking to the nucleus. Here we microinject capsids into cells that lack receptors and followed their movements within the cell over time. In general the capsids remained close to the positions where they were injected, and most particles did not move to the vicinity of or enter the nucleus. When 70 kDa-dextran was injected along with the capsids that did not enter the nucleus in significant amounts. Capsids conjugated to peptides containing the SV40 large T-antigen nuclear localization signal remained in the cytoplasm, although bovine serum albumen conjugated to the same peptide entered the nucleus rapidly. No effects of disruption of microfilaments, intermediate filaments, or microtubules on the distribution of the capsids were observed. These results suggest that movement of intact capsids within cells is primarily associated with passive processes.

  17. ROS-activated ATM-dependent phosphorylation of cytoplasmic substrates identified by large scale phosphoproteomics screen

    DEFF Research Database (Denmark)

    Kozlov, Sergei V; Waardenberg, Ashley J; Engholm-Keller, Kasper


    ATM (ataxia-telangiectasia, mutated) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signalling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoi......ATM (ataxia-telangiectasia, mutated) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signalling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle...... to identify cytoplasmic proteins altered in their phosphorylation state in control and A-T (ataxia-telangiectasia) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites...

  18. Serum from patients with various thrombopoietic disorders alters terminal cytoplasmic maturation of human megakaryocytes in vitro. (United States)

    Straneva, J E; Briddell, R A; Hui, S L; Hoffman, R


    Human bone marrow was depleted of progenitors (CFU-MK), but enriched for recognizable megakaryocytes (MK), and placed in cultures with serum from either normal donors (NABS) or patients with primary (PTS) or secondary (STS) thrombocytosis, autoimmune thrombocytopenia (ATS) or aplastic anemia (AAS). Mean MK diameters shifted during the 3-4 days of incubation. Endomitotic figure were visible and mean ploidy increased slightly during cytoplasmic maturation, where decreases in immature cells (stages 1 and 2) were accompanied by increases in the mature MK (stages 3 and 4). Cytoplasmic maturation was faster in AAS, ATS and STS than PTS or NABS; mean size and ploidy were similar in all cultures. Recognizable MK were not forced to undergo additional endoreduplication in response to stimulation. Only AAS augmented MK colony formation, which indicated that at least two humoral factors can regulate megakaryocytopoiesis at separate levels, the progenitors and morphologically recognizable MK.

  19. Transcytosis of Aminopeptidase N in caco-2 cells is mediated by a Non-cytoplasmic Signal

    DEFF Research Database (Denmark)

    Vogel, L K; Norén, Ove; Sjöström, H


    In Caco-2 cells, aminopeptidase N is transported to the apical membrane from the trans Golgi network by both the direct and the indirect pathway (Matter, K., Brauchbar, M., Bucher, K., and Hauri, H.-P. (1990) Cell 60, 429-437). The aim of this study was to determine the importance of the transmem......In Caco-2 cells, aminopeptidase N is transported to the apical membrane from the trans Golgi network by both the direct and the indirect pathway (Matter, K., Brauchbar, M., Bucher, K., and Hauri, H.-P. (1990) Cell 60, 429-437). The aim of this study was to determine the importance...... of the transmembrane or cytoplasmic domain of aminopeptidase N for transport of aminopeptidase N by the indirect pathway by analysis of mutated forms of aminopeptidase N recombinantly expressed in Caco-2 cells. A tail-less and two secretory forms of aminopeptidase N, all deprived of the cytoplasmic tail, were...

  20. Proteomic Analyses Reveal a Role of Cytoplasmic Droplets as an Energy Source during Epididymal Sperm Maturation (United States)

    Yuan, Shuiqiao; Zheng, Huili; Zheng, Zhihong; Yan, Wei


    A small portion of cytoplasm is generally retained as the cytoplasmic droplet (CD) on the flagellum of spermatozoa after spermiation in mice. CDs are believed to play a role in osmoadaptation by allowing water entrance or exit. However, many lines of evidence suggest that CDs may have roles beyond osmoregulation. To gain more insights, we purified CDs from murine epididymal spermatozoa and conducted proteomic analyses on proteins highly enriched in CDs. Among 105 proteins identified, 71 (68%) were enzymes involved in energy metabolism. We also found that sperm mitochondria underwent a reactivation process and glycolytic enzymes were further distributed and incorporated into different regions of the flagellum during epididymal sperm maturation. Both processes appeared to require CDs. Our data suggest that the CD represents a transient organelle that serves as an energy source essential for epididymal sperm maturation. PMID:24155961

  1. Antineutrophil cytoplasmic antibody–negative pauci-immune glomerulonephritis with massive intestinal bleeding

    Directory of Open Access Journals (Sweden)

    Miyeon Kim


    Full Text Available A 61-year-old woman was admitted to hospital because of generalized edema and proteinuria. Her renal function deteriorated rapidly. Serum immunoglobulin and complement levels were within normal ranges. An autoantibody examination showed negative for antinuclear antibody and antineutrophil cytoplasmic antibody. Histologic examination of a renal biopsy specimen revealed that all of the glomeruli had severe crescent formations with no immune deposits. The patient was treated with steroid pulse therapy with cyclophosphamide followed by oral prednisolone. Fifteen days later, she experienced massive recurrent hematochezia. Angiography revealed an active contrast extravasation in a branch of the distal ileal artery. We selectively embolized with a permanent embolic agent. On the 45th hospital day, the patient suddenly lost consciousness. Brain computed tomography showed intracerebral hemorrhage. We report a case of antineutrophil cytoplasmic antibody–negative pauci-immune glomerulonephritis with massive intestinal bleeding and cerebral hemorrhage.

  2. A study of the membrane association and regulatory effect of the phospholemman cytoplasmic domain. (United States)

    Hughes, Eleri; Whittaker, Christopher A P; Barsukov, Igor L; Esmann, Mikael; Middleton, David A


    Phospholemman (PLM) is a single-span transmembrane protein belonging to the FXYD family of proteins. PLM (or FXYD1) regulates the Na,K-ATPase (NKA) ion pump by altering its affinity for K(+) and Na(+) and by reducing its hydrolytic activity. Structural studies of PLM in anionic detergent micelles have suggested that the cytoplasmic domain, which alone can regulate NKA, forms a partial helix which is stabilized by interactions with the charged membrane surface. This work examines the membrane affinity and regulatory function of a 35-amino acid peptide (PLM(38-72)) representing the PLM cytoplasmic domain. Isothermal titration calorimetry and solid-state NMR measurements confirm that PLM(38-72) associates strongly with highly anionic phospholipid membranes, but the association is weakened substantially when the negative surface charge is reduced to a more physiologically relevant environment. Membrane interactions are also weakened when the peptide is phosphorylated at S68, one of the substrate sites for protein kinases. PLM(38-72) also lowers the maximal velocity of ATP hydrolysis (V(max)) by NKA, and phosphorylation of the peptide at S68 gives rise to a partial recovery of V(max). These results suggest that the PLM cytoplasmic domain populates NKA-associated and membrane-associated states in dynamic equilibrium and that phosphorylation may alter the position of the equilibrium. Interestingly, peptides representing the cytoplasmic domains of two other FXYD proteins, Mat-8 (FXYD3) and CHIF (FXYD4), have little or no interaction with highly anionic phospholipid membranes and have no effect on NKA function. This suggests that the functional and physical properties of PLM are not conserved across the entire FXYD family. Copyright © 2010. Published by Elsevier B.V.

  3. Glycoprotein cytoplasmic domain sequences required for rescue of a vesicular stomatitis virus glycoprotein mutant

    Energy Technology Data Exchange (ETDEWEB)

    Whitt, M.A.; Chong, L.; Rose, J.K. (Yale Univ. School of Medicine, New Haven, CT (USA))


    The authors have used transient expression of the wild-type vesicular stomatitis virus (VSV) glycoprotein (G protein) from cloned cDNA to rescue a temperature-sensitive G protein mutant of VSV in cells at the nonpermissive temperature. Using cDNAs encoding G proteins with deletions in the normal 29-amino-acid cytoplasmic domain, they determined that the presence of either the membrane-proximal 9 amino acids or the membrane-distal 12 amino acids was sufficient for rescue of the temperature-sensitive mutant. G proteins with cytoplasmic domains derived from other cellular or viral G proteins did not rescue the mutant, nor did G proteins with one or three amino acids of the normal cytoplasmic domain. Rescue correlated directly with the ability of the G proteins to be incorporated into virus particles. This was shown by analysis of radiolabeled particles separated on sucrose gradients as well as by electron microscopy of rescued virus after immunogold labeling. Quantitation of surface expression showed that all of the mutated G proteins were expressed less efficiently on the cell surface than was wild-type G protein. However, they were able to correct for differences in rescue efficiency resulting from differences in the level of surface expression by reducing wild-type G protein expression to levels equivalent to those observed for the mutated G proteins. The results provide evidence that at least a portion of the cytoplasmic domain is required for efficient assembly of the VSV G protein into virions during virus budding.

  4. A Case of Metastatic Angiosarcoma Diagnosed by Liquid-Based Preparation: Peculiar Cytoplasmic Changes


    Jung, Min Jung; Kim, Young Ok


    Angiosarcoma with predominantly epithelioid features is a rare soft tissue neoplasm and the interpretation of its cytopathologic findings may be difficult. We report a case of metastatic angiosarcoma with predominantly epithelioid features diagnosed by liquid-based cytology. The cytopathologic findings in this case differed from those of the conventional preparation and we found a clean background, no hyperchromatic nuclei and several cytoplasmic changes, including intracytoplasmic vacuoles w...

  5. Reprogramming of round spermatids by the germinal vesicle cytoplasm in mice.

    Directory of Open Access Journals (Sweden)

    Peng-Cheng Kong

    Full Text Available The birthrate following round spermatid injection (ROSI remains low in current and evidence suggests that factors in the germinal vesicle (GV cytoplasm and certain substances in the GV such as the nucleolus might be responsible for genomic reprogramming and embryonic development. However, little is known whether the reprogramming factors in GV oocyte cytoplasm and/or nucleolus in GV are beneficial to the reprogramming of round spermatids and development of ROSI embryos. Here, round spermatids were treated with GV cytolysates and injected this round spermatid alone or co-injected with GV oocyte nucleolus into mature metaphase II oocytes. Subsequent embryonic development was assessed morphologically and by Oct4 expression in blastocysts. There was no significant difference between experimental groups at the zygote to four-cell development stages. Blastocysts derived from oocytes which were injected with cytolysate treated-round spermatid alone or co-injected with nucleoli injection yielded 63.6% and 70.3% high quality embryos, respectively; comparable to blastocysts derived by intracytoplasmic sperm injection (ICSI, but higher than these oocytes which were co-injected with lysis buffer-treated round spermatids and nucleoli or injected with the lysis buffer-treated round spermatids alone. Furthermore, the proportion of live offspring resulting from oocytes which were co-injected with cytolysate treated-round spermatids and nucleoli or injected with cytolysate treated-round spermatids alone was higher than those were injected with lysis buffer treated-round spermaids, but comparable with the ICSI group. Our results demonstrate that factors from the GV cytoplasm improve round spermatid reprogramming, and while injection of the extra nucleolus does not obviously improve reprogramming its potential contribution, although which cannot be definitively excluded. Thus, some reprogramming factors are evidently present in GV oocyte cytoplasm and could

  6. Plasma exchange in antineutrophil cytoplasmic antibody-associated vasculitis--a 25-year perspective

    DEFF Research Database (Denmark)

    Szpirt, Wladimir M


    Demonstration of a pathogenic role for antineutrophil cytoplasmic antibodies (ANCA) underlies the scientific rationale for plasma exchange (PLEX) in the treatment of ANCA-associated vasculitis (AAV). Most clinical evidence of efficacy concerns the use of PLEX for the recovery of renal function...... in severe nephritis, when used in conjunction with immunosuppressive drug therapy. The development of PLEX for this indication, the strength of the clinical trial evidence supporting its use, its roles in other AAV indications and ongoing research are discussed....

  7. Differential effect of HDAC3 on cytoplasmic and nuclear huntingtin aggregates.

    Directory of Open Access Journals (Sweden)

    Tatsuo Mano

    Full Text Available Histone deacetylases (HDACs are potential therapeutic targets of polyglutamine (pQ diseases including Huntington's disease (HD that may function to correct aberrant transcriptional deactivation caused by mutant pQ proteins. HDAC3 is a unique class 1 HDAC found in both the cytoplasm and in the nucleus. However, the precise functions of HDAC3 in the two cellular compartments are only vaguely known. HDAC3 directly binds to huntingtin (Htt with short pQ and this interaction is important for suppressing neurotoxicity induced by HDAC3. With long pQ Htt, the interaction with HDAC3 is inhibited, and this supposedly promotes neuronal death, indicating that HDAC3 would be a good therapeutic target for HD. However, the knockout of one HDAC3 allele did not show any efficacy in reducing neurodegenerative symptoms in a mouse model of HD. Therefore, the role of HDAC3 in the pathogenesis of HD has yet to be fully elucidated. We attempted to resolve this issue by focusing on the different roles of HDAC3 on cytoplasmic and nuclear Htt aggregates. In addition to supporting the previous findings, we found that HDAC3 preferentially binds to nuclear Htt over cytoplasmic ones. Specific HDAC3 inhibitors increased the total amount of Htt aggregates by increasing the amount of nuclear aggregates. Both cytoplasmic and nuclear Htt aggregates were able to suppress endogenous HDAC3 activity, which led to decreased nuclear proteasome activity. Therefore, we concluded that Htt aggregates impair nuclear proteasome activity through the inhibition of HDAC3. Our findings provide new insights regarding cross-compartment proteasome regulation.

  8. Plant cytoplasmic GAPDH: redox post-translational modifications and moonlighting properties

    Directory of Open Access Journals (Sweden)

    Mirko eZaffagnini


    Full Text Available Glyceraldehyde-3-phosphate dehydrogenase (GAPDH is a ubiquitous enzyme involved in glycolysis and shown, particularly in animal cells, to play additional roles in several unrelated non-metabolic processes such as control of gene expression and apoptosis. This functional versatility is regulated, in part at least, by redox post-translational modifications that alter GAPDH catalytic activity and influence the subcellular localization of the enzyme. In spite of the well established moonlighting (multifunctional properties of animal GAPDH, little is known about non-metabolic roles of GAPDH in plants. Plant cells contain several GAPDH isoforms with different catalytic and regulatory properties, located both in the cytoplasm and in plastids, and participating in glycolysis and the Calvin-Benson cycle. A general feature of all GAPDH proteins is the presence of an acidic catalytic cysteine in the active site that is overly sensitive to oxidative modifications, including glutathionylation and S-nitrosylation. In Arabidopsis, oxidatively-modified cytoplasmic GAPDH has been successfully used as a tool to investigate the role of reduced glutathione, thioredoxins and glutaredoxins in the control of different types of redox post-translational modifications. Oxidative modifications inhibit GAPDH activity, but might enable additional functions in plant cells. Mounting evidence support the concept that plant cytoplasmic GAPDH may fulfill alternative, non-metabolic functions that are triggered by redox post-translational modifications of the protein under stress conditions. The aim of this review is to detail the molecular mechanisms underlying the redox regulation of plant cytoplasmic GAPDH in the light of its crystal structure, and to provide a brief inventory of the well known redox-dependent multi-facetted properties of animal GAPDH, together with the emerging roles of oxidatively-modified GAPDH in stress signaling pathways in plants.

  9. Generation of micronuclei during interphase by coupling between cytoplasmic membrane blebbing and nuclear budding.

    Directory of Open Access Journals (Sweden)

    Koh-ichi Utani

    Full Text Available Micronucleation, mediated by interphase nuclear budding, has been repeatedly suggested, but the process is still enigmatic. In the present study, we confirmed the previous observation that there are lamin B1-negative micronuclei in addition to the positive ones. A large cytoplasmic bleb was found to frequently entrap lamin B1-negative micronuclei, which were connected to the nucleus by a thin chromatin stalk. At the bottom of the stalk, the nuclear lamin B1 structure appeared broken. Chromatin extrusion through lamina breaks has been referred to as herniation or a blister of the nucleus, and has been observed after the expression of viral proteins. A cell line in which extrachromosomal double minutes and lamin B1 protein were simultaneously visualized in different colors in live cells was established. By using these cells, time-lapse microscopy revealed that cytoplasmic membrane blebbing occurred simultaneously with the extrusion of nuclear content, which generated lamin B1-negative micronuclei during interphase. Furthermore, activation of cytoplasmic membrane blebbing by the addition of fresh serum or camptothecin induced nuclear budding within 1 to 10 minutes, which suggested that blebbing might be the cause of the budding. After the induction of blebbing, the frequency of lamin-negative micronuclei increased. The budding was most frequent during S phase and more efficiently entrapped small extrachromosomal chromatin than the large chromosome arm. Based on these results, we suggest a novel mechanism in which cytoplasmic membrane dynamics pulls the chromatin out of the nucleus through the lamina break. Evidence for such a mechanism was obtained in certain cancer cell lines including human COLO 320 and HeLa. The mechanism could significantly perturb the genome and influence cancer cell phenotypes.

  10. Why cholesterol should be found predominantly in the cytoplasmic leaf of the plasma membrane

    CERN Document Server

    Giang, Ha


    In the mammalian plasma membrane, cholesterol can translocate rapidly between the exoplasmic and cytoplasmic leaves, and is found predominantly in the latter. We hypothesize that it is drawn to the inner leaf to reduce the bending free energy of the membrane caused by the presence there of phosphatidylethanolamine. Incorporating this mechanism into a model free energy for the bilayer, we calculate that approximately two thirds of the total cholesterol should be in the inner leaf.

  11. Actin filaments connected with the microtubules of lipotubuloids, cytoplasmic domains rich in lipid bodies and microtubules. (United States)

    Kwiatkowska, M; Popłońska, K; Stepiński, D


    Lipotubuloids, i.e., cytoplasmic domains containing an agglomeration of lipid bodies surrounded by half-unit membrane, entwined and held together by a system of microtubules, have been found in the ovary epidermis of Ornithogalum umbellatum. Ultrastructural studies demonstrated thin filaments in lipotubuloids that are probably actin filaments arranged parallel to microtubules. It is suggested that interaction of actin filaments with the microtubules determines the driving force for the rotary motion characteristic of lipotubuloids, as this movement is sensitive to cytochalasin B.

  12. Cytoplasmic BRMS1 expression in malignant melanoma is associated with increased disease-free survival

    Directory of Open Access Journals (Sweden)

    Slipicevic Ana


    Full Text Available Abstract Background/aims Breast cancer metastasis suppressor 1 (BRMS1 blocks metastasis in melanoma xenografts; however, its usefulness as a biomarker in human melanomas has not been widely studied. The goal was to measure BRMS1 expression in benign nevi, primary and metastatic melanomas and evaluate its impact on disease progression and prognosis. Methods Paraffin-embedded tissue from 155 primary melanomas, 69 metastases and 15 nevi was examined for BRMS1 expression using immunohistochemistry. siRNA mediated BRMS1 down-regulation was used to study impact on invasion and migration in melanoma cell lines. Results A significantly higher percentage of nevi (87%, compared to primary melanomas (20% and metastases (48%, expressed BRMS1 in the nucelus (p Waf1/Cip1 (p = 0.009. Cytoplasmic score index was inversely associated with nuclear p-Akt (p = 0.013 and positively associated with cytoplasmic p-ERK1/2 expression (p = 0.033. Nuclear BRMS1 expression in ≥ 10% of primary melanoma cells was associated with thicker tumors (p = 0.016 and decreased relapse-free period (p = 0.043. Nuclear BRMS1 was associated with expression of fatty acid binding protein 7 (FABP7; p = 0.011, a marker of invasion in melanomas. In line with this, repression of BRMS1 expression reduced the ability of melanoma cells to migrate and invade in vitro. Conclusion Our data suggest that BRMS1 is localized in cytoplasm and nucleus of melanocytic cells and that cellular localization determines its in vivo effect. We hypothesize that cytoplasmic BRMS1 restricts melanoma progression while nuclear BRMS1 possibly promotes melanoma cell invasion. Please see related article:

  13. Development of male sterile Eruca sativa carrying a Raphanus sativus/Brassica oleracea cybrid cytoplasm. (United States)

    Nothnagel, Thomas; Klocke, Evelyn; Schrader, Otto; Linke, Bettina; Budahn, Holger


    Alloplasmic male sterile breeding lines of Eruca sativa were developed by intergeneric hybridization with CMS- Brassica oleracea, followed by recurrent backcrosses and determination of the breeding value. Male sterile breeding lines of rocket salad (Eruca sativa) were developed by intergeneric hybridization with cytoplasmic male sterile (CMS) cauliflower (Brassica oleracea) followed by recurrent backcrosses. Five amphidiploid F1 plants (2n = 2x = 20, CE), achieved by manual crosses and embryo rescue, showed an intermediate habit. The plants were completely male sterile and lacked seed set after pollination with the Eruca parent. Allotetraploid F1-hybrid plants (4n = 4x = 40, CCEE) obtained after colchicine treatment were backcrossed six times with pollen of the Eruca parent to select alloplasmic diploid E. sativa lines. The hybrid status and the nucleo-cytoplasmic constellation were continuously controlled by RAPD and Southern analysis during subsequent backcrosses. The ploidy level was investigated by flow cytometry and chromosome analysis. Premeiotic (sporophytic) and postmeiotic (pollen abortive) defects during the anther development were observed in the alloplasmic E. sativus plants in comparison to the CMS-cauliflower donor. No further incompatibilities were noticed between the CMS-inducing cybrid cytoplasm and the E. sativa nuclear genome. The final alloplasmic E. sativa lines were diploid with 2n = 2x = 22 chromosomes and revealed complete male sterility and restored female fertility. Plant vigor and yield potential of the CMS-E. sativa BC5 lines were comparable to the parental E. sativus line. In conclusion, the employed cybrid-cytoplasm has been proven as a vital source of CMS for E. sativa. The developed lines are directly applicable for hybrid breeding of rocket salad.

  14. Regulation of TAK1/TAB1-mediated IL-1β signaling by cytoplasmic PPARβ/δ.

    Directory of Open Access Journals (Sweden)

    Josefine Stockert

    Full Text Available The peroxisome proliferator-activated receptor subtypes PPARα, PPARβ/δ, PPARγ are members of the steroid hormone receptor superfamily with well-established functions in transcriptional regulation. Here, we describe an unexpected cytoplasmic function of PPARβ/δ. Silencing of PPARβ/δ expression interferes with the expression of a large subset of interleukin-1β (IL-1β-induced target genes in HeLa cells, which is preceded by an inhibition of the IL-1β-induced phosphorylation of TAK1 and its downstream effectors, including the NFκBα inhibitor IκBα (NFKBIA and the NFκBα subunit p65 (RELA. PPARβ/δ enhances the interaction between TAK1 and the small heat-shock protein HSP27, a known positive modulator of TAK1-mediated IL-1β signaling. Consistent with these findings, PPARβ/δ physically interacts with both the endogenous cytoplasmic TAK1/TAB1 complex and HSP27, and PPARβ/δ overexpression increases the TAK1-induced transcriptional activity of NFκB. These observations suggest that PPARβ/δ plays a role in the assembly of a cytoplasmic multi-protein complex containing TAK1, TAB1, HSP27 and PPARβ/δ, and thereby participates in the NFκB response to IL-1β.

  15. Involvement of hGLD-2 in cytoplasmic polyadenylation of human p53 mRNA

    DEFF Research Database (Denmark)

    Glahder, Jacob-Andreas Harald; Norrild, Bodil


    Cytoplasmic polyadenylation is a post-transcriptional mechanism regulating mRNA stability and translation. The human p53 3'-untranslated region (3'-UTR) contains two regions similar to cytoplasmic polyadenylation elements (CPEs) just upstream of the poly(A) hexanucleotide. Evaluation of the p53 CPE......-like elements was performed by luciferase reporter assays, qPCR, and poly(A) assays. Herein, we report the down regulation of a luciferase reporter fused to the p53 3'-UTR, when human CPE-binding protein 1 (hCPEB1) is overexpressed. This inhibition is partially rescued when hCPEB1fused to hGLD-2 [a human...... cytoplasmic poly(A) polymerase] is overexpressed instead. The stability of a luciferase mRNA containing the p53 3'-UTR downstream, is decreased when hCPEB1 is overexpressed as seen by qPCR. Expression of hGLD-2 restores the mRNA stability. This is due to elongation of the poly(A) tail as seen by a PCR...

  16. Fluorescence studies on modes of cytochalasin B and phallotoxin action on cytoplasmic streaming in Chara (United States)


    Various investigations have suggested that cytoplasmic streaming in characean algae is driven by interaction between subcortical actin bundles and endoplasmic myosin. To further test this hypothesis, we have perfused cytotoxic actin-binding drugs and fluorescent actin labels into the cytoplasm of streaming Chara cells. Confirming earlier work, we find that cytochalasin B (CB) reversibly inhibits streaming. In direct contrast to earlier investigators, who have found phalloidin to be a potent inhibitor of movement in amoeba, slime mold, and fibroblastic cells, we find that phalloidin does not inhibit streaming in Chara but does modify the inhibitory effect of CB. Use of two fluorescent actin probes, fluorescein, isothiocyanate-heavy meromyosin (FITC-HMM) and nitrobenzoxadiazole-phallacidin (NBD-Ph), has permitted visualization of the effects of CB and phalloidin on the actin bundles. FITC-HMM labeling in perfused but nonstreaming cells has revealed a previously unobserved alteration of the actin bundles by CB. Phalloidin alone does not perceptibly alter the actin bundles but does block the alteration by CB if applied as a pretreatment, NBD-Ph perfused into the cytoplasm of streaming cells stains actin bundles without inhibiting streaming. NBD-Ph staining of actin bundles is not initially observed in cells inhibited by CB but does appear simultaneously with the recovery of streaming as CB leaks from the cells. The observations reported here are consistent with the established effects of phallotoxins and CB on actin in vitro and support the hypothesis that streaming is generated by actin-myosin interactions. PMID:6894146

  17. HDAC4 reduction: a novel therapeutic strategy to target cytoplasmic huntingtin and ameliorate neurodegeneration.

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    Michal Mielcarek


    Full Text Available Histone deacetylase (HDAC 4 is a transcriptional repressor that contains a glutamine-rich domain. We hypothesised that it may be involved in the molecular pathogenesis of Huntington's disease (HD, a protein-folding neurodegenerative disorder caused by an aggregation-prone polyglutamine expansion in the huntingtin protein. We found that HDAC4 associates with huntingtin in a polyglutamine-length-dependent manner and co-localises with cytoplasmic inclusions. We show that HDAC4 reduction delayed cytoplasmic aggregate formation, restored Bdnf transcript levels, and rescued neuronal and cortico-striatal synaptic function in HD mouse models. This was accompanied by an improvement in motor coordination, neurological phenotypes, and increased lifespan. Surprisingly, HDAC4 reduction had no effect on global transcriptional dysfunction and did not modulate nuclear huntingtin aggregation. Our results define a crucial role for the cytoplasmic aggregation process in the molecular pathology of HD. HDAC4 reduction presents a novel strategy for targeting huntingtin aggregation, which may be amenable to small-molecule therapeutics.

  18. Exosomal Secretion of Cytoplasmic Prostate Cancer Xenograft-derived Proteins *S⃞ (United States)

    Jansen, Flip H.; Krijgsveld, Jeroen; van Rijswijk, Angelique; van den Bemd, Gert-Jan; van den Berg, Mirella S.; van Weerden, Wytske M.; Willemsen, Rob; Dekker, Lennard J.; Luider, Theo M.; Jenster, Guido


    Novel markers for prostate cancer (PCa) are needed because current established markers such as prostate-specific antigen lack diagnostic specificity and prognostic value. Proteomics analysis of serum from mice grafted with human PCa xenografts resulted in the identification of 44 tumor-derived proteins. Besides secreted proteins we identified several cytoplasmic proteins, among which were most subunits of the proteasome. Native gel electrophoresis and sandwich ELISA showed that these subunits are present as proteasome complexes in the serum from xenograft-bearing mice. We hypothesized that the presence of proteasome subunits and other cytoplasmic proteins in serum of xenografted mice could be explained by the secretion of small vesicles by cancer cells, so-called exosomes. Therefore, mass spectrometry and Western blotting analyses of the protein content of exosomes isolated from PCa cell lines was performed. This resulted in the identification of mainly cytoplasmic proteins of which several had previously been identified in the serum of xenografted mice, including proteasome subunits. The isolated exosomes also contained RNA, including the gene fusion TMPRSS2-ERG product. These observations suggest that although their function is not clearly defined cancer-derived exosomes offer possibilities for the identification of novel biomarkers for PCa. PMID:19204029

  19. Development of Novel Cytoplasmic Male Sterile Source from Dongxiang Wild Rice (Oryza rufipogon

    Directory of Open Access Journals (Sweden)

    Xian-hua SHEN


    Full Text Available This study was conducted to develop and characterize a novel cytoplasmic male sterile (CMS source which was identified from Dongxiang wild rice (Oryza rufipogon by crossing Dongxiang wild rice as female with Zhongzao 35, an indica inbred variety, as male and continuous backcrossing with Zhongzao 35. Observation under optical microscope manifested that this novel CMS belonged to typical abortion type with less pollen compared with wild abortive type cytoplasm (CMS-WA. Sequential planting showed that this novel CMS has complete and stable male sterility. Testcross experiment showed that all the 24 tested materials including maintainer and restorer lines of CMS-WA and Honglian type cytoplasm (CMS-HL and other indica inbred varieties are the maintainers with complete maintaining ability, suggesting that this novel CMS has fertility restoration totally different from CMS-WA and CMS-HL and belongs to a novel type of CMS. So far, we only discovered a unique fertility restoration source for this novel CMS. Inheritance analysis showed that the fertility restoration of this CMS was governed by three pairs of independent dominant genes. Prospect for application of this novel CMS system in hybrid rice breeding was also discussed.

  20. Cytoplasmic proteasomes are not indispensable for cell growth in Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Hikaru; Arai, Naoko; Tanaka, Keiji, E-mail:; Saeki, Yasushi, E-mail:


    Highlights: •We succeeded to control the proteasome localization by the anchor-away technique. •Nuclear proteasome-depleted cells showed a lethal phenotype. •Cytoplasmic proteasomes are not indispensable for cell growth in dividing cells. -- Abstract: The 26S proteasome is an essential protease complex responsible for the degradation of ubiquitinated proteins in eukaryotic cells. In rapidly proliferating yeast cells, proteasomes are mainly localized in the nucleus, but the biological significance of the proteasome localization is still unclear. In this study, we investigated the relationship between the proteasome localization and the functions by the anchor-away technique, a ligand-dependent sequestration of a target protein into specific compartment(s). Anchoring of the proteasome to the plasma membrane or the ribosome resulted in conditional depletion of the nuclear proteasomes, whereas anchoring to histone resulted in the proteasome sequestration into the nucleus. We observed that the accumulation of ubiquitinated proteins in all the proteasome-targeted cells, suggesting that both the nuclear and cytoplasmic proteasomes have proteolytic functions and that the ubiquitinated proteins are produced and degraded in each compartment. Consistent with previous studies, the nuclear proteasome-depleted cells exhibited a lethal phenotype. In contrast, the nuclear sequestration of the proteasome resulted only in a mild growth defect, suggesting that the cytoplasmic proteasomes are not basically indispensable for cell growth in rapidly growing yeast cells.

  1. Assessment of prognostic significance of cytoplasmic survivin expression in advanced oesophageal cancer.

    Directory of Open Access Journals (Sweden)

    G Wallner


    Full Text Available Survivin is a member of the family of proteins, which inhibit apoptosis (inhibitor of apoptosis proteins - IAP. Expression of survivin was found in colorectal cancer, neuroblastoma, bladder cancer, non-small cell lung cancer, and breast cancer. There is some recent data indicating the correlation of poor prognosis and worse response to chemotherapy in patients with oesophageal squamous cell carcinoma (OSCC expressing survivin. The aim of the present study was to assess survivin expression in cancerous tissue of patients with advanced OSCC and to test the potential correlation between survivin expression and clinicopathological data. Forty two patients (mean age 58.36+/-8.97 yrs, who were oesophagectomised due to squamous cell carcinoma of the thoracic oesophagus between 1998 and 2000, were retrospectively analysed. Cytoplasmic survivin expression, examined immunohistochemically, was found in 35 (83.33% cases. No statistically significant correlation between survivin expression in the tumour and patients' gender, TNM stage, or vascular involvement was noted. The mean survival of patients with cytoplasmic survivin expression (17.81+/-5.51 months was not statistically different to those with negative survivin staining (16+/-6.28 months as assessed by Mantel-Cox test (p=0.49. Univariate regression analysis revealed UICC staging as the only predictor of survival in the analysed group (p<0.05. These results indicate that the cytoplasmic survivin expression does not seem to be the prognostic factor in advanced cases of OSCC.

  2. Cytoplasmic tail domain of glycoprotein B is essential for HHV-6 infection

    Energy Technology Data Exchange (ETDEWEB)

    Mahmoud, Nora F. [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Faculty of Pharmacy, Suez Canal University, Ismailia (Egypt); Jasirwan, Chyntia [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Division of Hepatobiliary, Department of Internal Medicine, Faculty of Medicine, University of Indonesia (Indonesia); Kanemoto, Satoshi; Wakata, Aika; Wang, Bochao; Hata, Yuuki [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Nagamata, Satoshi [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe (Japan); Kawabata, Akiko [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Tang, Huamin [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan); Department of Immunology, Nanjing Medical University, Nanjing (China); Mori, Yasuko, E-mail: [Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe (Japan)


    Human herpesvirus 6 (HHV-6) glycoprotein B (gB) is an abundantly expressed viral glycoprotein required for viral entry and cell fusion, and is highly conserved among herpesviruses. The present study examined the function of HHV-6 gB cytoplasmic tail domain (CTD). A gB CTD deletion mutant was constructed which, in contrast to its revertant, could not be reconstituted. Moreover, deletion of gB cytoplasmic tail impaired the intracellular transport of gB protein to the trans-Golgi network (TGN). Taken together, these results suggest that gB CTD is critical for HHV-6 propagation and important for intracellular transportation. - Highlights: • Glycoprotein B (gB) is highly conserved among herpesviruses. • HHV-6 gB is also abundantly expressed in virions. • In the present study, we showed the function of HHV-6 gB cytoplasmic tail domain (CTD). • We found that deletion of gB CTD impairs the intracellular transport of gB protein to the trans-Golgi network (TGN), and CTD of gB is critical for HHV-6 propagation.

  3. Dense Metal Plasma in a Solenoid for Ion Beam Neutralization

    Energy Technology Data Exchange (ETDEWEB)

    Anders, Andre; Kauffeldt, Marina; Oks, Efim M.; Roy, Prabir K.


    Space-charge neutralization is required to compress and focus a pulsed, high-current ion beam on a target for warm dense matter physics or heavy ion fusion experiments. We described approaches to produce dense plasma in and near the final focusing solenoid through which the ion beam travels, thereby providing an opportunity for the beam to acquire the necessary space-charge compensating electrons. Among the options are plasma injection from pulsed vacuum arc sources located outside the solenoid, and using a high current (> 4 kA) pulsed vacuum arc plasma from a ring cathode near the edge of the solenoid. The plasma distribution is characterized by photographic means, by an array of movable Langmuir probes, by a small single probe, and by evaluating Stark broadening of the Balmer H beta spectral line. In the main approach described here, the plasma is produced at several cathode spots distributed azimuthally on the ring cathode. It is shown that the plasma is essentially hollow, as determined by the structure of the magnetic field, though the plasma density exceeds 1014 cm-3 in practically all zones of the solenoid volume if the ring electrode is placed a few centimeters off the center of the solenoid. The plasma is non-uniform and fluctuating, however, since its density exceeds the ion beam density it is believed that this approach could provide a practical solution to the space charge neutralization challenge.

  4. Shrinkage/swelling of compacted clayey loose and dense soils (United States)

    Nowamooz, Hossein; Masrouri, Farimah


    This Note presents an experimental study performed on expansive compacted loose and dense samples using osmotic oedometers. Several successive wetting and drying cycles were applied in a suction range between 0 and 8 MPa under different values of constant net vertical stress (15, 30, and 60 kPa). During the suction cycles, the dense samples showed cumulative swelling strains, while the loose samples showed volumetric shrinkage accumulation. At the end of the suction cycles, the volumetric strains converged to an equilibrium stage that indicated elastic behavior of the swelling soil for any further hydraulic variations. At this stage, the compression curves for the studied soil at the different imposed suctions (0, 2, and 8 MPa) converged towards the saturated state curve for the high applied vertical stresses. We defined this pressure as the saturation stress(P). The compression curves provided sufficient data to examine the soil mechanical behavior at the equilibrium stage. To cite this article: H. Nowamooz, F. Masrouri, C. R. Mecanique 337 (2009).

  5. Synthesis of Dense and Chiral Dendritic Polyols Using Glyconanosynthon Scaffolds

    Directory of Open Access Journals (Sweden)

    Tze Chieh Shiao


    Full Text Available Most classical dendrimers are frequently built-up from identical repeating units of low valency (usually AB2 monomers. This strategy necessitates several generations to achieve a large number of surface functionalities. In addition, these typical monomers are achiral. We propose herein the use of sugar derivatives consisting of several and varied functionalities with their own individual intrinsic chirality as both scaffolds/core as well as repeating units. This approach allows the construction of chiral, dense dendrimers with a large number of surface groups at low dendrimer generations. Perpropargylated β-D-glucopyranoside, serving as an A5 core, together with various derivatives, such as 2-azidoethyl tetra-O-allyl-β-D-glucopyranoside, serving as an AB4 repeating moiety, were utilized to construct chiral dendrimers using “click chemistry” (CuAAC reaction. These were further modified by thiol-ene and thiol-yne click reactions with alcohols to provide dendritic polyols. Molecular dynamic simulation supported the assumption that the resulting polyols have a dense structure.

  6. Molecular Composition and Chemistry of Isolated Dense Cores (United States)

    Cook, Amanda; Boogert, A.


    The composition of molecular clouds and the envelopes and disks surrounding low mass protostars within them is still poorly known. There is little doubt that a large fraction of the molecules is frozen on grains, but the abundance of several crucial species (e.g. ammonia, methanol, ions) in the ices is still uncertain. In addition, prominent spectral features discovered decades ago are still not securely identified (e.g. the 6.85-micron absorption band). Gas phase and grain surface chemistry play pivotal roles in molecule formation, but numerous other processes could have significant impacts as well: shocks, thermal heating, irradiation of ices by ultraviolet photons and cosmic rays. Complex species could be formed this way, profoundly influencing cloud, disk and planetary/cometary chemistry. We have obtained Spitzer/IRS spectra of an unprecedented sample of sight-lines tracing 25 dense isolated cores. These cores physically differ from the large, cluster-forming molecular clouds (e.g. Ophiuchus, Perseus) that are commonly studied: they are less turbulent, colder, less dense, and likely longer lived. These IRS spectra of isolated cores thus provide unique information on ice formation and destruction mechanisms. Toward the same cores, we observed 33 highly extincted background stars as well, tracing the quiescent cloud medium against which the ices around protostars can be contrasted.

  7. Probing Dense Sprays with Gated, Picosecond, Digital Particle Field Holography

    Directory of Open Access Journals (Sweden)

    James Trolinger


    Full Text Available This paper describes work that demonstrated the feasibility of producing a gated digital holography system that is capable of producing high-resolution images of three-dimensional particle and structure details deep within dense particle fields of a spray. We developed a gated picosecond digital holocamera, using optical Kerr cell gating, to demonstrate features of gated digital holography that make it an exceptional candidate for this application. The Kerr cell gate shuttered the camera after the initial burst of ballistic and snake photons had been recorded, suppressing longer path, multiple scattered illumination. By starting with a CW laser without gating and then incorporating a picosecond laser and an optical Kerr gate, we were able to assess the imaging quality of the gated holograms, and determine improvement gained by gating. We produced high quality images of 50–200 μm diameter particles, hairs and USAF resolution charts from digital holograms recorded through turbid media where more than 98% of the light was scattered from the field. The system can gate pulses as short as 3 mm in pathlength (10 ps, enabling image-improving features of the system. The experiments lead us to the conclusion that this method has an excellent capability as a diagnostics tool in dense spray combustion research.

  8. Dense image registration through MRFs and efficient linear programming. (United States)

    Glocker, Ben; Komodakis, Nikos; Tziritas, Georgios; Navab, Nassir; Paragios, Nikos


    In this paper, we introduce a novel and efficient approach to dense image registration, which does not require a derivative of the employed cost function. In such a context, the registration problem is formulated using a discrete Markov random field objective function. First, towards dimensionality reduction on the variables we assume that the dense deformation field can be expressed using a small number of control points (registration grid) and an interpolation strategy. Then, the registration cost is expressed using a discrete sum over image costs (using an arbitrary similarity measure) projected on the control points, and a smoothness term that penalizes local deviations on the deformation field according to a neighborhood system on the grid. Towards a discrete approach, the search space is quantized resulting in a fully discrete model. In order to account for large deformations and produce results on a high resolution level, a multi-scale incremental approach is considered where the optimal solution is iteratively updated. This is done through successive morphings of the source towards the target image. Efficient linear programming using the primal dual principles is considered to recover the lowest potential of the cost function. Very promising results using synthetic data with known deformations and real data demonstrate the potentials of our approach.

  9. Hydrogen recycle and isotope exchange from dense carbon films

    Energy Technology Data Exchange (ETDEWEB)

    Clausing, R.E.; Heatherly, L.


    Dense carbon films were prepared by deposition from hydrogen plasmas to which methane was added. The initial hydrogen recycle coefficient from the films ranges from more than two to less than one. The films contain large amounts of hydrogen (up to 50 at. %). They adjust themselves to provide recycling coefficients near unity. Isotope changeover times tend to be long. The reservoir of hydrogen instantly available to the plasma to maintain or stabilize the recycle coefficient and isotopic composition of the plasma is 10/sup 15/ cm/sup -2/ or greater depending on film preparation, temperature, and prior plasma exposure conditions. Simulator observations tend to support and improve the understanding of the observations in TEXTOR and JET; however, they also point out the need for control of film deposition and operating parameters to provide desirable and reproducible properties. The films and the hydrogen isotopes they contain can be removed easily by plasma processes. Since the hydrogen in these films is relatively immobile except in the zone reached by energetic particles, or at temperatures above 400/sup 0/C, dense carbon films may be useful in managing the tritium recovery from near-term fusion experiments.

  10. Enhanced Dense Gas Fraction in Ultraluminous Infrared Galaxies (United States)

    Juneau, S.; Narayanan, D. T.; Moustakas, J.; Shirley, Y. L.; Bussmann, R. S.; Kennicutt, R. C., Jr.; Vanden Bout, P. A.


    We present a detailed analysis of the relation between infrared luminosity and molecular line luminosity, for a variety of molecular transitions, using a sample of 34 nearby galaxies spanning a broad range of infrared luminosities (1010 L sun enhanced HCN(1-0)/CO(1-0) luminosity ratio observed in ULIRGs can be successfully reproduced using numerical models with fixed chemical abundances and without AGN-induced chemistry effects. We extend this analysis to a total of 10 molecular line ratios by combining the following transitions: CO(1-0), HCO+(1-0), HCO+(3-2), HCN(1-0), and HCN(3-2). Our results suggest that AGNs reside in systems with higher dense gas fraction, and that chemistry or other effects associated with their hard radiation field may not dominate (NGC 1068 is one exception). Galaxy merger could be the underlying cause of increased dense gas fraction, and the evolutionary stage of such mergers may be another determinant of the HCN/CO luminosity ratio.

  11. Thermophysical properties of multi-shock compressed dense argon

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Q. F., E-mail:; Zheng, J.; Gu, Y. J.; Chen, Y. L.; Cai, L. C. [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, P. O. Box 919-102, Mianyang, Sichuan (China); Shen, Z. J. [Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, P. O. Box 8009-26, Beijing 10086 (China)


    In contrast to the single shock compression state that can be obtained directly via experimental measurements, the multi-shock compression states, however, have to be calculated with the aid of theoretical models. In order to determine experimentally the multiple shock states, a diagnostic approach with the Doppler pins system (DPS) and the pyrometer was used to probe multiple shocks in dense argon plasmas. Plasma was generated by a shock reverberation technique. The shock was produced using the flyer plate impact accelerated up to ∼6.1 km/s by a two-stage light gas gun and introduced into the plenum argon gas sample, which was pre-compressed from the environmental pressure to about 20 MPa. The time-resolved optical radiation histories were determined using a multi-wavelength channel optical transience radiance pyrometer. Simultaneously, the particle velocity profiles of the LiF window was measured with multi-DPS. The states of multi-shock compression argon plasma were determined from the measured shock velocities combining the particle velocity profiles. We performed the experiments on dense argon plasmas to determine the principal Hugonoit up to 21 GPa, the re-shock pressure up to 73 GPa, and the maximum measure pressure of the fourth shock up to 158 GPa. The results are used to validate the existing self-consistent variational theory model in the partial ionization region and create new theoretical models.

  12. Thermophysical properties of multi-shock compressed dense argon (United States)

    Chen, Q. F.; Zheng, J.; Gu, Y. J.; Chen, Y. L.; Cai, L. C.; Shen, Z. J.


    In contrast to the single shock compression state that can be obtained directly via experimental measurements, the multi-shock compression states, however, have to be calculated with the aid of theoretical models. In order to determine experimentally the multiple shock states, a diagnostic approach with the Doppler pins system (DPS) and the pyrometer was used to probe multiple shocks in dense argon plasmas. Plasma was generated by a shock reverberation technique. The shock was produced using the flyer plate impact accelerated up to ˜6.1 km/s by a two-stage light gas gun and introduced into the plenum argon gas sample, which was pre-compressed from the environmental pressure to about 20 MPa. The time-resolved optical radiation histories were determined using a multi-wavelength channel optical transience radiance pyrometer. Simultaneously, the particle velocity profiles of the LiF window was measured with multi-DPS. The states of multi-shock compression argon plasma were determined from the measured shock velocities combining the particle velocity profiles. We performed the experiments on dense argon plasmas to determine the principal Hugonoit up to 21 GPa, the re-shock pressure up to 73 GPa, and the maximum measure pressure of the fourth shock up to 158 GPa. The results are used to validate the existing self-consistent variational theory model in the partial ionization region and create new theoretical models.

  13. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F


    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  14. Spaced resolved analysis of suprathermal electrons in dense plasma

    Directory of Open Access Journals (Sweden)

    Moinard A.


    Full Text Available The investigation of the hot electron fraction is a crucial topic for high energy density laser driven plasmas: first, energy losses and radiative properties depend strongly on the hot electron fraction and, second, in ICF hohlraums suprathermal electrons preheat the D-T-capsule and seriously reduce the fusion performance. In the present work we present our first experimental and theoretical studies to analyze single shot space resolved hot electron fractions inside dense plasmas via optically thin X-ray line transitions from autoionizing states. The benchmark experiment has been carried out at an X-pinch in order to create a dense, localized plasma with a well defined symmetry axis of hot electron propagation. Simultaneous high spatial and spectral resolution in the X-ray spectral range has been obtained with a spherically bent quartz Bragg crystal. The high performance of the X-ray diagnostics allowed to identify space resolved hot electron fractions via the X-ray spectral distribution of multiple excited states.

  15. Dense neuron clustering explains connectivity statistics in cortical microcircuits.

    Directory of Open Access Journals (Sweden)

    Vladimir V Klinshov

    Full Text Available Local cortical circuits appear highly non-random, but the underlying connectivity rule remains elusive. Here, we analyze experimental data observed in layer 5 of rat neocortex and suggest a model for connectivity from which emerge essential observed non-random features of both wiring and weighting. These features include lognormal distributions of synaptic connection strength, anatomical clustering, and strong correlations between clustering and connection strength. Our model predicts that cortical microcircuits contain large groups of densely connected neurons which we call clusters. We show that such a cluster contains about one fifth of all excitatory neurons of a circuit which are very densely connected with stronger than average synapses. We demonstrate that such clustering plays an important role in the network dynamics, namely, it creates bistable neural spiking in small cortical circuits. Furthermore, introducing local clustering in large-scale networks leads to the emergence of various patterns of persistent local activity in an ongoing network activity. Thus, our results may bridge a gap between anatomical structure and persistent activity observed during working memory and other cognitive processes.

  16. Signatures of personality on dense 3D facial images. (United States)

    Hu, Sile; Xiong, Jieyi; Fu, Pengcheng; Qiao, Lu; Tan, Jingze; Jin, Li; Tang, Kun


    It has long been speculated that cues on the human face exist that allow observers to make reliable judgments of others' personality traits. However, direct evidence of association between facial shapes and personality is missing from the current literature. This study assessed the personality attributes of 834 Han Chinese volunteers (405 males and 429 females), utilising the five-factor personality model ('Big Five'), and collected their neutral 3D facial images. Dense anatomical correspondence was established across the 3D facial images in order to allow high-dimensional quantitative analyses of the facial phenotypes. In this paper, we developed a Partial Least Squares (PLS) -based method. We used composite partial least squares component (CPSLC) to test association between the self-tested personality scores and the dense 3D facial image data, then used principal component analysis (PCA) for further validation. Among the five personality factors, agreeableness and conscientiousness in males and extraversion in females were significantly associated with specific facial patterns. The personality-related facial patterns were extracted and their effects were extrapolated on simulated 3D facial models.

  17. Modeling the multiphase flow in a dense medium cyclone

    Energy Technology Data Exchange (ETDEWEB)

    Wang, B.; Chu, K.W.; Yu, A.B.; Vince, A. [University of New South Wales, Sydney, NSW (Australia)


    A mathematical model is proposed to describe the multiphase flow in a dense-medium cyclone (DMC). In this model, the volume of fluid multiphase model is first used to determine the shape and position of the air core, and then the mixture multiphase model is employed to describe the flow of the dense medium (comprising finely ground magnetite in water) and the air core, where the turbulence is described by the Reynolds stress model. The results of fluid flow are finally used in the simulation of coal particle flow described by the stochastic Lagrangian particle tracking model. The validity of the proposed approach is verified by the reasonably good agreement between the measured and predicted results under different conditions. The flow features in a DMC are then examined in terms of factors such as flow field, pressure drop, particle trajectories, and separation efficiency. The results are used to explain the key characteristics of flow in DMCs, such as the origin of a short-circuit flow, the flow pattern, and the motion of coal particles. Moreover, the so-called surging phenomenon is examined in relation to the instability of fluid flow. The model offers a convenient method to investigate the effects of variables related to geometrical and operational conditions on the performance of DMCs.

  18. Handover management in dense cellular networks: A stochastic geometry approach

    KAUST Repository

    Arshad, Rabe


    Cellular operators are continuously densifying their networks to cope with the ever-increasing capacity demand. Furthermore, an extreme densification phase for cellular networks is foreseen to fulfill the ambitious fifth generation (5G) performance requirements. Network densification improves spectrum utilization and network capacity by shrinking base stations\\' (BSs) footprints and reusing the same spectrum more frequently over the spatial domain. However, network densification also increases the handover (HO) rate, which may diminish the capacity gains for mobile users due to HO delays. In highly dense 5G cellular networks, HO delays may neutralize or even negate the gains offered by network densification. In this paper, we present an analytical paradigm, based on stochastic geometry, to quantify the effect of HO delay on the average user rate in cellular networks. To this end, we propose a flexible handover scheme to reduce HO delay in case of highly dense cellular networks. This scheme allows skipping the HO procedure with some BSs along users\\' trajectories. The performance evaluation and testing of this scheme for only single HO skipping shows considerable gains in many practical scenarios. © 2016 IEEE.

  19. Regulation of H+ Extrusion and Cytoplasmic pH in Maize Root Tips Acclimated to a Low-Oxygen Environment. (United States)

    Xia, J. H.; Roberts, JKM.


    We tested the hypothesis that H+ extrusion contributes to cytoplasmic pH regulation and tolerance of anoxia in maize (Zea mays) root tips. We studied root tips of whole seedlings that were acclimated to a low-oxygen environment by pretreatment in 3% (v/v) O2. Acclimated root tips characteristically regulate cytoplasmic pH near neutrality and survive prolonged anoxia, whereas nonacclimated tips undergo severe cytoplasmic acidosis and die much more quickly. We show that the plasma membrane H+-ATPase can operate under anoxia and that net H+ extrusion increases when cytoplasmic pH falls. However, at an external pH near 6.0, H+ extrusion contributes little to cytoplasmic pH regulation. At more acidic external pH values, net H+ flux into root tips increases dramatically, leading to a decrease in cytoplasmic pH and reduced tolerance of anoxia. We present evidence that, under these conditions, H+ pumps are activated to partly offset acidosis due to H+ influx and, thereby, contribute to cytoplasmic pH regulation and tolerance of anoxia. The regulation of H+ extrusion under anoxia is discussed with respect to the acclimation response and mechanisms of intracellular pH regulation in aerobic plant cells.

  20. A cytoplasmic activator of DNA replication is involved in signal transduction in antigen-specific T cell lines. (United States)

    Wong, R L; Clark, R B; Gutowski, J K; Katz, M E; Fresa, K L; Cohen, S


    Cytoplasmic extracts prepared from T cell lines undergoing antigen-specific, interleukin-2 (IL-2)-dependent proliferation were tested for their ability to induce DNA synthesis in isolated, quiescent nuclei. A tetanus toxoid (TET)-specific T cell line, established from peripheral blood of a normal human volunteer, was stimulated in the presence of relevant antigen and 1 unit/ml IL-2. Cytoplasmic extracts prepared from these cells were capable of inducing DNA synthesis in isolated, quiescent nuclei. The ability of cytoplasmic extracts to induce DNA synthesis in isolated, quiescent nuclei. The ability of cytoplasmic extracts to induce DNA synthesis in isolated nuclei correlated positively with the degree of proliferation induced in these cells. In contrast, incubation of this T cell line in the absence of antigen failed to induce proliferation and cytoplasmic extracts prepared from these cells induced little to no DNA synthesis in isolated, quiescent nuclei. The factor present in the cytoplasm of T cells stimulated with relevant antigen in the presence of IL-2 is similar, if not identical, to a factor which we have previously demonstrated in cytoplasmic extracts prepared from transformed lymphoblastoid cell lines and from mitogenically stimulated normal human peripheral blood mononuclear cells. This factor, which we have called activator of DNA replication (ADR) is a heat-labile protein, and is inactivated by treatment with protease inhibitors, including aprotinin. The ability of cytoplasmic extracts from T cells undergoing antigen-specific, IL-2-dependent proliferation to induce DNA synthesis in isolated, quiescent nuclei was markedly inhibited in the presence of aprotinin, providing strong evidence that a cytoplasmic activator of DNA replication, ADR, is involved in the signal transduction process for antigen-specific, IL-2-dependent T cell proliferation. ADR may represent a common intracellular mediator of DNA synthesis in activated and transformed lymphocytes.

  1. A novel nucleo-cytoplasmic hybrid clone formed via androgenesis in polyploid gibel carp

    Directory of Open Access Journals (Sweden)

    Zhou Li


    Full Text Available Abstract Background Unisexual vertebrates have been demonstrated to reproduce by gynogenesis, hybridogenesis, parthenogenesis, or kleptogenesis, however, it is uncertain how the reproduction mode contributes to the clonal diversity. Recently, polyploid gibel carp has been revealed to possess coexisting dual modes of unisexual gynogenesis and sexual reproduction and to have numerous various clones. Using sexual reproduction mating between clone D female and clone A male and subsequent 7 generation multiplying of unisexual gynogenesis, we have created a novel clone strain with more than several hundred millions of individuals. Here, we attempt to identify genetic background of the novel clone and to explore the significant implication for clonal diversity contribution. Methods Several nuclear genome markers and one cytoplasmic marker, the mitochondrial genome sequence, were used to identify the genetic organization of the randomly sampled individuals from different generations of the novel clone. Results Chromosome number, Cot-1 repetitive DNA banded karyotype, microsatellite patterns, AFLP profiles and transferrin alleles uniformly indicated that nuclear genome of the novel clone is identical to that of clone A, and significantly different from that of clone D. However, the cytoplasmic marker, its complete mtDNA genome sequence, is same to that of clone D, and different from that of clone A. Conclusions The present data indicate that the novel clone is a nucleo-cytoplasmic hybrid between the known clones A and D, because it originates from the offspring of gonochoristic sexual reproduction mating between clone D female and clone A male, and contains an entire nuclear genome from the paternal clone A and a mtDNA genome (cytoplasm from the maternal clone D. It is suggested to arise via androgenesis by a mechanism of ploidy doubling of clone A sperm in clone D ooplasm through inhibiting the first mitotic division. Significantly, the selected nucleo-cytoplasmic

  2. Coordinated movement of cytoplasmic and transmembrane domains of RyR1 upon gating.

    Directory of Open Access Journals (Sweden)

    Montserrat Samsó


    Full Text Available Ryanodine receptor type 1 (RyR1 produces spatially and temporally defined Ca2+ signals in several cell types. How signals received in the cytoplasmic domain are transmitted to the ion gate and how the channel gates are unknown. We used EGTA or neuroactive PCB 95 to stabilize the full closed or open states of RyR1. Single-channel measurements in the presence of FKBP12 indicate that PCB 95 inverts the thermodynamic stability of RyR1 and locks it in a long-lived open state whose unitary current is indistinguishable from the native open state. We analyzed two datasets of 15,625 and 18,527 frozen-hydrated RyR1-FKBP12 particles in the closed and open conformations, respectively, by cryo-electron microscopy. Their corresponding three-dimensional structures at 10.2 A resolution refine the structure surrounding the ion pathway previously identified in the closed conformation: two right-handed bundles emerging from the putative ion gate (the cytoplasmic "inner branches" and the transmembrane "inner helices". Furthermore, six of the identifiable transmembrane segments of RyR1 have similar organization to those of the mammalian Kv1.2 potassium channel. Upon gating, the distal cytoplasmic domains move towards the transmembrane domain while the central cytoplasmic domains move away from it, and also away from the 4-fold axis. Along the ion pathway, precise relocation of the inner helices and inner branches results in an approximately 4 A diameter increase of the ion gate. Whereas the inner helices of the K+ channels and of the RyR1 channel cross-correlate best with their corresponding open/closed states, the cytoplasmic inner branches, which are not observed in the K+ channels, appear to have at least as important a role as the inner helices for RyR1 gating. We propose a theoretical model whereby the inner helices, the inner branches, and the h1 densities together create an efficient novel gating mechanism for channel opening by relaxing two right

  3. Nucleocapsid Protein from Fig Mosaic Virus Forms Cytoplasmic Agglomerates That Are Hauled by Endoplasmic Reticulum Streaming (United States)

    Ishikawa, Kazuya; Miura, Chihiro; Maejima, Kensaku; Komatsu, Ken; Hashimoto, Masayoshi; Tomomitsu, Tatsuya; Fukuoka, Misato; Yusa, Akira; Yamaji, Yasuyuki


    ABSTRACT Although many studies have demonstrated intracellular movement of viral proteins or viral replication complexes, little is known about the mechanisms of their motility. In this study, we analyzed the localization and motility of the nucleocapsid protein (NP) of Fig mosaic virus (FMV), a negative-strand RNA virus belonging to the recently established genus Emaravirus. Electron microscopy of FMV-infected cells using immunogold labeling showed that NPs formed cytoplasmic agglomerates that were predominantly enveloped by the endoplasmic reticulum (ER) membrane, while nonenveloped NP agglomerates also localized along the ER. Likewise, transiently expressed NPs formed agglomerates, designated NP bodies (NBs), in close proximity to the ER, as was the case in FMV-infected cells. Subcellular fractionation and electron microscopic analyses of NP-expressing cells revealed that NBs localized in the cytoplasm. Furthermore, we found that NBs moved rapidly with the streaming of the ER in an actomyosin-dependent manner. Brefeldin A treatment at a high concentration to disturb the ER network configuration induced aberrant accumulation of NBs in the perinuclear region, indicating that the ER network configuration is related to NB localization. Dominant negative inhibition of the class XI myosins, XI-1, XI-2, and XI-K, affected both ER streaming and NB movement in a similar pattern. Taken together, these results showed that NBs localize in the cytoplasm but in close proximity to the ER membrane to form enveloped particles and that this causes passive movements of cytoplasmic NBs by ER streaming. IMPORTANCE Intracellular trafficking is a primary and essential step for the cell-to-cell movement of viruses. To date, many studies have demonstrated the rapid intracellular movement of viral factors but have failed to provide evidence for the mechanism or biological significance of this motility. Here, we observed that agglomerates of nucleocapsid protein (NP) moved rapidly

  4. CRISPR/Cas9-mediated mutation revealed cytoplasmic tail is dispensable for IZUMO1 function and male fertility

    DEFF Research Database (Denmark)

    Young, Samantha A M; Miyata, Haruhiko; Satouh, Yuhkoh


    IZUMO1 is a protein found in the head of spermatozoa that has been identified as essential for sperm-egg fusion. Its binding partner in the egg has been discovered (JUNO); however, the roles of several domains within IZUMO1 remain unexplored. One such domain is the C-terminus, which undergoes major...... phosphorylation changes in the cytoplasmic portion of the protein during rat epididymal transit. However, the cytoplasmic tail of IZUMO1 in many species is highly variable, ranging from 55 to one amino acid. Therefore, to understand the role of the cytoplasmic tail of IZUMO1 in mouse, we utilised the gene...

  5. Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM

    DEFF Research Database (Denmark)

    Briegel, Ariane; Ortega, Davi R; Mann, Petra


    motile bacteria contain one or more additional, sometimes purely cytoplasmic, chemoreceptor systems. Vibrio cholerae contains three chemotaxis clusters (I, II, and III). Here, using electron cryotomography, we explore V. cholerae's cytoplasmic chemoreceptor array and establish that it is formed...

  6. Kinetic theory molecular dynamics and hot dense matter: theoretical foundations. (United States)

    Graziani, F R; Bauer, J D; Murillo, M S


    Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD

  7. Propagation of Electromagnetic Waves in Extremely Dense Media

    CERN Document Server

    Masood, Samina


    We study the propagation of electromagnetic (EM) waves in extremely dense exotic systems with very unique properties. These EM waves develop a longitudinal component due to its interaction with the medium. Renormalization scheme of QED is used to understand the propagation of EM waves in both longitudinal and transverse directions. The propagation of EM waves in a quantum statistically treatable medium affects the properties of the medium itself. The electric permittivity and the magnetic permeability of the medium are modified and influence the related behavior of the medium. All the electromagnetic properties of a medium become a function of temperature and chemical potential of the medium. We study in detail the modifications of electric permittivity and magnetic permeability and other related properties of a medium in the superdense stellar objects.

  8. Charged current neutrino interactions in hot and dense matter (United States)

    Roberts, Luke F.; Reddy, Sanjay


    We derive the charged current absorption rate of electron and antielectron neutrinos in dense matter using a fully relativistic approach valid at arbitrary matter degeneracy. We include mean field energy shifts due to nuclear interactions and the corrections due to weak magnetism. The rates are derived both from the familiar Fermi's golden rule and from the techniques of finite temperature field theory, and are shown to be equivalent. In various limits, these results can also be used to calculate neutral current opacities. We find that some pieces of the response have been left out in previous derivations and their contribution at high density can be significant. Useful formulas and detailed derivations are presented and we provide a new open-source implementation of these opacities for use in radiation hydrodynamic simulations of core-collapse supernovae and neutron star mergers.

  9. The physics of hot and dense quark-gluon matter

    Energy Technology Data Exchange (ETDEWEB)

    Kharzeev, Dmitri E. [Stony Brook Univ., NY (United States)


    This technical report describes the work done under the DOE grant DE-FG-88ER41723 (final award number DE-SC0005645), "The physics of hot and dense quark-gluon matter", during the year of 12/01/2010 through 11/30/2011. As planned in the proposal, the performed research focused along two main thrusts: 1) topological effects in hot quark-gluon matter and 2) phenomenology of relativistic heavy ion collisions. The results of research are presented in 12 papers published in reputable refereed journals (Physical Review Letters, Physical Review, Physics Letters and Nuclear Physics). All of the performed research is directly related to the experimental programs of DOE, especially at the Relativistic Heavy Ion Collider. Much of it also has broader interdisciplinary implications - for example, the work on the non-dissipative chiral magnetic current is directly relevant for quantum computing. The attached report describes the performed work in detail.

  10. Solubility of dense CO2 in two biocompatible acrylate copolymers

    Directory of Open Access Journals (Sweden)

    A. R. C. Duarte


    Full Text Available Biocompatible polymers and copolymers are frequently being used as part of controlled delivery systems. These systems can be prepared using a "clean and environment friendly" technology like supercritical fluids. One great advantage of this process is that compressed carbon dioxide has excellent plasticizing properties and can swell most biocompatible polymeric matrixes, thus promoting drug impregnation processes. Mass sorption of two acrylate biocompatible copolymers contact with supercritical carbon dioxide is reported. Equilibrium solubility of dense carbon dioxide in poly(methylmethacrylate-co-ethylhexylacrylate and poly(methylmethacrylate-co-ethylhexylacrylate-co-ethyleneglycoldimethacrylate was studied by a static method at 10.0 MPa and 313 K. The reticulated copolymer had Fickean behavior and its diffusion coefficient was calculated, under operating conditions.


    Energy Technology Data Exchange (ETDEWEB)

    Schnee, Scott; Brunetti, Nathan; Friesen, Rachel [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Di Francesco, James; Johnstone, Doug; Pon, Andy [National Research Council Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road Victoria, BC V9E 2E7 (Canada); Caselli, Paola, E-mail: [School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT (United Kingdom)


    We present a survey of HCO{sup +} (3-2) observations pointed toward dense cores with previous measurements of N(N{sub 2}D{sup +})/N(N{sub 2}H{sup +}). Of the 26 cores in this survey, 5 show the spectroscopic signature of outward motion, 9 exhibit neither inward nor outward motion, 11 appear to be infalling, and 1 is not detected. We compare the degree of deuterium fractionation with infall velocities calculated from the HCO{sup +} spectra and find that those cores with [D]/[H] > 0.1 are more likely to have the signature of inward motions than cores with smaller [D]/[H] ratios. Infall motions are also much more common in cores with masses exceeding their thermal Jeans masses. The fastest infall velocity measured belongs to one of the two protostellar cores in our survey, L1521F, and the observed motions are typically on the order of the sound speed.

  12. Myoglobin entrapment in poly(vinyl alcohol dense membranes

    Directory of Open Access Journals (Sweden)

    K. C. S. Figueiredo


    Full Text Available Our goal in this study was the immobilization of myoglobin in poly(vinyl alcohol dense membranes. Glutaraldehyde was investigated both as the crosslinking agent, aiming to increase the membrane stability in aqueous medium, and as the vehicle to bind myoglobin and PVA. Reaction and membrane synthesis were carried simultaneously in mild operating conditions in order to maintain the native protein folding. Membrane characterization comprised the water swelling degree, DSC, TGA, UV-visible spectroscopy, FTIR analysis and oxygen transport in a dialysis cell. The incorporation of myoglobin in the film decreased the water swelling degree and improved the membrane thermal properties compared to unmodified PVA membrane. The reduction of ferric iron in the prosthetic group of the protein to the ferrous form was observed. The increased affinity between oxygen and the immobilized myoglobin did not favor the release of this solute from the biocarrier.

  13. Locally optimal resource allocation algorithm for dense femtocells (United States)

    Murthy, Chethana R.; Kavitha, C.


    Femtocell is a small low power base station for maximizing the indoor coverage and capacity for cellular users. These base stations can serve users with different access policies. As the Macrocell shares its limited resource - spectrum with the underlying Femtocell, there is a need for efficient resource allocation strategy that benefits all types of users, especially when user density is more and depends on the sub-carrier availability, users' quality of service requirements. This paper proposes a resource allocation strategy to model different user requirements in a dense environment. The approach selects locally optimal solution based on the users' priority and give fair trade-off between various network parameters without degrading the overall system capacity.

  14. Dense and Sparse Matrix Operations on the Cell Processor

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Samuel W.; Shalf, John; Oliker, Leonid; Husbands,Parry; Yelick, Katherine


    The slowing pace of commodity microprocessor performance improvements combined with ever-increasing chip power demands has become of utmost concern to computational scientists. Therefore, the high performance computing community is examining alternative architectures that address the limitations of modern superscalar designs. In this work, we examine STI's forthcoming Cell processor: a novel, low-power architecture that combines a PowerPC core with eight independent SIMD processing units coupled with a software-controlled memory to offer high FLOP/s/Watt. Since neither Cell hardware nor cycle-accurate simulators are currently publicly available, we develop an analytic framework to predict Cell performance on dense and sparse matrix operations, using a variety of algorithmic approaches. Results demonstrate Cell's potential to deliver more than an order of magnitude better GFLOP/s per watt performance, when compared with the Intel Itanium2 and Cray X1 processors.

  15. Estimation of Dense Image Flow Fields in Fluids

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Conradsen, Knut; Ersbøll, Bjarne Kjær


    The estimation of flow fields from time sequences of satellite imagery has a number of important applications. For visualisation of cloud or sea ice movements in sequences of crude temporal sampling a satisfactory non-blurred temporal interpolation can be performed only when the flow field...... of the local energy distribution, which is sampled using a set of 3-D spatio-temporal filters. The estimated local energy distribution also allows us to compute a confidence measure of the estimated local normal flow. The algorithm furthermore utilises Markovian random fields in order to integrate the local...... estimates of normal flows into a dense flow field using measures of spatial smoothness. To obtain smoothness we will constrain first order derivatives of the flow field. The performance of the algorithm is illustrated by the estimation of the flow fields corresponding to a sequence of Meteosat thermal...

  16. Formation of dense cellulose monolayers on silver surfaces

    Directory of Open Access Journals (Sweden)

    Soo Whan Choi


    Full Text Available The adsorption of a new cellulose derivative,6-O-(2,3-bis(thiosulfato propyl-oxy-2-hydroxy-propyl-cellulose (TSHP, onto silver surfaces was investigated by means of ellipsometry, contact angle measurements and X-ray photoelectron spectroscopy (XPS. The results showed that the formation of a dense TSHP monolayer on silver surfaces is an irreversible and slow process. Based on XPS results a model was proposed to explain the chemisorption of TSHP on silver substrates. This model considers the homolytical cleavage of the thiosulfate groups attached to the cellulose chains with the formation of thio radicals, which bind covalently to the silver surface. The formation of silver thiolates lead to a stable TSHP monolayer on silver surfaces.

  17. Laser Ignition of an Isentropically Compressed Dense Z-Pinch (United States)

    Winterberg, F.


    A dense z-pinch generated by a high voltage discharge over a corrugated helical sawtooth-shaped capillary tube with a solid DT core, is by shear flow stabilized against the m = 0 and m= 1 magnetohydrodynamic instabilities, and by rotational flow against the Rayleigh-Taylor instability. The shear-and rotational flow result from jet formation by the corrugated surface. A programmed voltage pulse can then isentropically compress the DT core to high densities, and if ignited at one end by a petawatt laser pulse, a thermonuclear detonation wave can be launched propagating along the z-pinch channel. The proposed z-pinch burn should also work without tritium as a thermonuclear detonation wave in deuterium.

  18. Kinetic theory and long range correlations in moderately dense gases

    Energy Technology Data Exchange (ETDEWEB)

    Petrosky, T.; Prigogine, I. [Univ. of Texas, Austin, TX (United States)


    The complex spectral representation of the Liouville operator is applied to moderately dense gases interacting through hard-core potentials in arbitrary d-dimensional spaces. It is shown that Markovian kinetic equations exist for all d. This provides an answer to the long standing question do kinetic equations exist in two dimensional systems. The non-Markovian effects, such as the long-time tails for arbitrary n-mode coupling, are estimated by superposition of the Markovian evolutions in each subspace as introduced in our spectral decomposition. The long-time tail effects invalidate the traditional kinetic theory based on a truncation of BBGKY hierarchy for d < 4, as well as the Green-Kubo formalism, as there appear contributions of order t{sup -1}, t{sup -{1/2}},... coming from multiple mode-mode couplings even for d = 3.

  19. Fast, Dense Low Cost Scintillator for Nuclear Physics

    Energy Technology Data Exchange (ETDEWEB)

    Woody, Craig


    We have studied the morphology, transparency, and optical properties of SrHfO{sub 3}:Ce ceramics. Ceramics can be made transparent by carefully controlling the stoichiometry of the precursor powders. When fully dense, transparent samples can be obtained. Ceramics with a composition close to stoichiometry (Sr:Hf ~ 1) appear to show good transparency and a reasonable light yield several times that of BGO. The contact and distance transparency of ceramics hot-pressed at about 1450ºC is very good, but deteriorates at increasingly higher hot-press temperatures. If these ceramics can be produced in large quantities and sizes, at low cost, they may be of considerable interest for PET and CT.

  20. Dense Matter Characterization by X-ray Thomson Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Landen, O L; Glenzer, S H; Edwards, M J; Lee, R W; Collins, G W; Cauble, R C; Hsing, W W; Hammel, B A


    We discuss the extension of the powerful technique of Thomson scattering to the x-ray regime for providing an independent measure of plasma parameters for dense plasmas. By spectrally-resolving the scattering, the coherent (Rayleigh) unshifted scattering component can be separated from the incoherent Thomson component, which is both Compton and Doppler shifted. The free electron density and temperature can then be inferred from the spectral shape of the high frequency Thomson scattering component. In addition, as the plasma temperature is decreased, the electron velocity distribution as measured by incoherent Thomson scattering will make a transition from the traditional Gaussian Boltzmann distribution to a density-dependent parabolic Fermi distribution to. We also present a discussion for a proof-of-principle experiment appropriate for a high energy laser facility.

  1. Quantum Control of Open Systems and Dense Atomic Ensembles (United States)

    DiLoreto, Christopher

    Controlling the dynamics of open quantum systems; i.e. quantum systems that decohere because of interactions with the environment, is an active area of research with many applications in quantum optics and quantum computation. My thesis expands the scope of this inquiry by seeking to control open systems in proximity to an additional system. The latter could be a classical system such as metal nanoparticles, or a quantum system such as a cluster of similar atoms. By modelling the interactions between the systems, we are able to expand the accessible state space of the quantum system in question. For a single, three-level quantum system, I examine isolated systems that have only normal spontaneous emission. I then show that intensity-intensity correlation spectra, which depend directly on the density matrix of the system, can be used detect whether transitions share a common energy level. This detection is possible due to the presence of quantum interference effects between two transitions if they are connected. This effect allows one to asses energy level structure diagrams in complex atoms/molecules. By placing an open quantum system near a nanoparticle dimer, I show that the spontaneous emission rate of the system can be changed "on demand" by changing the polarization of an incident, driving field. In a three-level, Lambda system, this allows a qubit to both retain high qubit fidelity when it is operating, and to be rapidly initialized to a pure state once it is rendered unusable by decoherence. This type of behaviour is not possible in a single open quantum system; therefore adding a classical system nearby extends the overall control space of the quantum system. An open quantum system near identical neighbours in a dense ensemble is another example of how the accessible state space can be expanded. I show that a dense ensemble of atoms rapidly becomes disordered with states that are not directly excited by an incident field becoming significantly populated

  2. Dense hadron star in quark degree of freedom

    Directory of Open Access Journals (Sweden)

    Tzeng Yiharn


    Full Text Available The quark degree of freedom may play an important role as one studies dense hadron stars which can help to understand the universe origin. We add a temperature dependence to the effective quark mass adopted from a quark-quark interaction on the QCD basis to probe properties of the star in the quark degree of freedom. Based on this interaction, the quark matter’s equation of state is obtained and its thermodynamic characteristics is investigated in detail. Stability of a star made of such matter is examined with and without strange quarks. The Tolman-Oppenheimer-Volkov equation along with the condition that dm=dr = 4πr2E are used to calculate mass and radius of such a star. Exact computations are made to calculate the star’s radius and mass at several temperatures. Comparisons of results from these temperatures are made and the significance is carefully investigated and discussed.

  3. Quantum statistical mechanics of dense partially ionized hydrogen. (United States)

    Dewitt, H. E.; Rogers, F. J.


    The theory of dense hydrogenic plasmas beginning with the two component quantum grand partition function is reviewed. It is shown that ionization equilibrium and molecular dissociation equilibrium can be treated in the same manner with proper consideration of all two-body states. A quantum perturbation expansion is used to give an accurate calculation of the equation of state of the gas for any degree of dissociation and ionization. In this theory, the effective interaction between any two charges is the dynamic screened potential obtained from the plasma dielectric function. We make the static approximation; and we carry out detailed numerical calculations with the bound and scattering states of the Debye potential, using the Beth-Uhlenbeck form of the quantum second virial coefficient. We compare our results with calculations from the Saha equation.

  4. An integral equation model for warm and hot dense mixtures

    CERN Document Server

    Starrett, C E; Daligault, J; Hamel, S


    In Starrett and Saumon [Phys. Rev. E 87, 013104 (2013)] a model for the calculation of electronic and ionic structures of warm and hot dense matter was described and validated. In that model the electronic structure of one "atom" in a plasma is determined using a density functional theory based average-atom (AA) model, and the ionic structure is determined by coupling the AA model to integral equations governing the fluid structure. That model was for plasmas with one nuclear species only. Here we extend it to treat plasmas with many nuclear species, i.e. mixtures, and apply it to a carbon-hydrogen mixture relevant to inertial confinement fusion experiments. Comparison of the predicted electronic and ionic structures with orbital-free and Kohn-Sham molecular dynamics simulations reveals excellent agreement wherever chemical bonding is not significant.

  5. Thermodynamic and dynamical properties of dense ICF plasma

    Directory of Open Access Journals (Sweden)

    Gabdullin Maratbek T.


    Full Text Available In present work, thermodynamic expressions were obtained through potentials that took into consideration long-range many-particle screening effects as well as short-range quantum-mechanical effects and radial distribution functions (RDFs. Stopping power of the projectile ions in dense, non-isothermal plasma was considered. One of the important values that describe the stopping power of the ions in plasma is the Coulomb logarithm. We investigated the stopping power of ions in inertial confinement fusion (ICF plasma and other energetic characteristics of fuel. Calculations of ions energy losses in the plasma for different values of the temperature and plasma density were carried out. A comparison of the calculated data of ion stopping power and energy deposition with experimental and theoretical results of other authors was also performed.

  6. Structured sublinear compressive sensing via dense belief propagation

    CERN Document Server

    Dai, Wei; Pham, Hoa Vin


    Compressive sensing (CS) is a sampling technique designed for reducing the complexity of sparse data acquisition. One of the major obstacles for practical deployment of CS techniques is the signal reconstruction time and the high storage cost of random sensing matrices. We propose a new structured compressive sensing scheme, based on codes of graphs, that allows for a joint design of structured sensing matrices and logarithmic-complexity reconstruction algorithms. The compressive sensing matrices can be shown to offer asymptotically optimal performance when used in combination with Orthogonal Matching Pursuit (OMP) methods. For more elaborate greedy reconstruction schemes, we propose a new family of dense list decoding belief propagation algorithms, as well as reinforced- and multiple-basis belief propagation algorithms. Our simulation results indicate that reinforced BP CS schemes offer very good complexity-performance tradeoffs for very sparse signal vectors.

  7. Dense Persistent Pupillary Membrane in an Adult Patient

    Directory of Open Access Journals (Sweden)

    Yesim Altay


    Full Text Available Persistent pupillary membranes (PPM are congenital abnormalities which results from an incomplete involution of tunica vasculosa lentis and are rarely seen in adults. A thirty-year old man applied to the hospital with the complaint of uncommon-looking pupils and progressive blurring of vision in the left eye. On examination, uncorrected visual acuity (Snellen were 20/100 in the right eye and 20/640 in the left eye with amblyopia. On biomicroscopic examination, there were bilateral dense PPM and cataract in the left eye. Visual field analysis of right and left eyes showed great narrowing of visual fields. We present our case in order to emphasize that analysis of visual field of patients with PPM is as important as central vision when planning its treatment. For planning treatment of patients with PPM, visual impairment, size of pupillary opening, and visual field analysis should be considered.

  8. Hysteresis losses in a dense superparamagnetic nanoparticle assembly

    Directory of Open Access Journals (Sweden)

    S. A. Gudoshnikov


    Full Text Available The hysteresis losses of a dense assembly of magnetite nanoparticles with an average diameter D = 25 nm are measured in the frequency range f = 10 – 200 kHz for magnetic field amplitudes up to H0 = 400 Oe. The low frequency hysteresis loops of the assembly are obtained by means of integration of the electro-motive force signal arising in a small pick-up coil wrapped around a sample which contains 1 – 5 mg of a magnetite powder. It is proved experimentally that the specific absorption rate diminishes approximately 4.5 times when the sample aspect ratio decreases from 11.4 to 1. Theoretical estimate shows that experimentally measured hysteresis loops can be approximately described only by taking into account appreciable contributions of magnetic nanoparticles of both very small, D 30 nm, diameters. Thus the wide particle size distribution has to be assumed.

  9. Additive Manufacturing of Dense Hexagonal Boron Nitride Objects

    Energy Technology Data Exchange (ETDEWEB)

    Marquez Rossy, Andres E [ORNL; Armstrong, Beth L [ORNL; Elliott, Amy M [ORNL; Lara-Curzio, Edgar [ORNL


    The feasibility of manufacturing hexagonal boron nitride objects via additive manufacturing techniques was investigated. It was demonstrated that it is possible to hot-extrude thermoplastic filaments containing uniformly distributed boron nitride particles with a volume concentration as high as 60% and that these thermoplastic filaments can be used as feedstock for 3D-printing objects using a fused deposition system. Objects 3D-printed by fused deposition were subsequently sintered at high temperature to obtain dense ceramic products. In a parallel study the behavior of hexagonal boron nitride in aqueous solutions was investigated. It was shown that the addition of a cationic dispersant to an azeotrope enabled the formulation of slurries with a volume concentration of boron nitride as high as 33%. Although these slurries exhibited complex rheological behavior, the results from this study are encouraging and provide a pathway for manufacturing hexagonal boron nitride objects via robocasting.

  10. Model-checking dense-time Duration Calculus

    DEFF Research Database (Denmark)

    Fränzle, Martin


    Since the seminal work of Zhou Chaochen, M. R. Hansen, and P. Sestoft on decidability of dense-time Duration Calculus [Zhou, Hansen, Sestoft, 1993] it is well-known that decidable fragments of Duration Calculus can only be obtained through withdrawal of much of the interesting vocabulary...... of this logic. While this was formerly taken as an indication that key-press verification of implementations with respect to elaborate Duration Calculus specifications were also impossible, we show that the model property is well decidable for realistic designs which feature natural constraints...... suitably sparser model classes we obtain model-checking procedures for rich subsets of Duration Calculus. Together with undecidability results also obtained, this sheds light upon the exact borderline between decidability and undecidability of Duration Calculi and related logics....

  11. Field electron emission from dense array of microneedles of tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Okuyama, F.; Aoyagi, M.; Kitai, T.; Ishikawa, K.


    Characteristics of field electron emission from the dense array of microneedles of tungsten prepared on a tungsten filament were measured at an environmental pressure of approx.1 x 10/sup -8/ Torr (1.33 x 10/sup -6/ Pa). Electron emission was not uniform over the filament surface, but the variation of emission current with applied voltage explicitly obeyed the Fowler-Nordheim relationship. At an emission current of approx.10/sup -4/ A, a vacuum arc was induced that led to a permanent change in current-voltage characteristic. Current fluctuation was dependent on emitter temperature and applied voltage, and the lowest fluctuation of about 4% was routinely obtained at approx.550 K and at applied voltages several percent lower than the arc-inducing voltage. Macroscopic current density amounted to approx.20-80 mA/cm/sup 2/ at the best stability.

  12. A Simple Analytical Model for Dense WDM/OOK Systems (United States)


    partial fulfillment of the requirements for the degree of MASTER OF SCIENCE IN ELECTRICAL ENGINEERING from the NAVAL POSTGRADUATE SCHOOL June, 1994...Electrical and Computer Engineering ii ABSTRACT We derive the closed form expression for the bit error probability of dense WDM systems employing an...L 2 Af2 -m.+2jRe{ 2jZ ~Z k*O m$O 47 T 1A2A.d.&I(- e 2cT)I _Ajl (e11c __e__) JISACIK ,A- ’’_ 11- A.:T + ± A1 2 1=-L bk+oba 0~ k*0 m*0 +2PRe T~ If2 -3b

  13. Potential of mean force for electrical conductivity of dense plasmas (United States)

    Starrett, C. E.


    The electrical conductivity in dense plasmas can be calculated with the relaxation-time approximation provided that the interaction potential between the scattering electron and the ion is known. To date there has been considerable uncertainty as to the best way to define this interaction potential so that it correctly includes the effects of ionic structure, screening by electrons and partial ionization. Current approximations lead to significantly different results with varying levels of agreement when compared to bench-mark calculations and experiments. We present a new way to define this potential, drawing on ideas from classical fluid theory to define a potential of mean force. This new potential results in significantly improved agreement with experiments and bench-mark calculations, and includes all the aforementioned physics self-consistently.

  14. Dense plasma focus (DPF) accelerated non radio isotopic radiological source (United States)

    Rusnak, Brian; Tang, Vincent


    A non-radio-isotopic radiological source using a dense plasma focus (DPF) to produce an intense z-pinch plasma from a gas, such as helium, and which accelerates charged particles, such as generated from the gas or injected from an external source, into a target positioned along an acceleration axis and of a type known to emit ionizing radiation when impinged by the type of accelerated charged particles. In a preferred embodiment, helium gas is used to produce a DPF-accelerated He2+ ion beam to a beryllium target, to produce neutron emission having a similar energy spectrum as a radio-isotopic AmBe neutron source. Furthermore, multiple DPFs may be stacked to provide staged acceleration of charged particles for enhancing energy, tunability, and control of the source.

  15. Shear Yielding and Shear Jamming of Dense Hard Sphere Glasses. (United States)

    Urbani, Pierfrancesco; Zamponi, Francesco


    We investigate the response of dense hard sphere glasses to a shear strain in a wide range of pressures ranging from the glass transition to the infinite-pressure jamming point. The phase diagram in the density-shear strain plane is calculated analytically using the mean-field infinite-dimensional solution. We find that just above the glass transition, the glass generically yields at a finite shear strain. The yielding transition in the mean-field picture is a spinodal point in presence of disorder. At higher densities, instead, we find that the glass generically jams at a finite shear strain: the jamming transition prevents yielding. The shear yielding and shear jamming lines merge in a critical point, close to which the system yields at extremely large shear stress. Around this point, highly nontrivial yielding dynamics, characterized by system-spanning disordered fractures, is expected.

  16. Warm dense mater: another application for pulsed power hydrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Reinovsky, Robert Emil [Los Alamos National Laboratory


    Pulsed Power Hydrodynamics (PPH) is an application of low-impedance pulsed power, and high magnetic field technology to the study of advanced hydrodynamic problems, instabilities, turbulence, and material properties. PPH can potentially be applied to the study of the properties of warm dense matter (WDM) as well. Exploration of the properties of warm dense matter such as equation of state, viscosity, conductivity is an emerging area of study focused on the behavior of matter at density near solid density (from 10% of solid density to slightly above solid density) and modest temperatures ({approx}1-10 eV). Conditions characteristic of WDM are difficult to obtain, and even more difficult to diagnose. One approach to producing WDM uses laser or particle beam heating of very small quantities of matter on timescales short compared to the subsequent hydrodynamic expansion timescales (isochoric heating) and a vigorous community of researchers are applying these techniques. Pulsed power hydrodynamic techniques, such as large convergence liner compression of a large volume, modest density, low temperature plasma to densities approaching solid density or through multiple shock compression and heating of normal density material between a massive, high density, energetic liner and a high density central 'anvil' are possible ways to reach relevant conditions. Another avenue to WDM conditions is through the explosion and subsequent expansion of a conductor (wire) against a high pressure (density) gas background (isobaric expansion) techniques. However, both techniques demand substantial energy, proper power conditioning and delivery, and an understanding of the hydrodynamic and instability processes that limit each technique. In this paper we will examine the challenges to pulsed power technology and to pulsed power systems presented by the opportunity to explore this interesting region of parameter space.

  17. Mapping topographic plant location properties using a dense matching approach (United States)

    Niederheiser, Robert; Rutzinger, Martin; Lamprecht, Andrea; Bardy-Durchhalter, Manfred; Pauli, Harald; Winkler, Manuela


    Within the project MEDIALPS (Disentangling anthropogenic drivers of climate change impacts on alpine plant species: Alps vs. Mediterranean mountains) six regions in Alpine and in Mediterranean mountain regions are investigated to assess how plant species respond to climate change. The project is embedded in the Global Observation Research Initiative in Alpine Environments (GLORIA), which is a well-established global monitoring initiative for systematic observation of changes in the plant species composition and soil temperature on mountain summits worldwide to discern accelerating climate change pressures on these fragile alpine ecosystems. Close-range sensing techniques such as terrestrial photogrammetry are well suited for mapping terrain topography of small areas with high resolution. Lightweight equipment, flexible positioning for image acquisition in the field, and independence on weather conditions (i.e. wind) make this a feasible method for in-situ data collection. New developments of dense matching approaches allow high quality 3D terrain mapping with less requirements for field set-up. However, challenges occur in post-processing and required data storage if many sites have to be mapped. Within MEDIALPS dense matching is used for mapping high resolution topography for 284 3x3 meter plots deriving information on vegetation coverage, roughness, slope, aspect and modelled solar radiation. This information helps identifying types of topography-dependent ecological growing conditions and evaluating the potential for existing refugial locations for specific plant species under climate change. This research is conducted within the project MEDIALPS - Disentangling anthropogenic drivers of climate change impacts on alpine plant species: Alps vs. Mediterranean mountains funded by the Earth System Sciences Programme of the Austrian Academy of Sciences.

  18. Study of exciton transfer in dense quantum dot nanocomposites (United States)

    Guzelturk, Burak; Hernandez-Martinez, Pedro Ludwig; Sharma, Vijay Kumar; Coskun, Yasemin; Ibrahimova, Vusala; Tuncel, Donus; Govorov, Alexander O.; Sun, Xiao Wei; Xiong, Qihua; Demir, Hilmi Volkan


    Nanocomposites of colloidal quantum dots (QDs) integrated into conjugated polymers (CPs) are key to hybrid optoelectronics, where engineering the excitonic interactions at the nanoscale is crucial. For such excitonic operation, it was believed that exciton diffusion is essential to realize nonradiative energy transfer from CPs to QDs. In this study, contrary to the previous literature, efficient exciton transfer is demonstrated in the nanocomposites of dense QDs, where exciton transfer can be as efficient as 80% without requiring the assistance of exciton diffusion. This is enabled by uniform dispersion of QDs at high density (up to ~70 wt%) in the nanocomposite while avoiding phase segregation. Theoretical modeling supports the experimental observation of weakly temperature dependent nonradiative energy transfer dynamics. This new finding provides the ability to design hybrid light-emitting diodes that show an order of magnitude enhanced external quantum efficiencies.Nanocomposites of colloidal quantum dots (QDs) integrated into conjugated polymers (CPs) are key to hybrid optoelectronics, where engineering the excitonic interactions at the nanoscale is crucial. For such excitonic operation, it was believed that exciton diffusion is essential to realize nonradiative energy transfer from CPs to QDs. In this study, contrary to the previous literature, efficient exciton transfer is demonstrated in the nanocomposites of dense QDs, where exciton transfer can be as efficient as 80% without requiring the assistance of exciton diffusion. This is enabled by uniform dispersion of QDs at high density (up to ~70 wt%) in the nanocomposite while avoiding phase segregation. Theoretical modeling supports the experimental observation of weakly temperature dependent nonradiative energy transfer dynamics. This new finding provides the ability to design hybrid light-emitting diodes that show an order of magnitude enhanced external quantum efficiencies. Electronic supplementary

  19. Effective Field Theories for Hot and Dense Matter

    Directory of Open Access Journals (Sweden)

    Blaschke D.


    Full Text Available The lecture is divided in two parts. The first one deals with an introduction to the physics of hot, dense many-particle systems in quantum field theory [1, 2]. The basics of the path integral approach to the partition function are explained for the example of chiral quark models. The QCD phase diagram is discussed in the meanfield approximation while QCD bound states in the medium are treated in the rainbow-ladder approximation (Gaussian fluctuations. Special emphasis is devoted to the discussion of the Mott effect, i.e. the transition of bound states to unbound, but resonant scattering states in the continnum under the influence of compression and heating of the system. Three examples are given: (1 the QCD model phase diagram with chiral symmetry ¨ restoration and color superconductivity [3], (2 the Schrodinger equation for heavy-quarkonia [4], and (2 Pions [5] as well as Kaons and D-mesons in the finite-temperature Bethe-Salpeter equation [6]. We discuss recent applications of this quantum field theoretical approach to hot and dense quark matter for a description of anomalous J/ψ supression in heavy-ion collisions [7] and for the structure and cooling of compact stars with quark matter interiors [8]. The second part provides a detailed introduction to the Polyakov-loop Nambu–Jona-Lasinio model [9] for thermodynamics and mesonic correlations [10] in the phase diagram of quark matter. Important relationships of low-energy QCD like the Gell-Mann–Oakes–Renner relation are generalized to finite temperatures. The effect of including the coupling to the Polyakov-loop potential on the phase diagram and mesonic correlations is discussed. An outlook is given to effects of nonlocality of the interactions [11] and of mesonic correlations in the medium [12] which go beyond the meanfield description.

  20. Current and Perspective Applications of Dense Plasma Focus Devices (United States)

    Gribkov, V. A.


    Dense Plasma Focus (DPF) devices' applications, which are intended to support the main-stream large-scale nuclear fusion programs (NFP) from one side (both in fundamental problems of Dense Magnetized Plasma physics and in its engineering issues) as well as elaborated for an immediate use in a number of fields from the other one, are described. In the first direction such problems as self-generated magnetic fields, implosion stability of plasma shells having a high aspect ratio, etc. are important for the Inertial Confinement Fusion (ICF) programs (e.g. as NIF), whereas different problems of current disruption phenomenon, plasma turbulence, mechanisms of generation of fast particles and neutrons in magnetized plasmas are of great interest for the large devices of the Magnetic Plasma Confinement—MPC (e.g. as ITER). In a sphere of the engineering problems of NFP it is shown that in particular the radiation material sciences have DPF as a very efficient tool for radiation tests of prospect materials and for improvement of their characteristics. In the field of broad-band current applications some results obtained in the fields of radiation material sciences, radiobiology, nuclear medicine, express Neutron Activation Analysis (including a single-shot interrogation of hidden illegal objects), dynamic non-destructive quality control, X-Ray microlithography and micromachining, and micro-radiography are presented. As the examples of the potential future applications it is proposed to use DPF as a powerful high-flux neutron source to generate very powerful pulses of neutrons in the nanosecond (ns) range of its duration for innovative experiments in nuclear physics, for the goals of radiation treatment of malignant tumors, for neutron tests of materials of the first wall, blankets and NFP device's constructions (with fluences up to 1 dpa per a year term), and ns pulses of fast electrons, neutrons and hard X-Rays for brachytherapy.

  1. Consequences of the Solar System passage through dense interstellar clouds

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    A. G. Yeghikyan


    Full Text Available Several consequences of the passage of the solar system through dense interstellar molecular clouds are discussed. These clouds, dense (more than 100 cm-3, cold (10–50 K and extended (larger than 1 pc, are characterized by a gas-to-dust mass ratio of about 100, by a specific power grain size spectrum (grain radii usually cover the range 0.001–3 micron and by an average dust-to-gas number density ratio of about 10-12. Frequently these clouds contain small-scale (10–100 AU condensations with gas concentrations ranging up to 10 5 cm-3. At their casual passage over the solar system they exert pressures very much enhanced with respect to today’s standards. Under these conditions it will occur that the Earth is exposed directly to the interstellar flow. It is shown first that even close to the Sun, at 1 AU, the cloud’s matter is only partly ionized and should mainly interact with the solar wind by charge exchange processes. Dust particles of the cloud serve as a source of neutrals, generated by the solar UV irradiation of dust grains, causing the evaporation of icy materials. The release of neutral atoms from dust grains is then followed by strong influences on the solar wind plasma flow. The behavior of the neutral gas inflow parameters is investigated by a 2-D hydrodynamic approach to model the interaction processes. Because of a reduction of the heliospheric dimension down to 1 AU, direct influence of the cloud’s matter to the terrestrial environment and atmosphere could be envisaged.Key words. Interplanetary physics (heliopause and solar wind termination; interplanetary dust; interstellar gas

  2. Heterozygous alleles restore male fertility to cytoplasmic male-sterile radish (Raphanus sativus L.): a case of overdominance. (United States)

    Wang, Zhi Wei; De Wang, Chuan; Wang, Chuan; Gao, Lei; Mei, Shi Yong; Zhou, Yuan; Xiang, Chang Ping; Wang, Ting


    The practice of hybridization has greatly contributed to the increase in crop productivity. A major component that exploits heterosis in crops is the cytoplasmic male sterility (CMS)/nucleus-controlled fertility restoration (Rf) system. Through positional cloning, it is shown that heterozygous alleles (RsRf3-1/RsRf3-2) encoding pentatricopeptide repeat (PPR) proteins are responsible for restoring fertility to cytoplasmic male-sterile radish (Raphanus sativus L.). Furthermore, it was found that heterozygous alleles (RsRf3-1/RsRf3-2) show higher expression and RNA polymerase II occupancy in the CMS cytoplasmic background compared with their homozygous alleles (RsRf3-1/RsRf3-1 or RsRf3-2/RsRf3-2). These data provide new insights into the molecular mechanism of fertility restoration to cytoplasmic male-sterile plants and illustrate a case of overdominance.

  3. Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system

    Energy Technology Data Exchange (ETDEWEB)

    Lountos, George T.; Tropea, Joseph E.; Waugh, David S. (SAIC); (NCI)


    The Yersinia pestis YscD protein is an essential component of the type III secretion system. YscD consists of an N-terminal cytoplasmic domain (residues 1-121), a transmembrane linker (122-142) and a large periplasmic domain (143-419). Both the cytoplasmic and the periplasmic domains are required for the assembly of the type III secretion system. Here, the structure of the YscD cytoplasmic domain solved by SAD phasing is presented. Although the three-dimensional structure is similar to those of forkhead-associated (FHA) domains, comparison with the structures of canonical FHA domains revealed that the cytoplasmic domain of YscD lacks the conserved residues that are required for binding phosphothreonine and is therefore unlikely to function as a true FHA domain.

  4. Plasma exchange and glucocorticoid dosing in the treatment of anti-neutrophil cytoplasm antibody associated vasculitis (PEXIVAS)

    DEFF Research Database (Denmark)

    Walsh, Michael; Merkel, Peter A; Peh, Chen Au


    Granulomatosis with polyangiitis (GPA, Wegener's) and microscopic polyangiitis (MPA) are small vessel vasculitides collectively referred to as anti-neutrophil cytoplasm antibody-associated vasculitis (AAV). AAV is associated with high rates of morbidity and mortality due to uncontrolled disease...

  5. Dehydration-induced redistribution of amphiphilic molecules between cytoplasm and lipids is associated with desiccation tolerance in seeds

    NARCIS (Netherlands)

    Buitink, J.; Leprince, O.; Hoekstra, F.A.


    This study establishes a relationship between desiccation tolerance and the transfer of amphiphilic molecules from the cytoplasm into lipids during drying, using electron paramagnetic resonance spectroscopy of amphiphilic spin probes introduced into imbibed radicles of pea (Pisum sativum) and

  6. A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.). (United States)

    Tanaka, Yoshiyuki; Tsuda, Mizue; Yasumoto, Keita; Yamagishi, Hiroshi; Terachi, Toru


    Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS) is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF) created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138. Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3 kb, similarity >99.9%). It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size) that are non-syntenic to normal-type genome, and the gene orf138 was found to be located at the edge of the

  7. A complete mitochondrial genome sequence of Ogura-type male-sterile cytoplasm and its comparative analysis with that of normal cytoplasm in radish (Raphanus sativus L.

    Directory of Open Access Journals (Sweden)

    Tanaka Yoshiyuki


    Full Text Available Abstract Background Plant mitochondrial genome has unique features such as large size, frequent recombination and incorporation of foreign DNA. Cytoplasmic male sterility (CMS is caused by rearrangement of the mitochondrial genome, and a novel chimeric open reading frame (ORF created by shuffling of endogenous sequences is often responsible for CMS. The Ogura-type male-sterile cytoplasm is one of the most extensively studied cytoplasms in Brassicaceae. Although the gene orf138 has been isolated as a determinant of Ogura-type CMS, no homologous sequence to orf138 has been found in public databases. Therefore, how orf138 sequence was created is a mystery. In this study, we determined the complete nucleotide sequence of two radish mitochondrial genomes, namely, Ogura- and normal-type genomes, and analyzed them to reveal the origin of the gene orf138. Results Ogura- and normal-type mitochondrial genomes were assembled to 258,426-bp and 244,036-bp circular sequences, respectively. Normal-type mitochondrial genome contained 33 protein-coding and three rRNA genes, which are well conserved with the reported mitochondrial genome of rapeseed. Ogura-type genomes contained same genes and additional atp9. As for tRNA, normal-type contained 17 tRNAs, while Ogura-type contained 17 tRNAs and one additional trnfM. The gene orf138 was specific to Ogura-type mitochondrial genome, and no sequence homologous to it was found in normal-type genome. Comparative analysis of the two genomes revealed that radish mitochondrial genome consists of 11 syntenic regions (length >3 kb, similarity >99.9%. It was shown that short repeats and overlapped repeats present in the edge of syntenic regions were involved in recombination events during evolution to interconvert two types of mitochondrial genome. Ogura-type mitochondrial genome has four unique regions (2,803 bp, 1,601 bp, 451 bp and 15,255 bp in size that are non-syntenic to normal-type genome, and the gene orf138

  8. Cytokeratin 7 and Antimitochondrial Antibody Expressions in the Differential Diagnosis of Renal Epithelial Neoplasms with Eosinophlic Cytoplasm

    Directory of Open Access Journals (Sweden)

    Ayhan Ozcan


    Full Text Available Objectives: The distinction between epithelial renal tumors with eosinophilic cytoplasm, namely, chromophobe renal cell carcinoma (ChRCC, clear cell (conventional renal cell carcinoma (ECRCC with eosinophilic cytoplasm, and oncocytoma may remain questionable in some cases because of overlapping morphologic features. We evaluated cytokeratin 7 (CK 7 and antimitochondrial antibody (AMA expressions to determine their potential value in distinguishing these tumors. Methods: In this study, 24 renal tumors were included. They consisted of 9 ChRCCs, 11 oncocytomas and 4 ECRCCs. Immunoperoxidase staining for CK 7 and AMA were performed. Results: CK 7 staining: All ChRCCs showed strong cytoplasmic immunoreactivity with conspicuous peripheral accentuation. All ECRCCs and oncocytomas were negative for CK 7. AMA staining: All ChRCCs showed diffuse cytoplasmic, coarse-granular immunostaining with peripheral accentuation. In all ECRCCs, diffuse cytoplasmic was observed with randomly distributed coarse-granular staining. All oncocytomas demonstrated diffuse cytoplasmic, but fine-granular staining. Combined interpretation of CK 7 and AMA stainings: Seven of eight ChRCCs showed combined AMA (+ with diffuse cytoplasmic coarse-granular with peripheral accentuation and CK 7 (+. All oncocytomas were CK 7 (- and AMA (+. All ECRCCs was also CK 7 (- and AMA (+ like oncocytomas, but the staining pattern of AMA was randomly distributed, and coarse-granular, rather than fine-granular which was observed in all of the oncocytomas. Conclusion: These results suggest that the combined interpretation of CK 7 and AMA may provide a better approach in the differential diagnosis of renal epithelial tumors with eosinophilic cytoplasm, in addition to the relatively well-known distinctive immunostaining patterns of AMA. [J Interdiscipl Histopathol 2012; 1(1.000: 11-15

  9. The cytoplasmic domain of Ig alpha is necessary and sufficient to support efficient early B cell development. (United States)

    Pike, Kelly A; Iacampo, Sandra; Friedmann, Jennifer E; Ratcliffe, Michael J H


    The B cell receptor complex (BcR) is essential for normal B lymphocyte function, and surface BcR expression is a crucial checkpoint in B cell development. However, functional requirements for chains of the BcR during development remain controversial. We have used retroviral gene transfer to introduce components of the BcR into chicken B cell precursors during embryonic development. A chimeric heterodimer, in which the cytoplasmic domains of chicken Igalpha and Igbeta are expressed by fusion with the extracellular and transmembrane domains of murine CD8alpha and CD8beta, respectively, targeted the cytoplasmic domains of the BcR to the cell surface in the absence of extracellular BcR domains. Expression of this chimeric heterodimer supported all early stages of embryo B cell development: bursal colonization, clonal expansion, and induction of repertoire diversification by gene conversion. Expression of the cytoplasmic domain of Igalpha, in the absence of the cytoplasmic domain of Igbeta, was not only necessary, but sufficient to support B cell development as efficiently as the endogenous BcR. In contrast, expression of the cytoplasmic domain of Igbeta in the absence of the cytoplasmic domain of Igalpha failed to support B cell development. The ability of the cytoplasmic domain of Igalpha to support early B cell development required a functional Igalpha immunoreceptor tyrosine-based activation motif. These results support a model in which expression of surface IgM following productive V(D)J recombination in developing B cell precursors serves to chaperone the cytoplasmic domain of Igalpha to the B cell surface, thereby initiating subsequent stages of development.

  10. Cytoplasmic changes and developmental competence of bovine oocytes cryopreserved without cumulus cells

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    S Modina


    Full Text Available The cryopreservation of female gametes is still an open problem because of their structural sensitivity to the coolingand- freezing process and to the exposure to cryoprotectants. The present work was aimed to study the effect of vitrification on immature bovine oocytes freed of cumulus cell investment before freezing. To verify the feasibility and efficiency of denuded oocyte (DO cryopreservation, the cytoplasmic alterations eventually induced either by cell removal or by the vitrification process were analyzed. In particular, the migration of cortical granules and Ca++ localization were studied. In addition, the localization and distribution of microtubules and microfilaments in immature fresh and vitrified DOs were evaluated. Finally, to establish whether the removal of cumulus cells influenced developmental competence, DOs were thawed after vitrification, matured in vitro and fertilized; then presumptive zygotes were cultured to reach the blastocyst stage. The results indicate that mechanical removal of cumulus cells from immature bovine oocytes does not affect their maturation competence but reduces the blastocyst rate when compared with intact cumulus oocyte complexes (COCs. The findings indicate further that the vitrification process induces changes of cytoplasmic components. However, the composition of the manipulation medium used to remove cumulus cells plays a crucial role in reducing the injuries caused by cryopreservation in both cytoplasmic and nuclear compartments. In fact, the presence of serum exerts a sort of protection, significantly improving both oocyte maturation and blastocyst rates. In conclusion, we demonstrate that denuded immature oocytes can be vitrified after cumulus cells removal and successfully develop up, after thawing, to the blastocyst stage, following in vitro maturation and fertilization.

  11. Cell cycle-dependent microtubule-based dynamic transport of cytoplasmic dynein in mammalian cells.

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    Takuya Kobayashi

    Full Text Available BACKGROUND: Cytoplasmic dynein complex is a large multi-subunit microtubule (MT-associated molecular motor involved in various cellular functions including organelle positioning, vesicle transport and cell division. However, regulatory mechanism of the cell-cycle dependent distribution of dynein has not fully been understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we report live-cell imaging of cytoplasmic dynein in HeLa cells, by expressing multifunctional green fluorescent protein (mfGFP-tagged 74-kDa intermediate chain (IC74. IC74-mfGFP was successfully incorporated into functional dynein complex. In interphase, dynein moved bi-directionally along with MTs, which might carry cargos such as transport vesicles. A substantial fraction of dynein moved toward cell periphery together with EB1, a member of MT plus end-tracking proteins (+TIPs, suggesting +TIPs-mediated transport of dynein. In late-interphase and prophase, dynein was localized at the centrosomes and the radial MT array. In prometaphase and metaphase, dynein was localized at spindle MTs where it frequently moved from spindle poles toward chromosomes or cell cortex. +TIPs may be involved in the transport of spindle dyneins. Possible kinetochore and cortical dyneins were also observed. CONCLUSIONS AND SIGNIFICANCE: These findings suggest that cytoplasmic dynein is transported to the site of action in preparation for the following cellular events, primarily by the MT-based transport. The MT-based transport may have greater advantage than simple diffusion of soluble dynein in rapid and efficient transport of the limited concentration of the protein.

  12. The SARS Coronavirus 3a protein binds calcium in its cytoplasmic domain. (United States)

    Minakshi, Rinki; Padhan, Kartika; Rehman, Safikur; Hassan, Md Imtaiyaz; Ahmad, Faizan


    The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) is a positive stranded RNA virus with ∼30kb genome. Among all open reading frames (orfs) of this virus, the orf3a is the largest, and encodes a protein of 274 amino acids, named as 3a protein. Sequence analysis suggests that the orf3a aligned to one calcium pump present in Plasmodium falciparum and the enzyme glutamine synthetase found in Leptospira interrogans. This sequence similarity was found to be limited only to amino acid residues 209-264 which form the cytoplasmic domain of the orf3a. Furthermore, this region was predicted to be involved in the calcium binding. Owing to this hypothesis, we were driven to establish its calcium binding property in vitro. Here, we expressed and purified the cytoplasmic domain of the 3a protein, called Cyto3a, as a recombinant His-tagged protein in the E. coli. The calcium binding nature was established by performing various staining methods such as ruthenium red and stains-all. (45)Ca overlay method was also done to further support the data. Since the 3a protein forms ion channels, we were interested to see any conformational changes occurring in the Cyot3a upon calcium binding, using fluorescence spectroscopy and circular dichroism. These studies clearly indicate a significant change in the conformation of the Cyto3a protein after binding with calcium. Our results strongly suggest that the cytoplasmic domain of the 3a protein of SARS-CoV binds calcium in vitro, causing a change in protein conformation. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. Transforming growth factor beta-independent shuttling of Smad4 between the cytoplasm and nucleus. (United States)

    Pierreux, C E; Nicolás, F J; Hill, C S


    Smad4 plays a pivotal role in all transforming growth factor beta (TGF-beta) signaling pathways. Here we describe six widely expressed alternatively spliced variants of human Smad4 with deletions of different exons in the linker, the region of Smad4 that separates the two well-conserved MH1 and MH2 domains. All these Smad4 variants form complexes with activated Smad2 and Smad3 and are incorporated into DNA-binding complexes with the transcription factor Fast-1, regardless of the amount of linker they contain. However, sequences encoded by exons 5 to 7 in the linker are essential for transcriptional activation. Most importantly, our observation that different Smad4 isoforms have different subcellular localizations has led us to the identification of a functional CRM1-dependent nuclear export signal in the Smad4 linker and a constitutively active nuclear localization signal in the N-terminal MH1 domain. In the absence of TGF-beta signaling, we conclude that Smad4 is rapidly and continuously shuttling between the nucleus and the cytoplasm, the distribution of Smad4 between the nucleus and the cytoplasm being dictated by the relative strengths of the nuclear import and export signals. We demonstrate that inhibition of CRM1-mediated nuclear export by treatment of cells with leptomycin B results in endogenous Smad4 accumulating very rapidly in the nucleus. Endogenous Smad2 and Smad3 are completely unaffected by leptomycin B treatment, indicating that the nucleocytoplasmic shuttling is specific for Smad4. We propose that, upon TGF-beta signaling, complex formation between Smad4 and activated Smad2 or -3 leads to nuclear accumulation of Smad4 through inhibition of its nuclear export. We demonstrate that after prolonged TGF-beta signaling Smad2 becomes dephosphorylated and Smad2 and Smad4 accumulate back in the cytoplasm.

  14. Transforming Growth Factor β-Independent Shuttling of Smad4 between the Cytoplasm and Nucleus (United States)

    Pierreux, Christophe E.; Nicolás, Francisco J.; Hill, Caroline S.


    Smad4 plays a pivotal role in all transforming growth factor β (TGF-β) signaling pathways. Here we describe six widely expressed alternatively spliced variants of human Smad4 with deletions of different exons in the linker, the region of Smad4 that separates the two well-conserved MH1 and MH2 domains. All these Smad4 variants form complexes with activated Smad2 and Smad3 and are incorporated into DNA-binding complexes with the transcription factor Fast-1, regardless of the amount of linker they contain. However, sequences encoded by exons 5 to 7 in the linker are essential for transcriptional activation. Most importantly, our observation that different Smad4 isoforms have different subcellular localizations has led us to the identification of a functional CRM1-dependent nuclear export signal in the Smad4 linker and a constitutively active nuclear localization signal in the N-terminal MH1 domain. In the absence of TGF-β signaling, we conclude that Smad4 is rapidly and continuously shuttling between the nucleus and the cytoplasm, the distribution of Smad4 between the nucleus and the cytoplasm being dictated by the relative strengths of the nuclear import and export signals. We demonstrate that inhibition of CRM1-mediated nuclear export by treatment of cells with leptomycin B results in endogenous Smad4 accumulating very rapidly in the nucleus. Endogenous Smad2 and Smad3 are completely unaffected by leptomycin B treatment, indicating that the nucleocytoplasmic shuttling is specific for Smad4. We propose that, upon TGF-β signaling, complex formation between Smad4 and activated Smad2 or -3 leads to nuclear accumulation of Smad4 through inhibition of its nuclear export. We demonstrate that after prolonged TGF-β signaling Smad2 becomes dephosphorylated and Smad2 and Smad4 accumulate back in the cytoplasm. PMID:11074002

  15. Divergent evolution in the cytoplasmic domains of PRLR and GHR genes in Artiodactyla

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    Li Meng-Hua


    Full Text Available Abstract Background Prolactin receptor (PRLR and growth hormone receptor (GHR belong to the large superfamily of class 1 cytokine receptors. Both of them have been identified as candidate genes affecting key quantitative traits, like growth and reproduction in livestock. We have previously studied the molecular anatomy of the cytoplasmic domain of GHR in different cattle breeds and artiodactyl species. In this study we have analysed the corresponding cytoplasmic signalling region of PRLR. Results We sequenced PRLR gene exon 10, coding for the major part of the cytoplasmic domain, from cattle, American bison, European bison, yak, sheep, pig and wild boar individuals. We found different patterns of variation in the two receptors within and between ruminants and pigs. Pigs and bison species have no variation within GHR exon 10, but show high haplotype diversity for the PRLR exon 10. In cattle, PRLR shows lower diversity than GHR. The Bovinae PRLR haplotype network fits better the known phylogenetic relationships between the species than that of the GHR, where differences within cattle breeds are larger than between the different species in the subfamily. By comparison with the wild boar haplotypes, a high number of subsequent nonsynonymous substitutions seem to have accumulated in the pig PRLR exon 10 after domestication. Conclusion Both genes affect a multitude of traits that have been targets of selection after domestication. The genes seem to have responded differently to different selection pressures imposed by human artificial selection. The results suggest possible effects of selective sweeps in GHR before domestication in the pig lineage or species divergence in the Bison lineage. The PRLR results may be explained by strong directional selection in pigs or functional switching.

  16. Accessory factors of cytoplasmic viral RNA sensors required for antiviral innate immune response

    Directory of Open Access Journals (Sweden)

    Hiroyuki eOshiumi


    Full Text Available Type I interferon (IFN induces many antiviral factors in host cells. RIG-I-like receptors (RLRs are cytoplasmic viral RNA sensors that trigger the signal to induce the innate immune response that includes type I IFN production. RIG-I and MDA5 are RLRs that form nucleoprotein filaments along viral double-stranded RNA, resulting in the activation of MAVS adaptor molecule. The MAVS protein forms a prion-like aggregation structure, leading to type I IFN production. RIG-I and MDA5 undergo post-translational modification. TRIM25 and Riplet ubiquitin ligases deliver a K63-linked polyubiquitin moiety to the RIG-I N-terminal caspase activation and recruitment domains (CARDs and C-terminal region; the polyubiquitin chain then stabilizes the two-CARD tetramer structure required for MAVS assembly. MDA5 activation is regulated by phosphorylation. RIOK3 is a protein kinase that phosphorylates the MDA5 protein in a steady state, and PP1α/γ dephosphorylate this protein, resulting in its activation. RIG-I and MDA5 require cytoplasmic RNA helicases for their efficient activation. LGP2, another RLR, is an RNA helicase involved in RLR signaling. This protein does not possess N-terminal CARDs and thus cannot trigger downstream signaling by itself. Recent studies have revealed that this protein modulates MDA5 filament formation, resulting in enhanced type I IFN production. Several other cytoplasmic RNA helicases are involved in RLR signaling. DDX3, DHX29, DHX36, and DDX60 RNA helicases have been reported to be involved in RLR-mediated type I IFN production after viral infection. However, the underlying mechanism is largely unknown. Future studies are required to reveal the role of RNA helicases in the RLR signaling pathway.

  17. Recombinant expression and characterization of the cytoplasmic rice β-glucosidase Os1BGlu4.

    Directory of Open Access Journals (Sweden)

    Chen Rouyi

    Full Text Available The Os1BGlu4 β-glucosidase is the only glycoside hydrolase family 1 member in rice that is predicted to be localized in the cytoplasm. To characterize the biochemical function of rice Os1BGlu4, the Os1bglu4 cDNA was cloned and used to express a thioredoxin fusion protein in Escherichia coli. After removal of the tag, the purified recombinant Os1BGlu4 (rOs1BGlu4 exhibited an optimum pH of 6.5, which is consistent with Os1BGlu4's cytoplasmic localization. Fluorescence microscopy of maize protoplasts and tobacco leaf cells expressing green fluorescent protein-tagged Os1BGlu4 confirmed the cytoplasmic localization. Purified rOs1BGlu4 can hydrolyze p-nitrophenyl (pNP-β-D-glucoside (pNPGlc efficiently (kcat/Km  =  17.9 mM(-1 · s(-1, and hydrolyzes pNP-β-D-fucopyranoside with about 50% the efficiency of the pNPGlc. Among natural substrates tested, rOs1BGlu4 efficiently hydrolyzed β-(1,3-linked oligosaccharides of degree of polymerization (DP 2-3, and β-(1,4-linked oligosaccharide of DP 3-4, and hydrolysis of salicin, esculin and p-coumaryl alcohol was also detected. Analysis of the hydrolysis of pNP-β-cellobioside showed that the initial hydrolysis was between the two glucose molecules, and suggested rOs1BGlu4 transglucosylates this substrate. At 10 mM pNPGlc concentration, rOs1BGlu4 can transfer the glucosyl group of pNPGlc to ethanol and pNPGlc. This transglycosylation activity suggests the potential use of Os1BGlu4 for pNP-oligosaccharide and alkyl glycosides synthesis.

  18. Cytoplasmic PELP1 and ERRgamma protect human mammary epithelial cells from Tam-induced cell death. (United States)

    Girard, Brian J; Regan Anderson, Tarah M; Welch, Siya Lem; Nicely, Julie; Seewaldt, Victoria L; Ostrander, Julie H


    Tamoxifen (Tam) is the only FDA-approved chemoprevention agent for pre-menopausal women at high risk for developing breast cancer. While Tam reduces a woman's risk of developing estrogen receptor positive (ER+) breast cancer, the molecular mechanisms associated with risk reduction are poorly understood. Prior studies have shown that cytoplasmic proline, glutamic acid and leucine rich protein 1 (PELP1) promotes Tam resistance in breast cancer cell lines. Herein, we tested for PELP1 localization in breast epithelial cells from women at high risk for developing breast cancer and found that PELP1 was localized to the cytoplasm in 36% of samples. In vitro, immortalized HMECs expressing a nuclear localization signal (NLS) mutant of PELP1 (PELP1-cyto) were resistant to Tam-induced death. Furthermore, PELP1-cyto signaling through estrogen-related receptor gamma (ERRγ) promoted cell survival in the presence of Tam. Overexpression of ERRγ in immortalized HMECs protected cells from Tam-induced death, while knockdown of ERRγ sensitized PELP1-cyto expressing HMECs to Tam. Moreover, Tam-induced HMEC cell death was independent of apoptosis and involved accumulation of the autophagy marker LC3-II. Expression of PELP1-cyto and ERRγ reduced Tam-induced LC3-II accumulation, and knockdown of ERRγ increased LC3-II levels in response to Tam. Additionally, PELP1-cyto expression led to the upregulation of MMP-3 and MAOB, known PELP1 and ERRγ target genes, respectively. Our data indicate that cytoplasmic PELP1 induces signaling pathways that converge on ERRγ to promote cell survival in the presence of Tam. These data suggest that PELP1 localization and/or ERRγ activation could be developed as tissue biomarkers for Tam responsiveness.

  19. Cytoplasmic PELP1 and ERRgamma protect human mammary epithelial cells from Tam-induced cell death.

    Directory of Open Access Journals (Sweden)

    Brian J Girard

    Full Text Available Tamoxifen (Tam is the only FDA-approved chemoprevention agent for pre-menopausal women at high risk for developing breast cancer. While Tam reduces a woman's risk of developing estrogen receptor positive (ER+ breast cancer, the molecular mechanisms associated with risk reduction are poorly understood. Prior studies have shown that cytoplasmic proline, glutamic acid and leucine rich protein 1 (PELP1 promotes Tam resistance in breast cancer cell lines. Herein, we tested for PELP1 localization in breast epithelial cells from women at high risk for developing breast cancer and found that PELP1 was localized to the cytoplasm in 36% of samples. In vitro, immortalized HMECs expressing a nuclear localization signal (NLS mutant of PELP1 (PELP1-cyto were resistant to Tam-induced death. Furthermore, PELP1-cyto signaling through estrogen-related receptor gamma (ERRγ promoted cell survival in the presence of Tam. Overexpression of ERRγ in immortalized HMECs protected cells from Tam-induced death, while knockdown of ERRγ sensitized PELP1-cyto expressing HMECs to Tam. Moreover, Tam-induced HMEC cell death was independent of apoptosis and involved accumulation of the autophagy marker LC3-II. Expression of PELP1-cyto and ERRγ reduced Tam-induced LC3-II accumulation, and knockdown of ERRγ increased LC3-II levels in response to Tam. Additionally, PELP1-cyto expression led to the upregulation of MMP-3 and MAOB, known PELP1 and ERRγ target genes, respectively. Our data indicate that cytoplasmic PELP1 induces signaling pathways that converge on ERRγ to promote cell survival in the presence of Tam. These data suggest that PELP1 localization and/or ERRγ activation could be developed as tissue biomarkers for Tam responsiveness.

  20. Fluoride enhances transfection activity of carbonate apatite by increasing cytoplasmic stability of plasmid DNA

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, E.H., E-mail: [Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan (Malaysia)


    Highlights: {yields} Cytoplasmic stability of plasmid DNA is enhanced by fluoride incorporation into carbonate apatite carrier. {yields} Fluoridated carbonate apatite promotes a robust increase in transgene expression. {yields} Controlled dissolution of fluoridated carbonate apatite in endosomal acidic environment might buffer the endosomes and prevent degradation of the released DNA. -- Abstract: Intracellular delivery of a functional gene or a nucleic acid sequence to specifically knockdown a harmful gene is a potential approach to precisely treat a critical human disease. The intensive efforts in the last few decades led to the development of a number of viral and non-viral synthetic vectors. However, an ideal delivery tool in terms of the safety and efficacy has yet to be established. Recently, we have developed pH-sensing inorganic nanocrystals of carbonate apatite for efficient and cell-targeted delivery of gene and gene-silencing RNA. Here we show that addition of very low level of fluoride to the particle-forming medium facilitates a robust increase in transgene expression following post-incubation of the particles with HeLa cells. Confocal microscopic observation and Southern blotting prove the cytoplasmic existence of plasmid DNA delivered by likely formed fluoridated carbonate apatite particles while degradation of plasmid DNA presumably by cytoplasmic nucleases was noticed following delivery with apatite particles alone. The beneficial role of fluoride in enhancing carbonate apatite-mediated gene expression might be due to the buffering potential of generated fluoridated apatite in endosomal acidic environment, thereby increasing the half-life of delivered plasmid DNA.

  1. Tau-mediated nuclear depletion and cytoplasmic accumulation of SFPQ in Alzheimer's and Pick's disease.

    Directory of Open Access Journals (Sweden)

    Yazi D Ke

    Full Text Available Tau dysfunction characterizes neurodegenerative diseases such as Alzheimer's disease (AD and frontotemporal lobar degeneration (FTLD. Here, we performed an unbiased SAGE (serial analysis of gene expression of differentially expressed mRNAs in the amygdala of transgenic pR5 mice that express human tau carrying the P301L mutation previously identified in familial cases of FTLD. SAGE identified 29 deregulated transcripts including Sfpq that encodes a nuclear factor implicated in the splicing and regulation of gene expression. To assess the relevance for human disease we analyzed brains from AD, Pick's disease (PiD, a form of FTLD, and control cases. Strikingly, in AD and PiD, both dementias with a tau pathology, affected brain areas showed a virtually complete nuclear depletion of SFPQ in both neurons and astrocytes, along with cytoplasmic accumulation. Accordingly, neurons harboring either AD tangles or Pick bodies were also depleted of SFPQ. Immunoblot analysis of human entorhinal cortex samples revealed reduced SFPQ levels with advanced Braak stages suggesting that the SFPQ pathology may progress together with the tau pathology in AD. To determine a causal role for tau, we stably expressed both wild-type and P301L human tau in human SH-SY5Y neuroblastoma cells, an established cell culture model of tau pathology. The cells were differentiated by two independent methods, mitomycin C-mediated cell cycle arrest or neuronal differentiation with retinoic acid. Confocal microscopy revealed that SFPQ was confined to nuclei in non-transfected wild-type cells, whereas in wild-type and P301L tau over-expressing cells, irrespective of the differentiation method, it formed aggregates in the cytoplasm, suggesting that pathogenic tau drives SFPQ pathology in post-mitotic cells. Our findings add SFPQ to a growing list of transcription factors with an altered nucleo-cytoplasmic distribution under neurodegenerative conditions.

  2. Prospective study of radioimmunoassay for antibodies against neutrophil cytoplasm in diagnosis of systemic vasculitis

    Energy Technology Data Exchange (ETDEWEB)

    Savage, C.O.S.; Winearls, C.G.; Jones, S.; Marshall, P.D.; Lockwood, C.M.


    The diagnosis and management of Wegener's granulomatosis and microscopic polyarteritis are complicated by the lack of specific diagnostic tests. The diagnostic performance of a solid-phase radioimmunoassay, which detects the autoantibodies against neutrophil cytoplasm present in these disorders, was assessed in a prospective study of patients with suspected vasculitis and/or rapidly progressive nephritis. The assay had a sensitivity and specificity of 96% when carried out in combination with a specific inhibition stage and indirect immunofluorescence staining of alcohol-fixed normal neutrophils.

  3. Nuclear envelope breakdown is under nuclear not cytoplasmic control in sea urchin zygotes. (United States)

    Sluder, G; Thompson, E A; Rieder, C L; Miller, F J


    Nuclear envelope breakdown (NEB) and entry into mitosis are though to be driven by the activation of the p34cdc2-cyclin B kinase complex or mitosis promoting factor (MPF). Checkpoint control mechanisms that monitor essential preparatory events for mitosis, such as DNA replication, are thought to prevent entry into mitosis by downregulating MPF activation until these events are completed. Thus, we were surprised to find that when pronuclear fusion in sea urchin zygotes is blocked with Colcemid, the female pronucleus consistently breaks down before the male pronucleus. This is not due to regional differences in the time of MPF activation, because pronuclei touching each other break down asynchronously to the same extent. To test whether NEB is controlled at the nuclear or cytoplasmic level, we activated the checkpoint for the completion of DNA synthesis separately in female and male pronuclei by treating either eggs or sperm before fertilization with psoralen to covalently cross-link base-paired strands of DNA. When only the maternal DNA is cross-linked, the male pronucleus breaks down first. When the sperm DNA is cross-linked, male pronuclear breakdown is substantially delayed relative to female pronuclear breakdown and sometimes does not occur. Inactivation of the Colcemid after female NEB in such zygotes with touching pronuclei yields a functional spindle composed of maternal chromosomes and paternal centrosomes. The intact male pronucleus remains located at one aster throughout mitosis. In other experiments, when psoralen-treated sperm nuclei, over 90% of the zygote nuclei do not break down for at least 2 h after the controls even though H1 histone kinase activity gradually rises close to, or higher than, control mitotic levels. The same is true for normal zygotes treated with aphidicolin to block DNA synthesis. From these results, we conclude that NEB in sea urchin zygotes is controlled at the nuclear, not cytoplasmic, level, and that mitotic levels of

  4. Functional Analysis of the Transmembrane and Cytoplasmic Domains of Pcdh15a in Zebrafish Hair Cells. (United States)

    Maeda, Reo; Pacentine, Itallia V; Erickson, Timothy; Nicolson, Teresa


    Protocadherin 15 (PCDH15) is required for mechanotransduction in sensory hair cells as a component of the tip link. Isoforms of PCDH15 differ in their cytoplasmic domains (CD1, CD2, and CD3), but share the extracellular and transmembrane (TMD) domains, as well as an intracellular domain known as the common region (CR). In heterologous expression systems, both the TMD and CR of PCDH15 have been shown to interact with members of the mechanotransduction complex. The in vivo significance of these protein-protein interaction domains of PCDH15 in hair cells has not been determined. Here, we examined the localization and function of the two isoforms of zebrafish Pcdh15a (CD1 and CD3) in pcdh15a-null mutants by assessing Pcdh15a transgene-mediated rescue of auditory/vestibular behavior and hair cell morphology and activity. We found that either isoform alone was able to rescue the Pcdh15a-null phenotype and that the CD1- or CD3-specific regions were dispensable for hair bundle integrity and labeling of hair cells with FM4-64, which was used as a proxy for mechanotransduction. When either the CR or TMD domain was deleted, the mutated proteins localized to the stereocilial tips, but were unable to rescue FM4-64 labeling. Disrupting both domains led to a complete failure of Pcdh15a to localize to the hair bundle. Our findings demonstrate that the TMD and cytoplasmic CR domains are required for the in vivo function of Pcdh15a in zebrafish hair cells.SIGNIFICANCE STATEMENT Tip links transmit force to mechanotransduction channels at the tip of hair bundles in sensory hair cells. One component of tip links is Protocadherin 15 (PCDH15). Here, we demonstrate that, when transgenically expressed, either zebrafish Pcdh15a-cytodomain 1 (CD1) or Pcdh15a-CD3 can rescue the phenotype of a pcdh15a-null mutant. Even when lacking the specific regions for CD1 or CD3, truncated Pcdh15a that contains the so-called common region (CR) at the cytoplasmic/membrane interface still has the ability to

  5. Ebolavirus VP35 interacts with the cytoplasmic dynein light chain 8. (United States)

    Kubota, Toru; Matsuoka, Mayumi; Chang, Tsung-Hsien; Bray, Mike; Jones, Steven; Tashiro, Masato; Kato, Atsushi; Ozato, Keiko


    The viral protein VP35 of ebolavirus (EBOV) is implicated to have diverse roles in the viral life cycle. We employed a yeast two-hybrid screen to search for VP35 binding partners and identified the cytoplasmic dynein light chain (DLC8) as a protein that interacts with VP35. Mapping analysis unraveled a consensus motif, SQTQT, within VP35 through which VP35 binds to DLC8. The disruption of DLC8 binding does not affect the ability of VP35 to inhibit type I IFN production. Given that VP35 from various EBOV species interacts with DLC8, this interaction may have a role in regulating the EBOV life cycle.

  6. Ebolavirus VP35 Interacts with the Cytoplasmic Dynein Light Chain 8§ ▿


    Kubota, Toru; Matsuoka, Mayumi; Chang, Tsung-Hsien; Bray, Mike; Jones, Steven,; Tashiro, Masato; Kato, Atsushi; Ozato, Keiko


    The viral protein VP35 of ebolavirus (EBOV) is implicated to have diverse roles in the viral life cycle. We employed a yeast two-hybrid screen to search for VP35 binding partners and identified the cytoplasmic dynein light chain (DLC8) as a protein that interacts with VP35. Mapping analysis unraveled a consensus motif, SQTQT, within VP35 through which VP35 binds to DLC8. The disruption of DLC8 binding does not affect the ability of VP35 to inhibit type I IFN production. Given that VP35 from v...

  7. Partial structural characterization of the cytoplasmic domain of the erythrocyte membrane protein, band 3. (United States)

    Appell, K C; Low, P S


    The cytoplasmic domain of band 3 was released from spectrin-depleted, acetic acid-stripped erythrocyte membrane vesicles by mild chymotryptic digestion. After purification by ion exchange and gel filtration chromatography, the fragment preparation was found to be greater than 90% pure on polyacrylamide disc gels in the presence of 0.2% sodium dodecyl sulfate. The subunit Mr from the electrophoretic procedure was estimated at approximately 40,000. The isolated cytoplasmic fragment ws judged to be a dimer, since (i) the unmodified fragment and its disulfide-cross-linked (dimeric) counterpart eluted in the same peak fraction from a Sephacryl S-200 gel filtration column, and (ii) the sedimentation velocity molecular weight of the native fragment was calculated to be approximately 95,000. No evidence of either larger or smaller aggregates was obtained. The frictional ratio of the fragment was measured at 1.6, suggesting a highly elongated morphology. The circular dichroism spectrum of the fragment corresponded to approximately 37% alpha helix. Titration of the cytoplasmic fragment over the physiological pH range gave rise to a reversible 2-fold increase in the intrinsic fluorescence quantum yield (lambda ex, 290 nm; lambda em, 335 nm) between pH 6 and 9. Computer analysis of the data yielded a temperature-dependent apparent pKa of 7.8 at 37 degrees C and 8.1 at 20 degrees C, both with Hill coefficients less than or equal to 1. Calorimetric experiments revealed a similar sensitivity to pH, where the denaturation temperature of the fragment titrated from 74 degrees C at pH 6 to 59 degrees C at pH 8.5, with an apparent pKa of 7.3 and a Hill coefficient less than 1. The enthalpies and widths at half-height of the transitions were also exquisitely sensitive to pH. The fluorescence and calorimetric data could all be described by the titration of a single ionizable group of apparent pKa of 7.8 at 37 degrees C and delta pKa/degrees C of -0.018. The ionization of this critical

  8. Rapid and Sustained Nuclear-Cytoplasmic ERK Oscillations Induced by Epidermal Growth Factor

    Energy Technology Data Exchange (ETDEWEB)

    Shankaran, Harish; Ippolito, Danielle L.; Chrisler, William B.; Resat, Haluk; Bollinger, Nikki; Opresko, Lee K.; Wiley, H. S.


    Mathematical modeling has predicted that ERK activity should oscillate in response to cell stimulation, but this has never been observed. To explore this inconsistency, we expressed an ERK1-GFP fusion protein in mammary epithelial cells. Following EGF stimulation, we observed rapid and continuous ERK oscillations between the nucleus and cytoplasm with a periodicity of approximately 15 minutes. These oscillations were remarkably persistent (>45 cycles), displayed an asymmetric waveform, and were highly dependent on cell density, essentially disappearing at confluency. We conclude that the ERK pathway is an intrinsic oscillator. Although the functional implications of the observed oscillations are uncertain, this property can be used to continuously monitor ERK activity in single cells.

  9. Isolation of cell nuclei using inert macromolecules to mimic the crowded cytoplasm.

    Directory of Open Access Journals (Sweden)

    Ronald Hancock

    Full Text Available Cell nuclei are commonly isolated and studied in media which include millimolar concentrations of cations, which conserve the nuclear volume by screening the negative charges on chromatin and maintaining its compaction. However, two factors question if these ionic conditions correctly reproduce the environment of nuclei in vivo: the small-scale motion and conformation of chromatin in vivo are not reproduced in isolated nuclei, and experiments and theory suggest that small ions in the cytoplasm are not free in the soluble phase but are predominantly bound to macromolecules. We studied the possible role in maintaining the structure and functions of nuclei in vivo of a further but frequently overlooked property of the cytoplasm, the crowding or osmotic effects caused by diffusible macromolecules whose concentration, measured in several studies, is in the range of 130 mg/ml. Nuclei which conserved their volume in the cell and their ultrastructure seen by electron microscopy were released from K562 cells in media containing the inert polymer 70 kDa Ficoll (50% w/v or 70 kDa dextran (35% w/v to replace the diffusible cytoplasmic molecules which were dispersed on cell lysis with digitonin, with 100 microM K-Hepes buffer as the only source of ions. Immunofluorescence labelling and experiments using cells expressing GFP-fusion proteins showed that internal compartments (nucleoli, PML and coiled bodies, foci of RNA polymerase II were conserved in these nuclei, and nascent RNA transcripts could be elongated. Our observations are consistent with the hypothesis that crowding by diffusible cytoplasmic macromolecules is a crucial but overlooked factor which supports the nucleus in vivo by equilibrating the opposing osmotic pressure cause by the high concentration of macromolecules in the nucleus, and suggest that crowded media provide more physiological conditions to study nuclear structure and functions. They may also help to resolve the long-standing paradox

  10. Marker-assisted identification of restorer gene(s) in iso-cytoplasmic restorer lines of WA cytoplasm in rice and assessment of their fertility restoration potential across environments. (United States)

    Kumar, Amit; Bhowmick, Prolay Kumar; Singh, Vikram Jeet; Malik, Manoj; Gupta, Ashish Kumar; Seth, R; Nagarajan, M; Krishnan, S Gopala; Singh, Ashok Kumar


    Iso-cytoplasmic restorers possess the same male sterile cytoplasm as the cytoplasmic male sterile (CMS) lines, thereby minimizing the potential cyto-nuclear conflict in the hybrids. Restoration of fertility of the wild abortive CMS is governed by two major genes namely, Rf3 and Rf4. Therefore, assessing the allelic status of these restorer genes in the iso-cytoplasmic restorers using molecular markers will not only help in estimating the efficiency of these genes either alone or in combination, in fertility restoration in the hybrids in different environments, but will also be useful in determining the efficacy of these markers. In the present study, the efficiency of molecular markers in identifying genotypes carrying restorer allele of the gene(s) Rf3 and Rf4, restoring male fertility of WA cytoplasm in rice was assessed in a set of 100 iso-cytoplasmic rice restorers using gene linked as well as candidate gene based markers. In order to validate the efficacy of markers in identifying the restorers, a sub-set of selected 25 iso-cytoplasmic rice restorers were crossed with four different cytoplasmic male sterile lines namely, IR 79156A, IR 58025A, Pusa 6A and RTN 12A, and the pollen and spikelet fertility of the F1s were evaluated at three different locations. Marker analysis showed that Rf4 was the predominant fertility restorer gene in the iso-cytoplasmic restorers and Rf3 had a synergistic effect on fertility restoration. The efficiency of gene based markers, DRCG-RF4-14 and DRRM-RF3-10 for Rf4 (87%) and Rf3 (84%) genes was higher than respective gene-linked SSR markers RM6100 (80%) and RM3873 (82%). It is concluded that the gene based markers can be effectively used in identifying fertility restorer lines obviating the need for making crosses and evaluating the F1s. Though gene based markers are more efficient, there is a need to identify functional polymorphisms which can provide 100% efficiency. Three iso-cytoplasmic restorers namely, PRR 300, PRR 363 and

  11. Distribution of dense breasts using screening mammography in Korean women: a retrospective observational study


    Bae, Jong-Myon; Shin, Sang Yop; Kim, Eun Hee; Kim, Yoon-Nam; Nam, Chung Mo


    OBJECTIVES: This retrospective observational study evaluated the distribution of dense breasts by age group among healthy Korean women. METHODS: Participants were women aged 30 years and older who voluntarily underwent screening mammography between January 2007 and December 2011. Women who received the Breast Imaging Reporting and Data System for mammographic density of 3 or 4 were defined as having dense breasts. The proportion of women with dense breasts (PDB, %) was calculated by dividing ...

  12. Dense Medium Plasma Water Purification Reactor (DMP WaPR) Project (United States)

    National Aeronautics and Space Administration — The Dense Medium Plasma Water Purification Reactor offers significant improvements over existing water purification technologies used in Advanced Life Support...

  13. The Green Bank Ammonia Survey: Dense Cores under Pressure in Orion A (United States)

    Kirk, Helen; Friesen, Rachel K.; Pineda, Jaime E.; Rosolowsky, Erik; Offner, Stella S. R.; Matzner, Christopher D.; Myers, Philip C.; Di Francesco, James; Caselli, Paola; Alves, Felipe O.; Chacón-Tanarro, Ana; Chen, How-Huan; Chun-Yuan Chen, Michael; Keown, Jared; Punanova, Anna; Seo, Young Min; Shirley, Yancy; Ginsburg, Adam; Hall, Christine; Singh, Ayushi; Arce, Héctor G.; Goodman, Alyssa A.; Martin, Peter; Redaelli, Elena


    We use data on gas temperature and velocity dispersion from the Green Bank Ammonia Survey and core masses and sizes from the James Clerk Maxwell Telescope Gould Belt Survey to estimate the virial states of dense cores within the Orion A molecular cloud. Surprisingly, we find that almost none of the dense cores are sufficiently massive to be bound when considering only the balance between self-gravity and the thermal and non-thermal motions present in the dense gas. Including the additional pressure binding imposed by the weight of the ambient molecular cloud material and additional smaller pressure terms, however, suggests that most of the dense cores are pressure-confined.

  14. Densely Aligned Graphene Nanoribbon Arrays and Bandgap Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Su, Justin [Stanford Univ., CA (United States); Chen, Changxin [Stanford Univ., CA (United States); Gong, Ming [Stanford Univ., CA (United States); Kenney, Michael [Stanford Univ., CA (United States)


    Graphene has attracted great interest for future electronics due to its high mobility and high thermal conductivity. However, a two-dimensional graphene sheet behaves like a metal, lacking a bandgap needed for the key devices components such as field effect transistors (FETs) in digital electronics. It has been shown that, partly due to quantum confinement, graphene nanoribbons (GNRs) with ~2 nm width can open up sufficient bandgaps and evolve into semiconductors to exhibit high on/off ratios useful for FETs. However, a challenging problem has been that, such ultra-narrow GNRs (~2 nm) are difficult to fabricate, especially for GNRs with smooth edges throughout the ribbon length. Despite high on/off ratios, these GNRs show very low mobility and low on-state conductance due to dominant scattering effects by imperfections and disorders at the edges. Wider GNRs (>5 nm) show higher mobility, higher conductance but smaller bandgaps and low on/off ratios undesirable for FET applications. It is highly desirable to open up bandgaps in graphene or increase the bandgaps in wide GNRs to afford graphene based semiconductors for high performance (high on-state current and high on/off ratio) electronics. Large scale ordering and dense packing of such GNRs in parallel are also needed for device integration but have also been challenging thus far. It has been shown theoretically that uniaxial strains can be applied to a GNR to engineer its bandgap. The underlying physics is that under uniaxial strain, the Dirac point moves due to stretched C-C bonds, leading to an increase in the bandgap of armchair GNRs by up to 50% of its original bandgap (i.e. bandgap at zero strain). For zigzag GNRs, due to the existence of the edge states, changes of bandgap are smaller under uniaxial strain and can be increased by ~30%. This work proposes a novel approach to the fabrication of densely aligned graphene nanoribbons with highly smooth edges afforded by anisotropic etching and uniaxial strain for

  15. Modelling compressible dense and dilute two-phase flows (United States)

    Saurel, Richard; Chinnayya, Ashwin; Carmouze, Quentin


    Many two-phase flow situations, from engineering science to astrophysics, deal with transition from dense (high concentration of the condensed phase) to dilute concentration (low concentration of the same phase), covering the entire range of volume fractions. Some models are now well accepted at the two limits, but none are able to cover accurately the entire range, in particular regarding waves propagation. In the present work, an alternative to the Baer and Nunziato (BN) model [Baer, M. R. and Nunziato, J. W., "A two-phase mixture theory for the deflagration-to-detonation transition (DDT) in reactive granular materials," Int. J. Multiphase Flow 12(6), 861 (1986)], initially designed for dense flows, is built. The corresponding model is hyperbolic and thermodynamically consistent. Contrarily to the BN model that involves 6 wave speeds, the new formulation involves 4 waves only, in agreement with the Marble model [Marble, F. E., "Dynamics of a gas containing small solid particles," Combustion and Propulsion (5th AGARD Colloquium) (Pergamon Press, 1963), Vol. 175] based on pressureless Euler equations for the dispersed phase, a well-accepted model for low particle volume concentrations. In the new model, the presence of pressure in the momentum equation of the particles and consideration of volume fractions in the two phases render the model valid for large particle concentrations. A symmetric version of the new model is derived as well for liquids containing gas bubbles. This model version involves 4 characteristic wave speeds as well, but with different velocities. Last, the two sub-models with 4 waves are combined in a unique formulation, valid for the full range of volume fractions. It involves the same 6 wave speeds as the BN model, but at a given point of space, 4 waves only emerge, depending on the local volume fractions. The non-linear pressure waves propagate only in the phase with dominant volume fraction. The new model is tested numerically on various

  16. Cytoplasmic inheritance of parent–offspring cell structure in the clonal diatom Cyclotella meneghiniana (United States)

    Shimada, Masakazu


    In cytoplasmic inheritance, structural states of a parent cell could be transmitted to offspring cells via two mechanisms. The first is referred to as the hangover of parent structure, where the structure itself remains and faithfully transmits within offspring cells; the second is structural inheritance, wherein the parent structure functions as a template for development of new offspring structure. We estimated to what extent the parent structure affects the development of offspring structure by structural inheritance, using a clone of the diatom Cyclotella meneghiniana. The cell has two siliceous valves (a cell wall part at both cell poles): one is inherited from the parent and the other is newly formed. We estimated cytoplasmic heritability by comparing valve traits (central fultoportulae (CTFP), striae, central area, and cell diameter) of parent and new offspring valves, using single-cell isolation and valve labelling. Parent–offspring valve trait regressions showed that all traits, except CTFP, were significantly correlated. We formulated a quantitative genetic model considering the diatom inheritance system and revealed short-term rapid evolution compared with other inheritance systems. Diatom structural inheritance will have evolved to enable clonal populations to rapidly acquire and maintain suitable structures for temporal changes in environments and life-cycle stages. PMID:27807268

  17. Differential Proteomic Analysis of Anthers between Cytoplasmic Male Sterile and Maintainer Lines in Capsicum annuum L.

    Directory of Open Access Journals (Sweden)

    Zhiming Wu


    Full Text Available Cytoplasmic male sterility (CMS, widely used in the production of hybrid seeds, is a maternally inherited trait resulting in a failure to produce functional pollen. In order to identify some specific proteins associated with CMS in pepper, two-dimensional gel electrophoresis (2-DE was applied to proteomic analysis of anthers/buds between a CMS line (designated NA3 and its maintainer (designated NB3 in Capsicum annuum L. Thirty-three spots showed more than 1.5-fold in either CMS or its maintainer. Based on mass spectrometry, 27 spots representing 23 distinct proteins in these 33 spots were identified. Proteins down-regulated in CMS anthers/buds includes ATP synthase D chain, formate dehydrogenase, alpha-mannosidas, RuBisCO large subunit-binding protein subunit beta, chloroplast manganese stabilizing protein-II, glutathione S-transferase, adenosine kinase isoform 1T-like protein, putative DNA repair protein RAD23-4, putative caffeoyl-CoA 3-O-methyltransferase, glutamine synthetase (GS, annexin Cap32, glutelin, allene oxide cyclase, etc. In CMS anthers/buds, polyphenol oxidase, ATP synthase subunit beta, and actin are up-regulated. It was predicted that male sterility in NA3 might be related to energy metabolism turbulence, excessive ethylene synthesis, and suffocation of starch synthesis. The present study lays a foundation for future investigations of gene functions associated with pollen development and cytoplasmic male sterility, and explores the molecular mechanism of CMS in pepper.

  18. Cytoplasmic inheritance of parent-offspring cell structure in the clonal diatom Cyclotella meneghiniana. (United States)

    Shirokawa, Yuka; Shimada, Masakazu


    In cytoplasmic inheritance, structural states of a parent cell could be transmitted to offspring cells via two mechanisms. The first is referred to as the hangover of parent structure, where the structure itself remains and faithfully transmits within offspring cells; the second is structural inheritance, wherein the parent structure functions as a template for development of new offspring structure. We estimated to what extent the parent structure affects the development of offspring structure by structural inheritance, using a clone of the diatom Cyclotella meneghiniana The cell has two siliceous valves (a cell wall part at both cell poles): one is inherited from the parent and the other is newly formed. We estimated cytoplasmic heritability by comparing valve traits (central fultoportulae (CTFP), striae, central area, and cell diameter) of parent and new offspring valves, using single-cell isolation and valve labelling. Parent-offspring valve trait regressions showed that all traits, except CTFP, were significantly correlated. We formulated a quantitative genetic model considering the diatom inheritance system and revealed short-term rapid evolution compared with other inheritance systems. Diatom structural inheritance will have evolved to enable clonal populations to rapidly acquire and maintain suitable structures for temporal changes in environments and life-cycle stages. © 2016 The Author(s).

  19. Uptake and degradation of cytoplasmic RNA by lysosomes in the perfused rat liver

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    Heydrick, S.J.; Lardeux, B.; Mortimore, G.E.


    The release of (/sup 14/C)cytidine has been shown previously to be a valid marker for RNA degradation in rat hepatocytes. The breakdown of RNA measured with this marker in perfused livers prelabeled in vivo with (6-/sup 14/C)orotic acid was found to be regulated acutely by perfusate amino acids over a wide range, from 0.29 to 3.48%/h. This regulation paralleled that of lysosomal proteolysis. Chloroquine inhibited RNA degradation 60-70%. In subsequent cell fractionation studies labelled cytidine was released; the distribution of this release paralleled that of a lysosomal marker enzyme. The release plateaued after two hours, defining a distinct lysosomal pool of RNA. The lysosomal location of the RNA pool was confirmed in experiments where a 22% increase in the apparent pool size was obtained by lowering the homogenate pH from 7.0 to 5.5. The pool size correlated linearly with the rate of RNA degradation measured during perfusion, giving a turnover constant in reasonable agreement with values reported for autophagy. These results indicate that cytoplasmic RNA degradation occurs primarily in the lysosome and is regulated under these conditions by the amino acid control of lysosomal sequestration of cytoplasm.

  20. Cytoplasmic proteasomes are not indispensable for cell growth in Saccharomyces cerevisiae. (United States)

    Tsuchiya, Hikaru; Arai, Naoko; Tanaka, Keiji; Saeki, Yasushi


    The 26S proteasome is an essential protease complex responsible for the degradation of ubiquitinated proteins in eukaryotic cells. In rapidly proliferating yeast cells, proteasomes are mainly localized in the nucleus, but the biological significance of the proteasome localization is still unclear. In this study, we investigated the relationship between the proteasome localization and the functions by the anchor-away technique, a ligand-dependent sequestration of a target protein into specific compartment(s). Anchoring of the proteasome to the plasma membrane or the ribosome resulted in conditional depletion of the nuclear proteasomes, whereas anchoring to histone resulted in the proteasome sequestration into the nucleus. We observed that the accumulation of ubiquitinated proteins in all the proteasome-targeted cells, suggesting that both the nuclear and cytoplasmic proteasomes have proteolytic functions and that the ubiquitinated proteins are produced and degraded in each compartment. Consistent with previous studies, the nuclear proteasome-depleted cells exhibited a lethal phenotype. In contrast, the nuclear sequestration of the proteasome resulted only in a mild growth defect, suggesting that the cytoplasmic proteasomes are not basically indispensable for cell growth in rapidly growing yeast cells. Copyright © 2013 Elsevier Inc. All rights reserved.

  1. Internal epithelia in Drosophila display rudimentary competence to form cytoplasmic networks of transgenic human vimentin. (United States)

    Gullmets, Josef; Torvaldson, Elin; Lindqvist, Julia; Imanishi, Susumu Y; Taimen, Pekka; Meinander, Annika; Eriksson, John E


    Cytoplasmic intermediate filaments (cIFs) are found in all eumetazoans, except arthropods. To investigate the compatibility of cIFs in arthropods, we expressed human vimentin (hVim), a cIF with filament-forming capacity in vertebrate cells and tissues, transgenically in Drosophila Transgenic hVim could be recovered from whole-fly lysates by using a standard procedure for intermediate filament (IF) extraction. When this procedure was used to test for the possible presence of IF-like proteins in flies, only lamins and tropomyosin were observed in IF-enriched extracts, thereby providing biochemical reinforcement to the paradigm that arthropods lack cIFs. In Drosophila, transgenic hVim was unable to form filament networks in S2 cells and mesenchymal tissues; however, cage-like vimentin structures could be observed around the nuclei in internal epithelia, which suggests that Drosophila retains selective competence for filament formation. Taken together, our results imply that although the filament network formation competence is partially lost in Drosophila, a rudimentary filament network formation ability remains in epithelial cells. As a result of the observed selective competence for cIF assembly in Drosophila, we hypothesize that internal epithelial cIFs were the last cIFs to disappear from arthropods.-Gullmets, J., Torvaldson, E., Lindqvist, J., Imanishi, S. Y., Taimen, P., Meinander, A., Eriksson, J. E. Internal epithelia in Drosophila display rudimentary competence to form cytoplasmic networks of transgenic human vimentin. © FASEB.

  2. No influence of Indy on lifespan in Drosophila after correction for genetic and cytoplasmic background effects.

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    Janne M Toivonen


    Full Text Available To investigate whether alterations in mitochondrial metabolism affect longevity in Drosophila melanogaster, we studied lifespan in various single gene mutants, using inbred and outbred genetic backgrounds. As positive controls we included the two most intensively studied mutants of Indy, which encodes a Drosophila Krebs cycle intermediate transporter. It has been reported that flies heterozygous for these Indy mutations, which lie outside the coding region, show almost a doubling of lifespan. We report that only one of the two mutants lowers mRNA levels, implying that the lifespan extension observed is not attributable to the Indy mutations themselves. Moreover, neither Indy mutation extended lifespan in female flies in any genetic background tested. In the original genetic background, only the Indy mutation associated with altered RNA expression extended lifespan in male flies. However, this effect was abolished by backcrossing into standard outbred genetic backgrounds, and was associated with an unidentified locus on the X chromosome. The original Indy line with long-lived males is infected by the cytoplasmic symbiont Wolbachia, and the longevity of Indy males disappeared after tetracycline clearance of this endosymbiont. These findings underscore the critical importance of standardisation of genetic background and of cytoplasm in genetic studies of lifespan, and show that the lifespan extension previously claimed for Indy mutants was entirely attributable to confounding variation from these two sources. In addition, we saw no effects on lifespan of expression knockdown of the Indy orthologues nac-2 and nac-3 in the nematode Caenorhabditis elegans.

  3. [Anti-neutrophil cytoplasmic antibodies (ANCA) in patients with symptomatic and asymptomatic HIV infection]. (United States)

    Habegger de Sorrentino, A; Motta, P; Iliovich, E; Sorrentino, A P


    The cytopathic effect of HIV on CD4 T cells, as well as the active autoimmune mechanism occurring during infection, have been documented. Of the cytokines involved in the pathogenesis of AIDS, the main one produced by the monocyte-macrophage series is tumor necrosis factor alfa (TNF alpha). This cytokine induces antigens such as proteinase 3 (Pr 3) or mieloperoxidase (MPO). Anti-neutrophil cytoplasmic antibodies (ANCA) are directed against this type of PMN antigens. In the present paper, the role of anti-neutrophil cytoplasmic antibodies (ANCA) in HIV infected patients as responsible for autoimmune phenomena in relation to opportunistic infections, was studied. A total of 88 serum samples belonging to 49 asymptomatic and 39 symptomatic HIV infected patients were tested for ANCA by an indirect immunofluorescence (IIF) test over a neutrophil substrate. ANCA were detected in 53.8% of symptomatic patients as compared to 4.1% in asymptomatic cases (p tuberculosis is a frequent finding in HIV infected patients from Northeastern Argentina. When the presence of ANCA in TB(+) HIV(+) and TB(+) HIV(-) patients was studied, it was seen that positive-ANCA significantly correlated with the first group (p pulmonar TB, could indicate that the virus may not be responsible for the induction of these antibodies.

  4. A single Danio rerio hars gene encodes both cytoplasmic and mitochondrial histidyl-tRNA synthetases.

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    Ashley L Waldron

    Full Text Available Histidyl tRNA Synthetase (HARS is a member of the aminoacyl tRNA synthetase (ARS family of enzymes. This family of 20 enzymes is responsible for attaching specific amino acids to their cognate tRNA molecules, a critical step in protein synthesis. However, recent work highlighting a growing number of associations between ARS genes and diverse human diseases raises the possibility of new and unexpected functions in this ancient enzyme family. For example, mutations in HARS have been linked to two different neurological disorders, Usher Syndrome Type IIIB and Charcot Marie Tooth peripheral neuropathy. These connections raise the possibility of previously undiscovered roles for HARS in metazoan development, with alterations in these functions leading to complex diseases. In an attempt to establish Danio rerio as a model for studying HARS functions in human disease, we characterized the Danio rerio hars gene and compared it to that of human HARS. Using a combination of bioinformatics, molecular biology, and cellular approaches, we found that while the human genome encodes separate genes for cytoplasmic and mitochondrial HARS protein, the Danio rerio genome encodes a single hars gene which undergoes alternative splicing to produce the respective cytoplasmic and mitochondrial versions of Hars. Nevertheless, while the HARS genes of humans and Danio differ significantly at the genomic level, we found that they are still highly conserved at the amino acid level, underscoring the potential utility of Danio rerio as a model organism for investigating HARS function and its link to human diseases in vivo.

  5. Impact-Free Measurement of Microtubule Rotations on Kinesin and Cytoplasmic-Dynein Coated Surfaces.

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    Aniruddha Mitra

    Full Text Available Knowledge about the three-dimensional stepping of motor proteins on the surface of microtubules (MTs as well as the torsional components in their power strokes can be inferred from longitudinal MT rotations in gliding motility assays. In previous studies, optical detection of these rotations relied on the tracking of rather large optical probes present on the outer MT surface. However, these probes may act as obstacles for motor stepping and may prevent the unhindered rotation of the gliding MTs. To overcome these limitations, we devised a novel, impact-free method to detect MT rotations based on fluorescent speckles within the MT structure in combination with fluorescence-interference contrast microscopy. We (i confirmed the rotational pitches of MTs gliding on surfaces coated by kinesin-1 and kinesin-8 motors, (ii demonstrated the superiority of our method over previous approaches on kinesin-8 coated surfaces at low ATP concentration, and (iii identified MT rotations driven by mammalian cytoplasmic dynein, indicating that during collective motion cytoplasmic dynein side-steps with a bias in one direction. Our novel method is easy to implement on any state-of-the-art fluorescence microscope and allows for high-throughput experiments.

  6. Cytoplasmic streaming in Drosophila oocytes varies with kinesin activity and correlates with the microtubule cytoskeleton architecture. (United States)

    Ganguly, Sujoy; Williams, Lucy S; Palacios, Isabel M; Goldstein, Raymond E


    Cells can localize molecules asymmetrically through the combined action of cytoplasmic streaming, which circulates their fluid contents, and specific anchoring mechanisms. Streaming also contributes to the distribution of nutrients and organelles such as chloroplasts in plants, the asymmetric position of the meiotic spindle in mammalian embryos, and the developmental potential of the zygote, yet little is known quantitatively about the relationship between streaming and the motor activity which drives it. Here we use Particle Image Velocimetry to quantify the statistical properties of Kinesin-dependent streaming during mid-oogenesis in Drosophila. We find that streaming can be used to detect subtle changes in Kinesin activity and that the flows reflect the architecture of the microtubule cytoskeleton. Furthermore, based on characterization of the rheology of the cytoplasm in vivo, we establish estimates of the number of Kinesins required to drive the observed streaming. Using this in vivo data as the basis of a model for transport, we suggest that the disordered character of transport at mid-oogenesis, as revealed by streaming, is an important component of the localization dynamics of the body plan determinant oskar mRNA.

  7. Cytoplasmic streaming in plant cells emerges naturally by microfilament self-organization. (United States)

    Woodhouse, Francis G; Goldstein, Raymond E


    Many cells exhibit large-scale active circulation of their entire fluid contents, a process termed cytoplasmic streaming. This phenomenon is particularly prevalent in plant cells, often presenting strikingly regimented flow patterns. The driving mechanism in such cells is known: myosin-coated organelles entrain cytoplasm as they process along actin filament bundles fixed at the periphery. Still unknown, however, is the developmental process that constructs the well-ordered actin configurations required for coherent cell-scale flow. Previous experimental works on streaming regeneration in cells of Characean algae, whose longitudinal flow is perhaps the most regimented of all, hint at an autonomous process of microfilament self-organization driving the formation of streaming patterns during morphogenesis. Working from first principles, we propose a robust model of streaming emergence that combines motor dynamics with both microscopic and macroscopic hydrodynamics to explain how several independent processes, each ineffectual on its own, can reinforce to ultimately develop the patterns of streaming observed in the Characeae and other streaming species.

  8. Host cytoplasmic processing bodies assembled by Trypanosoma cruzi during infection exert anti-parasitic activity. (United States)

    Seto, Eri; Onizuka, Yoko; Nakajima-Shimada, Junko


    Processing bodies (PBs) are cytoplasmic granules containing mRNAs and proteins involved in translation and degradation of mRNAs. PBs are constitutively present in cells and are induced to accumulate when external stressors including microbial infection are applied to cells, followed by a rapid translational arrest. We have examined the impact of Trypanosoma cruzi (T. cruzi, Tc) infection on host cytoplasmic PB assembly. Within 24h post-infection, we found the average number of PB foci per cell increased by more than 2-fold. Protein levels of PB components were unaltered during infection. These results indicated that Tc infection caused accumulation of PBs by changing the localization pattern of PB protein components. To elucidate the role of the accumulated PBs on Tc infection, we knocked down PBs using a siRNA specific for PB components EDC4 and Lsm14A, which are involved in mRNA decapping and translational repression, respectively. We observed that the inhibition of PB accumulation significantly enhanced the infectivity and growth of intracellular amastigotes. Depletion of PBs did not affect nitric oxide (NO) production during Tc infection, indicating that the growth promotion was not caused by modulation of NO-mediated killing of Tc. Our results suggest that the accumulated PBs partially contribute to anti-parasitic responses by manipulating the host's mRNA metabolism. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  9. X-ray powder pattern analysis of cytoplasmic polyhedrosis virus inclusion bodies

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    Di, X.; Sun, Y.K.; McCrae, M.A.; Rossmann, M.G. (Purdue Univ., West lafayette, IN (USA))


    Cytoplasmic polyhedrosis virus is an insect reovirus which is occluded in crystalline inclusion bodies that form in the mid-gut of certain insects. Inclusion bodies of cytoplasmic polyhedrosis virus from Bombyx mori were isolated and purified. These crystalline bodies, about 1-3 microns in linear size, were compacted in a capillary tube while immersed in buffer. X-ray diffraction photographs showed powder rings, extending to 8.2 A resolution, which could be indexed with a cell measuring a = b = 49.9 +/- 0.4 A, c = 41.5 +/- 0.4 A, alpha = beta = gamma = 90 degrees. The polyhedrin protein, which is the major component of the inclusion body, has a molecular weight of about 30,000 daltons and, hence, there are probably two molecules in the unit cell. Thus, the unit cell is monoclinic or possibly triclinic. A Patterson derived from the measured powder pattern intensities, assuming monoclinic symmetry, could be interpreted in terms of a molecule with two larger globes. Such a structure is roughly consistent with the breakdown of the polyhedrin into two larger fragments of molecular weight 17,000 and 14,000 when raising the pH to near 10. Under these conditions the inclusion bodies disintegrate, releasing virus and catalyzing the proteolysis of the polyhedrin.

  10. Nocturnal changes in leaf growth of Populus deltoides are controlled by cytoplasmic growth. (United States)

    Matsubara, Shizue; Hurry, Vaughan; Druart, Nathalie; Benedict, Catherine; Janzik, Ingar; Chavarría-Krauser, Andrés; Walter, Achim; Schurr, Ulrich


    Growing leaves do not expand at a constant rate but exhibit pronounced diel growth rhythms. However, the mechanisms giving rise to distinct diel growth dynamics in different species are still largely unknown. As a first step towards identifying genes controlling rate and timing of leaf growth, we analysed the transcriptomes of rapidly expanding and fully expanded leaves of Populus deltoides Bartr. ex. Marsh at points of high and low expansion at night. Tissues with well defined temporal growth rates were harvested using an online growth-monitoring system based on a digital image sequence processing method developed for quantitative mapping of dicot leaf growth. Unlike plants studied previously, leaf growth in P. deltoides was characterised by lack of a base-tip gradient across the lamina, and by maximal and minimal growth at dusk and dawn, respectively. Microarray analysis revealed that the nocturnal decline in growth coincided with a concerted down-regulation of ribosomal protein genes, indicating deceleration of cytoplasmic growth. In a subsequent time-course experiment, Northern blotting and real-time RT-PCR confirmed that the ribosomal protein gene RPL12 and a cell-cycle gene H2B were down-regulated after midnight following a decrease in cellular carbohydrate concentrations. Thus, we propose that the spatio-temporal growth pattern in leaves of P. deltoides primarily arises from cytoplasmic growth whose activity increases from afternoon to midnight and thereafter decreases in this species.

  11. Association of nad7a Gene with Cytoplasmic Male Sterility in Pigeonpea

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    Pallavi Sinha


    Full Text Available Cytoplasmic male sterility (CMS has been exploited in the commercial pigeonpea [ (L. Millsp.] hybrid breeding system; however, the molecular mechanism behind this system is unknown. To understand the underlying molecular mechanism involved in A CMS system derived from (Haines Maesen, 34 mitochondrial genes were analyzed for expression profiling and structural variation analysis between CMS line (ICRISAT Pigeonpea A line, ICPA 2039 and its cognate maintainer (ICPB 2039. Expression profiling of 34 mitochondrial genes revealed nine genes with significant fold differential gene expression at ≤ 0.01, including one gene, , with 1366-fold higher expression in CMS line as compared with the maintainer. Structural variation analysis of these mitochondrial genes identified length variation between ICPA 2039 and ICPB 2039 for (subunit of gene. Sanger sequencing of and genes in the CMS and the maintainer lines identified two single nucleotide polymorphisms (SNPs in upstream region of and a deletion of 10 bp in in the CMS line. Protein structure evaluation showed conformational changes in predicted protein structures for between ICPA 2039 and ICPB 2039 lines. All above analyses indicate association of gene with the CMS for A cytoplasm in pigeonpea. Additionally, one polymerase chain reaction (PCR based Indel marker ( has been developed and validated for testing genetic purity of A derived CMS lines to strengthen the commercial hybrid breeding program in pigeonpea.

  12. Red blood cell thickness is evolutionarily constrained by slow, hemoglobin-restricted diffusion in cytoplasm. (United States)

    Richardson, Sarah L; Swietach, Pawel


    During capillary transit, red blood cells (RBCs) must exchange large quantities of CO 2 and O 2 in typically less than one second, but the degree to which this is rate-limited by diffusion through cytoplasm is not known. Gas diffusivity is intuitively assumed to be fast and this would imply that the intracellular path-length, defined by RBC shape, is not a factor that could meaningfully compromise physiology. Here, we evaluated CO 2 diffusivity (D CO2 ) in RBCs and related our results to cell shape. D CO2 inside RBCs was determined by fluorescence imaging of [H + ] dynamics in cells under superfusion. This method is based on the principle that H + diffusion is facilitated by CO 2 /HCO 3 - buffer and thus provides a read-out of D CO2 . By imaging the spread of H + ions from a photochemically-activated source (6-nitroveratraldehyde), D CO2 in human RBCs was calculated to be only 5% of the rate in water. Measurements on RBCs containing different hemoglobin concentrations demonstrated a halving of D CO2 with every 75 g/L increase in mean corpuscular hemoglobin concentration (MCHC). Thus, to compensate for highly-restricted cytoplasmic diffusion, RBC thickness must be reduced as appropriate for its MCHC. This can explain the inverse relationship between MCHC and RBC thickness determined from >250 animal species.

  13. Holophytochrome-Interacting Proteins in Physcomitrella: Putative Actors in Phytochrome Cytoplasmic Signaling. (United States)

    Ermert, Anna Lena; Mailliet, Katharina; Hughes, Jon


    Phytochromes are the principle photoreceptors in light-regulated plant development, primarily acting via translocation of the light-activated photoreceptor into the nucleus and subsequent gene regulation. However, several independent lines of evidence indicate unambiguously that an additional cytoplasmic signaling mechanism must exist. Directional responses in filament tip cells of the moss Physcomitrella patens are steered by phy4 which has been shown to interact physically with the blue light receptor phototropin at the plasma membrane. This complex might perceive and transduce vectorial information leading to cytoskeleton reorganization and finally a directional growth response. We developed yeast two-hybrid procedures using photochemically functional, full-length phy4 as bait in Physcomitrella cDNA library screens and growth assays under different light conditions, revealing Pfr-dependent interactions possibly associated with phytochrome cytoplasmic signaling. Candidate proteins were then expressed in planta with fluorescent protein tags to determine their intracellular localization in darkness and red light. Of 14 candidates, 12 were confirmed to interact with phy4 in planta using bimolecular fluorescence complementation. We also used database information to study their expression patterns relative to those of phy4. We discuss the likely functional characteristics of these holophytochrome-interacting proteins (HIP's) and their possible roles in signaling.

  14. Signaling from the cytoplasm to the nucleus in striatal medium-sized spiny neurons

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    Miriam eMatamales


    Full Text Available Striatal medium-sized spiny neurons (MSNs receive massive glutamate inputs from the cerebral cortex and thalamus and are a major target of dopamine projections. Interaction between glutamate and dopamine signaling is crucial for the control of movement and reward-driven learning, and its alterations are implicated in several neuropsychiatric disorders including Parkinson’s disease and drug addiction. Long-lasting forms of synaptic plasticity are thought to depend on transcription of gene products that alter the structure and/or function of neurons. Although multiple signal transduction pathways regulate transcription, little is known about signal transmission between the cytoplasm and the nucleus of striatal neurons and its regulation. Here we review the current knowledge of the signaling cascades that target the nucleus of MSNs, most of which are activated by cAMP and/or Ca2+. We outline the mechanisms by which signals originating at the plasma membrane and amplified in the cytoplasm are relayed to the nucleus, through the regulation of several protein kinases and phosphatases and transport through the nuclear pore. We also summarize the identified mechanisms of transcription regulation and chromatin remodeling in MSNs that appear to be important for behavioral adaptations, and discuss their relationships with epigenetic regulation.

  15. Holophytochrome-interacting proteins in Physcomitrella: putative actors in phytochrome cytoplasmic signaling

    Directory of Open Access Journals (Sweden)

    Anna Lena eErmert


    Full Text Available Phytochromes are the principle photoreceptors in light-regulated plant development, primarily acting via translocation of the light-activated photoreceptor into the nucleus and subsequent gene regulation. However, several independent lines of evidence indicate unambiguously that an additional cytoplasmic signaling mechanism must exist. Directional responses in filament tip cells of the moss Physcomitrella patens are steered by phy4 which has been shown to interact physically with the blue light receptor phototropin at the plasma membrane. This complex might perceive and transduce vectorial information leading to cytoskeleton reorganization and finally a directional growth response. We developed yeast two-hybrid procedures using photochemically-functional, full-length phy4 as bait in Physcomitrella cDNA library screens and growth assays under different light conditions, revealing Pfr-dependent interactions possibly associated with phytochrome cytoplasmic signaling. Candidate proteins were then expressed in planta with fluorescent protein tags to determine their intracellular localization in darkness and red light. Of 14 candidates, 12 were confirmed to interact with phy4 in planta using bimolecular fluorescence complementation. We discuss the roles these putative holophytochrome-interacting proteins (HIP's might have in signaling.

  16. Structural and functional consequences of tyrosine phosphorylation in the LRP1 cytoplasmic domain. (United States)

    Betts, Gina N; van der Geer, Peter; Komives, Elizabeth A


    The cytoplasmic domain of LRP1 contains two NPXY motifs that have been shown to interact with signaling proteins. In previous work, we showed that Tyr(4507) in the distal NPXY motif is phosphorylated by v-Src, whereas denaturation of the protein was required for phosphorylation of Tyr(4473) in the membraneproximal NPXY motif. Amide H/D exchange studies reveal that the distal NPXY motif is fully solvent-exposed, whereas the proximal one is not. Phosphopeptide mapping combined with in vitro and in vivo kinase experiments show that Tyr(4473) can be phosphorylated, but only if Tyr(4507) is phosphorylated or substituted with glutamic acid. Amide H/D exchange experiments indicate that solvent accessibility increases across the entire LRP1 cytoplasmic region upon phosphorylation at Tyr(4507); in particular the NPXY(4473) motif becomes much more exposed. This differential phosphorylation is functionally relevant: binding of Snx17, which is known to bind at the proximal NPXY motif, is inhibited by phosphorylation at Tyr(4473). Conversely, Shp2 binds most strongly when both of the NPXY motifs in LRP1 are phosphorylated.

  17. Interrelationship Between Cytoplasmic Retroviral Gag Concentration and Gag-Membrane Association (United States)

    Fogarty, Keir H.; Berk, Serkan; Grigsby, Iwen F.; Chen, Yan; Mansky, Louis M.; Mueller, Joachim D.


    The early events in the retrovirus assembly pathway, particularly the timing and nature of Gag translocation from the site of protein translation to the inner leaflet of the plasma membrane, are poorly understood. We have investigated the interrelationship between cytoplasmic Gag concentration and plasma membrane association using complementary live-cell biophysical fluorescence techniques in real-time with both the human T-cell leukemia virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1) Gag proteins. In particular, dual-color, z-scan fluorescence fluctuation spectroscopy (dcz-FFS) in conjunction with total internal reflection fluorescence (TIRF) and conventional, epi-illumination imaging were utilized. Our results demonstrate that HTLV-1 Gag is capable of membrane targeting and particle assembly at low (i.e., nM) cytoplasmic concentrations, and that there is a critical threshold concentration (approaching μM) prior to the observation of HIV-1 Gag associated with the plasma membrane. These observations imply fundamental differences between HIV-1 and HTLV-1 Gag trafficking and membrane association. PMID:24316368

  18. Transcriptional regulation of Culex pipiens mosquitoes by Wolbachia influences cytoplasmic incompatibility.

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    Sofia B Pinto


    Full Text Available Cytoplasmic incompatibility (CI induced by the endosymbiont Wolbachia pipientis causes complex patterns of crossing sterility between populations of the Culex pipiens group of mosquitoes. The molecular basis of the phenotype is yet to be defined. In order to investigate what host changes may underlie CI at the molecular level, we examined the transcription of a homolog of the Drosophila melanogaster gene grauzone that encodes a zinc finger protein and acts as a regulator of female meiosis, in which mutations can cause sterility. Upregulation was observed in Wolbachia-infected C. pipiens group individuals relative to Wolbachia-cured lines and the level of upregulation differed between lines that were reproductively incompatible. Knockdown analysis of this gene using RNAi showed an effect on hatch rates in a Wolbachia infected Culex molestus line. Furthermore, in later stages of development an effect on developmental progression in CI embryos occurs in bidirectionally incompatible crosses. The genome of a wPip Wolbachia strain variant from Culex molestus was sequenced and compared with the genome of a wPip variant with which it was incompatible. Three genes in inserted or deleted regions were newly identified in the C. molestus wPip genome, one of which is a transcriptional regulator labelled wtrM. When this gene was transfected into adult Culex mosquitoes, upregulation of the grauzone homolog was observed. These data suggest that Wolbachia-mediated regulation of host gene expression is a component of the mechanism of cytoplasmic incompatibility.

  19. Most human proteins made in both nucleus and cytoplasm turn over within minutes.

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    Sabyasachi Baboo

    Full Text Available In bacteria, protein synthesis can be coupled to transcription, but in eukaryotes it is believed to occur solely in the cytoplasm. Using pulses as short as 5 s, we find that three analogues--L-azidohomoalanine, puromycin (detected after attaching fluors using 'click' chemistry or immuno-labeling, and amino acids tagged with 'heavy' 15N and 13C (detected using secondary ion mass spectrometry--are incorporated into the nucleus and cytoplasm in a process sensitive to translational inhibitors. The nuclear incorporation represents a significant fraction of the total, and labels in both compartments have half-lives of less than a minute; results are consistent with most newly-made peptides being destroyed soon after they are made. As nascent RNA bearing a premature termination codon (detected by fluorescence in situ hybridization is also eliminated by a mechanism sensitive to a translational inhibitor, the nuclear turnover of peptides is probably a by-product of proof-reading the RNA for stop codons (a process known as nonsense-mediated decay. We speculate that the apparently-wasteful turnover of this previously-hidden ('dark-matter' world of peptide is involved in regulating protein production.

  20. Operational characteristics of a high voltage dense plasma focus (United States)

    Woodall, D. M.


    A high voltage dense plasma focus powered by a single stage Marx bank was designed, built and operated. The maximum bank parameters are: voltage--120 kV, energy--20 kJ, short circuit current--600kA. The bank impedance is about 200 millohms. The plasma focus center electrode diameter is 1.27 cm. The outer electrode diameter is 10.16 cm. Rundown length is about 10 cm, corresponding to a bank quarter period of about 900 millohms ns. Rundown L is about 50 milliohms. The context of this work is established with a review of previous plasma focus theoretical, experimental and computational work and related topics. Theoretical motivation for high voltage operation is presented. The design, construction and operation of this device are discussed in detail. Results and analysis of measurements obtained are presented. Device operation was investigated primarily at 80 kV (9 kJ), with a gas fill of about 1 torr H2, plus 3-5 percent A. The following diagnostics were used: gun voltage and current measurements; filtered, time resolved x ray PIN measurements of the pinch region; time integrated x ray pinhole photographs of the pinch region; fast frame visible light photographs of the sheath during rundown; and B probe measurements of the current sheath shortly before collapse.